Model systems in stem cell biology

Spontaneous Differentiation of Human Neural Stem Cells on Nanodiamonds

The potential use of stem cells in regenerative medicine requires the ability to be able to control stem cell fate as cellular networks are developed. Here, nanodiamonds (≈10 nm) are supported on glass and shown to be an excellent host for the attachment and proliferation of human neural stem cells. Moreover, it is shown that spontaneous differentiation into neurons occurs on nanodiamonds. The use of variously oxygen terminated and hydrogen terminated nanodiamonds has been explored. It is shown that O-ND monolayers promote the differentiation of human neural stem cells into neurons with increased total neurite length, degree of branching, and density of neurites when compared with H-NDs or the glass control. The total number of neurites and total neurite length expressing MAP2, a protein enriched in dendrites, is over five times higher for spontaneously differentiated neurones on the O-NDs compared to the control. The fact that inexpensive nanodiamonds can be attached through simple sonication from water on 2D and 3D shapes indicates significant promise for their potential as biomaterials in which neuro-regenerative diseases can be studied.

What is a stem cell?

The historical roots of the stem cell concept are traced with respect to its usage in embryology and in hematology. The modern consensus definition of stem cells, comprising both pluripotent stem cells in culture and tissue-specific stem cells in vivo, is explained and explored. Methods for identifying stem cells are discussed with respect to cell surface markers, telomerase, label retention and transplantability, and properties of the stem cell niche are explored. The CreER method for identifying stem cells in vivo is explained, as is evidence in favor of a stochastic rather than an obligate asymmetric form of cell division. In conclusion, it is found that stem cells do not possess any unique and specific molecular markers; and stem cell behavior depends on the environment of the cell as well as the stem cell's intrinsic qualities. Furthermore, the stochastic mode of division implies that stem cell behavior is a property of a cell population not of an individual cell. In this sense, stem cells do not exist in isolation but only as a part of multicellular system. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Methods and Principles Adult Stem Cells, Tissue Renewal, and Regeneration > Environmental Control of Stem Cells.

Generative models: Human embryonic stem cells and multiple modeling relations

Model organisms are at once scientific models and concrete living things. It is widely assumed by philosophers of science that (1) model organisms function much like other kinds of models, and (2) that insofar as their scientific role is distinctive, it is in virtue of representing a wide range of biological species and providing a basis for generalizations about those targets. This paper uses the case of human embryonic stem cells (hESC) to challenge both assumptions. I first argue that hESC can be considered model organisms, analogous to classic examples such as Escherichia coli and Drosophila melanogaster. I then discuss four contrasts between the epistemic role of hESC in practice, and the assumptions about model organisms noted above. These contrasts motivate an alternative view of model organisms as a network of systems related constructively and developmentally to one another. I conclude by relating this result to other accounts of model organisms in recent philosophy of science.

In-silico models of stem cell and developmental systems

Understanding how developmental systems evolve over time is a key question in stem cell and developmental biology research. However, due to hurdles of existing experimental techniques, our understanding of these systems as a whole remains partial and coarse. In recent years, we have been constructing in-silico models that synthesize experimental knowledge using software engineering tools. Our approach integrates known isolated mechanisms with simplified assumptions where the knowledge is limited. This has proven to be a powerful, yet underutilized, tool to analyze the developmental process. The models provide a means to study development in-silico by altering the model’s specifications, and thereby predict unforeseen phenomena to guide future experimental trials. To date, three organs from diverse evolutionary organisms have been modeled: the mouse pancreas, the C. elegans gonad, and partial rodent brain development. Analysis and execution of the models recapitulated the development of the organs, anticipated known experimental results and gave rise to novel testable predictions. Some of these results had already been validated experimentally. In this paper, I review our efforts in realistic in-silico modeling of stem cell research and developmental biology and discuss achievements and challenges. I envision that in the future, in-silico models as presented in this paper would become a common and useful technique for research in developmental biology and related research fields, particularly regenerative medicine, tissue engineering and cancer therapeutics.

Multi-scale computational modeling of developmental biology

MOTIVATION

Normal development of multicellular organisms is regulated by a highly complex process in which a set of precursor cells proliferate, differentiate and move, forming over time a functioning tissue. To handle their complexity, developmental systems can be studied over distinct scales. The dynamics of each scale is determined by the collective activity of entities at the scale below it.

RESULTS

I describe a multi-scale computational approach for modeling developmental systems and detail the methodology through a synthetic example of a developmental system that retains key features of real developmental systems. I discuss the simulation of the system as it emerges from cross-scale and intra-scale interactions and describe how an in silico study can be carried out by modifying these interactions in a way that mimics in vivo experiments. I highlight biological features of the results through a comparison with findings in Caenorhabditis elegans germline development and finally discuss about the applications of the approach in real developmental systems and propose future extensions.

AVAILABILITY AND IMPLEMENTATION

The source code of the model of the synthetic developmental system can be found in www.wisdom.weizmann.ac.il/~yaki/MultiScaleModel.

CONTACT

yaki.setty@gmail.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

The maize root stem cell niche: a partnership between two sister cell populations

Using transcript profile analysis, we explored the nature of the stem cell niche in roots of maize (Zea mays). Toward assessing a role for specific genes in the establishment and maintenance of the niche, we perturbed the niche and simultaneously monitored the spatial expression patterns of genes hypothesized as essential. Our results allow us to quantify and localize gene activities to specific portions of the niche: to the quiescent center (QC) or the proximal meristem (PM), or to both. The data point to molecular, biochemical and physiological processes associated with the specification and maintenance of the niche, and include reduced expression of metabolism-, redox- and certain cell cycle-associated transcripts in the QC, enrichment of auxin-associated transcripts within the entire niche, controls for the state of differentiation of QC cells, a role for cytokinins specifically in the PM portion of the niche, processes (repair machinery) for maintaining DNA integrity and a role for gene silencing in niche stabilization. To provide additional support for the hypothesized roles of the above-mentioned and other transcripts in niche specification, we overexpressed, in Arabidopsis, homologs of representative genes (eight) identified as highly enriched or reduced in the maize root QC. We conclude that the coordinated changes in expression of auxin-, redox-, cell cycle- and metabolism-associated genes suggest the linkage of gene networks at the level of transcription, thereby providing additional insights into events likely associated with root stem cell niche establishment and maintenance.

Regeneration: Thomas Hunt Morgan's window into development

Early in his career Thomas Hunt Morgan was interested in embryology and dedicated his research to studying organisms that could regenerate. Widely regarded as a regeneration expert, Morgan was invited to deliver a series of lectures on the topic that he developed into a book, Regeneration (1901). In addition to presenting experimental work that he had conducted and supervised, Morgan also synthesized and critiqued a great deal of work by his peers and predecessors. This essay probes into the history of regeneration studies by looking in depth at Regeneration and evaluating Morgan's contribution. Although famous for his work with fruit fly genetics, studying Regeneration illuminates Morgan's earlier scientific approach which emphasized the importance of studying a diversity of organisms. Surveying a broad range of regenerative phenomena allowed Morgan to institute a standard scientific terminology that continues to inform regeneration studies today. Most importantly, Morgan argued that regeneration was a fundamental aspect of the growth process and therefore should be accounted for within developmental theory. Establishing important similarities between regeneration and development allowed Morgan to make the case that regeneration could act as a model of development. The nature of the relationship between embryogenesis and regeneration remains an active area of research.

Phenotypic evolutionary models in stem cell biology: replacement, quiescence, and variability

Phenotypic evolutionary models have been used with great success in many areas of biology, but thus far have not been applied to the study of stem cells except for investigations of cancer. We develop a framework that allows such modeling techniques to be applied to stem cells more generally. The fundamental modeling structure is the stochastic kinetics of stem cells in their niche and of transit amplifying and fully differentiated cells elsewhere in the organism, with positive and negative feedback. This formulation allows graded signals to be turned into all or nothing responses, and shows the importance of looking beyond the niche for understanding how stem cells behave. Using the deterministic version of this framework, we show how competition between different stem cell lines can be analyzed, and under what circumstances stem cells in a niche will be replaced by other stem cells with different phenotypic characteristics. Using the stochastic version of our framework and state dependent life history theory, we show that the optimal behavior of a focal stem cell will involve long periods of quiescence and that a population of identical stem cells will show great variability in the times at which activity occurs; we compare our results with classic ones on quiescence and variability in the hematopoietic system.

Banking on it: public policy and the ethics of stem cell research and development

If the therapeutic potential of stem cell-based therapies is ever realized, demand for stem cells and derivative tissues will be tremendous and will create new challenges for health care systems, especially publicly funded health care systems. We propose a framework for the ethical analysis of stem cell research and development that considers the welfare of communities, tissue recipients, and cell sources in relation to a range of stem cell production and distribution options. Ethical desiderata include: equitable access, maximized potential therapeutic benefit across demographic and disease groups, and reasonable cost. Other ethical priorities include the minimization of stem cell line and tissue wastage, risk of immune rejection, risk of transmitting diseases, the use of human embryos, and risk to those contributing source cells. We array plausible sources of stem cells and distribution strategies to characterize 12 potential models for producing and distributing cells and tissues in the future. We describe "personalized", "matched", and "universalized" models, and compare the ethical acceptability of these models. Popular and scientific discourses about stem cells typically emphasize personalized or matched stem cell distribution models. We show that universalized models may ultimately best serve the interest of taxpayers, communities and patients who hold high stakes in the therapeutic success of stem cell science. They are therefore highly worthy of scientific pursuit. This conclusion is provisional and the framework must be reapplied as scientific knowledge, technological capacity and ethical mores evolve.

The science and ethics of making part-human animals in stem cell biology

The National Academy of Sciences recently issued voluntary guidelines to govern human embryonic stem cell research. Among other restrictions, these guidelines prohibit certain kinds of combinations of human and nonhuman animal cells, and call for ethics review and oversight of any protocol involving the transfer of human embryonic stem cells into nonhuman animals. In this essay, I discuss the history of and scientific rationales for combining human cells with cells of nonhuman animals, and critically assess the most recent attempts to limit such research on moral grounds--and find them lacking. Nonetheless, as I show, this research remains scientifically and morally contested. I then explore whether and how the NAS's recommended Embryonic Stem Cell Research and Oversight committees will allow for scientifically well-informed moral assessment of this controversial, but possibly important, research.

(Re)defining stem cells

Stem-cell nomenclature is in a muddle! So-called stem cells may be self-renewing or emergent, oligopotent (uni- and multipotent) or pluri- and totipotent, cells with perpetual embryonic features or cells that have changed irreversibly. Ambiguity probably seeped into stem cells from common usage, flukes in biology's history beginning with Weismann's divide between germ and soma and Haeckel's biogenic law and ending with contemporary issues over the therapeutic efficacy of adult versus embryonic cells. Confusion centers on tissue dynamics, whether stem cells are properly members of emerging or steady-state populations. Clarity might yet be achieved by codifying differences between cells in emergent populations, including embryonic stem and embryonic germ (ES and EG) cells in tissue culture as opposed to self-renewing (SR) cells in steady-state populations.