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ABSTRACT: Clostridium polysaccharolyticum DSM 1801

PROVIDER: PRJEB17055 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	FOHN01.dat.gz	Other
	FOHN01.fasta.gz	Fasta.gz
	FOHN01.master.dat	Other
	FOHN01.dat.gz	Other

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[Clostridium] polysaccharolyticum DSM 1801

Project description:Clostridium polysaccharolyticum DSM 1801 genome sequencing

| PRJNA303218 | ENA

Metabolic inhibition of Clostridium thermocellum M1570 by pentose sugars.

Project description:Differential RNA-Seq analyses to investigate the basis for metabolic inhibition of Clostridium thermocellum M1570 by xylose. The M1570 strain was developed in the C. thermocellum DSM 1313 Δhpt background strain. Lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta) genes are deleted (Argyros DA, Tripathi SA, Barrett TF, Rogers SR, Feinberg LF, Olson DG, Foden JM, Miller BB, Lynd LR, Hogsett DA, Caiazza NC: High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. Appl Environ Microbiol 2010, 77:8288-8294 )

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University of Manitoba/MGCB2 C thermocellum RNA-seq Experiment

Project description:Determine overall gene expression profiles; RNA expression observed in stationary relative to exponential phase cells of strain Clostridum thermocellum (ATCC 27405) grown on cellobiose; Comparative RNA expression of 3 Clostridium thermocellu strains (DSM 1237, 2650, and 4150) grown to mid exponential phase on cellobiose; Verify whether observed differences in fermentation end-product ratios are reflected in differences in RNA expression profiles. RNA-seq data will be compared with the same experiments performed with proteomic experiments; Compare gene expression across relative strains.

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RNA-seq analysis of Clostridium beijerinckii DSM 6423 at early exponential, acetogenic, and solventogenic growth phase on rhamnose compared to glucose

Project description:This experiment aim was to characterize the catabolism of L-rhamnose of Clostridium beijerinckii DSM 6423 by transcriptomic analysis, generating new insights and knowledge on utilization of L-rhamnose for production of chemicals, including Isopropanol, Butanol, Ethanol (IBE) and 1,2-propandiol. These analysis on cultures grown on L-rhamnose compared to D-glucose grown cultures showed upregulation of the L-rhamnose-related clusters and genes, and lower expression of the solventogenic genes, which was reflected in the products formed.

2019-01-14 | E-MTAB-7487 | biostudies-arrayexpress

GPR183 mediates the capacity of the novel CD47-CD19 bispecific antibody TG-1801 to heighten ublituximab-umbralisib (U2) anti-lymphoma activity

Project description:Targeted therapies have considerably improved the survival rate of B-cell non-Hodgkin lymphoma (B-NHL) patients in the last decade; however, most subtypes remain incurable. TG-1801, a bispecific antibody that targets CD47 selectively on CD19+ B-cells, is under clinical evaluation in relapsed/refractory B-NHL patients either as a single-agent or in combination with ublituximab, a CD20 antibody, which is also being combined with the PI3Kδ/CK1e inhibitor, umbralisib (“U2”-regimen). In this study, we demonstrated that TG-1801 potentiates ublituximab-mediated antibody-dependent cell death (ADCC) and antibody-dependent cell phagocytosis (ADCP), leading to an additive anti-tumour effect of the TG-1801/U2 combination in B-NHL co-cultures. Accordingly, in a B-NHL xenotransplant model, the triplet achieved a 93% tumour growth inhibition, with 40% of the animals remaining tumour-free 35 days after the last dosing. Transcriptomic analysis further uncovered the upregulation of the G protein-coupled receptor, GPR183, as a crucial event associated with TG-1801/U2 synergism, while pharmacological blockade or genetic depletion of this factor impaired ADCP initiation, as well as cytoskeleton remodelling and cell migration, in B-NHL cultures exposed to the drug combination. Thus, our results set the preclinical rationale and support a combination strategy of TG-1801 with PI3Kδ- and CD20-targeting agents in patients with B-NHL.

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Project description:Investigation of sulfur metabolism in Clostridium thermocellum DSM 1313 ∆hpt, to determine growth and gene expression when the organism is incubated with either the oxidized (i.e., sulfate) or the reduced and assimilated (i.e., cysteine) forms of sulfur. A sulfite reductase (∆hpt ∆SO3R) knockout mutant to limit sulfur assimilation was created to compare the resulting gene expression patterns by RNAseq transciptomics against the parental strain (∆hpt) when both are grown in the presence of sulfate. Additionally, we bypass the sulfate auxotrophy of the mutant by providing assimilated sulfur in the form of cysteine to determine whether growth is restored to normal and whether methionine can be biosynthesized by yet uncharacterized pathways in this organism.

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Project description:RNA expression observed in stationary relative to exponential phase cells of strain Clostridum thermocellum (ATCC 27405) grown on cellobiose. b) Comparative RNA expression of 3 Clostridium thermocellu strains (DSM 1237, 2650, and 4150) grown to mid exponential phase on cellobiose. There are 2 purposes for this experiment. 1) Purpose 1 was to verify whether observed differences in fermentation end-product ratios are reflected in differences in RNA expression profiles. Micro Array data will be compared with the same experiments performed with RNA seq and with proteomic experiments. Purpose 2 was to improve our general understanding of the genomes of these strains by doing the experiments on a chip that combined the current genome information for all three strains. It is expected that the Micro Array will confirm that these genomes as currently available are incomplete.

2014-10-26 | GSE51743 | GEO

Project description:Investigation of whole genome gene expression level changes in Lactococcus lactis KCTC 3769T,L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T . This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains. A one chip study using total RNA recovered from of L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T . For the the transcriptome of of L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T was analyzed using the Lactococcus lactis KCTC 3769T microarray platform

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