Effect of iBET762+ on transcriptome of 20861 and 20863 W12 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Alison McBride
PROVIDER: E-GEOD-75987 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2014-01-14 | E-GEOD-53810 | biostudies-arrayexpress
Project description:The high cellulose digestion capability of the anaerobic thermophilic bacterium, Clostridium thermocellum, can be attributed to its efficient glycoside hydrolase system, consisting of both a free-enzyme system and a cellulosomal system, wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins into large protein complexes bound to the bacterial cell wall. Using an integrated series of experiments encompassing polysaccharide depolymerization assays, direct biochemical analyses and transcriptomics, we show herein that, in addition to cell-bound cellulosomes and M-bM-^@M-^\freeM-bM-^@M-^] enzymes, C. thermocellum naturally employs a system of cell-free cellulosomes that are not designed to be tethered to the cell and can diffuse away to attack polysaccharide substrates at some distance from the cell. By characterizing the cells and the secretomes of a series of mutants in which genes for either individual scaffoldins or combinations thereof are deleted, we demonstrate that the cellulosome is far more important in cellulose degradation than are the free enzymes, and that the primary scaffoldin CipA is much more important for the action of the cellulosomes than is the collective contribution of the secondary scaffoldins. Extensive transcriptomics analyses confirm the above results and extend the study to the effects of scaffoldin deletions on the organism as a whole. To gain insights into the transcriptome profiles of C. thermocellum strains when various cellulosomal scaffoldin genes were deleted. High quality RNA was extracted from C. thermocellum grown on cellulose. Transcriptome profiles were obtained at one time point during actively growing fermentations, mid exponential phase when 50% of the substrate had been consumed.
2015-02-28 | E-GEOD-63883 | biostudies-arrayexpress
Project description:The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates A twenty-four array study using total RNA recovered from three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates
2015-08-27 | E-GEOD-72413 | biostudies-arrayexpress
Project description:Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol. Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production. Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth. This perceived redox imbalance may be in part responsible for the mentioned bioproductivity limitations. Toward better understanding the redox metabolism of C. thermocellum, we analyzed gene expression, using microarrays, during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which we observed to change fermentation redox potential. High quality RNA was extracted from C. thermocellum grown on cellobiose in chemostat culture and exposed, separately, to methyl viologen and hydrogen peroxide. Transcriptome profiles were obtained at seven time points during actively growing fermentations, 3 minutes, 15 minutes, 35 minutes, 7 hours, 14 hours, 50 hours, and 60 hours after beginning exposure to each stressor. Exposure treatments were carried out in duplicate and reference/untreated samples were taken before and between treatments, after flushing of stressor chemicals and re-equilibration of growth conditions.
2015-07-29 | E-GEOD-71465 | biostudies-arrayexpress
Project description:Clostridium thermocellum is a leading candidate organism for implementing a consolidated bioprocessing (CBP) strategy for biofuel production due to its native ability to rapidly consume cellulose and its existing ethanol production pathway. C. thermocellum converts cellulose and cellobiose to lactate, formate, acetate, H2, ethanol, amino acids, and other products. Elimination of the pathways leading to products such as H2 could redirect carbon flux towards ethanol production. Rather than delete each hydrogenase individually, we targeted a hydrogenase maturase gene (hydG), which is involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes by assembling the active site. This functionally inactivated all three Fe-Fe hydrogenases simultaneously, as they were unable to make active enzymes. In the ∆hydG mutant, the [NiFe] hydrogenase-encoding ech was also deleted to obtain a mutant that functionally lacks all hydrogenase. The ethanol yield increased nearly 2-fold in ∆hydG∆ech compared to wild type, and H2 production was below the detection limit. Interestingly, ∆hydG and ∆hydG∆ech exhibited improved growth in the presence of acetate in the medium. Transcriptomic and proteomic analysis reveal that genes related to sulfate transport and metabolism were up-regulated in the presence of added acetate in ∆hydG, resulting in altered sulfur metabolism. Further genomic analysis of this strain revealed a mutation in the bi-functional alcohol/aldehyde dehydrogenase adhE gene, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities, whereas the wild type strain can only utilize NADH. This is the exact same adhE mutation found in ethanol-tolerant C. thermocellum strain E50C, but ∆hydG∆ech is not more ethanol tolerant than the wild type. Targeting protein post-translational modification is a promising new approach to target multiple enzymes simultaneously for metabolic engineering. A seventeen array study using total RNA recovered from fermentation cultures of three strains (parental, ∆hydG and ∆hydG∆ech) of Clostridium thermocellum DSM1313. Cells were harvested at an OD 0.4-0.5 from cultures grown in the presence of additional 5mM acetate and compared to untreated controls. At least two biological replicates were performed for each treatment and control condition.
2014-01-15 | E-GEOD-54082 | biostudies-arrayexpress
Project description:Shotgun proteomics was conducted with blood plasma samples collected from woody breast chickens compared with non-woody breast control broilers at 4- and 8 wks of age.
2021-09-07 | PXD026896 | Pride
Project description:Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production to produce bioethanol directly from cellulosic biomass. However, few transcriptomic studies have been reported so far for C. thermocellum using biomass as carbon source. In this study, samples were taken from exponential and stationary phases of C. thermocellum cells growing in MTC media with pretreated switchgrass as carbon source, and transcriptomic profiling change of C. thermocellum during different growth phase was investigated using both expression array and tiling array. This study will help the understanding of gene expression of C. thermocellum using cellulosic biomass as carbon source and the knowledge will facilitate future metabolic engineering effort for strain improvement. [HX12 expression array]: A eleven array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different growth phase of T2 and T3 with switchgrass as carbon source. Two biological replicates used for each phase. [3Plex tiling array]: A six array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different growth phase of T2 and T3 with switchgrass as carbon source. Two biological replicates used for each phase.
2014-05-08 | E-GEOD-26926 | biostudies-arrayexpress
Project description:Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of its ethanol stress response have not been elucidated fully. Methodology/Principal Findings In this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. Conclusions Our study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated “omics” approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress. A sixteen array study using total RNA recovered from wild-type cultures of Zymomonas mobilis subsp mobilis ZM4 at different time points of 6, 10, 13.5, and 26h post-inoculation with 6% (v/v) treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.
2013-09-04 | E-GEOD-21165 | biostudies-arrayexpress
Project description:Rainbow darter (Etheostoma caeruleum) are a small benthic fish found in North America. This species is sensitive to sewage effluent in the environment, showing the presence of intersex in up to 80% of males in near-field areas in the Grand River, ON. To learn more about the molecular events associated with intersex, we developed a customized oligonucleotide microarray (4x180K) with next generation sequencing (454 Roche) to characterize molecular responses in the gonad. Transcriptomics was performed on both males and females from both a reference site and a polluted site. Males with and without intersex from the polluted site were compared to the control males. Rainbow darter were sampled from from the Grand River in May 2011. Fish were selected according to the location, gonad maturity, and intersex index. Reference fish were taken from the upstream to the urban area; exposed fish were taken from downstream of from Kitchener MWWE treatment plant.
2014-05-22 | E-GEOD-57394 | biostudies-arrayexpress
Project description:Background: Microalgae can make a significant contribution towards meeting global renewable energy needs in both lipid-based liquid biofuel and hydrogen biofuel. The development of energy-related products and chemicals from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. We have developed a de novo sequencing, annotation, and quantitation pipeline that can be applied to unsequenced organisms for effective quantitative gene expression profiling. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular hydrogen (H2) under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of hydrogen photoproduction in this organism. Results: In this work, we measured rates of hydrogen production and extracted RNA from samples of C. moewusii following various lengths of dark anaerobic incubation. RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of hydrogen photoproduction. One hundred fifty six million reads generated from seven samples were then used for de novo assembly after data trimming. The BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 39,136 contigs, which were then used as the reference transcripts for RNA-Seq analysis. Nearly 98% transcripts had Blast hits, although more than one-third were annotated as hypothetical proteins. The expression value of RNA-Seq results was imported into statistical software for data quality control, normalization, and subsequent statistical analyses such as One-way ANOVA and K-means Clustering. Our results indicated that more transcripts were differentially expressed during the period of early and higher hydrogen photoproduction, and fewer transcripts were differentially expressed when rates of hydrogen photoproduction decreased. Conclusions: Herein, we have described a workflow to analyze RNA-Seq data without reference genome sequence information, which can be applied to the rapid development of other unsequenced microorganisms (both prokaryotic and eukaryotic) with the potential for development as fuel production strains. This study provided the first transcriptomic RNA-Seq dataset, as well as biological insights into the metabolic changes that occur concomitant with induction of hydrogen photoevolution in C. moewusii, which can help further development of this organism as a hydrogen photoproduction strain. Examine time course gene differential expression post anaerobic induction for hydrogen production
2013-09-04 | E-GEOD-46225 | biostudies-arrayexpress