Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic hybridization of Methanobacteria to identify the diversity in strains on manure and olive mill waste.

ABSTRACT: Population dynamics of methanogenic genera was investigated in pilot anaerobic digesters. Cattle manure and two-phase olive mill wastes were codigested at a 3:1 ratio in two reactors operated at 37 ï¾°C and 55 ï¾°C. Other two reactors were run with either residue at 37 ï¾°C. Sludge DNA extracted from samples taken from all four reactors on days 4, 14 and 28 of digestion was used for hybridisation with the AnaeroChip, an oligonucleotide microarray targeting those groups of methanogenic archaea that are commonly found under mesophilic and thermophilic conditions (Franke-Whittle et al. 2009, in press, doi:10.1016/j.mimet.2009.09.017).

ORGANISM(S): Methanobacteria

SUBMITTER: Marta Goberna

PROVIDER: E-MEXP-2453 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Adaptation of methanogenic communities to the cofermentation of cattle excreta and olive mill wastes at 37 degrees C and 55 degrees C.

Goberna Marta M Gadermaier Maria M García Carlos C Wett Bernhard B Insam Heribert H

Applied and environmental microbiology 20100730 19

The acclimatization of methanogens to two-phase olive mill wastes (TPOMW) was investigated in pilot fermenters started up with cattle excreta (37°C) and after changing their feed to excreta plus TPOMW (37°C or 55°C) or TPOMW alone (37°C) until a steady state was reached (28 days). Methanogenic diversity was screened using a phylogenetic microarray (AnaeroChip), and positive targets were quantified by real-time PCR. Results revealed high phylogenetic richness, with representatives of three out of ...[more]

PMID: 20675446

Similar Datasets

Transcription profiling of Trichoderma reesei QM6a to assess the cellular effects of expression of misfolded CBHI molecules

Project description:Cultures were grown at 28 oC for 48 h on a shaker at 250 rpm. MG132 (60 ï¾µM, final concentration) in phenylmethylsulfonyl fluoride (PMSF) was added after 46 h or PMSF was added alone to the cultures without MG132. Following sample collection, mycelia were washed with 0.9 % (w/v) NaCl in RNAse-free (diethyl pyrocarbonite [DEPC]-treated) water, frozen in liquid nitrogen and stored at -80 oC.

2009-05-29 | E-MEXP-2190 | biostudies-arrayexpress

Transcription profiling of Candida albicans after induction of tet-OP4 promoter-EFG1 fusion under normoxia

Project description:Transformants either containing pCS1 (strain CCS1) or pNIM as control (strain CCS2) were induced by doxycycline (40 ï¾µg/ml) for the indicated times (T0-T10, 0 to 10 min) in aerated hypha-inducing medium (10 % serum, 37 ï¾°C). For each time point, cDNA of CCS1 and CCS2 were co-hybridised to microarrays and ratios of expression were calculated for each gene. Each gene is represented by duplicate spots on the DNA microarrays.

2009-04-07 | E-MEXP-2117 | biostudies-arrayexpress

Transcription profiling by array of C. albicans genes after induction of tet-OP4 promoter-EFG1 fusion under hypoxia.

Project description:Transformants either containing pCS1 (strain CCS1) or pNIM as control (strain CCS2) were induced by doxycycline (40 ï¾µg/ml) for the indicated times (T0-T10, 0 to 10 min) in hypha-inducing medium (10 % serum, 37 ï¾°C) under a stream of 93.8 % nitrogen, 6 % CO2 and 0.2 % oxygen. For each time point, cDNA of CCS1 and CCS2 were co-hybridised to microarrays and ratios of expression were calculated for each gene. Each gene is represented by duplicate spots on the DNA microarrays.

2010-03-18 | E-MEXP-2119 | biostudies-arrayexpress

partial-nitritation anammox reactor

Project description:Identify and characterize two distinct communities, the aerobic community and the anaerobic community in the partial nitritation/anammox reactors using metaproteomics approach

2019-07-26 | PXD009787 | Pride

Transcription profiling of honey bees for identification of changes in transcript abundance relating to Colony Collapse Disorder

Project description:Remaining adult bees in colonies suffering from CCD at apiaries in Florida, California and Pennsylvania were collected during the winter of 2006-2007. The health of CCD colonies was scored at the time of collection as either ï¾severeï¾ or ï¾mildï¾ depending on the apparent strength of the colony. ï¾Historicalï¾ bees, collected prior to the appearance of CCD and hence ostensibly healthy, were collected in 2004 and 2005 from colonies set up on new equipment and not receiving any miticide treatments from apiaries of The Pennsylvania State University near State College, PA. A combination looped, common-reference microarray design was used to compare historical and CCD samples with each other; a blend of RNA isolated from healthy colonies (collected near Urbana, IL in July 2007) served as reference. The microarray experiment compared the guts of bees from mildly and severely afflicted colonies collected in apiaries experiencing CCD on the East Coast (Florida and Pennsylvania) and West Coast (California) with a common reference.

2009-08-15 | E-MEXP-2292 | biostudies-arrayexpress

Anaerobic biogas plants via LC-MS/MS

Project description:Anaerobic degradation (AD) of heterogeneous agricultural substrates is a complex process involving a diverse microbial community. While microbial community composition of a variety of biogas plants (BPs) is well described, little is known about metabolic processes and microbial interaction patterns. Here, we analyzed 16 large-scale BPs using metaproteomics. All metabolic steps of AD were observed in the metaproteome, and multivariate analyses indicated that they were shaped by temperature, pH, volatile fatty acid content and substrate types. Biogas plants can be subdivided into hydrogenotrophic, acetoclastic or a mixture of both methanogenic pathways based on their process parameters, taxonomic and functional metaproteome. Network analyses showed large differences in metabolic and microbial interaction patterns. Both, number of interactions and interaction partners were highly dependent on the prevalent methanogenic pathway for most species. Nevertheless, we observed a highly conserved metabolism of different abundant Pseudomonas spp. for all BPs indicating a key role during AD in carbohydrate hydrolysis irrespectively of variabilities in substrate input and process parameters. Thus, Pseudomonas spp. are of high importance for robust and versatile AD food webs, which highlight a large variety of downstream metabolic processes for their respective methanogenic pathways.

2019-11-11 | PXD014605 | Pride

Transcription profiling by array of human renal proximal tubular cells of young or senescent replicative age; or high or low reactive oxygen species.

Project description:Renal Proximal Tubular Cells of young / senescent replicative age or high / low reactive oxygen species content were profiled using an Affymetrix Chip Platform. Sample classifications: Young refers to the in vitro age of early passage cells. Senescent indicates cells at the end of their in vitro life span, having entered an irreversible growth arrest. SortHI refers to cells with high intracellular reactive oxygen species content that were sorted by FACS according to a bright FL1 fluorescence after staining with 1 ï¾µM CM-H2DCFDA (Molecular Probes Cat No C6827). SortLO refers to cells with low intracellular reactive oxygen species content that were sorted by FACS according to a dim FL1 fluorescence after staining with 1 ï¾µM CM-H2DCFDA.

2011-01-15 | E-MEXP-2683 | biostudies-arrayexpress

Transcription profiling by array of human olfactory ecto-mesenchymal stem cells in familial dysautonomia

Project description:Exploration of transcriptome expression in 5 control and 4 familial dysautonomia (FD) human olfactory ecto-mesenchymal stem cells (hOE-MSCs) at very early (P1 and P2) and later (P5 and P9) cell passages.

2011-01-01 | E-MTAB-281 | biostudies-arrayexpress

Meta-transcriptomic analysis of the response of river biofilms to pharmaceutical products using anonymous DNA microarray

Project description:Low concentrations of pharmaceutical compounds were shown to induce transcriptional responses in isolated microorganisms, which could have consequences on ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two distinct rivers and supplemented with environmentally relevant doses of four pharmaceutical products (erythromycin-ER, gemfibrozil-GM, sulfamethazine-SN and sulfamethoxazole-SL). To follow the expression of functional genes, we constructed a 9,600 features anonymous DNA microarray platform onto which cDNA from the various biofilms was hybridized. The reactor design for biofilm development has been previously described (Lawrence et al., 2004; Lawrence et al., 2000). Two duplicate experiments were carried out, with reactors being inoculated with either water from the WC (nutrient rich) or the SSR (nutrient poor). Treatments consisted in the addition of various pharmaceutical compounds: 1 µg l-1 erythromycin (ER), 1 µg l-1 gemfibrozil (GM), 0.5 µg l-1 sulfamethazine (SN), 0.5 µg l-1 sulfamethoxazole (SL). Nothing was added to control reactors (CO). All treatments were replicated independently three times. A reference sample (composite sample from Wascana Creek reactors used to construct the microarray) was hybridized (Cy5) on each slide.

2010-07-06 | E-GEOD-20501 | biostudies-arrayexpress

Transcription profiling of human embryonic kidney cell line HEK293T to investigate the effects of overexpression of FoxO4 or mutated FoxO4 in presence or absence of p300

Project description:Effects of overexpression of FoxO4 or mutated FoxO4 in presence or absence of p300 overexpression

2009-07-30 | E-MTAB-4 | biostudies-arrayexpress