Project description:To better understand the molecular mechanisms of SP cells, we screened the miRNAs expression patterns in the SP compared with the MP cells. MiRCURY™ LNA array analysis of sorted SP and MP cells from two relapsed myeloma patients with more than 70% bone marrow plasma cells were performed.
Project description:Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes. Examination of CTCF and RAD21 binding sites in THP-1 cell.
Project description:A clone encoding carboxymethylcellulase activity was isolated during functional screening of a human gut metagenomic library using Lactococcus lactis MG1363 as heterologous host. The insert sequence revealed a glycoside hydrolase family 9 (GH9) catalytic domain with sequence similarity to a gene from Coprococcus sp. ART55/1, which is closely related to Coprocococcus eutactus. Surveys of available genomes indicated a limited distribution of GH9 domains among dominant human colonic anaerobes. Genomes of two Coprococcus-related strains showed the presence of two GH9-encoding and four GH5-encoding genes, however, the strains did not appear to be able to degrade cellulose. Instead, they grew well on beta-glucans and one of the strains also showed growth on galactomannan, galactan and glucomannan. Gene expression and proteomic analysis of Coprococcus sp. ART55/1 grown on cellobiose, beta-glucan and lichenan led to a similar change in expression in comparison to glucose. On beta-glucan and lichenan only, one of the four GH5 genes was strongly upregulated. Growth on glucomannan lead to a transcriptional response of many genes, in particular a strong upregulation of glycoside hydrolases involved in mannan degradation. Thus, beta-glucans are a major growth substrate for species related to Coprococcus eutactus, with glucomannan and galactans alternative substrates for some strains.
Project description:This project is a proteomic comparison of Hyphomicrobium sp. MC8b grown with dichloromethane or with methanol. The datasets were obtained using a pan-proteomic database built by merging the predicted proteomes from the annotated genomes of 13 Hyphomicrobium strains.
Project description:Kentrophoros ciliates are found worldwide in coastal marine sediment, and have an obligate symbiosis with sulfur-oxidizing Gammaproteobacteria called Candidatus Kentron. The genomes of different Kentron species suggest that they are chemolithoheterotrophs, producing new biomass from organic carbon substrates. We investigated the metaproteome of Kentrophoros sp. H and its symbiont (from two sites in the Mediterranean), to verify that hypothesized pathways of carbon and energy metabolism are indeed expressed, and to estimate the stable isotope fractionation in biomass, which can be a signature of the carbon sources used by the organism.