Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae

Hayes, Andrew; Zhang, Nianshu; Wu, Jian; Butler, Philip R.; Hauser, Nicole; Hoheisel, Jöerg; Lim, Fei Ling; Sharrocks, Andrew D.; Oliver, Stephen G.

doi:10.1016/s1046-2023(02)00032-4

Cited by 83 publications

(75 citation statements)

References 19 publications

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“…Progress is, however, being made in the use of chemostat culture for exploitation of functional genomics. The effect of growthrate-dependent factors can obscure observations made in batch culture, as elegantly demonstrated by Hayes et al (2002). The transcription factor Mcm1 is involved in the regulation of the cell cycle in S. cerevisiae.…”

Section: Application Of the Chemostat To The Functionalgenomic Eramentioning

confidence: 99%

“…This study demonstrates the power of the chemostat for transcriptional profiling by revealing genes sets hidden by secondary growth effects. Subsequently, transcriptional profiling of chemostat-grown cultures from nitrogen-or carbon-limited cultures, at two different specific growth rates, showed that expression profiles gained from known genes can be exploited to gain further insight into functions of unknown genes, and into the molecular basis of growth rate control (Hayes et al, 2002).…”

Section: Application Of the Chemostat To The Functionalgenomic Eramentioning

confidence: 99%

“…Studies such those of Hayes et al (2002), Kolkman et al (2004), Piper et al (2002) and Wu et al (2004) highlight the enhanced reproducibility of transcriptome, proteome, metabolome and metabolic engineering data obtained from steady-state chemostat cultures. The carefully controlled and defined physiological conditions obtainable in chemostat cultures enable the acquisition of reliable biological samples for analysis by multiple functional genomic techniques, resulting in, to paraphrase Delneri et al (2001), 'a truly integrative biology of model organisms'.…”

Section: Continuous Culture As An Aid To Reproducibility and Functionmentioning

confidence: 99%

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Continuous culture – making a comeback?

2005

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The heyday of continuous culture was in the 1960s, when its versatility and reproducibility were used to address fundamental problems in diverse microbiological fields such as biochemistry, ecology, genetics and physiology. The advent of molecular genetics in the 1970s and 1980s led to a decline in the popularity of continuous culture as a standard laboratory tool. The current trend of studying global proteomics, transcriptomics and metabolomics requires reproducible, reliable and biologically homogeneous datasets with which to approach a given problem. The use of continuous culture techniques can aid the acquisition of such data, and continuous cultures offer advantages over biologically heterogeneous batch cultures, where secondary growth and stress effects can often mask subtle physiological differences and trends. This review is intended to remind microbiologists of the value of continuous cultivation in a wide range of biological investigations, and describes some advantages and recent advances in applications of continuous culture in post-genomic studies.

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Section: Application Of the Chemostat To The Functionalgenomic Eramentioning

confidence: 99%

Section: Application Of the Chemostat To The Functionalgenomic Eramentioning

confidence: 99%

Section: Continuous Culture As An Aid To Reproducibility and Functionmentioning

confidence: 99%

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Continuous culture – making a comeback?

2005

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“…The mixture was heated at 100°C for 3 min. Hybridization was carried out as described by Hayes et al [17].…”

Section: Microarray Hybridizationmentioning

confidence: 99%

Global gene expression profiles for the growth phases of Trichophyton rubrum

Liu

Leng

et al. 2011

Sci. China Life Sci.

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Trichophyton rubrum (T. rubrum) is a common superficial fungus. Molecular and genetic studies of T. rubrum are still limited. In this paper, we report the global analysis of gene expression profiles at different growth phases using cDNA microarray technology. A total of 2044 differentially expressed genes were obtained and clustered into three expression patterns. Our data confirmed previous results that many mRNAs were pre-stored in the conidia of T. rubrum. Transcriptional profiling and function analysis showed that some glycolytic enzymes share similar expression patterns and may be coregulated during the transition of growth phases. Some genes involved in small GTPase signaling pathways, and in cAMP-dependent and MAPK regulation pathways were induced in response to the growth dynamics of T. rubrum. Although the detailed biological roles of these T. rubrum genes are still unknown, our results suggest that these genes may be involved in regulation mechanisms in the life cycle of the fungus.

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“…However, the application of some of these techniques at a global, genome-wide, scale can be too onerous (Brown et al, 2001). With the recent development of hybridisation-array technology (Schena et al, 1995;Lashkari et al, 1997;Wodicka et al, 1997;Gasch et al, 2000), gene expression studies are increasingly being used for functional discovery, analysis and experimental annotation of reference genomes (Hughes et al, 2000;Shoemaker et al, 2001;Hayes et al, 2002;Bono et al, 2003;Levine and Tjian, 2003;Yamada et al, 2003). Microarrays are also being applied in analyses of differential expression in cells and tissues, gene discovery, drug screening and diagnostics (US Patent 6544742;2003124581;2003180774;WO Patent 0218646).…”

Section: Post-genomic Studies Perspective New Challengesmentioning

confidence: 99%

Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics

Castrillo¹,

Oliver²

2004

BMB Reports

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The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, 'systems biology' studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).

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Hybridization array technology coupled with chemostat culture: Tools to interrogate gene expression in Saccharomyces cerevisiae

Cited by 83 publications

References 19 publications

Continuous culture – making a comeback?

Continuous culture – making a comeback?

Global gene expression profiles for the growth phases of Trichophyton rubrum

Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics

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