NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.
StemBook is an open access collection of invited, original, peer-reviewed chapters covering a range of topics related to stem cell biology written by top researchers in the field at the Harvard Stem Cell Institute and worldwide. StemBook is aimed at stem cell and non-specialist researchers.
In addition to the contributions of the editorial board and the stem cell research community, the project is being done in collaboration with several other enterprises including Harvard’s Initiative in Innovative Computing. The Initiative in Innovative Computing created the Scientific Collaboration Framework (SCF), the extensible software infrastructure used for the project. SCF and the StemBook project were funded, in part, by a generous grant from an anonymous foundation and also appreciates the input of WormBase's Textpresso team.
Contents
- About StemBook
- Cellular and nuclear reprogramming
- Inducing pluripotencyKit T Rodolfa.Published September 30, 2008.
- Stem cells in animal models of regenerationKyle A Gurley and Alejandro Sánchez Alvarado.Published December 31, 2008.
- Small RNAs – their biogenesis, regulation and function in embryonic stem cellsJoshua E Babiarz and Robert Blelloch.Published May 31, 2009.
- Introduction
- The Biogenesis of miRNAs and related small RNAs
- The role of small RNAs in embryonic stem cells
- Transcriptional regulation of the miRNA content of a cell
- Post-transcriptional regulation of the processing of miRNAs
- miRNAs and induced pluripotency
- Non-canonical miRNAs and endogenous siRNAs
- Conclusions
- References
- Inducing pluripotency
- Ectoderm specification and differentiation
- The cranial sensory nervous system: specification of sensory progenitors and placodesAndrea Streit.Published December 15, 2008.
- Introduction
- Sensory placodes and their derivatives
- A unique territory of multipotent sensory progenitors
- Six and Eya genes and their role in placode development
- Induction of the placode territory through combinatorial signalling
- Specification of individual placodes from common field
- Conclusions
- References
- Tooth organogenesis and regenerationIrma Thesleff and Mark Tummers.Published January 31, 2009.
- Morphogenesis and cell differentiation during tooth development
- Cell and tissue interactions and signaling centers
- Regulation and molecular basis of odontogenic competence
- Regeneration capacity and stem cells in mammalian teeth
- Mouse incisor stem cell niche
- Molecular regulation of the stem cell niche
- Future perspectives for stem cell – based tooth bioengineering
- References
- Melanocyte stem cellsMasatake Osawa.Published June 30, 2009.
- Limbal epithelial stem cells of the corneaGenevieve A Secker and Julie T Daniels.Published June 30, 2009.
- Neural crest-derived stem cellsOlga Shakhova and Lukas Sommer.Published May 4, 2010.
- The cranial sensory nervous system: specification of sensory progenitors and placodes
- Endoderm specification and differentiation
- Pancreatic stem cellsL Charles Murtaugh and Daniel Kopinke.Published July 11, 2008.
- Introduction
- The normal pancreas: embryonic development and adult homeostasis
- Pancreatic regeneration: re-growth or re-differentiation?
- The exception that proves the rule: pancreatic duct ligation
- Duct-to-islet differentiation: in vitro veritas?
- From embryonic stem cell to beta-cell
- Conclusions
- Acknowledgements
- References
- Specification and patterning of the respiratory systemWellington V Cardoso and Darrell N Kotton.Published July 16, 2008.
- Introduction
- Specification of respiratory progenitors in the foregut
- Fgf signaling and induction of respiratory cell fate
- Activation of Fgf10-Fgfr2b signaling in lung progenitors is critical for bud morphogenesis
- Gene interactions in the prospective respiratory field control Fgf10 expression and patterning of the lung primordium
- Retinoids in early lung development
- Dorsal-ventral (D-V) patterning and tracheal-esophageal separation
- Gata6 in lung development
- Canonical Wnt signaling in lung cell fate decisions
- Chromatin remodeling and development
- Do residual lung epithelial stem/progenitor cells remain after lung development is complete?
- Embryonic stem cells and lung epithelial differentiation
- Concluding remarks and perspectives
- References
- Liver developmentAaron M Zorn.Published October 31, 2008.
- Endoderm specificationAnne Grapin-Botton.Published November 30, 2008.
- Pancreatic stem cells
- Epigenetics
- Epigenetic Mechanisms Controlling Mesodermal SpecificationMaria Jose Barrero and Juan Carlos Izpisua Belmonte.Published December 10, 2012.
- Imaging chromatin in embryonic stem cellsEran Meshorer.Published July 11, 2008.
- Epigenetic silencing during early lineage commitmentHoward Cedar and Yehudit Bergman.Published April 30, 2009.
- The chromatin signature of pluripotent cellsKy Sha and Laurie A Boyer.Published May 31, 2009.
- Stem cells, cancer, and epigeneticsStephen B Baylin.Published October 31, 2009.
- Introduction
- Relationships bewteen promoter DNA hypermethylation, genes which regulate stem/progenitor cells, and initiation of human cancer
- Mouse knockout studies of the gene, hypermethylated in cancer 1 (HIC1), indicate that stem/progenitor cell related, epigenetic abnormalities, can contribute to the initiation of cancer
- Relationships between a regulatory chromatin pattern in embryonic cells, abnormal promoter DNA hypermethylation, and cell progression to cancer
- Future directions
- References
- Epigenetic Mechanisms Controlling Mesodermal Specification
- Genomics and proteomics
- Proteomic studies of stem cellsJianlong Wang, Jennifer J Trowbridge, Sridhar Rao, and Stuart H Orkin.Published July 14, 2008.
- Genome-wide transcription factor localization and function in stem cellsWai-Leong Tam and Bing Lim.Published September 15, 2008.
- Introduction
- Key regulators of pluripotency
- The transcriptional landscape in ESCs
- The transcriptional landscape in somatic stem cells
- Reactivating pluripotency
- Cell type-dependent regulation of distinct circuitries
- The integration of microRNAs in transcription circuits
- Perspectives
- Acknowledgements
- References
- The pluripotent transcriptomeMarica Grskovic and Miguel Ramalho-Santos.Published October 10, 2008.
- Introduction
- Molecular signature of pluripotent stem cells
- Co-expression to co-regulation: regulatory pathways
- Novel genes and splice variants
- Is everything transcribed? In every ES cell?
- Differences between mouse and human ES cells
- Expression of the pluripotent transcriptome in cancer
- In vivo transcriptomics – a germline connection?
- Concluding remarks
- Acknowledgements
- References
- Proteomic studies of stem cells
- Germ cell and somatic stem cell biology in reproduction
- Regulation of spermatogoniaQing Zhou and Michael D Griswold.Published July 14, 2008.
- piRNA function in germline developmentJaspreet S Khurana and William E Theurkauf.Published July 30, 2008.
- The role of microRNAs in germline differentiationSteve Reynolds and Hannele Ruohola-Baker.Published September 15, 2008.
- Germline stem cell nichesTing Xie.Published September 30, 2008.
- The anatomically simplest GSC niche in C. elegans
- The first structurally and functionally defined GSC niche in the Drosophila ovary
- The structurally and mechanistically well-studied GSC niche in the Drosophila testis
- The complex GSC niche yet to be defined structurally and functionally in the mouse testis
- Commonalities and differences in different GSC niches
- Conclusions and future directions
- References
- Uterine stem cellsJose Teixeira, Bo R Rueda, and James K Pru.Published September 30, 2008.
- Modeling germ cell differentiationNiels Geijsen and George Q Daley.Published November 30, 2008.
- Lineage analysis of stem cellsDT Fox, LX Morris, T Nystul, and AC Spradling.Published January 31, 2009.
- Somatic stem cells of the ovary and their relationship to human ovarian cancersHenry L Chang, David T MacLaughlin, and Patricia K Donahoe.Published April 30, 2009.
- Sex differentiation in mouse and man and subsequent development of the female reproductive organsNelson A Arango, Ph.D. and Patricia K Donahoe, M.D.Published September 30, 2010.
- C. elegans germline stem cells and their nicheJudith Kimble and Hannah Seidel.Published November 15, 2013.
- Regulation of spermatogonia
- Manufacturing
- Regulatory challenges for the manufacture and scale-out of autologous cell therapiesPaul Hourd, Amit Chandra, Nick Medcalf, and David J Williams.Published March 31, 2014.
- From production to patient: challenges and approaches for delivering cell therapiesKaren Coopman and Nick Medcalf.Published March 31, 2014.
- Regulatory challenges for the manufacture and scale-out of autologous cell therapies
- Mesoderm specification and differentiation
- Epigenetic Mechanisms Controlling Mesodermal SpecificationMaria Jose Barrero and Juan Carlos Izpisua Belmonte.Published December 10, 2012.
- Mouse kidney developmentAlan J Davidson.Published January 15, 2009.
- AdiposeApril Cook and Chad Cowan.Published March 31, 2009.
- Adult mesenchymal stem cellsErnestina Schipani and Henry M Kronenberg.Published January 31, 2009.
- Introduction
- Are mesenchymal stem cells distinct from hematopoietic stem cells?
- Have mesenchymal stem cells specific cell-surface antigens?
- Are pluripotent stem cells present in the bone marrow?
- What is the developmental origin of mesenchymal stem cells?
- Is there a “niche” for mesenchymal stem cells?
- Why studying MSCs?
- A future perspective
- Acknowledgments
- References
- Epigenetic Mechanisms Controlling Mesodermal Specification
- Niche biology, homing, and migration
- Hematopoietic stem cell traffickingClaire Magnon and Paul S Frenette.Published July 14, 2008.
- The neural stem cell microenvironmentIlias Kazanis, Justin Lathia, Lara Moss, and Charles ffrench-Constant.Published August 31, 2008.
- Hematopoietic stem cell trafficking
- Renewal
- Aging and stem cell renewalHaroldo Silva and Irina M Conboy.Published July 15, 2008.
- Quiescent stem cells in the nicheFumio Arai and Toshio Suda.Published July 11, 2008.
- Mechanisms regulating stem cell polarity and the specification of asymmetric divisionsHila Toledano and D Leanne Jones.Published March 31, 2009.
- Aging and stem cell renewal
- Stem cell immunology
- Immunologic targeting of the cancer stem cellCatherine J Wu.Published December 15, 2008.
- Immunological considerations for cell therapy using human embryonic stem cell derivativesMicha Drukker.Published December 16, 2008.
- Introduction
- Expression of histocompatibility antigens on u/dhESCs
- Expression of T-cell regulating signals in u/dhESCs
- T-cell response against u/dhESCs measured by functional assays
- Interaction of natural killer cells with hESCs
- Generation of patient-specific isogenic hESC lines
- Conclusions
- Acknowledgments
- References
- Mouse models of graft-versus-host diseasePavan Reddy and James LM Ferrara.Published February 28, 2009.
- Prospects for ensuring acceptance of ES cell-derived tissuesKathy O Lui, Paul J Fairchild, and Herman Waldmann.Published September 30, 2010.
- Introduction
- Central tolerance
- esDC as a negative vaccine against graft rejection
- Immunological privilege of ES cell-derived tissues
- Proposed mechanisms of natural privilege operating in ES cell-derived tissues
- Induction of donor-specific tolerance for ES cell-derived tissues
- Conclusion
- Acknowledgements
- References
- Immunologic targeting of the cancer stem cell
- Therapeutic prospects
- The hematopoietic stem cell nicheLouise E Purton and David T Scadden.Published November 15, 2008.
- Hematopoietic inductive microenvironments and the hematopoietic stem cell niche: a historical perspective
- Cell types that have been identified to form prospective HSC niches
- Are all HSC niches equal?
- What regulates the HSC niches?
- When niches turn bad- evidence for roles of the HSC niches in hematopoietic diseases
- Acknowledgments
- References
- Medical applications of epidermal stem cellsGaelle Lapouge and Cédric Blanpain.Published November 15, 2008.
- Mesenchymal stromal cells as a drug delivery systemLata G Menon, Veronica J Shi, and Rona S Carroll.Published January 15, 2009.
- Egress and Mobilization of Hematopoietic Stem and Progenitor Cells: A Dynamic Multi-facet ProcessKfir Lapid, Chen Glait-Santar, Shiri Gur-Cohen, Jonathan Canaani, Orit Kollet, and Tsvee Lapidot.Published December 10, 2012.
- Introduction
- Cytokine-induced mobilization
- The SDF-1/CXCR4 pathway
- HSPC mobilization and intracellular signaling
- Adhesion molecules and loss of retention
- Proteolytic activity
- The fibrinolytic system
- The dynamics of the HSC niche and BM microenvironment during mobilization
- Involvement of the innate immunity
- The nervous system
- Stem cell mobilization viewed in the clinical context
- Concluding remarks
- References
- Cord blood hematopoietic stem cell transplantationHal E Broxmeyer.Published May 26, 2010.
- The hematopoietic stem cell niche
- Tissue engineering
- Combining stem cells and biomaterial scaffolds for constructing tissues and cell deliveryStephanie M Willerth and Shelly E Sakiyama-Elbert.Published July 9, 2008.
- Autologous Approaches to Tissue EngineeringBeatrice Dionigi and Dario O Fauza.Published December 10, 2012.
- Flow perfusion culture of mesenchymal stem cells for bone tissue engineeringF Kurtis Kasper, Jiehong Liao, James D Kretlow, Vassilios I Sikavitsas, and Antonios G Mikos.Published August 15, 2008.
- Prevalence and significance of bone defects
- Current clinical strategies for bone regeneration
- Tissue engineering-based clinical approaches and considerations for bone regeneration
- Bone regeneration by progenitor cell transplantation
- Bone tissue induction into polymer scaffolds
- Flow perfusion culture enhances osteogenic differentiation of mesenchymal stem cells
- Fluid flow increases mineralized bone-like extracellular matrix deposition in a dose-dependent manner
- In vitro culture duration and stage of osteogenic differentiation of transplanted mesenchymal stem cells affect in vivo osteogenicity of in vitro generated bone-like extracellular matrix constructs
- Mineralized matrix deposition by mesenchymal stem cells in flow perfusion culture increases with increasing fluid shear forces
- Scaffold mesh size affects the osteogenic differentiation of mesenchymal stem cells cultured in a flow perfusion bioreactor
- The initial cell phenotype and degree of cell adhesion to titanium fiber mesh scaffolds affects the ectopic bone formation response in vivo
- In vitro generated bone-like extracellular matrix influences the osteogenic differentiation of mesenchymal stem cells in vitro
- In vitro generated bone-like extracellular matrix and fluid shear stress synergistically enhance osteogenic differentiation of mesenchymal stem cells in vitro
- Flow perfusion culture of mesenchymal stem cells results in the generation of an extracellular matrix containing bone-related growth factors
- The preculture period of mesenchymal stem cells in osteogenic media influences the in vivo bone forming potential of the cells
- An in vitro generated extracellular matrix supports tissue infiltration and promotes blood vessel formation at an ectopic site in vivo
- An in vitro generated bone-like extracellular matrix enhances the osteogenic gene expression of mesenchymal stem cells
- Flow perfusion culture promotes infiltration and spatial distribution of mesenchymal stem cells within electrospun poly(ε-caprolactone) microfiber and multilayer nanofiber/microfiber scaffolds
- Summary
- Acknowledgements
- References
- Engineering microenvironments to control stem cell fate and functionShawdee Eshghi and David V Schaffer.Published September 11, 2008.
- The role of bone marrow-derived stem cells in lung regeneration and repairElizabeth K Sage, Michael R Loebinger, Julia Polak, and Sam M Janes.Published September 30, 2008.
- Mechanical control of stem cell differentiationDaniel M Cohen and Christopher S Chen.Published October 31, 2008.
- Skin tissue engineeringDavid J Wong and Howard Y Chang.Published March 31, 2009.
- Molecular imaging of stem cellsMartin Rodriguez-Porcel, Joseph C Wu, and Sanjiv Sam Gambhir.Published July 30, 2009.
- Combining stem cells and biomaterial scaffolds for constructing tissues and cell delivery
- Protocols
- Pluripotent Cells
- Embryoid body formation from human pluripotent stem cells in chemically defined E8 mediaYongshun Lin and Guokai Chen.Published June 1, 2014.
- Genome editing in human pluripotent stem cellsDerek T Peters, Chad A Cowan, and Kiran Musunuru.Published April 29, 2013.
- Splitting hPSCs with DispaseMark Tomishima.Published December 10, 2012.
- Splitting hESC/hiPSC lines with EDTA in feeder free conditionsGuokai Chen.Published December 10, 2012.
- Splitting hESC/hiPSC lines on MEF using AccutaseHyesoo Kim.Published December 10, 2012.
- General Spinfection ProtocolW Travis Berggren, Margaret Lutz, and Veronica Modesto.Published December 10, 2012.
- Assessment of human pluripotent stem cells with PluriTestFranz-Josef Müller, Björn Brändl, and Jeanne F Loring.Published December 10, 2012.
- Conditioning pluripotent stem cell media with mouse embryonic fibroblasts (MEF-CM)Mark Tomishima.Published June 10, 2012.
- Feeder-independent culture protocol – EDTA splittingWiCell.Published June 10, 2012.
- Feeder dependent (MEF) culture protocol – collagenase passagingWiCell.Published June 10, 2012.
- iPSC derivation from fibroblast in chemically defined mediumGuokai Chen.Published June 10, 2012.
- Cryopreservation of human pluripotent stem cells in defined conditionsGuokai Chen.Published June 10, 2012.
- Formation of embryoid bodies from Matrigel dots protocolMargaret Lutz and Travis Berggren.Published June 10, 2012.
- Teratoma formation: A tool for monitoring pluripotency in stem cell researchWendy Y Zhang, Patricia E de Almeida, and Joseph C Wu.Published June 10, 2012.
- Basic pluripotent stem cell culture protocolsAuthors: Maria Borowski, Maria Giovino-Doherty, Lan Ji, Meng-Jiao Shi, Kelly P Smith, and Joseph Laning.Published June 10, 2012.
- Embryoid body formation from human pluripotent stem cells in chemically defined E8 media
- Reprogramming
- iPSC Reprogramming from Human Peripheral Blood Using Sendai Virus Mediated Gene TransferWenli Yang, Jason A Mills, Spencer Sullivan, Ying Liu, Deborah L French, and Paul Gadue.Published June 10, 2012.
- Protocol for making retroviral reprogramming factorsMargaret Lutz, Veronica Modesto, and Athanasia Panopoulos.Published June 10, 2012.
- Hematopoietic differentiationKyung-Dal Choi, Maxim Vodyanik, and Igor I Slukvin.Published June 10, 2012.
- Robust generation of hepatocyte-like cells from human embryonic stem cell populationsCN Medine, B Lucendo-Villarin, W Zhou, CC West, and DC Hay.Published June 10, 2012.
- Monolayer endoderm differentiation from human ESCsX Cheng, L Ying, L Lu, AM Galvão, JA Mills, HC Lin, DN Kotton, SS Shen, MC Nostro, JK Choi, MJ Weiss, DL French, and P Gadue.Published June 10, 2012.
- Blood - SeV derived fibroblast generated iPSCsLaurence Daheron and Sunita D'Souza.Published June 10, 2012.
- Protocol for directed differentiation of human pluripotent stem cells toward a hepatocyte fateJun Cai, Ann DeLaForest, Joseph Fisher, Amanda Urick, Thomas Wagner, Kirk Twaroski, Max Cayo, Masato Nagaoka, and Stephen A Duncan.Published June 10, 2012.
- iPSC Reprogramming from Human Peripheral Blood Using Sendai Virus Mediated Gene Transfer
- Ectoderm
- Midbrain dopamine neurons from hESCsMark Tomishima.Published June 10, 2012.
- Neural induction – Dual SMAD inhibitionMark Tomishima.Published June 10, 2012.
- Midbrain dopamine neurons from hESCs
- Endoderm
- Pancreatic differentiationM Cristina Nostro, Farida Sarangi, Shinichiro Ogawa, Audrey Holtzinger, Barbara Corneo, Xueling Li, Suzanne J Micallef, In-Hyun Park, Christina Basford, Michael B Wheeler, George Q Daley, Andrew G Elefanty, Edouard G Stanley, and Gordon Keller.Published June 10, 2012.
- Robust generation of hepatocyte-like cells from human embryonic stem cell populationsCN Medine, B Lucendo-Villarin, W Zhou, CC West, and DC Hay.Published June 10, 2012.
- Monolayer endoderm differentiation from human ESCsX Cheng, L Ying, L Lu, AM Galvão, JA Mills, HC Lin, DN Kotton, SS Shen, MC Nostro, JK Choi, MJ Weiss, DL French, and P Gadue.Published June 10, 2012.
- Protocol for directed differentiation of human pluripotent stem cells toward a hepatocyte fateJun Cai, Ann DeLaForest, Joseph Fisher, Amanda Urick, Thomas Wagner, Kirk Twaroski, Max Cayo, Masato Nagaoka, and Stephen A Duncan.Published June 10, 2012.
- Pancreatic differentiation
- Mesoderm
- Generation of human induced pluripotent stem cells from peripheral blood using the STEMCCA lentiviral vectorAndreia Gianotti-Sommer, Sarah S Rozelle, Spencer Sullivan, Jason A Mills, Seon-Mi Park, Brenden W Smith, Amulya M Iyer, Deborah L French, Darrell N Kotton, Paul Gadue, George J Murphy, and Gustavo Mostoslavsky.Published April 29, 2013.
- Hematopoietic differentiationKyung-Dal Choi, Maxim Vodyanik, and Igor I Slukvin.Published June 10, 2012.
- Chondrocyte protocolRachel A Oldershaw, Melissa A Baxter, Emma T Lowe, Nicola Bates, Lisa M Grady, Francesca Soncin, Daniel R Brison, Timothy E Hardingham, and Susan J Kimber.Published June 10, 2012.
- Blood - SeV derived fibroblast generated iPSCsLaurence Daheron and Sunita D'Souza.Published June 10, 2012.
- Generation of human induced pluripotent stem cells from peripheral blood using the STEMCCA lentiviral vector
- Cell Imaging
- Analyzing the genomic integrity of stem cellsUri Ben-David and Nissim Benvenisty.Published June 10, 2012.
- Analyzing the genomic integrity of stem cells
- Pluripotent Cells
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