Transcription profiling of yeast cells (homozygous deletion mutants of BY4743) grown in chemostats, sampled at steady state. Glucose and ammonium limitation, dilution rates 0.1 and 0.2 hr-1, gene deletions HO and HAP4 applied
ABSTRACT: S. cerevisiae cells (homozygous deletion mutants of BY4743) grown in chemostats, sampled at steady state. Glucose and ammonium limitation, dilution rates 0.1 and 0.2 hr-1, gene deletions HO and HAP4 applied.
New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods.Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets ...[more]
Project description:Deletion mutants of S. cerevisiae 4743 were grown in glucose-limited continuous chemostats (D = 0.2h-1). The deletion mutants used were: Homozygous deletion mutants of HAP4, OXA1, BCS1, RIP1, MBA1 and MIG1. Heterozygous deletion mutants of HAP4, RIP1 and MIG1.
Project description:Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples. Two samples cultured in minimum media with abundant ammonium (MM) or minute ammonium (MM-N)
Project description:A three-factor design was applied to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures of Saccharomyces cerevisiae.
Project description:Investigation of lipid metabolism as a function of three experimental factors: 1) aerobicity (aerobic vs anaerobic, or 'A' vs 'O'), 2) nutrient limitation (carbon vs nitrogen limitation, or 'C' vs 'N'), 3) temperature (30C vs 15C, or 'T' vs 't') using a full factorial design.
Project description:Physiological effects of carbon dioxide and impact on genome-wide transcript profiles were analysed in chemostat cultures of Saccharomyces cerevisiae. In anaerobic, glucose-limited chemostat cultures grown at atmospheric pressure, cultivation under CO2-saturated conditions had only a marginal (<10%) impact on the biomass yield. Conversely, a 25% decrease of the biomass yield was found in aerobic, glucose-limited chemostat cultures aerated with a mixture of 79% CO2 and 21% O2. This observation indicated that respiratory metabolism is more sensitive to CO2 than fermentative metabolism. Consistent with the more pronounced physiological effects of CO2 in respiratory cultures, the number of CO2-responsive transcripts was higher in aerobic cultures than in anaerobic cultures. Many genes involved in mitochondrial functions showed a transcriptional response to elevated CO2 concentrations. This is consistent with an uncoupling effect of CO2 and/or intracellular bicarbonate on the mitochondrial inner membrane. Other transcripts that showed a significant transcriptional response to elevated CO2 included NCE103 (probably encoding carbonic anhydrase), PCK1 (encoding PEP carboxykinase) and members of the IMD gene family (encoding isozymes of inosine monophosphate dehydrogenase Experiment Overall Design: Knowledge on the genome-wide transcriptional response of S. cerevisiae to high CO2 concentrations may provide a deeper insight into the molecular mechanisms of CO2 stress. Such insight is essential to develop metabolic-engineering strategies for improving CO2 tolerance. Furthermore, identification of ‘signature transcripts’ that uniquely respond to CO2 stress may be applicable for diagnosing the CO2 status of industrial fermentations. It has recently been demonstrated that the combination of chemostat cultivation with DNA-microarray-based transcriptome analysis offers a powerful and reproducible approach to identify the transcriptional responses of yeasts to environmental parameters For this reason, in the present study we used chemostat cultures of S. cerevisiae to quantify the effect of CO2 on respiring and fermenting cells, and to determine the genome-wide transcriptional responses of this yeast to high CO2 concentrations.
Project description:First part of the time-course transcriptomic profilling of the oleaginous yeast Yarrowia lipolytica, obtained during a controlled decellerostat (D-stat) setup. A nitrogen limitation was applied during the course of the D-stat to initiate and control de novo biolipid synthesis. Yarrowia lipolytica Agilent microarray, one-color staining. Each time sample was spotted in triplicate. A reference condition was spotted in quadruplicate, based on a RNA pool from three samples obtained during the biomass production phase.