Project description:Amycolatopsis sp. BX17 is an actinobacterium isolated from milpa soils that antagonizes the phytopathogenic fungus Fusarium graminearum. Metabolites secreted by the actinobacterium cultured in medium without glucose inhibited 100% the mycelial growth of F. graminearum RH1, while in medium supplemented with 20 g/L of glucose inhibition was 65%. With the aim of studying how the metabolism of strain BX17 is modulated by glucose, as the main carbon source, media with 0 and 20 g/L glucose were selected to analyze the intracellular proteins by quantitative label-free proteomic analysis.
Project description:Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Similar mechanisms and gene transcripts are assumed to be involved in the host defense response because both pathogens are biotrophic fungi. The main objective of our study was to identify co-regulated mRNAs that show a change in expression pattern after inoculation with Pst or Bgt, and to identify mRNAs specific to the fungal stress response. In the present study, cDNA libraries were constructed from leaves inoculated with Pst or Bgt at 0, 1, 2 and 3 days post-inoculation (dpi) with three biological replicates, and then sequenced using the Illumina HiSeq™ 2000 platform. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:Lignin modifications and the exoproteome of three aromatic catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. Samples were digested with trypsin, then analyzed by LC-MS/MS. Data was searched with MSGF+ and abundances inferred using PNNL's DMS and MTS Processing pipeline
Project description:PPARγ is a master transcriptional regulator of adipogenesis. Hence, the identification of PPARγ coactivators should help reveal mechanisms controlling gene expression in adipose tissue development and physiology. We show that the non-coding RNA Steroid receptor RNA Activator, SRA, associates with PPARγ and coactivates PPARγ-dependent reporter gene expression. Overexpression of SRA in ST2 adipocyte precursor cells promotes their differentiation into adipocytes. Conversely, knockdown of endogenous SRA inhibits 3T3-L1 preadipocyte differentiation. Microarray analysis reveals hundreds of SRA-responsive genes in adipocytes, including genes in cell cycle, insulin and TNFα signaling pathways. Some functions of SRA may involve mechanisms other than coactivation of PPARγ. SRA increases insulin-stimulated glucose uptake in adipocytes. SRA promotes S-phase entry during mitotic clonal expansion, decreases expression of cyclin-dependent kinase inhibiters p21Cip1 and p27Kip1, and increases phosphorylation of Cdk1/Cdc2. SRA also inhibits the TNFα-induced phosphorylation of c-Jun NH2-terminal kinase. In conclusion, SRA enhances adipogenesis and adipocyte function through multiple pathways.
Project description:We performed Chromatin Isolation by RNA Purification (ChIRP) of SRA and ChIP of p68 following by high-throughput sequencing in NTERA2 cell line. We find that SRA localizes with p68 genome-wide at genes whose function is involved in embryonic development.
Project description:S. coelicolor spore stocks were diluted to 2x108 cfu/mL and 0.5ul was spotted onto a 60x15mm petri dish with 4ml ISP2 agar, resulting in agar approximately 2 mm thick. For interactions, 0.5 ul of an Amycolatopsis sp. AA4 stock (8x108 cfu/mL) was spotted 0.75 cm away from the S. coelicolor spot. Interactions were grown for 4 days at 30°C, then imaged or harvested for RNA isolation. Biomass was collected after 4 days of growth at 30°C using a cell scraper. For the patches growing alone, the entire patch was collected and one sample consists of three whole patches combined. For the patches in interactions, only half of the patch, the side closest to the initiator strain, was collected and one sample consists of five half patches. Precaution was taken to not scrape up any of the interacting strain.
Project description:S. coelicolor spore stocks were diluted to 2x108 cfu/mL and 0.5ul was spotted onto a 60x15mm petri dish with 4ml ISP2 agar, resulting in agar approximately 2 mm thick. For interactions, 0.5 ul of an Amycolatopsis sp. AA4 stock (8x108 cfu/mL) was spotted 0.75 cm away from the S. coelicolor spot. Interactions were grown for 4 days at 30°C, then imaged or harvested for RNA isolation. Biomass was collected after 4 days of growth at 30°C using a cell scraper. For the patches growing alone, the entire patch was collected and one sample consists of three whole patches combined. For the patches in interactions, only half of the patch, the side closest to the initiator strain, was collected and one sample consists of five half patches. Precaution was taken to not scrape up any of the interacting strain.