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 ﾰC and 55 ﾰC. Other two reactors were run with either residue at 37 ﾰC. 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).
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]
Project description:The aim of the study was to use microarray for profiling the microbiota in anaerobic digestion process. The probes are ssDNA molecules that are ligated into circular molecules if a complementary target sequence is present in the sample DNA. Ligated probes are PCR amplified with a labeled primer, and the amplicons are hybridized on DNA microarray by tag sequences.
Project description:Cultures were grown at 28 oC for 48 h on a shaker at 250 rpm. MG132 (60 ﾵM, 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.
Project description:Synechococcus elongatus PCC7942 wild type, the IdiB-free S.elongatus mutant K10 (Michel et al. 1999; Microbiology, 145: page 1473-1484) and the IdiC-merodiploid mutant MuD (Pietsch et al. 2007, Photosynth. Res. 94: page 91-108) were cultivated in BG11 medium, continuously bubbled with 2%CO2-enriched air and illuminated with fluorescent bulbs with a light intensity of 100 ﾵmol photons m-s s-1. After an inoculation of a cell density of OD750nm 0.3 the cells were cultivated with iron-sufficient or iron-deficient BG11 medium. The growth time for wild type was 24h and 72h. The two mutants were cultivated for 72h only. Possible differences in the RNA amount after the cultivation with or without iron were examined using the microarray technique. .
Project description:With the aim of investigating the genome-wide postprandial effects of single servings ingestion of milk and yogurt on gene expression in the blood cells of human subjects and to identify the downstream physiological processes regulated by the differentially expressed genes we conducted a randomized, controlled, single blinded, crossover study on 6 healthy male individuals. 540g of milk or yogurt was ingested after an overnight fasting. Blood samples were collected before (0h) and 2h, 4h, 6h after the ingestion and the blood cell transcriptome was analyzed using a linear kinetic analysis.
Project description:Transcription profiling of Physcomitrella patens Reute strain gametophore, mature sporophyte and spore stage. These samples are part of an large-scale expression data set for the model moss Physcomitrella patens.
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.
Project description:To study the composition of mRNPs containing TcDhh1, we carried out immunoprecipitation assays with anti-TcDhh1 and epimastigotes lysates. Pre-immune serum was used as control. We also carried out a ribonomic approach to identify the mRNAs present within the TcDhh1 immunoprecipitated complexes. For this purpose, competitive microarray hibridizations were performed against negative controls, the non-precipitated fraction.