Project description:The response of P. putida CSV86 in response to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with either naphthalene (0.1%) alone or along with glucose (0.25%) as carbon source and different concentration of ammonium nitrate. For nitrogen limiting 0.1% NH4N03 was added in the medium and for nitrogen rich 1% NH4N03 was used. As control CSV86 was also grown in 1X Luria Broth with glucose as additional carbon source. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.
Project description:The response of P. putida KT2440 (PB2440) to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with 2mM glucose as carbon source and different concentration of ammonium chloride as nitrogen source. For nitrogen limiting condition 2mM ammonium chloride was used whereas, for nitrogen rich condition 20mM ammonium chloride was added in the medium. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.
Project description:The response of P. putida CF600 to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with 2mM phenol as carbon source and different concentration of ammonium chloride as nitrogen source. For nitrogen limiting condition 2mM ammonium chloride was used whereas, for nitrogen rich condition 20mM ammonium chloride was added in the medium. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.
Project description:The thermophilic filamentous fungi Myceliophthora thermophila (Sporotrichum thermophile) and Thielavia terrestris are proficient decomposers of cellulose, suggesting that they will be a rich source of thermostable industrial enzymes for lignocellulose degradation. To identify the genes and proteins involved in this process, we explored the transcriptomes of M. thermophila and T. terrestris growing at 45 ºC on either glucose, alfalfa, or barley straw by short-read sequencing of extracted mRNA. To better understand the adaptations that allow these fungi to grow at elevated temperatures, we compared their transcriptomes when growing at 34C to their transcritomes at 45C, and also to the transcriptome of the related fungus Chaetomium globosum, which does not grow at 45C. RNA was extracted from cultures in early growth stage growing with glucose, alfalfa, or barley straw as carbon source at 34C or 45C (M. thermophila and T. terrestris); duplicate cultures were sampled in some conditions.
Project description:Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.
Project description:Purpose: Examining the transcriptome of human gut bacteria that grow on seaweed polysaccharides as a sole carbon source Methods: Strains were grown on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro. Fold change was calculated as seaweed polysaccharide over galactose with n=2 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth, RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1% of the overall average RPKM expression level. READS WERE ANALYZED .......GABRIEL FILL IN Results: We identified novel polysaccharide utiilization loci in 5 strains of human gut bacteria
Project description:Neosartorya fischeri is a fungi that is able to grow in petroleum asphaltenes as sole carbon source. Here, was investigated which enzymes were up regulated
Project description:The gut bacterium Coprococcus sp. ART55/1 has been found to encode two genes containing glycoside hydrolase family 9 (GH9) catalytic domains. These genes are hypothesised to impact upon the ability of this bacteria to utilise different carbon sources. To further investigate the role of these genes, as well as the wider transcriptome, Coprococcus sp. ART55/1 was grown on five different carbon sources - beta-glucan, lichenan, cellobiose, glucose and glucomannan - and the transcriptional response was investigated using RNA sequencing.