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Dynamics of two oscillation phenotypes in S. cerevisiae [4hr]

ABSTRACT: Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient. Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle.

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE30052 | GEO | 2012/04/17

SECONDARY ACCESSION(S): PRJNA155161

REPOSITORIES: GEO

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Dynamics of two oscillation phenotypes in S. cerevisiae [4hr]

Project description:Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient. Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle. High-resolution samples over time were collected for CEN.PK113-7D oscillating with 4 hour period.

2012-04-16 | E-GEOD-30052 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae [2hr]

2012-04-16 | E-GEOD-30051 | biostudies-arrayexpress

Dynamics of two oscillation phenotypes in S. cerevisiae [2hr]

2012-04-17 | GSE30051 | GEO

Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122

Project description:Genetic and environmental stresses are known factors that influence an organisms phenotype. Time is rarely taken into consideration when studying phenotypic changes in cells. Time-resolved microarray data revealed genome-wide transcriptional changes in yeast strain CEN.PK122 oscillating with~2 periods. We mapped the global patterns of transcriptional oscillationsinto a 3-dimensional map to represent different cellular phenotypes ofoscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. High-resolution samples over time were collected for CEN.PK122 oscillating with 2 h period.

2012-04-16 | E-GEOD-30054 | biostudies-arrayexpress

Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122

2012-04-17 | GSE30054 | GEO

Budding yeast respiratory oscillations in a transient state

Project description:RNAseq analysis of budding yeast respiratory oscillations was performed at high temporal resolution (4 min, 24 samples), covering 2.5 cycles of the short period oscillation of the IFO 0233 strain of budding yeast. This and related systems were previously analyzed by microarrays and RNAseq, but the expression of noncoding transcripts has not been analyzed. The oscillations were recorded by online measurements and the system underwent a multi-generational transient, where periods first gradually decreased (from 0.7 h to 0.6 h), and then a bifurcation of system dynamics occurred. After this bifurcation periods were longer but the oscillation was unstable. The RNAseq samples were taken in the 2.5 cycles before this bifurcation occurred, i.e., the data provides a snapshot of a transient state of the respiratory oscillations.

2022-07-11 | E-MTAB-11901 | biostudies-arrayexpress

Oscillating gene expression determines competence for periodic branching in the Arabidopsis root

Project description:The Oscillation Zone (OZ) of unsynchronized roots was disected and divided into an upper (OZ2) and lower (OZ1) half . Samples were ordered according to DR5:GUS expression as analyzed by real time PCR to find periodic expression patterns

2010-09-12 | GSE21611 | GEO

Role of Astrocytes in critical periods

Project description:Brain postnatal development is characterized by critical periods of experience dependent remodeling. Maturation of local circuits inhibitory neurons terminate this period of enhanced plasticity. Astroglial cells are known to influence excitatory and inhibitory synaptic transmission as well as network activity through active signaling mechanisms. Although these can be developmentally regulated, the role of astrocytes in the timing of post-natal critical period is unknown. Here we show in the visual cortex that astrocytes con-trol the maturation of inhibitory neurons and thereby closure of the critical period. We uncover a novel underlying pathway involving regulation of the extracellular matrix that allows interneurons maturation via astroglial connexin signaling. We find that timing of the critical period closure is controlled by a marked upregulation of the astroglial protein connexin 30 that inhibits expression of the matrix degrading enzyme MMP9 through the RhoA-GTPase pathway. Our results thus demonstrate that astrocytes not only influ-ence neuronal activity but are also key elements in the experience–dependent wiring of brain circuits. Therefore, astrocytes represent a new cellular partner to consider in our understanding of the post-natal shaping of neuronal activities, hence providing a new target to alleviate malfunctions associated to im-paired closure of the critical period and settling of synaptic circuits.

2022-05-12 | PXD020448 | Pride

Oscillating gene expression determines competence for periodic branching in the Arabidopsis root

Project description:The Oscillation Zone (OZ) of unsynchronized roots was dissected and divided into an upper (OZ2) and lower (OZ1) half . Samples were ordered according to DR5:GUS expression as analyzed by real time PCR to find periodic expression patterns Seedlings were grown for 5 days. 39 individual roots were dissected for RNA extraction. These microarray samples profile a specific region of the root tip designated as the Oscillation zone. Arrangement of the samples in the following order: OZ1-1, OZ1-4, OZ1-23, OZ1-14, OZ1-17, OZ1-2, OZ1-6, OZ1-13, OZ1-15, OZ1-16, OZ1-10, OZ1-32, OZ1-3, OZ1-31, OZ1-22, OZ1-35, OZ1-19, OZ1-9, OZ1-33, OZ1-20, OZ2-4, OZ2-23, OZ2-14, OZ2-6, OZ2-13, OZ2-15, OZ2-10, OZ2-32, OZ2-22, OZ2-35, OZ2-19, OZ2-9, OZ2-20, OZ2-36, OZ2-39, OZ2-21, OZ2-40, OZ2-38, OZ2-1, was used to identify periodic expression patterns.

2010-09-12 | E-GEOD-21611 | biostudies-arrayexpress

A perturbation in the system leads to period doubling

Project description:Perturbation of the gated-synchrony system in yeast with phenelzine, an antidepressant drug used in the treatment of affective disorders in humans, leads to a rapid lengthening in the period of the genome-wide transcriptional oscillation. The effect is a concerted, genome-scale change in expression that is first seen in genes maximally expressed in the late-reductive phase of the cycle, doubling the length of the reductive phase within two cycles after treatment. Clustering of genes based on their temporal patterns of expression yielded just three super clusters whose trajectories through time could then be mapped into a simple 3D figure. In contrast to transcripts in the late-reductive phase, most transcripts do not show transients in expression relative to others in their temporal cluster but change their period in a concerted fashion. Mapping the trajectories of the transcripts into low-dimensional surfaces that can be represented by simple systems of differential equations provides a readily testable model of the dynamic architecture of phenotype. In this system, period doubling may be a preferred pathway for phenotypic change. As a practical matter, low-amplitude, genome-wide oscillations, a ubiquitous but often unrecognized attribute of phenotype, could be a source of seemingly intractable biological noise in microarray studies. Keywords: Time Course Experiment

2007-10-12 | GSE9302 | GEO

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