Structure of the Digestive Tube in the Holothurian Eupentacta fraudatrix (Holothuroidea: Dendrochirota)

In the holothurian Eupentacta fraudatrix,the gut wall exhibits trilaminar organization. It consists of an inner digestive epithelium, a middle layer of connective tissue, and an outer mesothelium (coelomic epithelium). The pharynx, esophagus, and stomach are lined with a cuticular epithelium composed of T-shaped cells. The lining epithelium of the intestine and cloaca lacks a cuticle and consists of columnar vesicular enterocytes. Mucocytes are also encountered in the digestive epithelium. The connective tissue layer is composed of a ground substance, which houses collagen fibers, amoebocytes, morula cells, and fibroblasts. The gut mesothelium is a pseudostratified epithelium, which is dominated by peritoneal and myoepithelial cells and also includes the perikarya and processes of the neurons of the hyponeural plexus and vacuolated cells.     

Induction of proepicardial marker gene expression by the liver bud

Cells of the coronary vessels arise from a unique extracardiac mesothelial cell population, the proepicardium, which develops posterior to the sinoatrial region of the looping-stage heart. Although contribution of the proepicardial cells to cardiac development has been studied extensively, it remains unresolved how the proepicardium is induced and specified in the mesoderm during embryogenesis. It is known, however, that the proepicardium develops from the mesothelium that overlays the liver bud. Here, we show that the expression of proepicardial marker genes - Wt1, capsulin (epicardin, pod1, Tcf21) and Tbx18, can be induced in na?ve mesothelial cells by the liver bud, both in vitro and in vivo. Lateral embryonic explants, when co-cultured with the liver bud, were induced to express these proepicardial marker genes. The same induction of the marker genes was detected in vivo when a quail liver bud was implanted in the posterior-lateral regions of a chick embryo. This ectopic induction of marker gene expression was not evident when other endodermal tissues, such as the lung bud or stomach, were implanted. This inductive response to the liver bud was not detectable in host embryos before stage 12 (16-somite stage). These results suggest that, after a specific developmental stage, a large area of the mesothelium becomes competent to express proepicardial marker genes in response to localized liver-derived signal(s). The developmentally regulated competency of mesothelium and a localized inductive signal might play a role in restricting the induction of the proepicardial marker gene expression to a specific region of the mesothelium. The data might also provide a foundation for future engineering of a coronary vascular progenitor population.     

Establishment of enhancer detection lines expressing GFP in the gut of the ascidian Ciona intestinalis

The gut is a tubular, endodermal organ for digesting food and absorbing nutrients. In this study, we characterized eight enhancer detection lines that express green fluorescent protein (GFP) in the whole or part of the digestive tube of the ascidian Ciona intestinalis. Three enhancer detection lines for the pyloric gland, a structure associated with the digestive tube, were also analyzed. These lines are valuable markers for analyzing the mechanisms of development of the gut. Based on the GFP expression of the enhancer detection lines together with morphological characteristics, the digestive tube of Ciona can be subdivided into at least 10 compartments in which different genetic cascades operate. Causal insertion sites of the enhancer detection lines were identified, and the expression pattern of the genes near the insertion sites were characterized by means of whole-mount in situ hybridization. We have characterized four and two genes that were specifically or strongly expressed in the digestive tube and pyloric gland, respectively. The present data provide the basic information and useful resources for studying gut formation in Ciona.     

Transdifferentiation in holothurian gut regeneration

It has recently been shown that the whole spectrum of cell types constituting a multicellular organism can be generated from stem cells. Our study provides an example of an alternative mechanism of tissue repair. Injection of distilled water into the coelomic cavity of the holothurian Eupentacta fraudatrix results in the loss of the whole digestive tract, except the cloaca. The new gut reforms from two separate rudiments. One rudiment appears at the anterior end of the body and extends posteriorly. The second rudiment grows anteriorly from the cloaca. In the anterior rudiment, the luminal epithelium (normally derived from endoderm) develops de novo through direct transdifferentiation of the coelomic epithelial cells (mesodermal in origin). In the posterior rudiment, the luminal epithelium originates from the lining epithelium of the cloaca. After 27 days, the two rudiments come into contact and fuse to form a continuous digestive tube lined with a fully differentiated luminal epithelium. Thus in this species, the luminal epithelia of the anterior and posterior gut rudiments develop from two different cell sources-i.e., from the mesodermally derived mesothelium and the endodermally derived epithelium of the cloacal lining, respectively. Our data suggest that differentiated cells of echinoderms are capable of transdifferentiation into other cell types.     

The receptor tyrosine kinase RET regulates hindgut colonization by sacral neural crest cells

The enteric nervous system (ENS) is formed from vagal and sacral neural crest cells (NCC). Vagal NCC give rise to most of the ENS along the entire gut, whereas the contribution of sacral NCC is mainly limited to the hindgut. This, and data from heterotopic quail-chick grafting studies, suggests that vagal and sacral NCC have intrinsic differences in their ability to colonize the gut, and/or to respond to signalling cues within the gut environment. To better understand the molecular basis of these differences, we studied the expression of genes known to be essential for ENS formation, in sacral NCC within the chick hindgut. Our results demonstrate that, as in vagal NCC, Sox10, EdnrB, and Ret are expressed in sacral NCC within the gut. Since we did not detect a qualitative difference in expression of these ENS genes we performed DNA microarray analysis of vagal and sacral NCC. Of 11 key ENS genes examined from the total data set, Ret was the only gene identified as being highly differentially expressed, with a fourfold increase in expression in vagal versus sacral NCC. We also found that over-expression of RET in sacral NCC increased their ENS developmental potential such that larger numbers of cells entered the gut earlier in development, thus promoting the fate of sacral NCC towards that of vagal NCC.     

Developmental genetics of the Drosophila gut: specification of primordia, subdivision and overt-differentiation.

The Drosophila gut is composed of three major parts, the foregut, midgut and hindgut, which arise from anterior and posterior invaginations of the early blastoderm. We review the process of the specification of the gut primordia, subsequent subdivision and region-specific cell differentiation in terms of developmental genetics. Graded activities of maternal signals at anterior and posterior terminal domains of the blastoderm, being mediated by activities of two zygotic gap genes, tailless and huckebein, lead to the activation of key genes that determine the gut primordia: serpent (GATA factor gene) for the endodermal midgut; brachyenteron (Brachyury homolog) for the ectodermal hindgut. fork head (HNF-3 homolog) and caudal (Cdx homolog) are also essential for the development of all gut primordia or hindgut primordium, respectively. Subdivision of the midgut epithelium is regulated by inductive signals emanating from the visceral mesoderm, which is under the control of HOM-C genes. In contrast, pattern formation of the ectodermal foregut and hindgut is regulated by secreted signaling molecules, such as Wingless (Wnt homolog), Hedgehog and Decapentaplegic (Bmp-4 homolog), as in the case of segmented structures and imaginal discs. Finally, the gut is subdivided into at least 36 compartments that are recognized asminimum tissue units of regional differentiation. A few genes that are responsible for determining and maintaining the state of overt-differentiation of the compartments have also been reported. A marked feature of the genetic mechanism of the gut development is the unexpectedly wide spectrum of the similarities of relevant genes and regulatory pathways of gene expression between Drosophila and vertebrates, which may imply a prototypic style of body plan common to protostomes and deuterostomes.     

Unique and conserved aspects of gut development in zebrafish

Although the development of the digestive system of humans and vertebrate model organisms has been well characterized, relatively little is known about how the zebrafish digestive system forms. We define developmental milestones during organogenesis of the zebrafish digestive tract, liver, and pancreas and identify important differences in the way the digestive endoderm of zebrafish and amniotes is organized. Such differences account for the finding that the zebrafish digestive system is assembled from individual organ anlagen, whereas the digestive anlagen of amniotes arise from a primitive gut tube. Despite differences of organ morphogenesis, conserved molecular programs regulate pharynx, esophagus, liver, and pancreas development in teleosts and mammals. Specifically, we show that zebrafish faust/gata-5 is a functional ortholog of gata-4, a gene that is essential for the formation of the mammalian and avian foregut. Further, extraembryonic gata activity is required for this function in zebrafish as has been shown in other vertebrates. We also show that a loss-of-function mutation that perturbs sonic hedgehog causes defects in the development of the esophagus that parallel those associated with targeted disruption of this gene in mammals. Perturbation of sonic hedgehog also affects zebrafish liver and pancreas development, and these effects occur in a reciprocal fashion, as has been described during mammalian liver and ventral pancreas development. Together, these data define aspects of digestive system development necessary for the characterization of zebrafish mutants. Given the similarities of teleost and mammalian digestive physiology and anatomy, these findings have implications for developmental and evolutionary studies as well as research of human diseases, such as diabetes, liver cirrhosis, and cancer.     

Early mouse endoderm is patterned by soluble factors from adjacent germ layers

Endoderm that forms the respiratory and digestive tracts is a sheet of approximately 500-1000 cells around the distal cup of an E7.5 mouse embryo. Within 2 days, endoderm folds into a primitive gut tube from which numerous organs will bud. To characterize the signals involved in the developmental specification of this early endoderm, we have employed an in vitro assay using germ layer explants and show that adjacent germ layers provide soluble, temporally specific signals that induce organ-specific gene expression in endoderm. Furthermore, we show that FGF4 expressed in primitive streak-mesoderm can induce the differentiation of endoderm in a concentration-dependent manner. We conclude that the differentiation of gastrulation-stage endoderm is directed by adjacent mesoderm and ectoderm, one of the earliest reported patterning events in formation of the vertebrate gut tube.     

Clonally related cells are restricted to organ boundaries early in the development of the chicken gut to form compartment boundaries

The gut organs are all derived from a simple, undifferentiated, linear gut tube. We analyzed the lineage relationships of cells derived from this gut tube in chicken embryos, determining where the progeny of a single cell are located within the gut. We find that daughter cells derived from a single progenitor can populate both the gizzard (chicken stomach) and the small intestine early in development, but that clonally related cells are restricted to a single organ by stage 12. We also find that clonally related cells can populate different mesodermal layers within the radial axis of the gut throughout all of the stages tested in these experiments. Many genes that have organ-specific expression patterns within the gut have been isolated. The onset of these restricted expression patterns correlates with the time that clonal boundaries appear to form, suggesting that these genes might be involved in the establishment of compartment boundaries, which prevent cells on one side of the boundary from intermingling with cells on the other side of the boundary.     

Novel tissue units of regional differentiation in the gut epithelium of Drosopbila,as revealed by P-element-mediated detection of enhancer

We analysed spatial patterns of expression of a lacZ reporter gene in the gut of Drosophila larvae that had been transformed with a P-element-lacZ vector to identify regional differences in gene expression. lacZ-positive epithelial cells formed distinct domains with discrete transverse and longitudinal boundaries along the gut tube. Boundaries were often found at sites at which morphological boundaries were not obvious. The gut epithelium was subdivided into 36 compartments by the boundaries. We refer to these novel compartments as tissue compartments. The lacZ-positive domain of each strain appeared as a single tissue compartment or as a combination of several tissue compartments. The tissue compartment is considered to be a unit of regional differentiation. The spatial organization of the tissue compartments may represent the floor plan, determined by genes that control the regional differentiation of this nonsegmental organ. Correspondence to: R. Murakami     

Discovering Functional Modules across Diverse Maize Transcriptomes Using COB,the Co-Expression Browser

Tools that provide improved ability to relate genotype to phenotype have the potential to accelerate breeding for desired traits and to improve our understanding of the molecular variants that underlie phenotypes. The availability of large-scale gene expression profiles in maize provides an opportunity to advance our understanding of complex traits in this agronomically important species. We built co-expression networks based on genome-wide expression data from a variety of maize accessions as well as an atlas of different tissues and developmental stages. We demonstrate that these networks reveal clusters of genes that are enriched for known biological function and contain extensive structure which has yet to be characterized. Furthermore, we found that co-expression networks derived from developmental or tissue atlases as compared to expression variation across diverse accessions capture unique functions. To provide convenient access to these networks, we developed a public, web-based Co-expression Browser (COB), which enables interactive queries of the genome-wide networks. We illustrate the utility of this system through two specific use cases: one in which gene-centric queries are used to provide functional context for previously characterized metabolic pathways, and a second where lists of genes produced by mapping studies are further resolved and validated using co-expression networks.     

The serosal mesothelium is a major source of smooth muscle cells of the gut vasculature

Most internal organs are situated in a coelomic cavity and are covered by a mesothelium. During heart development, epicardial cells (a mesothelium) move to and over the heart, undergo epithelial-mesenchymal transition (EMT), and subsequently differentiate into endothelial and vascular smooth muscle cells. This is thought to be a unique process in blood vessel formation. Still, structural and developmental similarities between the heart and gut led us to test the hypothesis that a conserved or related mechanism may regulate blood vessel development to the gut, which, similar to the heart, is housed in a coelomic cavity. By using a combination of molecular genetics, vital dye fate mapping, organ culture and immunohistochemistry, we demonstrate that the serosal mesothelium is the major source of vasculogenic cells in developing mouse gut. Our studies show that the gut is initially devoid of a mesothelium but that serosal mesothelial cells expressing the Wilm's tumor protein (Wt1) move to and over the gut. Subsequently, a subset of these cells undergoes EMT and migrates throughout the gut. Using Wt1-Cre genetic lineage marking of serosal cells and their progeny, we demonstrate that these cells differentiate to smooth muscle of all major blood vessels in the mesenteries and gut. Our data reveal a conserved mechanism in blood vessel formation to coelomic organs, and have major implications for our understanding of vertebrate organogenesis and vascular deficiencies of the gut.     

Identification of oscillatory genes in somitogenesis from functional genomic analysis of a human mesenchymal stem cell model

During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 h period consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 h, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3a(tm1Amc) mutants but not in Dll3(pu) mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro.     

HPK1, a hematopoietic protein kinase activating the SAPK/JNK pathway.

In mammalian cells, a specific stress-activated protein kinase (SAPK/JNK) pathway is activated in response to inflammatory cytokines, injury from heat, chemotherapeutic drugs and UV or ionizing radiation. The mechanisms that link these stimuli to activation of the SAPK/JNK pathway in different tissues remain to be identified. We have developed and applied a PCR-based subtraction strategy to identify novel genes that are differentially expressed at specific developmental points in hematopoiesis. We show that one such gene, hematopoietic progenitor kinase 1 (hpk1), encodes a serine/threonine kinase sharing similarity with the kinase domain of Ste20. HPK1 specifically activates the SAPK/JNK pathway after transfection into COS1 cells, but does not stimulate the p38/RK or mitogen-activated ERK signaling pathways. Activation of SAPK requires a functional HPK1 kinase domain and HPK1 signals via the SH3-containing mixed lineage kinase MLK-3 and the known SAPK activator SEK1. HPK1 therefore provides an example of a cell type-specific input into the SAPK/JNK pathway. The developmental specificity of its expression suggests a potential role in hematopoietic lineage decisions and growth regulation.