Digital Gene Expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea

The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking. Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC. DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes

Advances in Aquatic Invertebrate Stem Cell Research

This publication is based upon work from COST Action ’16203 MARISTEM Stem cells of marine/aquatic invertebrates: from basic research to innovative applications’, supported by COST (European Cooperation in Science and Technology).COST (European Cooperation in Science and Technology) is a funding agency for research and innovation networks. Our Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation.www.cost.eu Aquatic invertebrates represent the largest biodiversity and the widest phylogenetic radiation on Earth, with more than 2 million known species. Up until a few years ago, their use as model organisms in biological research was limited by the paucity of omics data. Recently, the situation has rapidly changed and is still changing. Today, the genomes and various transcriptomes of many aquatic invertebrate species, as well as many recombinant proteins of invertebrate origin, are available. New technologies have revolutionized the available toolbox of research methodologies. This explains the rising interest of researchers in the use of aquatic invertebrates as reliable model organisms.In contrast to the prevalence of diverse oligopotent and unipotent stem cells in vertebrates, aquatic invertebrates (especially non-ecdysozoan invertebrates) exhibit multiple adult cell types with stem cellattributes characterized by multipotency and pluripotency; furthermore, these give rise to cell lineages characteristic of more than a single germ layer, sometimes with somatic and germ line potentials. In addition, unlike vertebrates, aquatic invertebrate adult stem cells are disseminated and widespread inside the animal body, are not associated with a regulatory microenvironment (niche) and do participate in aging and regeneration phenomena. These properties can help us to better understand the processes and phenomena in mammalian stem cell biology, such as natural chimerism and cancer, aging and senescence, immunity and autoimmune responses, which are all difficult to explain or understand in the human context.The COST Action 16203 MARISTEM "Stem cells of marine/aquatic invertebrates: from basic research to innovative applications" started in 2017 with the aim to foster the knowledge of the biology of aquatic invertebrates stem cells and strengthen the European community of researchers on aquatic invertebrate stem cells in order to build innovative ideas relevant to various biomedical disciplines. This book represents one of the deliverables of the Action and collects part of the materials produced during the past 3 years within the network as a tool to disseminate and render available what has been achieved up to now. We hope that this book will be useful to scientists interested in stem cells of non-model organisms, with particular reference to aquatic invertebrates

Advances in Aquatic Invertebrate Stem Cell Research

This publication is based upon work from COST Action ’16203 MARISTEM Stem cells of marine/aquatic invertebrates: from basic research to innovative applications’, supported by COST (European Cooperation in Science and Technology). COST (European Cooperation in Science and Technology) is a funding agency for research and innovation networks. Our Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. Aquatic invertebrates represent the largest biodiversity and the widest phylogenetic radiation on Earth, with more than 2 million known species. Up until a few years ago, their use as model organisms in biological research was limited by the paucity of omics data. Recently, the situation has rapidly changed and is still changing. Today, the genomes and various transcriptomes of many aquatic invertebrate species, as well as many recombinant proteins of invertebrate origin, are available. New technologies have revolutionized the available toolbox of research methodologies. This explains the rising interest of researchers in the use of aquatic invertebrates as reliable model organisms. In contrast to the prevalence of diverse oligopotent and unipotent stem cells in vertebrates, aquatic invertebrates (especially non-ecdysozoan invertebrates) exhibit multiple adult cell types with stem cell attributes characterized by multipotency and pluripotency; furthermore, these give rise to cell lineages characteristic of more than a single germ layer, sometimes with somatic and germ line potentials. In addition, unlike vertebrates, aquatic invertebrate adult stem cells are disseminated and widespread inside the animal body, are not associated with a regulatory microenvironment (niche) and do participate in aging and regeneration phenomena. These properties can help us to better understand the processes and phenomena in mammalian stem cell biology, such as natural chimerism and cancer, aging and senescence, immunity and autoimmune responses, which are all difficult to explain or understand in the human context. The COST Action 16203 MARISTEM "Stem cells of marine/aquatic invertebrates: from basic research to innovative applications" started in 2017 with the aim to foster the knowledge of the biology of aquatic invertebrates stem cells and strengthen the European community of researchers on aquatic invertebrate stem cells in order to build innovative ideas relevant to various biomedical disciplines. This book represents one of the deliverables of the Action and collects part of the materials produced during the past 3 years within the network as a tool to disseminate and render available what has been achieved up to now. We hope that this book will be useful to scientists interested in stem cells of non-model organisms, with particular reference to aquatic invertebrate

Advances in Aquatic Invertebrate Stem Cell Research

This publication is based upon work from COST Action ’16203 MARISTEM Stem cells of marine/aquatic invertebrates: from basic research to innovative applications’, supported by COST (European Cooperation in Science and Technology). COST (European Cooperation in Science and Technology) is a funding agency for research and innovation networks. Our Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. Aquatic invertebrates represent the largest biodiversity and the widest phylogenetic radiation on Earth, with more than 2 million known species. Up until a few years ago, their use as model organisms in biological research was limited by the paucity of omics data. Recently, the situation has rapidly changed and is still changing. Today, the genomes and various transcriptomes of many aquatic invertebrate species, as well as many recombinant proteins of invertebrate origin, are available. New technologies have revolutionized the available toolbox of research methodologies. This explains the rising interest of researchers in the use of aquatic invertebrates as reliable model organisms. In contrast to the prevalence of diverse oligopotent and unipotent stem cells in vertebrates, aquatic invertebrates (especially non-ecdysozoan invertebrates) exhibit multiple adult cell types with stem cell attributes characterized by multipotency and pluripotency; furthermore, these give rise to cell lineages characteristic of more than a single germ layer, sometimes with somatic and germ line potentials. In addition, unlike vertebrates, aquatic invertebrate adult stem cells are disseminated and widespread inside the animal body, are not associated with a regulatory microenvironment (niche) and do participate in aging and regeneration phenomena. These properties can help us to better understand the processes and phenomena in mammalian stem cell biology, such as natural chimerism and cancer, aging and senescence, immunity and autoimmune responses, which are all difficult to explain or understand in the human context. The COST Action 16203 MARISTEM "Stem cells of marine/aquatic invertebrates: from basic research to innovative applications" started in 2017 with the aim to foster the knowledge of the biology of aquatic invertebrates stem cells and strengthen the European community of researchers on aquatic invertebrate stem cells in order to build innovative ideas relevant to various biomedical disciplines. This book represents one of the deliverables of the Action and collects part of the materials produced during the past 3 years within the network as a tool to disseminate and render available what has been achieved up to now. We hope that this book will be useful to scientists interested in stem cells of non-model organisms, with particular reference to aquatic invertebrate

Homeobox genes in the development and regeneration of the cephalochordate Branchiostoma lanceolatum and the polychaete annelid Spirobranchus lamarcki

The development of complex animal morphology requires the extremely sophisticated spatiotemporal coordination of cell behaviour and communication. Homeobox genes encode transcription factors that are deployed in developmental processes to control the expression of other genes in particular locations and contexts. Many homeobox genes are highly conserved and act in similar roles between distantly-related animals that derive from the roles of their ancestral orthologues. The way that these genes have differentially evolved between taxa, and the effect that these changes have on the development and morphology of animals, is critical to our understanding of metazoan evolution. One particular developmental context, the regeneration of missing tissue, offers a unique perspective on evolutionary developmental biology because of its relationship to ontogenic development and its surprising diversity of retention and process between animal taxa. I examined the homeobox gene content of transcriptomes taken from the mature and regenerating tissue of the post-anal tail of Branchiostoma lanceolatum, a well-studied cephalochordate with a highly conserved genome, and the evolutionarily novel operculum of Spirobranchus lamarcki, a sedentarian annelid. In S. lamarcki regeneration, a diverse variety of homeobox genes is expressed, and the regenerative expression response is substantial. The discovery of several difficult-to-classify homeobox genes lead to the substantial expansion and improvement of the classification of a variety of homeobox genes undergoing unusual rapid and expansive evolution in the Spiralia, including dozens of TALE and PRD class genes, a new orthology group, and a strange S. lamarcki Hox gene. In B. lanceolatum, a similar diversity of expressed genes is observed but a milder regenerative response. One transcriptomic sequence in particular, identified as Pax3/7, led to the discovery that this well-studied gene has a previously unnoticed duplication in cephalochordates. This discovery has implications for ongoing study of vertebrate and cephalochordate neural plate border evolution

Whole-Body Regeneration

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. 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 thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field

Whole-Body Regeneration

This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. 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 thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field