Project description:Mitochondrial rRNAs play important roles in regulating mtDNA-encoded gene expression and energy metabolism subsequently. However, the proteins that regulate mitochondrial 16S rRNA processing remain poorly understood. Herein, we generated adipose-specific Wbscr16-/- mice and cells, both of which exhibited dramatic mitochondrial changes. Subsequently, WBSCR16 was identified as a 16S rRNA-binding protein essential for the cleavage of 16S rRNA-mt-tRNALeu, facilitating 16S rRNA processing and mitochondrial ribosome assembly. Additionally, WBSCR16 recruited RNase P subunit MRPP3 to nascent 16S rRNA and assisted in this specific cleavage. Furthermore, evidence showed that adipose-specific Wbscr16 ablation promotes energy wasting via lipid preference in brown adipose tissue, leading to excess energy expenditure and resistance to obesity. In contrast, overexpression of WBSCR16 upregulated 16S rRNA processing and induced a preference for glucose utilization in both transgenic mouse models and cultured cells. These findings suggest that WBSCR16 plays essential roles in mitochondrial 16S rRNA processing in mammals, and is the key mitochondrial protein to balance glucose and lipid metabolism.
Project description:The goal of this growth chamber experiment was to investigate the effects of diverse soil microbial communities on the transcriptional responses of plants to drought. Specifically, we sought to understand how soil microbiomes' past exposure to water-limited conditions (either long-term exposure to dry conditions in low-precipitation sites, or recent acute drought) impacted their interactions with plants. Six soils collected from remnant prairies crossing a steep precipitation gradient in Kansas, USA were used as the starting microbial communities. Thirty-two pots (or mesocosms) of each soil were divided among four treatments: droughted or well-watered, and with or without a host plant (Tripsacum dactyloides) in a factorial design. The soil mesocosms were "conditioned" in these treatments for five months. (Metagenome and metatranscriptome data from the baseline soils and the post-conditioning soils are available in a separate BioProject on NCBI SRA and GEO). Then, a microbial slurry extracted from each of the 192 conditioned soils was used to inoculate 4 plants in a subsequent experiment (the “Test Phase”): one pot per combination of watering treatment (droughted or control) and host species (Zea mays or Tripsacum dactyloides). After 4 weeks (for maize) or 5 weeks (for eastern gamagrass) we harvested one crown root per plant for 16S rRNA sequencing and another crown root for RNA-seq. The 16S and RNA-seq data for these plants (both species) are contained in this BioProject. Note that 16S rRNA sequencing data are available for all plants in this experiment, but we conducted RNA-seq only for a subset (all plants grown in microbiomes originating from the 2 driest and 2 wettest collection sites).
Project description:The goal of this growth chamber experiment was to investigate the effects of diverse soil microbial communities on the transcriptional responses of plants to drought. Specifically, we sought to understand how soil microbiomes' past exposure to water-limited conditions (either long-term exposure to dry conditions in low-precipitation sites, or recent acute drought) impacted their interactions with plants. Six soils collected from remnant prairies crossing a steep precipitation gradient in Kansas, USA were used as the starting microbial communities. Thirty-two pots (or mesocosms) of each soil were divided among four treatments: droughted or well-watered, and with or without a host plant (Tripsacum dactyloides) in a factorial design. The soil mesocosms were "conditioned" in these treatments for five months. (Metagenome and metatranscriptome data from the baseline soils and the post-conditioning soils are available in a separate BioProject on NCBI SRA and GEO). Then, a microbial slurry extracted from each of the 192 conditioned soils was used to inoculate 4 plants in a subsequent experiment (the “Test Phase”): one pot per combination of watering treatment (droughted or control) and host species (Zea mays or Tripsacum dactyloides). After 4 weeks (for maize) or 5 weeks (for eastern gamagrass) we harvested one crown root per plant for 16S rRNA sequencing and another crown root for RNA-seq. The 16S and RNA-seq data for these plants (both species) are contained in this BioProject. Note that 16S rRNA sequencing data are available for all plants in this experiment, but we conducted RNA-seq only for a subset (all plants grown in microbiomes originating from the 2 driest and 2 wettest collection sites).
Project description:We found that mainstream cigarette smoking (4 cigarettes/day, 5 days/week for 2 weeks using Kentucky Research Cigarettes 3R4F) resulted in >20% decrease in the percentage of normal Paneth cell population in Atg16l1 T300A mice but showed minimal effect in wildtype littermate control mice, indicating that Atg16l1 T300A polymorphism confers sensitivity to cigarette smoking-induced Paneth cell damage. We performed 16S rRNA sequencing to identify potential microbiota changes associated with Paneth cell defect in Atg16l1 T300A mice exposed to cigarette smoking. Female mice were used at 4-5 weeks of age. Cigarette smoking was performed using smoking chamber with the dosage and schedule as described above. The fecal samples from the mice were collected for 16S rRNA sequencing analysis after completing 6 weeks of smoking.
Project description:Iron-rich pelagic aggregates (iron snow) were collected directly onto silicate glass filters using an electronic water pump installed below the redoxcline. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA/rRNA sequences were sorted by SortmeRNA. mRNA sequences were blast against NCBI-non redundant protein database and the outputs were meganized in MEGAN to do functional analysis. rRNA sequences were further sorted against bacterial/archeal 16S rRNA, eukaryotic 18S rRNA and 10,000 rRNA sequences of bacterial 16S rRNA, eukaryotic 18S rRNA were subset to do taxonomy analysis.
Project description:A phylogenetic microarray targeting 66 families described in the human gut microbiota has been developped aud used to monitor the gut microbiota's structure and diversity. The microarray format provided by Agilent and used in this study is 8x15K. A study with a total of 4 chips was realized. Arrays 1 and 2: Hybridization with 100ng of labelled 16S rRNA gene amplicons from a mock community sample and 250ng of labelled 16S rRNA gene amplicons from 1 faecal sample. Each Agilent-030618 array probe (4441) was synthetized in three replicates. Arrays 3 and 4: Hybridization with 250ng of labelled 16S rRNA gene amplicons from 2 faecal samples. Each Agilent-40558 array probe (4441) was synthetized in three replicates.
Project description:IL22 induces antimicrobial peptides which influnce microbiota. We used 16s rRNA gene sequencing (16s DNA-seq) to analyze the microbiota with Fc or IL-22Fc treatment.