Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification
Project description:in vitro comparison between two MRSA grown in rich (BHI) and poor media (SNM), compared with the nasal metatranscriptome reads of S. aureus. Global expression profile of two MRSA strains of S.aureus harvested in two different growth phases and compared with a metatranscriptome nose sample of a S. aureus carrier.
Project description:in vitro comparison between two MRSA grown in rich (BHI) and poor media (SNM), compared with the nasal metatranscriptome reads of S. aureus.
Project description:We performed a biological and molecular characterization of the novel human multiple myeloma cell line CMA03/06, an IL-6-independent variant of CMA03 cell line previously established in our Institution. We showed that the CMA03/06 cells grows in the absence of IL-6 with a doubling time comparable to CMA03; the addition of IL-6 to the culture medium or co-culture with multipotent mesenchymal stromal cells does not induce an increase in proliferation rate. Interestingly, we provided evidence that IL-6 independence of CMA03/06 cells is not a consequence of the development of an autocrine IL-6 loop, even though the cells maintain the IL-6 signaling pathway responsiveness as demonstrated by STAT1 and STAT3 induction by IL-6. A slight constitutive activation of STAT3 has been observed in CMA03/06 cell line; however STAT3 silencing in CMA03/06 cells did not affect their viability and proliferation suggesting that this pathway is not the only responsible for the IL-6 independency of CMA03/06 cell line. The new cell line showed a lower susceptibility to camptothecin-induced apoptosis compared to CMA03 cells, whereas an increased induction of apoptosis was observed in CMA03/06 cell line after Bortezomib treatment which may suggest the involvement NF-kB pathway in the IL-6 independent growth and survival of CMA03/06 cells. Finally, global gene expression profiling analysis allowed the identification of a list of 308 modulated genes in CMA03/06 versus CMA03 cells, many of which particularly relevant for MM biology. Overall, the novel CMA03/06 cell line may represent a suitable model for studies investigating molecular mechanisms involved in clonal evolution towards IL-6 and/or stroma-independent growth and survival of myeloma cells.
Project description:We compiled a metatranscriptome by extracting total RNA (including ribosomes), reverse transcription and solexa sequencing. We obtained quantitative data on the transcription of each orf to assess the importance of each orf to the metabolism of Kuenenia stuttgartiensis
Project description:Atmospheric Particulate Matter (PM) is one of the leading environmental risk factors for the global burden of disease. Increasing epidemiological studies demonstrated that PM plays a significant role in CNS demyelinating disorders; however, there is no direct testimony of this, and yet the molecular mechanism by which the occurrence remains unclear. Using multiple in vivo and in vitro strategies, in the present study we demonstrate that PM exposure aggravates neuroinflammation, myelin injury, and dysfunction of movement coordination ability via boosting microglial pro-inflammatory activities, in both the pathological demyelination and physiological myelinogenesis animal models. Indeed, pharmacological disturbance combined with RNA-seq and ChIP-seq suggests that TLR-4/NF-κB signaling mediated a core network of genes that control PM-triggered microglia pathogenicity. In summary, our study defines a novel atmospheric environmental mechanism that mediates PM-aggravated microglia pathogenic activities, and establishes a systematic approach for the investigation of the effects of environmental exposure in neurologic disorders.
Project description:The clinical impact of aberrant CEBPA promoter methylation (PM) in AML is controversial discussed. The aim of this study was to clarify the significance of aberrant CEBPA PM with regard to clinical features in a cohort of 572 de novo AML with wildtype CEBPA and normal karyotype. The distal promoter was methylated in 54/572 cases (9.41%) whereas proximal PM was never detected. Methylation of the core promoter was detected in only 8 of 326 cases (2.45%) and thus seems to be a rare event in AML. There was no correlation between CEBPA distal PM, age, sex, white blood cell (WBC) count or Hb levels at diagnosis. We also were not able to detect a significant correlation between the presence of CEBPA distal PM and molecular mutations such as FLT3-ITD, NPM1, AML1, MLL-PTD and IDH1. Solely the frequency of IDH2R140 mutations was significantly reduced in CEBPA distal PM positive compared to CEBPA distal PM negative cases (p=0.01). Furthermore, analysis of CEBPA mRNA expression level revealed no difference between CEBPA distal PM positive and CEBPA distal PM negative cases, suggesting that CEBPA distal PM has no influence on CEBPA expression. CEBPA distal PM did not show impact on overall survival (OS), event free survival (EFS) or incidence of relapse. Also when other mutations were taken into regard no prognostic impact of CEBPA distal PM could be shown. In contrast, a distinct expression profile of CEBPA distal PM positive cases compared to CEBPA mutated and CEBPA distal PM negative cases was observed. In addition, a significantly higher frequency of CEBPA distal PM was detected in RUNX1-RUNX1T1 positive AML compared to the CEBPA witdtype cases. We conclude that the presence of aberrant CEBPA PM has no clinical relevance and is therefore a negligible prognostic marker in de novo AML with normal karyotype.
Project description:Chip-Seq on HepG2-human (fragmentation date:2016-06-05 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
