GEO DataSets

(Submitter supplied) The co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait for in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus (Csac) growing on individual monosaccharides (arabinose, fructose, galactose, glucose, mannose and xylose), mixtures of these sugars. more...

Organism:

Caldicellulosiruptor saccharolyticus

Type:

Expression profiling by array

Platform:

GPL6681

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caldicellulosiruptor saccharolyticus

Type:

Expression profiling by array

Platform:

GPL6681

15 Samples

Download data: TXT

(Submitter supplied) The co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait for in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on oligosaccharides (composed of glucose and xylose) compared to monosaccharides. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for a number of the 24 putative carbohydrate ATP-binding cassette (ABC) transporters in the C. more...

Organism:

Caldicellulosiruptor saccharolyticus

Type:

Expression profiling by array

Platform:

GPL6681

5 Samples

Download data: TXT

(Submitter supplied) Caldicellulosiruptor saccharolyticus is an extremely thermophilic, Gram-positive anaerobe, which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2 and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to co-utilize glucose and xylose, make this bacterium an attractive candidate for microbial bioenergy production. Glycolytic pathways and an ABC-type sugar transporter were significantly up-regulated during growth on glucose and xylose, indicating that C. more...

Organism:

Caldicellulosiruptor saccharolyticus

Type:

Expression profiling by array

Platform:

GPL6681

4 Samples

Download data: CSV

(Submitter supplied) Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays.

Organism:

Bacillus sp. N16-5

Type:

Expression profiling by array

Platform:

GPL15620

30 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caldicellulosiruptor bescii DSM 6725

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29511

24 Samples

Download data

(Submitter supplied) Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade various polysaccharide components of plant cell walls. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species C. saccharolyticus and C.bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to fourteen Caldicellulosiruptor species. more...

Organism:

Caldicellulosiruptor bescii DSM 6725

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29511

9 Samples

Download data

(Submitter supplied) Extremely thermophilic bacteria from the genus Caldicellulosiruptor can degrade various polysaccharide components of plant cell walls. Previous experimental studies identified a variety of carbohydrate-active enzymes in model species C. saccharolyticus and C.bescii, while prior transcriptomic experiments identified their putative carbohydrate uptake transporters. We investigated the mechanisms of transcriptional regulation of carbohydrate utilization genes using a comparative genomics approach applied to fourteen Caldicellulosiruptor species. more...

Organism:

Caldicellulosiruptor bescii DSM 6725

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29511

15 Samples

Download data: TXT, XLSX

(Submitter supplied) Investigation of whole genome gene expression levels in Clostridium acetobutylicum strain 824 grown individually on starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL9387

33 Samples

Download data: PAIR

(Submitter supplied) Hyperthermophilic bacteria of the genus Thermotoga are known to utilize a wide range of simple and complex polysaccharides. T. maritima's transcriptional response to a variety of mono- and poly-saccharides was previously studied to assign functions to genes involved in carbohydrate uptake and utilization. To compare and contrast closely-related members of the Thermotoga genus, a four-species microarray was developed by expanding a whole genome T. more...

Organism:

Thermotoga neapolitana; Thermotoga petrophila; Thermotoga maritima; Thermotoga sp. RQ2

Type:

Expression profiling by array

Platform:

GPL13655

4 Samples

Download data: CSV, GPR

(Submitter supplied) Phylogenetic, microbiological and comparative genomic analysis was used to examine the diversity among members of the genus Caldicellulosiruptor with an eye towards the capacity of these extremely thermophilic bacteria for degrading the complex carbohydrate content of plant biomass. Seven species from this genus (C. saccharolyticus, C. bescii (formerly Anaerocellum thermophilum), C. hydrothermalis, C. more...

Organism:

Caldicellulosiruptor bescii; Caldicellulosiruptor kronotskyensis; Caldicellulosiruptor saccharolyticus; Caldicellulosiruptor hydrothermalis; Caldicellulosiruptor owensensis; Caldicellulosiruptor acetigenus

Type:

Genome variation profiling by array

Platform:

GPL6681

6 Samples

Download data: CSV

(Submitter supplied) L. acidophilus cells, transferred at least five times in modified MRS medium (Barrangou et al, 2003) containing the carbohydrate of interest, were grown to an OD600 of 0.6, harvested and processed for microarray experiments (Azcarate-Peril et al, 2005). Keywords: other

Organism:

Lactobacillus acidophilus

Type:

Expression profiling by array

Platform:

GPL1401

28 Samples

Download data

(Submitter supplied) The transport of carbohydrates by Streptococcus mutans is accomplished by the phosphoenolpyruvate-phosphotrasferase system (PTS) and ATP-binding cassette (ABC) transporters. To undertake a global transcriptional analysis of all S. mutans sugar transporters simultaneously, we used a whole-genome expression microarray. Global transcription profiles of S. mutans UA159 were determined for several carbohydrates. more...

Organism:

Streptococcus mutans; Streptococcus mutans UA159

Type:

Expression profiling by array

Platform:

GPL4769

48 Samples

Download data: CEL, EXP

(Submitter supplied) Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2 and H2. C. bescii, C. kronotskyensis and C. saccharolyticus solubilized 38%, 36% and 29% (by weight) of unpretreated switchgrass (5 g/l), repectively, which was about half of the concentration of crystalline cellulose (Avicel, 5 g/l) that was solubilized under the same conditions. more...

Organism:

Caldicellulosiruptor bescii; Caldicellulosiruptor kronotskyensis; Caldicellulosiruptor saccharolyticus

Type:

Expression profiling by array

Platforms:

GPL20190 GPL20191 GPL6681

3 Samples

Download data: GPR

(Submitter supplied) The genome of the lignocellulose-degrading, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus encodes genes comprising clusters of glycoside hydrolases, ABC transporters and metabolic enzymes that are transcriptionally responsive to carbohydrates. Transcriptomic and biosolubilization analyses were used to determine if C. saccharolyticus could be deployed as a probe to assess the characteristics of plant biomass feedstocks and efficacy of pre-treatment methods, as these both relate to deconstruction strategies for biofuels production. more...

Organism:

Caldicellulosiruptor saccharolyticus

Type:

Expression profiling by array

Platform:

GPL6681

11 Samples

Download data: CSV, TXT