Phylogenetic analysis of developmental and postnatal mouse cell lineages

SUMMARY Fate maps depict how cells relate together through past lineage relationships, and are useful tools for studying developmental and somatic processes. However, with existing technologies, it has not been possible to generate detailed fate maps of complex organisms such as the mouse. We and others have therefore proposed a novel approach, "phylogenetic fate mapping," where patterns of somatic mutation carried by the individual cells of an animal are used to retrospectively deduce lineage relationships through phylogenetic inference. Here, we have cataloged genomic polymorphisms at 324 mutation-prone polyguanine tracts for nearly 300 cells isolated from a single mouse, and have explored the cells' lineage relationships both phylogenetically and through a network-based approach. We present a model of mouse embryogenesis, where an early period of substantial cell mixing is followed by more coherent growth of clones later. We find that cells from certain tissues have greater numbers of close relatives in other specific tissues than expected from chance, suggesting that those populations arise from a similar pool of ancestral lineages. Finally, we have investigated the dynamics of cell turnover (the frequency of cell loss and replacement) in postnatal tissues. This work offers a longitudinal study of developmental lineages, from conception to adulthood, and provides insight into basic questions of mouse embryology as well as the somatic processes that occur after birth.     

Stepwise specification of lymphocyte developmental lineages

B and T lymphocytes differentiate from multipotent precursors through distinct specification and commitment steps. New findings on the unique role of Pax5 in B-lineage commitment, dichotomous action of Notch signaling in B versus T cell development, and the gene expression changes comprising T-lineage specification and commitment now illuminate this process.     

Myogenic cell lineages.

For many years the mechanisms by which skeletal muscles in higher vertebrates come to be composed of diverse fiber types distributed in distinctive patterns has interested cell and developmental biologists. The fiber composition of skeletal muscles varies from class to class and from muscle to muscle within the vertebrates. The developmental basis for these events is the subject of this review. Because an individual multinucleate vertebrate skeletal muscle fiber is formed by the fusion of many individual myoblasts, more attention, in recent times, has been directed toward the origins and differences among myoblasts, and more emphasis has been placed on the lineal relationship of myoblasts to fibers. This is a review of studies related to the concepts of myogenic cell lineage in higher vertebrate development with emphases on some of the most challenging problems of myogenesis including the embryonic origins of myogenic precursor cells, the mechanisms of fiber type diversity and patterning, the distinctions among myoblasts during myogenesis, and the current hypotheses of how a variety of factors, intrinsic and extrinsic to the myoblast, determine the definitive phenotype of a muscle fiber.     

A bifurcating autoregression model for cell lineages with variable generation means.

The bifurcating autoregression model for cell lineage data is extended to allow for observations whose means vary from generation to generation. The maximum likelihood estimates of this extended model are found and used to estimate the generation means and overall variance. The model is also used to test for inherited effects as measured by mother-daughter correlation, and for environmental effects as measured by the sister-sister correlation, conditional on inherited effects. Applications to data sets on EMT6 cells and Escherichia coli are given.     

Inference of Euler angles for single-particle analysis by means of evolutionary algorithms

Single-particle analysis is one of the methods for structural studies of protein and macromolecules; it requires advanced image analysis of electron micrographics. Reconstructing three-dimensional (3D) structure from microscope images is not an easy analysis because of the low image resolution of images and lack of the directional information of images in 3D structure. To improve the resolution, different projections are aligned, classified, and averaged. Inferring the orientations of these images is so difficult that the task of reconstructing 3D structures depends upon the experience of researchers. But recently, a method to reconstruct 3D structures was automatically devised. In this paper, we propose a new method for determining Euler angles of projections by applying genetic algorithms. We empirically show that the proposed approach has improved the previous one in terms of computational time and acquired precision.     

Genetic analysis of developmental mechanisms in hydra: XIV. Identification of the cell lineages responsible for the altered developmental gradients in a mutant strain,reg-16

The developmental gradients of six chimeric strains of hydra produced from a normal strain (105) and a regeneration-deficient strain (reg-16) were analyzed. The reg-16 mutant has been shown to have a lower gradient of head-activation potential and a higher gradient of head-inhibition potential than the normal 105 strain. The chimeric animals consisted of different combinations of the three self-renewing cell lineages found in hydra (the ectodermal and endodermal epithelial cell lineages and the interstitial cell lineage) from each of the parental origins. To identify the cell lineages responsible for the abnormal gradients in reg-16, the head-activation and head-inhibition potentials of these cell lineage chimeras were assayed by lateral transplantation of tissue. The results obtained have provided evidence which indicates that the defect responsible for the low head-activation potential in reg-16 resides in its ectodermal and endodermal epithelial cell lineages, whereas the defect responsible for its high head-inhibition potential resides in its endodermal epithelial and interstitial cell lineages. The cellular localization of these defects is not identical but very similar to the cellular localization of the regenerative defects in reg-16. This finding is consistent with and supports the view that the abnormalities of the developmental gradients are correlated to the reduced head regenerative capacity in reg-16.     

Mapping of clonal lineages across developmental stages in human neural differentiation

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Marking cell lineages in living tissues

We have generated a novel genetic system to visualize cell lineages in living tissues at high resolution. Heat shock was used to trigger the excision of a specific transposon and activation of a fluorescent marker gene. A histone-YFP marker was used to allow identification of cell lineages and easy counting of cells. Constitutive expression of a green fluorescent membrane protein was used to provide a precise outline of all surrounding cells. Marked lineages can be induced from specific cells within the organism by targeted laser irradiation, and the fate of the marked cells can be followed non-invasively. We have used the system to map cell lineages originating from the initials of primary and lateral roots in Arabidopsis. The lineage marking technique enabled us to measure the differential contribution of primary root pericycle cell files to developing lateral root primordia. The majority of cells in an emerging lateral root primordium derive from the central file of pericycle founder cells while off-centre founder cells contribute only a minor proliferation of tissue near the base of the root. The system shows great promise for the detailed study of cell division during morphogenesis.     

Zebrafish model systems for developmental neurobehavioral toxicology

Zebrafish offer many advantages that complement classic mammalian models for the study of normal development as well as for the teratogenic effects of exposure to hazardous compounds. The clear chorion and embryo of the zebrafish allow for continuous visualization of the anatomical changes associated with development, which, along with short maturation times and the capability of complex behavior, makes this model particularly useful for measuring changes to the developing nervous system. Moreover, the rich array of developmental, behavioral, and molecular benefits offered by the zebrafish have contributed to an increasing demand for the use of zebrafish in behavioral teratology. Essential for this endeavor has been the development of a battery of tests to evaluate a spectrum of behavior in zebrafish. Measures of sensorimotor plasticity, emotional function, cognition and social interaction have been used to characterize the persisting adverse effects of developmental exposure to a variety of chemicals including therapeutic drugs, drugs of abuse and environmental toxicants. In this review, we present and discuss such tests and data from a range of developmental neurobehavioral toxicology studies using zebrafish as a model. Zebrafish provide a key intermediate model between high throughput in vitro screens and the classic mammalian models as they have the accessibility of in vitro models and the complex functional capabilities of mammalian models. Birth Defects Research (Part C) 99:14–23, 2013. © 2013 Wiley Periodicals, Inc.     

Endothelial cell lineages of the heart

During early gastrulation, vertebrate embryos begin to produce endothelial cells (ECs) from the mesoderm. ECs first form primitive vascular plexus de novo and later differentiate into arterial, venous, capillary, and lymphatic ECs. In the heart, the five distinct EC types (endocardial, coronary arterial, venous, capillary, and lymphatic) have distinct phenotypes. For example, coronary ECs establish a typical vessel network throughout the myocardium, whereas endocardial ECs form a large epithelial sheet with no angiogenic sprouting into the myocardium. Neither coronary arteries, veins, and capillaries, nor lymphatic vessels fuse with the endocardium or open to the heart chamber. The developmental stage during which the specific phenotype of each cardiac EC type is determined remains unclear. The mechanisms involved in EC commitment and diversity can however be more precisely defined by tracking the migratory patterns and lineage decisions of the precursors of cardiac ECs. Work carried out by the authors is supported in part by the NIH.     

Unfolding a chordate developmental program, one cell at a time: Invariant cell lineages, short-range inductions and evolutionary plasticity in ascidians

Ascidians were historically the first metazoans in which experimental embryology was carried out. These early works by Chabry and Conklin [Chabry, L., 1887. Embryologie normale et tératologique des Ascidie. Felix Alcan Editeur, Paris; Conklin, E., 1905. The organization and cell lineage of the ascidian egg. J. Acad., Nat. Sci. Phila. 13, 1], in particular, led to the idea that the developmental program of these animals was driven by the cell-autonomous inheritance of localised maternal determinants, rendered precise by the stereotyped pattern of invariant cell cleavages. Work in the past 20 years indeed identified several localised maternal determinants of the position of cleavage planes or of some early cell fates. The overwhelming majority of cells in the three germ layers, however, do not follow a cell-autonomous differentiation program. Instead, they respond to short-range signals, as described in this review. Careful analysis of cell-cell contacts suggests that a major function of the invariant position of cleavage plans, besides segregating competence factors, is to control the relative positions of inducing cells and those competent to respond. Surprisingly, while the cell lineage is very well conserved between the divergent species Halocynthia roretzi and Ciona intestinalis, the molecular nature of inducing signals can vary. The constraints on embryo anatomy thus appear stronger than those on the choice of individual regulatory molecules.     

Nestin expression in pancreatic exocrine cell lineages

Expression of nestin has been suggested to be a characteristic of pancreatic islet stem cells. To determine whether nestin is indeed expressed in such putative cells during embryonic development, or in the adult pancreas after injury, we performed a cell lineage analysis using two independent lines of transgenic mice encoding Cre recombinase under the control of rat nestin cis-regulatory sequences, each crossed with loxP-bearing R26R mice. F1 animals produced the reporter molecule beta-galactosidase only upon Cre-mediated recombination, thus solely in cells using (or having used) the transgenic nestin promoter. In early pancreatic primordia, beta-galactosidase was observed in mesenchymal and epithelial cells. At later developmental stages or in adults, vast clusters of acinar cells and few ductal cells were labeled, in addition to fibroblasts and vascular cells, but no endocrine cells were tagged by beta-galactosidase. This correlated with the transient expression, observed with an anti-nestin antibody, of endogenous nestin in about 5% of epithelial cells during development (whether in cord-forming arrangements or in nascent acini), and in vascular and mesenchymal structures. After partial pancreatectomy, there was a transient increase of the number of anti-nestin-labeled endothelial cells, but again, no endocrine cells bore beta-galactosidase. Together, these findings show that nestin is expressed in the pancreatic exocrine cell lineage, and suggest that consistent nestin expression is not a major feature of islet endocrine progenitor cells.     

Tracing the lineage of tracing cell lineages

The study of cell lineages has been, and remains, of crucial importance in developmental biology. It requires the identification of a cell or group of cells and of all of their descendants during embryonic development. Here, we provide a brief survey of how different techniques for achieving this have evolved over the last 100 years.     

Cell-free systems for capsid assembly of primate lentiviruses from three different lineages

We recently demonstrated that capsids from three main primate lentiviral lineages appear to form via a pathway of assembly intermediates in primate cells. Retroviral capsid assembly intermediates were initially identified and characterized using a cell-free system for assembly of immature HIV-1 capsids. Because cell-free capsid assembly systems are useful tools, we are interested in developing such systems for other primate lentiviruses besides HIV-1. Here we extend previous cell-free studies by showing that Gag proteins of HIV-2, from a second primate lentiviral lineage, progress from early intermediates to late intermediates and completed capsids over time. Additionally, we demonstrate that Gag proteins of SIVagm, from a third primate lentiviral lineage, associate with the cellular factor HP68 and complete assembly in this system. Therefore, cell-free systems reproduce assembly of Gag from three main primate lentiviral lineages, and can be used to compare mechanistic features of capsid assembly of genetically divergent primate lentiviruses.     

An interactive computer system for the analysis of cell lineages.

We have developed an interactive computer system for analysing cell lineage data. It can be utilized in studies of cell motility, cell division, cell differentiation, and cell aging. It has enabled us to document the heterogeneity of human foreskin fibroblasts in culture and to propose that loss of proliferative potential may mean that cells enter a state of differentiation which makes them unable to respond to mitotic stimulation. Our method, which enables us to apply immunological and cytochemical probes after recording the history of a cell lineage, should allow us to define precisely features which uniquely distinguish cycling from noncycling cells on an individual cell basis.     

Learning cluster-based classification systems with ant colony optimization algorithms

Classification is a data mining task the goal of which is to learn a model, from a training dataset, that can predict the class of a new data instance, while clustering aims to discover natural instance-groupings within a given dataset. Learning cluster-based classification systems involves partitioning a training set into data subsets (clusters) and building a local classification model for each data cluster. The class of a new instance is predicted by first assigning the instance to its nearest cluster and then using that cluster’s local classification model to predict the instance’s class. In this paper, we present an ant colony optimization (ACO) approach to building cluster-based classification systems. Our ACO approach optimizes the number of clusters, the positioning of the clusters, and the choice of classification algorithm to use as the local classifier for each cluster. We also present an ensemble approach that allows the system to decide on the class of a given instance by considering the predictions of all local classifiers, employing a weighted voting mechanism based on the fuzzy degree of membership in each cluster. Our experimental evaluation employs five widely used classification algorithms: naïve Bayes, nearest neighbour, Ripper, C4.5, and support vector machines, and results are reported on a suite of 54 popular UCI benchmark datasets.     

Control algorithms for artificial beta cell.

The evolution of control algorithms for closed-loop regulation of blood glucose levels is described. Because of the rapid response time of the BIOSTATOR Glucose Analyzer, a derivative algorithm can be applied to replace the previous generation of "predictor" algorithms for the calculation of dynamic insulin infusion rates.     

Stem cells and lineages of the intestine: a developmental and evolutionary perspective

The intestine consists of epithelial cells that secrete digestive enzymes and mucus (gland cells), absorb food particles (enterocytes), and produce hormones (endocrine cells). Intestinal cells are rapidly turned over and need to be replaced. In cnidarians, mitosis of differentiated intestinal cells accounts for much of the replacement; in addition, migratory, multipotent stem cells (interstitial cells) contribute to the production of intestinal cells. In other phyla, intestinal cell replacement is solely the function of stem cells entering the gut from the outside (such as in case of the neoblasts of platyhelminths) or intestinal stem cells located within the midgut epithelium (as in both vertebrates or arthropods). We will attempt in the following to review important aspects of midgut stem cells in different animal groups: where are they located, what types of lineages do they produce, and how do they develop. We will start out with a comparative survey of midgut cell types found across the animal kingdom; then briefly look at the specification of these cells during embryonic development; and finally focus on the stem cells that regenerate midgut cells during adult life. In a number of model systems, including mouse, zebrafish and Drosophila, the molecular pathways controlling intestinal stem cells proliferation and the specification of intestinal cell types are under intensive investigation. We will highlight findings of the recent literature, focusing on aspects that are shared between the different models and that point at evolutionary ancient mechanisms of intestinal cell formation.     

Model systems in developmental biology

The practical criteria by which developmental biologists choose their model systems have evolutionary correlates. The result is a sample that is not merely small, but biased in particular ways, for example towards species with rapid, highly canalized development. These biases influence both data collection and interpretation, and our views of how development works and which aspects of it are important.