GEO DataSets

(Submitter supplied) Background: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. Results: In this study, C. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL15992

43 Samples

Download data: TXT

(Submitter supplied) 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. However, C. thermocellum is relatively sensitive to ethanol compared to yeast. Previous studies have investigated the membrane and protein composition of wild-type and ethanol tolerant strains, but relatively little is known about the genome changes associated with the ethanol tolerant C. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL11186

30 Samples

Download data: CALLS, PAIR

(Submitter supplied) The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus 27405

Type:

Expression profiling by array

Platform:

GPL17171

8 Samples

Download data: CALLS, PAIR

(Submitter supplied) Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium. We are primarily interested in gene regulation by three predicted LacI regulators. more...

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

36 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by array

Platform:

GPL20749

32 Samples

Download data: TXT

(Submitter supplied) Background: The ability of Clostridium thermocellum ATCC 27405 wild-type strain to hydrolyze cellulose and ferment the degradation products directly to ethanol and other metabolic byproducts makes it an attractive candidate for consolidated bioprocessing of cellulosic biomass to biofuels. In this study, whole-genome microarrays were used to investigate the expression of C. thermocellum mRNA during growth on crystalline cellulose in controlled replicate batch fermentations. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL13640

39 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis revealed that genes involved in urea uptake and metabolism were significantly upregulated in the Clo1313_2031 deletion strain, suggesting that deletion of Clo1313_2031 mimics nitrogen starvation in C. thermocellum. Additionally, genes encoding the RNF-complex were also more highly expressed and in turn may have a potential role in increasing ethanol production.

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

8 Samples

Download data: TXT, XLSX

(Submitter supplied) Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. more...

Organism:

Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL16336

4 Samples

Download data: GPR

(Submitter supplied) Four C. thermocellum DSM-1313 derived strains were assessed using metabolite and DNA microarray tools in order to better understand carbon and electron flow within this organism. C. thermocellum is able to ferment cellulose into its fermentation end products L-lactate, acetate, formate, hydrogen gas, and ethanol, with the latter being the desired end product to be used as biorenewable fuel. In addition to the parent strain (genotype: hpt spo0A), strains with either or both of the genes encoding lactate dehydrogenase (ldh) and phosphate acetyltransferase (pta) deleted were studied. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by array

Platform:

GPL13117

24 Samples

Download data: XYS

(Submitter supplied) The main objective is to develop a strain tolerant to furfural for ethanol production from lignocellulosic hydrolysates. We compare gene expressions among three genetically modified S. cerevisiae (control, TAL-expressing and TAL-ADH expressing strain) under the presence and absence of furfural.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9294

12 Samples

Download data: TXT

(Submitter supplied) Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by array

Platform:

GPL6431

24 Samples

Download data: TXT

(Submitter supplied) Background: Lignocellulosic biomass is a promising renewable feedstock for the microbial production of fuels. To release the major fermentable sugars such as glucose and xylose, pretreatment, hydrolysis, and subsequent conditioning of biomass feedstock are needed. During this process, many toxic compounds are produced or introduced which subsequently inhibit microbial growth and in many cases the production titer and rate. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by genome tiling array

Platform:

GPL18675

30 Samples

Download data: TXT

(Submitter supplied) DNA sequences for the 3163 C. thermocellum ATCC 27405 predicted protein-encoding genes were obtained from The Joint Genome Institute using sequence assembled in November 2003. Oligonucleotide probes that represented the whole genome of C. thermocellum were designed using the CommOligo software and were commercially synthesized without modification (MWG Biotech, High Point, NC) in 96-well plates. The concentration of the probes was adjusted to 100 pmol/JlL, transferred to 384-well printing plates in a final concentration of 50% dimethyl sulfoxide using a BioMek FX liquid handling robot (Beckman-Coulter, Fullerton, CA) and then spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI) in a dust-free clean room maintained at 21°C and 50% relative humidity. more...

Organism:

Acetivibrio thermocellus ATCC 27405

1 Series

39 Samples

Download data: TXT

(Submitter supplied) Clostridium thermocellum forms adherent biofilms on lignocellulosic feedstock in a typical continuous cell-monolayer to efficiently break down and uptake cellulose hydrolysates. The adherent biofilm (i.e., sessile cells) may freely revert to the non-adherent form (i.e., planktonic cells) through generation of offspring cells or microenvironment constraints such as limited surface area. The two interdependent cell populations co-exist and have different contributions to culture activity and growth. more...

Organism:

Acetivibrio thermocellus 27405

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22495

8 Samples

Download data: XLSX

(Submitter supplied) Earlier studies pointed to the ability of C. thermocellum to exquisitely control gene expression in response to growth rate and the presence of insoluble cellulose or soluble compounds such as cellobiose. This microarray study was carried out in order to examine expression responses of the entire genome. The use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates.

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL10557

11 Samples

Download data: PAIR

(Submitter supplied) Heat alters biology from molecular to ecological levels, but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here, we provide a comprehensive picture of the molecular signatures of this process, by integrating multiomic and phenotypic data. In individual zebrafish embryos, repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow-down in concert with reduced responses to novel stimuli. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

12 Samples

Download data: TAB