Epigenetic alchemy for cell fate conversion

Recent progress in neural stem cell research shows that a number of extrinsic factors and intracellular mechanisms, including epigenetic modifications, are involved in the self-renewal of neural stem cells and in neuronal and glial differentiation. Remarkably, there is increasing evidence that the remodeling of chromatin structure and the alteration of epigenetic marks, including histone methylation and acetylation and DNA methylation, can cause committed cells to convert from one fate to another, and such converted cells are functional when transplanted in vivo. Thus, epigenetic research might generate the alchemy required to convert any non-neural stem cells into functional neural stem cells, which are few and difficult to extract from the adult central nervous system.     

A fungicide-responsive kinase as a tool for synthetic cell fate regulation

Engineered biological systems that precisely execute defined tasks have major potential for medicine and biotechnology. For instance, gene- or cell-based therapies targeting pathogenic cells may replace time- and resource-intensive drug development. Engineering signal transduction systems is a promising, yet presently underexplored approach. Here, we exploit a fungicide-responsive heterologous histidine kinase for pathway engineering and synthetic cell fate regulation in the budding yeast Saccharomyces cerevisiae. Rewiring the osmoregulatory Hog1 MAPK signalling system generates yeast cells programmed to execute three different tasks. First, a synthetic negative feedback loop implemented by employing the fungicide-responsive kinase and a fungicide-resistant derivative reshapes the Hog1 activation profile, demonstrating how signalling dynamics can be engineered. Second, combinatorial integration of different genetic parts including the histidine kinases, a pathway activator and chemically regulated promoters enables control of yeast growth and/or gene expression in a two-input Boolean logic manner. Finally, we implemented a genetic ‘suicide attack’ system, in which engineered cells eliminate target cells and themselves in a specific and controllable manner. Taken together, fungicide-responsive kinases can be applied in different constellations to engineer signalling behaviour. Sensitizing engineered cells to existing chemicals may be generally useful for future medical and biotechnological applications.     

A polynomial based model for cell fate prediction in human diseases

Background

Cell fate regulation directly affects tissue homeostasis and human health. Research on cell fate decision sheds light on key regulators, facilitates understanding the mechanisms, and suggests novel strategies to treat human diseases that are related to abnormal cell development.

Results

In this study, we proposed a polynomial based model to predict cell fate. This model was derived from Taylor series. As a case study, gene expression data of pancreatic cells were adopted to test and verify the model. As numerous features (genes) are available, we employed two kinds of feature selection methods, i.e. correlation based and apoptosis pathway based. Then polynomials of different degrees were used to refine the cell fate prediction function. 10-fold cross-validation was carried out to evaluate the performance of our model. In addition, we analyzed the stability of the resultant cell fate prediction model by evaluating the ranges of the parameters, as well as assessing the variances of the predicted values at randomly selected points. Results show that, within both the two considered gene selection methods, the prediction accuracies of polynomials of different degrees show little differences. Interestingly, the linear polynomial (degree 1 polynomial) is more stable than others. When comparing the linear polynomials based on the two gene selection methods, it shows that although the accuracy of the linear polynomial that uses correlation analysis outcomes is a little higher (achieves 86.62%), the one within genes of the apoptosis pathway is much more stable.

Conclusions

Considering both the prediction accuracy and the stability of polynomial models of different degrees, the linear model is a preferred choice for cell fate prediction with gene expression data of pancreatic cells. The presented cell fate prediction model can be extended to other cells, which may be important for basic research as well as clinical study of cell development related diseases.

     

MicroRNA regulation of stem cell fate

MicroRNAs modulate target gene expression and are essential for normal development, but how does this pathway impact cell fate decisions? In this issue of Cell Stem Cell, Ivey et al. (2008) find that muscle-specific microRNAs repress nonmuscle genes to direct embryonic stem cell differentiation to mesoderm and muscle.     

A fuel cell model in biological energy conversion

Consideration of the high energy conversion efficiency of biological systems leads to the idea that mechanical energy may arise via a series of steps, of which a rate-determining one occurs in a fuel-cell-like element. The mitochondrion is suggested as the site of such entities. The observed efficiency would be consistent with a potential loss of about 0.5 V. The supposed biological fuel cells would be able to act as an electrical power source, driving chemical reactions against their spontaneous direction.Considerations of electrical conductance in wet proteins shows that ohmic (i.e., non-interfacial) potential differences through mitochondrial membranes could be negligible. The cathodic reaction would be the reduction of oxygen, O₂+4H⁺+4e^–H₂O and the anodic reaction, 2NADH⁺2NAD+2H⁺+4e^–. The anodes are suggested as being molecular, buried in the invaginations of the inner membrane forming the cristae. The cathodes are located on enzymes which are probably on the inner side of the membrane but could be, respectively, on the outer (cathodic), and the inner (anodic) sides. The electron transport occurs though proteins within each membrane. The relation of the so-called fuel cell potentials to potentially observable membrane potentials, and those measured by fluorescent probes, are discussed.The fuel cells produce electrical energy and this energy is transferred to ADP by an electrolytic route, using electric power from the cells to work the endergonic ATP synthesis. Possible electrode reactions are suggested. An exponential dependence of the rate of ATP synthesis upon applied potential has been observed.Biological cells radiate electromagnetically in the 10⁹ to 10¹⁵ Hz region. Such phenomena support a fuel cell model of a biological cell because they demand the presence of mobile electrons.     

A macrophage cell model for pH and volume regulation

A whole-cell model of a macrophage (mphi) is developed to simulate pH and volume regulation during a NH4Cl prepulse challenge. The cell is assumed spherical, with a plasma membrane that separates the cytosolic and extracellular bathing media. The membrane contains background currents for Na+, K+ and Cl-, a Na(+)-K+ pump, a V-type H(+)-extruder (V-ATPase), and a leak pathway for NH4+. Cell volume is controlled by instantaneous osmotic balance between cytosolic and extracellular osmolytes. Simulations reveal that the mphi model can mimic alterations in measured pH(i) and cell volume (Vol(i)) data during and after delivery of an ammonia prepulse, which induces an acid load within the cell. Our analysis indicates that there are substantial problems in quantifying transporter-mediated H+ efflux solely from experimental observations of pH(i) recovery, as is commonly done in practice. Problems stemming from the separation of effects arise, since there is residual NH4+ dissociation to H+ inside the mphi during pH(i) recovery, as well as, proton extrusion via the V-ATPase. The core assumption of conventional measurement techniques used to estimate the H+ extrusion current (I(H)) is that the recovery phase is solely dependent on transporter-mediated H+ extrusion. However, our model predictions suggest that there are major problems in using this approach, due to the complex interactions between I(H), NH3/NH4+ buffering and NH3/NH4+ efflux during the active acid extrusion phase. That is, the conventional buffer capacity-based I(H) estimation must also take into account the perturbation that a prepulse challenge brings to the cytoplasmic acid buffer itself. The importance of this whole-cell model of mphipH(i) and volume regulation lies in its potential for extension to the characterization of several other types of non-excitable cells, such as the microglia (brain macrophage) and the T-lymphocyte.     

Molecular regulation of vertebrate retina cell fate

The specification of retinal cell fate is a multistep process that begins during early development and results from the spatio‐temporal coordination of cell cycle, cell differentiation, and morphogenesis. This review focuses on recent advances in understanding the molecular mechanisms underlying the distinct steps of retinal specification. Emphasis is placed on key regulatory events that control the multipotency of retinal progenitors, the generation of cell diversity, and the establishment of the clock that determines the ordered generation of retinal cell types. These basic studies have paved the way to the latest progress on the isolation and in vitro generation of retinal stem cells, which is presented in the light of possible therapeutic applications. Birth Defects Research (Part C) 87:284–295, 2009. © 2009 Wiley‐Liss, Inc.     

Redox regulation of plant stem cell fate

Despite the importance of stem cells in plant and animal development, the common mechanisms of stem cell maintenance in both systems have remained elusive. Recently, the importance of hydrogen peroxide (H₂O₂) signaling in priming stem cell differentiation has been extensively studied in animals. Here, we show that different forms of reactive oxygen species (ROS) have antagonistic roles in plant stem cell regulation, which were established by distinct spatiotemporal patterns of ROS‐metabolizing enzymes. The superoxide anion () is markedly enriched in stem cells to activate WUSCHEL and maintain stemness, whereas H₂O₂ is more abundant in the differentiating peripheral zone to promote stem cell differentiation. Moreover, H₂O₂ negatively regulates biosynthesis in stem cells, and increasing H₂O₂ levels or scavenging leads to the termination of stem cells. Our results provide a mechanistic framework for ROS‐mediated control of plant stem cell fate and demonstrate that the balance between and H₂O₂ is key to stem cell maintenance and differentiation.