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Stephen Cooper

Publications and source records attributed to Stephen Cooper.

15 recordsLinked to original sources
PubMed2004

Is whole-culture synchronization biology's 'perpetual-motion machine'?

Whole-culture or batch synchronization cannot, in theory, produce a synchronized culture because it violates a fundamental law that proposes that no batch treatment can alter the cell-age order of a culture. In analogy with the history of perpetual-motion machines, it is suggested that the study of these whole-culture 'synchronization' methods might lead to an understanding of general biological principles even though these methods cannot be used to study the normal cell cycle.

Cell Cycle↗
PubMed2004

Rejoinder: whole-culture synchronization cannot, and does not, synchronize cells.

There have been numerous proposals suggesting that whole-culture methods - in which all cells in a growing culture are treated identically - can synchronize cells. An explicit defense of these methods has been presented (Spellman and Sherlock, this issue, pp. 270-273, ). Here, this defense of whole-culture 'synchronization' is subjected to a critical evaluation leading to the conclusion that whole-culture synchronization cannot synchronize cells - at all. Whole-culture methods cannot produce a set of cells that reflects the size and genome composition of cells of any particular cell-cycle age during the normal cell cycle. Thus, in addition to the well-recognized problem of artifacts, it is proposed that experiments using whole-culture treatments (usually starvation or inhibition methods) are not suitable for cell-cycle analysis because these methods do not produce a synchronized culture.

Cell Cycle↗
PubMed2003

Microarray analysis of gene expression during the cell cycle.

Microarrays have been applied to the determination of genome-wide expression patterns during the cell cycle of a number of different cells. Both eukaryotic and prokaryotic cells have been studied using whole-culture and selective synchronization methods. The published microarray data on yeast, mammalian, and bacterial cells have been uniformly interpreted as indicating that a large number of genes are expressed in a cell-cycle-dependent manner. These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle. The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression. Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

Journal Article↗
PubMed2003

Risk of postnatal depression after emergency delivery.

AIM: To identify whether women having emergency delivery are at increased risk of developing postnatal depression (PND). METHODS: This is a retrospective comparative cohort study design. Two hundred and fifty Malaysian women were part of a previous study examining the prevalence of PND in a multiracial country and the effects of postnatal rituals. All women were at least 6 weeks post-partum when asked to complete the Edinburgh Postnatal Depression Scale (EPDS). Sociodemographic and birth data were obtained. RESULTS: Data collected were divided into two groups: 55 emergency delivery and 191 non-emergency delivery. There were four missing data. There was no significant difference in the mean age, parity, gestational period, baby birthweight, 5 min baby Apgar score and EPDS scores of the two groups. However, the analysis of PND indicated that women with emergency delivery had a relative risk of 1.81 compared with women with non-emergency delivery. The comparison of the two groups using chi2 indicated a significant (chi2 = 3.94, d.f. = 1, P = 0.04) increase in the presence of PND in the emergency delivery. CONCLUSION: When compared with women having non-emergency delivery, women having emergency delivery had about twice the risk of developing PND. Special attention to this group appears warranted.

Adult↗
PubMed2003

Reappraisal of serum starvation, the restriction point, G0, and G1 phase arrest points.

The restriction point in the G1 phase of the mammalian cell cycle is the oldest, best-known, and widely accepted control point regulating division cycle in mammalian cells. Origins of the restriction point and its subsequent history are reanalyzed here. The initial proposal of the restriction point has an alternative explanation, which is that cells arrested with a G1 phase amount of DNA can arise from the inhibition of a process or processes occurring throughout the cell cycle and are not restricted to any particular phase of the cell cycle or specifically related to any event in the G1 phase of the cell cycle. The initial evidence and subsequent analyses require reexamination. It is proposed that the arrest of cells with a particular DNA content equivalent to that in cells in the G1 phase of the division cycle does not mean there is any particular G1 phase control point.

Animals↗
PubMed2002

Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods.

Microarray analysis of gene expression during the yeast division cycle has led to the proposal that a significant number of genes in Saccharomyces cerevisiae are expressed in a cell-cycle-specific manner. Four different methods of synchronization were used for cell-cycle analysis. Randomized data exhibit periodic patterns of lesser strength than the experimental data. Thus the cyclicities in the expression measurements in the four experiments presented do not arise from chance fluctuations or noise in the data. However, when the degree of cyclicity for genes in different experiments are compared, a large degree of non-reproducibility is found. Re-examining the phase timing of peak expression, we find that three of the experiments (those using alpha-factor, CDC28 and CDC15 synchronization) show consistent patterns of phasing, but the elutriation synchrony results demonstrate a different pattern from the other arrest-release synchronization methods. Specific genes can show a wide range of cyclical behavior between different experiments; a gene with high cyclicity in one experiment can show essentially no cyclicity in another experiment. The elutriation experiment, possibly being the least perturbing of the four synchronization methods, may give the most accurate characterization of the state of gene expression during the normal, unperturbed cell cycle. Under this alternative explanation, the observed cyclicities in the other three experiments are a stress response to synchronization, and may not reproduce in unperturbed cells.

Cell Cycle↗
PubMed2002

Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization.

Microarray analysis of gene expression patterns for thousands of human genes has led to the proposal that a large number of genes are expressed in a cell-cycle-specific manner. The identification of cyclically expressed genes was based on Affymetrix microarray analysis of gene expression after double-thymidine block synchronization. A statistical reanalysis of the original data leads to three principal findings. (i) Randomized data exhibit periodic patterns of similar or greater strength than the experimental data. This finding suggests that all apparent cyclicities in the expression measurements may arise from chance fluctuations. (ii) The presence of cyclicity and the timing of peak cyclicity in a given gene are not reproduced in two replicate experiments. This fact suggests there is an uncontrolled source of experimental variation that is stronger than the innate variation of gene expression in cells over time. (iii) The amplitude of peak expression in the second cycle is not consistently smaller than the corresponding amplitude in the first cycle. This finding places doubt on the assumption that the cells are actually synchronized. We propose that the microarray results do not support the proposal that there are numerous cell-cycle-specifically expressed genes in human cells.

Cell Cycle↗
PubMed2002

Minimally disturbed, multicycle, and reproducible synchrony using a eukaryotic "baby machine".

A eukaryotic "baby machine" has been developed that produces synchronized cultures that display up to four synchronous cell cycles. That such cells can be produced implies that methods unable to produce successive synchronized cell cycles may not actually synchronize cells. But most important, the baby machine method now opens the way for the study of the cell cycle of minimally disturbed, artifact-free, well-synchronized, mammalian cells.

Animals↗
PubMed2002

Reappraisal of G1-phase arrest and synchronization by lovastatin.

It has been proposed that lovastatin arrests cells in the G1-phase of the division cycle, and that release from lovastatin inhibition produces a synchronized culture. A new method of methocel time-lapse-videography has been used to analyse cell division patterns following lovastatin treatment. Release of L1210 cells from lovastatin inhibition failed to produce synchronized divisions. Moreover, contrary to earlier proposals, lovastatin did not arrest cells with a G1-phase amount of DNA. Analysis of previous reports of 'synchronization' and growth-arrest support these findings. It is concluded that lovastatin neither synchronizes cells, nor arrests cells in the G1-phase of the division cycle.

Animals↗
PubMed2002

The Schaechter-Bentzon-Maaløe experiment and the analysis of cell cycle events in eukaryotic cells.

The Schaechter-Bentzon-Maaløe (SBM) experiment, performed more than 40 years ago, provides an important lesson for the analysis of the eukaryotic cell cycle. Before this experiment, temperature shifts had been used to synchronize bacteria and determine the pattern of DNA synthesis during the bacterial division cycle. These experiments indicated that DNA replication occurred during a fraction of the division cycle with gaps before and after DNA synthesis, a pattern similar to the eukaryotic division cycle. The SBM experiment studied DNA replication during the division cycle by labeling an unperturbed culture with a short pulse of tritiated thymidine. All cells were found to be labeled, indicating that unperturbed cells synthesize DNA throughout the division cycle. Thus, the SBM experiment was a control experiment demonstrating that artifacts can be introduced by synchronization methods. The idea of an control experiment under unperturbed conditions is proposed for the analysis of data on cell-cycle-specific gene expression in yeast and mammalian cells.

Artifacts↗
PubMedDate not supplied

How the change from FLM to FACS affected our understanding of the G1-phase of the cell cycle.

The frequency of labeled mitoses (FLM) method for analyzing cell-cycle phases necessitates a determination of cell-cycle interdivision times and the absolute lengths of the cell-cycle phases. The change to flow sorting (FACS) analysis, a simpler, less labor intensive, and more rapid method, eliminated determinations of absolute phase times, yielding only percents of cells exhibiting particular DMA contents. Without an interdivision time value, conversion of these fractions into absolute phase lengths is not possible. This change in methodology has led to an alteration in how the cell cycle is viewed. The FLM method allowed the conclusion that G1 phase variability resulted from constancy of S and G2 phase lengths. In contrast, with FACS analysis, slow growing cells exhibiting a large fraction of cells with a G1-phase amount of DMA appeared to be "arrested in G1 phase". The loss of absolute phase length determinations has therefore led to the proposals of G1-phase arrest, G1-phase controls, restriction points, and G0 phase. It is suggested that these G1-phase controls and phenomena require a critical reevaluation in the light of an alternative cell-cycle model that does not require or postulate such G1-phase controls.

Cell Cycle↗