Project description:Subjects with different allergic phenotypes showed distinct gut microbial patterns and functions. AD+FA subjects showed the mixtures of gut microbial patterns of FA and AD, while gut microbial pattern of FA seems to dominate in subjects with AD+FA
Project description:This SuperSeries is composed of the following subset Series: GSE36822: Clonal competition with alternating dominance in multiple myeloma [244kCGH] GSE36823: Clonal competition with alternating dominance in multiple myeloma [44kCGH] GSE36824: Clonal competition with alternating dominance in multiple myeloma [GEP] Refer to individual Series
Project description:Accurate description of a microbial community is an important first step in understanding the role of its components in ecosystem function. A method for surveying microbial communities termed Serial Analysis of Ribosomal DNA (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA gene from microbial communities. These tags are ligated to form concatemers comprised of 20-40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method’s utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. Comparison of duplicate profiles from one soil genomic DNA preparation revealed the method was highly reproducible. The large numbers of singleton tags together with non-parametric richness estimates indicated a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either numerical or diversity standpoints, low abundant taxa comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological role of these rare members of microbial communities in qualitative and quantitative terms. Keywords: SARD profiles, culture-independent study, microbial community survey, microbial census
Project description:In this work, we used a functional gene microarray approach (GeoChip) to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar
Project description:We investigated whether two sympatric Arctic charr morphs (Salvelinus alpinus) with contrasting feeding ecology, the small-benthic (SB) and the planktivorous (PL) charr of Thingvallavatn in Iceland, exhibit genetically based differences in gene expression variability, and how dominance would affect their hybrids. Through a common-garden experiment, we identified genes clusters with similar expression variability, most differing among the two morphs. In the hybrids, gene expression variability was substantially affected by maternal effects and biases towards the PL charr, while the expression of a minority of genes felt outside the range of parental values. These profiles of expression variability were consistent across mRNA and miRNA datasets. Predominant maternal effects and PL charr biases were also observed at the level of average gene expression, including candidate genes involved in the lower jaw development.
Project description:Plants deploy pattern recognition receptors to detect microbe- and damage-associated molecular patterns. Arabidopsis thaliana receptor-like protein RLP30 contributes to innate immunity to the necrotrophic fungus Sclerotinia sclerotiorum by recognizing SCLEROTINIA CULTURE FILTRATE ELICITOR 1 (SCFE1). Here we show that the S. sclerotiorum small cysteine-rich protein SCP1 accounts for elicitor activity of SCFE1. RLP30 recognizes SCP1 and its homologs from divergent fungi and oomycetes, as well as an SCP1-unrelated and conserved pattern from bacterial Pseudomonads. Stable expression of RLP30 in Nicotiana tabacum confers enhanced immunity to bacterial, fungal, and oomycete pathogens. Unlike Arabidopsis, which requires intact SCP1 for RLP30-mediated immunity, other Brassicaceae and Solanaceae respond to smaller immunogenic SCP1 epitopes. We conclude that Arabidopsis RLP30 recognizes immunogenic patterns from three microbial kingdoms and that mechanistically different SCP1 perception has evolved in other plant species, likely as a result of convergent evolution.
Project description:Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments.