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Background: Whole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and analyzing complex, high-dimensional data. Results: We developed WholeCellViz, a web-based software program for visually exploring and analyzing whole-cell simulations. WholeCellViz provides 14 animated visualizations, including metabolic and chromosome maps. These visualizations help researchers analyze model predictions by displaying predictions in their biological context. Furthermore, WholeCellViz enables researchers to compare predictions within and across simulations by allowing users to simultaneously display multiple visualizations. Conclusion: WholeCellViz was designed to facilitate exploration, analysis, and communication of whole-cell model data. Taken together, WholeCellViz helps researchers use whole-cell model simulations to drive advances in biology and bioengineering. [ABSTRACT FROM AUTHOR]

In plants, as in animals, most cells that constitute the organism limit their reproductive potential in order to provide collective support for the immortal germ line. And, as in animals, the mechanisms that restrict the proliferation of somatic cells in plants can fail, leading to tumours. There are intriguing similarities in tumorigenesis between plants and animals, including the involvement of the retinoblastoma pathway as well as overlap with mechanisms that are used for stem cell maintenance. However, plant tumours are less frequent and are not as lethal as those in animals. We argue that fundamental differences between plant and animal development make it much more difficult for individual plant cells to escape communal controls. [ABSTRACT FROM AUTHOR]

Regulatory machinery is focally organized in the interphase nucleus. The information contained in these focal nuclear microenvironments must be inherited during cell division to sustain physiologically responsive gene expression in progeny cells. Recent results suggest that focal mitotic retention of phenotypic transcription factors at promoters together with histone modifications and DNA methylation--a mechanism collectively known as gene bookmarking--is a novel parameter of inherited epigenetic control that sustains cellular identity after mitosis. The epigenetic signatures imposed by bookmarking poise genes for activation or suppression following mitosis. We discuss the implications of phenotypic transcription factor retention on mitotic chromosomes in biological control and disease. [ABSTRACT FROM AUTHOR]

No-one can have failed to notice the splash that induced pluripotent stem (iPS) cells have made in the few years since somatic cells were first reprogrammed to pluripotency. But what is their real promise, where should research efforts be focused, and are we at a stage where we can replace embryonic stem cells? Four pioneering iPS cell researchers offer their personal insights into these and other questions of current debate. As well expressing hope for the improved understanding and treatment of human disease, they urge caution over safety and propose the establishment of iPS cell banks. [ABSTRACT FROM AUTHOR]

It has been known for many years that cellular metabolism within the solid tumour is markedly different from that of the corresponding normal tissue. The transcription factor hypoxia-inducible factor 1 (HIF1) has been implicated in regulating many of the genes that are responsible for the metabolic difference. However, it remains unclear how this 'aerobic glycolysis', originally described by Otto Warburg, offers tumour cells a growth advantage. As discussed in this Perspective, new data suggests that this metabolic switch may provide a benefit to the tumour not by increasing glycolysis but by decreasing mitochondrial activity. [ABSTRACT FROM AUTHOR]

MYC in human epidermal stem cells can stimulate differentiation rather than uncontrolled proliferation. This discovery was, understandably, greeted with scepticism by researchers. However, subsequent studies have confirmed that MYC can stimulate epidermal stem cells to differentiate and have shed light on the underlying mechanisms. Two concepts that are relevant to cancer have emerged: first, MYC regulates similar genes in different cell types, but the biological consequences are context-dependent; and second, MYC activation is not a simple 'on/off' switch - the cellular response depends on the strength and duration of MYC activity, which in turn is affected by the many cofactors and regulatory pathways with which MYC interacts. [ABSTRACT FROM AUTHOR]

The accumulation of multiple mutations and alterations in the cancer genome underlies the complexity of cancer phenotypes. A consequence of these alterations is the deregulation of various cell-signalling pathways that control cell function. Molecular-profiling studies, particularly DNA microarray analyses, have the potential to describe this complexity. These studies also provide an opportunity to link pathway deregulation with potential therapeutic strategies. This approach, when coupled with other methods for identifying pathway activation, provides an opportunity to both match individual patients with the most appropriate therapeutic strategy and identify potential options for combination therapy. [ABSTRACT FROM AUTHOR]

Chemokines have long been known to orchestrate dendritic-cell migration in the body. However, recent evidence has shown that chemokines not only direct the trafficking of dendritic cells but also can regulate their maturation status. Here, we propose that this dual function of chemokines ensures that T cells and dendritic cells meet in T-cell regions of lymphoid organs and that antigen is presented in an immunologically optimal context for T-cell priming. [ABSTRACT FROM AUTHOR]

Most tumours are derived from a single cell that is transformed into a cancer-initiating cell (cancer stem cell) that has the capacity to proliferate and form tumours in vivo. However, the origin of the cancer stem cell remains elusive. Interestingly, during development and tissue repair the fusion of genetic and cytoplasmic material between cells of different origins is an important physiological process. Such cell fusion and horizontal gene-transfer events have also been linked to several fundamental features of cancer and could be important in the development of the cancer stem cell. [ABSTRACT FROM AUTHOR]