Comparative transcriptional analysis of Desulfovibrio G20 grown under syntrophic and respiratory condtions
ABSTRACT: Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis in chemostats at a high growth rate of 0.047h-1 5 replicates of coculture and 3 replicates of sulfate-limited monoculture
Project description:Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis or Methanospirillum hungatei in chemostats at a low growth rate of 0.027h-1. 7 samples of Desulfovibrio alaskensis strain G20 grown in syntrophic coculture on lactate with either Methanococcus maripaludis (4 replicates) or Methanospirillum hungatei (3 replicates), and 5 samples of sulfate-limited monoculture growth of strain G20 on lactate.
Project description:Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1) 2 replicates each for syntrophic coculture (M. maripaludis or M. hungatei pairing) and respiratory (sulfate- or pyruvate-limited) monoculture for both growth rates (0.027 and 0.047 h-1), and 4 replicates fermentative monoculture (gas flow rate through head space of bioreactor 10 ml/min (chemostats C91 and C93) or 1 ml/min (chemostats C92 and C94)
Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media and then pelleted and transferred to another media when they reached stationary phase. The Choline mutant was transferred to lacte/sulfate minimal media and choline/sulfate minimal media. The LysX mutant was transferred to minimal media with lysine and rich media. G20 was transferred to minimal media, choline/sulfate minimal media, lactate/choline/sulfate minimal media, minimal media with lysine, and rich media. We aimed to confirm or expand the regulons of each of the transposon interupted regulator mutants and compare gene expression responses of the regulators in different growth conditions. 10 samples were collected: 2 regulator mutants (2 conditions each), Desulfovibrio alaskensis G20 (5 conditions), 2 replicates for G20 minimal media condition. Control sample -G20 rich media.
Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase. We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants. 8 samples were collected: 7 regulator mutants and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.
Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase. We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants. 12 samples were collected: 10 regulator mutants, 1 mutant in a secretory protein and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.
Project description:Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing interspecies interactions is dependent, at least initially, on the availability of model systems with well-annotated genomes and tractable genetics. We employed controlled cultivation and next-generation sequencing technology to identify transcriptional responses of euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and a marine facultative aerobe Shewanella putrefaciens W3-18-1 to investigate the effect of C sources and C flux directions on the interactions between these organisms.
Project description:Murine BV2 microglia cells were transfected either with siRNA negative control or siRNA against caspase-3 for 48h. Later on some the of the BV2 transfected cells were co-cultured with C6 glioma cells during 6h. We used the SA Biosciences Mouse Wound Healing PCR Array (PAMM-121Z) to quantitate gene expression of relevant genes related to the wound healing process Glioma cells recruit and exploit microglia, resident immune cells of the brain, for their proliferation and invasion capability. The underlying molecular mechanism used by glioma cells to transform microglia into a tumor-supporting phenotype remains elusive. Here, we report that glioma-induced microglia conversion is coupled to a reduction of basal microglial caspase-3 activity, increased S-nitrosylation of mitochondria-associated caspase-3 through inhibition of thioredoxin-2 activity, and demonstrate that caspase-3 inhibition regulates microglial tumor-supporting function. Further, we identified nitric oxide synthase-2 (NOS2) activity originating from the glioma cells as a driving stimulus in the control of microglial caspase-3 activity. Repression of glioma NOS2 expression in vivo led to reduction in both microglia recruitment and tumor expansion, whereas depletion of the microglial caspase-3 gene promoted tumor growth. This study provides evidence that the inhibition of Trx2-mediated denitrosylation of SNO-procaspase-3 is part of the microglial pro-tumoral activation pathway initiated by glioma cancer cells. qPCR gene expression profiling. Three independent experiments of siControl BV2 monoculture, siCaspase3 BV2 monoculture, siControl BV2 cocultured 6h with C6 glioma cells and siCaspase3 BV2 cocultured 6h with C6 glioma cells. Equal amount total RNA from each culture was used for the gene expression analysis. Please note that the raw data for three independent experiments (prior to averaging the data) is provided in the 'Raw_Data_File_with_the_Ct_values_for_3_indep_experiments.txt'.
Project description:Objective: Assuming that mesenchymal stem cells adapt to the osteoarthritic joint environment to exert a chondroprotective effect, we aimed at investigating the molecular response set up by MSCs after priming by OA chondrocytes in cocultures. Design: We used primary human OA chondrocytes and adipose stem cells (ASCs) in mono- and cocultures and performed a high throughput secretome analysis. Among secreted proteins differentially induced in cocultures, we identified thrombospondin-1 (THBS1) as a potential candidate that could be involved in the chondroprotective effect of ASCs. Results: Secretome analysis revealed significant induction of THBS1in ASCs/chondrocytes cocultures at the mRNA and protein levels. Interestingly, we showed that THBS1 was up-regulated at late stages of MSC chondrogenic differentiation while recombinant THBS1 exerted a prochondrogenic effect on MSC. However, down-regulation of THBS1 in ASCs did not revert OA chondrocyte phenotype by decreasing hypertrophic and inflammatory markers. Nevertheless, down-regulation of THBS1 in ASCs reduced their immunosuppressive activity while recombinant THBS1 exerted an anti-inflammatory role on T lymphocytes. THBS1 function was evaluated in vivo in the collagenase-induced OA (CIOA) model by comparing ASCs expressing siTHBS1 and control ASCs. The OA protective effect of ASCs was reversed when THBS1 was down-regulated in ASCs indicating that THBS1 plays a role in the therapeutic effect of ASCs Conclusions: Our data gather some evidence that THBS1 exerts a pro-chondrogenic and anti-inflammatory function in vitro, which could partially explain a chondroprotective effect of ASCs in OA.
Project description:We previously described that the coculture of primary human osteoblasts (hOBs) and human umbilical vein endothelial cells (HUVECs) improves the differentiation of both cell types, leading to the formation of functional blood vessels and enhanced bone regeneration. The objective of this study was to further delineate the multifaceted interactions between both cell types. To investigate the proteome of hOBs after cocultivation with HUVECs we used stable isotope labeling by amino acids in cell culture