Search PubMed⌕ Search

Biomedical subjects

Stephen Cooper

Publications and source records attributed to Stephen Cooper.

At least 19 recordsLinked to original sources
PubMed2006

Distinguishing between linear and exponential cell growth during the division cycle: single-cell studies, cell-culture studies, and the object of cell-cycle research.

BACKGROUND: Two approaches to understanding growth during the cell cycle are single-cell studies, where growth during the cell cycle of a single cell is measured, and cell-culture studies, where growth during the cell cycle of a large number of cells as an aggregate is analyzed. Mitchison has proposed that single-cell studies, because they show variations in cell growth patterns, are more suitable for understanding cell growth during the cell cycle, and should be preferred over culture studies. Specifically, Mitchison argues that one can glean the cellular growth pattern by microscopically observing single cells during the division cycle. In contrast to Mitchison's viewpoint, it is argued here that the biological laws underlying cell growth are not to be found in single-cell studies. The cellular growth law can and should be understood by studying cells as an aggregate. RESULTS: The purpose or objective of cell cycle analysis is presented and discussed. These ideas are applied to the controversy between proponents of linear growth as a possible growth pattern during the cell cycle and the proponents of exponential growth during the cell cycle. Differential (pulse) and integral (single cell) experiments are compared with regard to cell cycle analysis and it is concluded that pulse-labeling approaches are preferred over microscopic examination of cell growth for distinguishing between linear and exponential growth patterns. Even more to the point, aggregate experiments are to be preferred to single-cell studies. CONCLUSION: The logical consistency of exponential growth--integrating and accounting for biochemistry, cell biology, and rigorous experimental analysis--leads to the conclusion that proposals of linear growth are the result of experimental perturbations and measurement limitations. It is proposed that the universal pattern of cell growth during the cell cycle is exponential.

Cell Culture Techniques↗
PubMed2006

Nocodazole does not synchronize cells: implications for cell-cycle control and whole-culture synchronization.

It has been predicted that nocodazole-inhibited cells are not synchronized because nocodazole-arrested cells with a G2-phase amount of DNA would not have a narrow cell-size range reflecting the cell size of some specific, presumably G2-phase, cell-cycle age. Size measurements of nocodazole-inhibited cells now fully confirm this prediction. Further, release from nocodazole inhibition does not produce cells that move through the cell cycle mimicking the passage of normal unperturbed cells through the cell cycle. Nocodazole, an archetypal whole-culture synchronization method, can inhibit growth to produce cells with a G2-phase amount of DNA, but such cells are not synchronized. Cells produced by a selective (i.e., non-whole-culture) method not only have a specific DNA content, but also have a narrow size distribution. The current view of cell-cycle control that is based on methods that are not suitable for cell-cycle analysis must therefore be reconsidered when results are based on whole-culture synchronization.

Animals↗
PubMed2006

Checkpoints and restriction points in bacteria and eukaryotic cells.

Bacterial checkpoints, analogous to those proposed to exist in eukaryotic cells, offer insights into the definition of a checkpoint. Examination of bacterial "checkpoint" or arrest phenomena illustrate problems with a too-casual application of the checkpoint idea to eukaryotic phenomena. The question raised here is whether there are cellular processes that "check" whether a cellular process is completed. It is possible that many eukaryotic "checkpoints" may not have "checking" functions. Some of the ubiquitous checkpoint phenomena widely described may be merely the result of the inherent incompleteness of earlier events preventing the initiation of subsequent events.

Animals↗
PubMed2006

Regulation of DNA synthesis in bacteria: Analysis of the Bates/Kleckner licensing/initiation-mass model for cell cycle control.

Bates and Kleckner have recently proposed that bacterial cell division is a licensing agent for a subsequent initiation of DNA replication. They also propose that initiation mass for DNA replication is not constant. These two proposals do not take into account older data showing that initiation of DNA replication can occur prior to the division event. This critical analysis is derived from measurements of DNA replication during the division cycle in cells growing at different, and more rapid, growth rates. Furthermore, mutants impaired in division can initiate DNA synthesis. The data presented by Bates and Kleckner do not support the proposal that initiation mass is variable, and the proposed pattern of DNA replication during the division cycle of the K12 cells analysed is not consistent with prior data on the pattern of DNA replication during the division cycle.

Cell Cycle↗
PubMed2005

Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu, Gaido and Wolfinger: on the analysis of gene expression during the normal, eukaryotic, cell cycle.

BACKGROUND: The paper of Liu, Gaido and Wolfinger on gene expression during the division cycle of HeLa cells using the data of Whitfield et al. are discussed in order to see whether their analysis is related to gene expression during the division cycle. RESULTS: The results of Liu, Gaido and Wolfinger demonstrate that different inhibition methods proposed to "synchronize" cells lead to different levels of gene expression. This result, in and of itself, should be taken as evidence that the original work of Whitfield et al. is flawed and should not be used to support the notion that the cells studied were synchronized or that the microarray analyses identify cell-cycle-regulated genes. Furthermore, the DNA content evidence presented by Whitfield et al. supports the proposal that the cells described as 'synchronized' are not synchronized. A comparison of the gene expression amplitudes from two different experiments indicates that the results are not reproducible. CONCLUSION: It is concluded that the analysis of Liu, Gaido, and Wolfinger is problematic because their work assumes that the cells they analyze are or were synchronized. The very fact that different inhibition methods lead to different degrees of gene expression should be taken as additional evidence that the experiments should be viewed skeptically rather than accepted as an approach to understanding gene expression during the cell cycle.

Cell Cycle↗
PubMed2005

Reanalysis of the protocol for in vitro synchronization of mammalian astrocytic cultures by serum deprivation.

Serum starvation of astrocytes for a period of time followed by refeeding has been proposed as a method to produce synchronized astrocytes. Here, it is proposed that the method neither synchronizes cells nor satisfies rigorous criteria for cell synchronization. The proposed non-selective, whole-culture synchronization protocol cannot, in theory, synchronize cells. The cells produced by the proposed serum starvation/refeeding protocol do not reflect the properties of any particular cell during the cell cycle. Cells produced by the published protocol will have a wide distribution of cell sizes, and therefore, the cells produced by starvation/refeeding will not model cells of any specific age during the division cycle. Thus, the proposed protocol will not produce a synchronized culture.

Animals↗
PubMed2004

Control and maintenance of mammalian cell size.

BACKGROUND: Conlon and Raff propose that mammalian cells grow linearly during the division cycle. According to Conlon and Raff, cells growing linearly do not need a size checkpoint to maintain a constant distribution of cell sizes. If there is no cell-size-control system, then exponential growth is not allowed, as exponential growth, according to Conlon and Raff, would require a cell-size-control system. DISCUSSION: A reexamination of the model and experiments of Conlon and Raff indicates that exponential growth is fully compatible with cell size maintenance, and that mammalian cells have a system to regulate and maintain cell size that is related to the process of S-phase initiation. Mammalian cell size control and its relationship to growth rate-faster growing cells are larger than slower growing cells-is explained by the initiation of S phase occurring at a relatively constant cell size coupled with relatively invariant S- and G2-phase times as interdivision time varies. SUMMARY: This view of the mammalian cell cycle, the continuum model, explains the mass growth pattern during the division cycle, size maintenance, size determination, and the kinetics of cell-size change following a shift-up from slow to rapid growth.

Animals↗
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↗