Computational Stem Cell Biology

This volume details methods and protocols to further the study of stem cells within the computational stem cell biology (CSCB) field. Chapters are divided into four sections covering the theory and practice of modeling of stem cell behavior, analyzing single cell genome-scale measurements, reconstructing gene regulatory networks, and metabolomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Stem Cell Biology: Methods and Protocols will be an invaluable guide to researchers as they explore stem cells from the perspective of computational biology.

Computational Biology for Stem Cell Research is an invaluable guide for researchers as they explore HSCs and MSCs in computational biology. With the growing advancement of technology in the field of biomedical sciences, computational approaches have reduced the financial and experimental burden of the experimental process. In the shortest span, it has established itself as an integral component of any biological research activity. HSC informatics (in silico) techniques such as machine learning, genome network analysis, data mining, complex genome structures, docking, system biology, mathematical modeling, programming (R, Python, Perl, etc.) help to analyze, visualize, network constructions, and protein-ligand or protein-protein interactions. This book is aimed at beginners with an exact correlation between the biomedical sciences and in silico computational methods for HSCs transplantation and translational research and provides insights into methods targeting HSCs properties like proliferation, self-renewal, differentiation, and apoptosis. Modeling Stem Cell Behavior: Explore stem cell behavior through animal models, bridging laboratory studies to real-world clinical allogeneic HSC transplantation (HSCT) scenarios. Bioinformatics-Driven Translational Research: Navigate a path from bench to bedside with cutting-edge bioinformatics approaches, translating computational insights into tangible advancements in stem cell research and medical applications. Interdisciplinary Resource: Discover a single comprehensive resource catering to biomedical sciences, life sciences, and chemistry fields, offering essential insights into computational tools vital for modern research.

"Computational biology in combination with large-scale biology has played a critical role in exploring the great potentials of embryonic stem cells, resulting in significant discoveries. This e-book brings together reviews and essays from different aspects"

The study of stem cell biology is under intensive investigations. Because stem cells have the unique capability to self-renew and differentiate into one or several cell types, they play a critical role in development, tissue homeostasis and regeneration. Stem cells also constitute promising cell candidates for cell therapy. The aim of this book is to provide an accurate knowledge on stem cell biology and regenerative medicine. This book will cover many topics in the field and is based on seminars given by recognized scientists involved the international master program on stem cell biology at the University Pierre and Marie Curie (UPMC) in Paris. Content Preface. Pierre Charbord and Charles Durand. 1) General concepts 1.Stem cell concepts. Charles Durand and Pierre Charbord. 2.Transcriptional regulation in stem cells. Eric Soler and Frank Grosveld. 3.DNA repair in stem cells. Leyla Vahidi Ferdousi and Miria Ricchetti. 4. Stem cells and epigenetic regulation. Emma L. Walton and Claire Francastel. 5. Hydra and the evolution of stem cells. Alexander Klimovich, Anna Marei Böhm and Thomas C.G. Bosch. 6. Ontogeny of stem cells. Thierry Jaffredo. 7. Regeneration in anamniotic vertebrates. Dunja Knapp. 8. Computational models of spatio-temporal stem cell organization. Peter Buske and Joerg Galle. 2) Pluripotent stem cells 9. X chromosome inactivation in stem cells and development. Agnese Loda, Friedemann Loos and Joost Gribnau. 10. Molecular machinery of reprogramming. Romain Desprat, Ollivier Milhavet and Jean-Marc Lemaitre. 11. Modeling human genetic disorders using induced pluripotent stem cells. Franck Lebrin. 3) Adult stem cells 12. Developmental biology of hematopoietic stem cells : Cellular aspects. Laurent Yvernogeau, Jean-Charles Boisset and Catherine Robin. 13. Developmental biology of haematopoietic stem cells: Cell intrinsic and extrinsic regulators of their emergence. Katrin Ottersbach. 14. Biology of hematopoietic stem cells in the adult. Marie-Laure Arcangeli, Rima Haddad, Francoise Pflumio. 15. Epithelial stem cells in the skin. Romain Fontaine, Mathieu Castela and Selim Aractingi. 16. Skeletal muscle stem cells. Elisa Negroni, Maximilien Bencze, Stéphanie Duguez, Gillian Butler-Browne and Vincent Mouly. 17. Mammary stem cells. Marie-Ange Deugnier, Marisa M. Faraldo and Marina A. Glukhova. 18. Intestinal stem cells. Silvia Fre. 19. Neural stem cells. Nathalie Kubis and Martin Catala. 20. Dental stem cells. Anne Poliard. 21. Bone marrow Mesenchymal Stem Cells: from stemness to stromal property of hematopoietic support. Pierre Charbord and Bruno Delorme. 22. Retinal stem cells. Olivier Goureau, Angélique Terray, Katherine S. Matho, Sacha Reichman, and Gael Orieux. 4) Stem cell-related diseases and therapy using stem cells 23. Leukemic stem cells: what the concept brings to disease and patient management. Berent Lunden and Christine Chomienne. 24. Stem cells for cardiac repair. Philippe Menasché. 25. Stem cells for red blood cell production. Christelle Mazurier, Guillaume F Rousseau, Luc Douay and Hélène Lapillonne. 26. Prospectives for therapy with stem cells in skeletal muscular diseases. Maximilien Bencze, Elisa Negroni, Vincent Mouly and Gillian Butler-Browne. 5) Regulatory and philosophical aspects 27. Legal framework for research on Human Embryonic Stem Cells in France and in Europe. Arnaud de Guerra, Emmanuelle Prada-Bordenave 28. Stem cell epistemological issues. Lucie Laplane. 29. Future outlook. Pierre Charbord and Charles Durand.

This book describes a global assessment of stem cell engineering research, achieved through site visits by a panel of experts to leading institutes, followed by dedicated workshops. The assessment made clear that engineers and the engineering approach with its quantitative, system-based thinking can contribute much to the progress of stem cell research and development. The increased need for complex computational models and new, innovative technologies, such as high-throughput screening techniques, organ-on-a-chip models and in vitro tumor models require an increasing involvement of engineers and physical scientists. Additionally, this book will show that although the US is still in a leadership position in stem cell engineering, Asian countries such as Japan, China and Korea, as well as European countries like the UK, Germany, Sweden and the Netherlands are rapidly expanding their investments in the field. Strategic partnerships between countries could lead to major advances of the field and scalable expansion and differentiation of stem cells. This study was funded by the National Science Foundation (NSF), the National Institutes of Health (NIH) and the National Institute of Standards and Technology (NIST).

Stem cells have been gaining a lot of attention in recent years. Their unique potential to self-renew and differentiate has turned them into an attractive model for the study of basic biological questions such as cell division, replication, transcription, cell fate decisions, and more. With embryonic stem (ES) cells that can generate each cell type in the mammalian body and adult stem cells that are able to give rise to the cells within a given lineage, basic questions at different developmental stages can be addressed. Importantly, both adult and embryonic stem cells provide an excellent tool for cell therapy, making stem cell research ever more pertinent to regenerative medicine. As the title The Cell Biology of Stem Cells suggests, our book deals with multiple aspects of stem cell biology, ranging from their basic molecular characteristics to the in vivo stem cell trafficking of adult stem cells and the adult stem-cell niche, and ends with a visit to regeneration and cell fate reprogramming. In the first chapter, “Early embryonic cell fate decisions in the mouse”, Amy Ralson and Yojiro Yamanaka describe the mechanisms that support early developmental decisions in the mouse pre-implantation embryo and the current understanding of the source of the most immature stem cell types, which includes ES cells, trophoblast stem (TS) cells and extraembryonic endoderm stem (XEN) cells.

Biology of Stem Cells and the Molecular Basis of the Stem State concentrates upon adult stem cells, particularly on mesenchymal cell populations, which is the author’s area of expertise. The text offers the reader a detailed description of the emergence of stem cell research and the dogmas that were created during the first decades of analysis of stem cell properties, particularly those of hemopoietic stem cells. Biology of Stem Cells and the Molecular Basis of the Stem State also introduces the reader to the commonly accepted notions regarding stem cell biology, with an emphasis on an alternative view of stemness, i.e. the stem state. In keeping with the popularity of this topic, Biology of Stem Cells and the Molecular Basis of the Stem State addresses the major controversies and points of dispute, among researchers in the stem cell field. Overall, Biology of Stem Cells and the Molecular Basis of the Stem State presents a well-rounded dialogue about stem cells as it not only concentrates upon the biological elements of stem cell, but also addresses the controversy and hype currently enveloping this popular subject.

Stem Cells: A Short Course is a comprehensive text for students delving into the rapidly evolving discipline of stem cell research. Comprised of eight chapters, the text addresses all of the major facets and disciplines related to stem cell biology and research. A brief history of stem cell research serves as an introduction, followed by coverage of stem cell fundamentals; chapters then explore embryonic and fetal amniotic stem cells, adult stem cells, nuclear reprogramming, and cancer stem cells. The book concludes with chapters on stem cell applications, including the role of stem cells in drug discovery and therapeutic applications in spinal cord injury, brain damage, neurological and autoimmune disorders, among others. Written by a leader in the field, Stem Cells: A Short Course appeals to both students and instructors alike, appealing to academic enthusiasm for stem cell research and applications.