Project description:Rhizobium leguminosarum bivar viciae strain 3841 was grown on AMS minimal medium with either succinate ammonia or glucose ammonia as carbon and nitrogen sources. Gene expression was compared between the two crabon sources. Total RNA was amplified using Genispheres SenseAmp kit.
Project description:Meta-proteomics analysis approach in the application of biogas production from anaerobic digestion has many advantages that has not been fully uncovered yet. This study aims to investigate biogas production from a stable 2-stage chicken manure fermentation system in chemical and biological perspective. The diversity and functional protein changes from the 1st stage to 2nd stage is a good indication to expose the differential metabolic processes in anaerobic digestion. The highlight of identified functional proteins explain the causation of accumulated ammonia and carbon sources for methane production. Due to the ammonia stress and nutrient limitation, the hydrogenotrophic methanogenic pathway is adopted as indicative of meta-proteomics data involving the key methanogenic substrates (formate and acetate). Unlike traditional meta-genomic analysis, this study could provide both species names of microorganism and enzymes to directly point the generation pathway of methane and carbon dioxide in investigating biogas production of chicken manure.
Project description:Gene expression in wildtype Rhizobium leguminosarum biovar viciae strain 3841 was comapred to a bacA mutant. All cultures were grown in the laboratory on AMS with glucose and ammonia as carbon and nitrogen sources.
Project description:Transcriptional profiling of the yeast Lachancea kluyveri when grown on minimal media with different compounds added as the sole nitrogen source. Cells grown on uracil, uridine, dihydrouracil and ammonia were profiled using cells grown on proline as the reference.
Project description:Purpose: To investigate the influence of the 40 genes on plasmid, we compared the transcript varies between the engineered strains and the wild-type strain in synthetic medium with different carbon sources (i.e., glucose, galactose and ethanol/glycerol media). Methods: Total mRNA profiles of the engineered strains and the wild-type strain were generated by deep sequencing, in triplicate, using BGIseq500. The sequence reads that passed quality filters were analyzed. Results: RNA sequencing results revealed that the transcript patterns were influenced dramatically by the carbon sources and there was no significant difference between the wild-type and engineered strains (that is, any change amounted to less than 10%)
Project description:We propose a carbon source dependent genetic regulatory network for the budding yeast Saccharomyces cerevisiae, derived from quantitative proteomic analyses integrated with bioinformatics knowledge of regulatory pathways and protein interactions. The proposed network, comprising 1247 transcription factor interactions and 126 chaperone interactions, defines the proteome shift in the cell when growing under different carbon sources. We used a label-free proteomics strategy to quantify alterations in protein abundance for S. cerevisiae when grown on minimal media using glucose, galactose, maltose and trehalose as sole carbon sources.
Project description:This experiment was performed to obtain strand-specific transcriptional profiles of haploid yeast in four different growth conditions. This helps to better understand how sense and antisense transcription changes as a function of growth condition and thus complements the protein-based data of the publication this dataset refers to.Haploid yeast (strain YMaM330) were grown to mid-log phase in one of 4 growth media: rich media with either glucose, galactose or ethanol (YPD, YPGal or YPE) as carbon sources or synthetic growth medium with glucose as a carbon source (SC). Strand-specific tiling arrays were then used to measure RNA levels of both coding and non-coding transcripts. We found the transcriptome to be very similar to diploid yeast and therefore used the annotation established in Xu Z., Nature, 2009. The expression profiles are available in a searchable web-database (http://steinmetzlab.embl.de//cgi-bin/viewKnopLabArray.pl?showSamples=KnopHaploidTest2&type=heatmap).
Project description:Escherichia coli culture was subjected to two different types of nutritional scenarios, abundant carbon/ nitrogen sources and scarce carbon/nitrogen medium. Study revealed that scarce medium adapted culture were more tolerant to hydrogen peroxide than abundant medium.
