Pollen microbiome
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ABSTRACT:
PROVIDER: PRJEB23282 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, we sequenced four small RNA libraries derived from mature pollens, in vitro germinated pollens, mature silks and pollinated silks of maize, respectively. In total, 161 known miRNAs belonging to 27 families and 82 novel miRNAs were identified. Of them, miRNAs involved in pollen-silk (pistil) interactions were analyzed. On the male side, miRNA differentially expressed between mature and germinated pollen were identified, some of them participate in pollen germination and tube growth. On the female side, silk-expressed miRNAs respond to pollination were also responsive to stresses, especially drought and fungal invasion. Furthermore, GO analysis of target genes revealed that members related to anxin signal transduction and gene expressional regulation were overrepresented.The results indicated that during pollen-silk interactions, miRNAs-mediated auxin signal transduction plays important roles, and miRNAs took part in complex transcriptional regulating network.
2013-03-02 | GSE44787 | GEO
Project description:Beehive microbiome from pollen and honey
| PRJEB45401 | ENA
Project description:Significant gut microbiota heterogeneity exists amongst UC patients though the clinical implications of this variance are unknown. European and South Asian UC patients exhibit distinct disease risk alleles, many of which regulate immune function and relate to variation in gut microbiota β-diversity. We hypothesized ethnically distinct UC patients exhibit discrete gut microbiotas with unique luminal metabolic programming that influence adaptive immune responses and relate to clinical status. Using parallel bacterial 16S rRNA and fungal ITS2 sequencing of fecal samples (UC n=30; healthy n=13), we corroborated previous observations of UC-associated depletion of bacterial diversity and demonstrated significant gastrointestinal expansion of Saccharomycetales as a novel UC characteristic. We identified four distinct microbial community states (MCS 1-4), confirmed their existence using microbiota data from an independent UC cohort, and show they co-associate with patient ethnicity and degree of disease severity. Each MCS was predicted to be uniquely enriched for specific amino acid, carbohydrate, and lipid metabolism pathways and exhibited significant luminal enrichment of metabolic products from these pathways. Using a novel in vitro human DC/T-cell assay we show that DC exposure to patient fecal water led to MCS -specific changes in T-cell populations, particularly the Th1:Th2 ratio, and that patients with the most severe disease exhibited the greatest Th2 skewing. Thus, based on ethnicity, microbiome composition, and associated metabolic dysfunction, UC patients may be stratified in a clinically and immunologically meaningful manner, providing a platform for the development of FMC-focused therapy. Fecal microbiome was assessed with Affymetrix PhyloChip arrays from patients with ulcerative colitis and healthy controls.
2016-07-25 | E-GEOD-78724 | biostudies-arrayexpress
Project description:In this study, we sequenced four small RNA libraries derived from mature pollens, in vitro germinated pollens, mature silks and pollinated silks of maize, respectively. In total, 161 known miRNAs belonging to 27 families and 82 novel miRNAs were identified. Of them, miRNAs involved in pollen-silk (pistil) interactions were analyzed. On the male side, miRNA differentially expressed between mature and germinated pollen were identified, some of them participate in pollen germination and tube growth. On the female side, silk-expressed miRNAs respond to pollination were also responsive to stresses, especially drought and fungal invasion. Furthermore, GO analysis of target genes revealed that members related to anxin signal transduction and gene expressional regulation were overrepresented.The results indicated that during pollen-silk interactions, miRNAs-mediated auxin signal transduction plays important roles, and miRNAs took part in complex transcriptional regulating network. Examination of 4 different tissues of maize to provide novel information for understanding the post-transcriptional regulations of pollen-pistil interactions
2013-03-02 | E-GEOD-44787 | biostudies-arrayexpress
Project description:Bacterial and fungal microbiota associated with the stigma of parasitic plant
| PRJEB43630 | ENA
Project description:Persistent mucosal inflammation and microbial infection are characteristic of Chronic Rhinosinusitis (CRS). Though mucosal microbiota dysbiosis is a characteristic feature of other chronic inflammatory diseases, the relationship between sinus microbiota composition and CRS is unknown. Here we demonstrate, using comparative microbiome profiling of a cohort of CRS patients and healthy subjects, that the sinus microbiota of CRS patients exhibit significantly reduced bacterial diversity. Characteristic of this community collapse is the depletion of multiple, phylogenetically distinct, Lactic Acid Bacteria and the concomitant increase in relative abundance of a single species, Corynebacterium tuberculostearicum. Recapitulating the conditions observed in our human cohort in a murine model confirmed the pathogenic potential of C. tuberculostearicum and the critical necessity for a replete mucosal microbiota to protect against this species. Moreover, we provide evidence that Lactobacillus sakei, identified from our comparative microbiome analyses as a potentially protective species, affords defense against C. tuberculostearicum sinus infection, even in the context of a depleted sinus bacterial community. These studies demonstrate that sinus mucosal health is highly dependent on the composition of the resident microbiota, and identifies a new sino-pathogen and a strong bacterial candidate for therapeutic intervention. A total of 14 samples were profiled for microbiome composition: 7 from non-sinusitis patients, and 7 from patients with clinically diagnosed chronic sinusitis.
2012-07-31 | E-GEOD-37850 | biostudies-arrayexpress
Project description:In this study, RNA-seq based comparative transcriptome analysis was used to study the genetic response of maize silk to pollen tube penetration and in comparison to the fungal invasion of Fusarium graminearum and Ustilago maydis. RNA-seq libraries of 8 tissues were generated from leaf, root, seed, pollen tube, silk, pollinated silk, infected silk with Fusarium and infected silk with Ustilago.
2019-03-17 | E-MTAB-4559 | biostudies-arrayexpress
Project description:We isolated tricellular pollen (TCP) and pollen mother cells (PMC) of rice using laser microdissection, and did microarray analysis with Agilent 44k rice array.
2010-07-31 | GSE17098 | GEO
Project description:Background: Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart. Results: A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during development of pollen and embryo sac in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of miRNAs-enriched during the development of pollen and embryo sac in autotetraploid rice revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development. However, only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression levels in pollen and embryo sac development. Of these DEM, osa-miR1436_L+3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21nt-phasiRNAs were detected both during pollen and embryo sac development, while 24nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development. Conclusion: The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-24nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice.
2017-03-09 | GSE90479 | GEO
Project description:Jasmonates are well known signaling components required for diverse processes ranging from wound and pathogen responses to regulation of developmental processes. A prominent feature of jasmonate biosynthesis or signaling mutants is the loss of fertility. In contrast to the male sterile phenotype of Arabidopsis mutants, the loss of the co-receptor protein COI1 in the tomato mutant jai1-1 results in female sterility with additional severe effects on stamen and pollen development. While a general model of jasmonate effects on male gametophyte development has been proposed to involve the regulation of water transport, the molecular details of this response are scarce. Here we show an extensive temporal profiling of the development, hormone content, transcriptome and metabolome of tomato stamen in six distinct stages of flower development in wild type and jai1-1. We found that the premature stamen desiccation of jai1-1 stamens and the preponed pollen maturation coincide with an accumulation of desiccation-related metabolites. The wild type shows a transient increase of jasmonates up to mid-flowering that is absent in jai1-1. This finding coincides with an early increase of the ethylene precursor ACC in jai1-1 that is similarly reflected in the increased expression of ethylene biosynthesis and response genes. Our data suggests an essential role of jasmonates in the temporal inhibition of ethylene production to prevent premature desiccation of stamens and to ensure proper timing in flower development.
2015-03-31 | E-MTAB-2752 | biostudies-arrayexpress