Discoveries In Developmental Biology Research Articles

"Sans doute habituée à une existence sédentaire": Des Esseintes's Turtle and the Residue of Naturalism

Abstract: This article analyzes the decorated turtle in Huysmans's 1884 À rebours . It argues that des Esseintes's unfortunate animal, which perishes under its heavy ornamentation, plays out the apprehensions of its owner and embodies the psychological and physical perils that await him. Turtles—fundamental to nineteenth-century discoveries in developmental biology as well as to Darwin's theories of evolution—are at once instructive specimens and labile signifiers in competing narratives: sites and objects of theorization. The narrator's use of this animal thus also amounts to an insertion of naturalism within the novel's storied decadence. To make this argument, this article examines the turtle episode in the context of late nineteenth-century scientific and fictional writings about turtles, including Jules Hosch's 1878 short story "Histoire d'une tortue et d'un étudiant."

CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data.

Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.

Derivation of Thyroid Follicular Cells From Pluripotent Stem Cells: Insights From Development and Implications for Regenerative Medicine.

Stem cell-based therapies to reconstitute in vivo organ function hold great promise for future clinical applications to a variety of diseases. Hypothyroidism resulting from congenital lack of functional thyrocytes, surgical tissue removal, or gland ablation, represents a particularly attractive endocrine disease target that may be conceivably cured by transplantation of long-lived functional thyroid progenitors or mature follicular epithelial cells, provided a source of autologous cells can be generated and a variety of technical and biological challenges can be surmounted. Here we review the emerging literature indicating that thyroid follicular epithelial cells can now be engineered in vitro from the pluripotent stem cells (PSCs) of mice, normal humans, or patients with congenital hypothyroidism. We review the in vivo embryonic development of the thyroid gland and explain how emerging discoveries in developmental biology have been utilized as a roadmap for driving PSCs, which resemble cells of the early embryo, into mature functional thyroid follicles in vitro. Finally, we discuss the bioengineering, biological, and clinical hurdles that now need to be addressed if the goals of life-long cure of hypothyroidism through cell- and/or gene-based therapies are to be attained.

Versatile CRISPR/Cas9-mediated mosaic analysis by gRNA-induced crossing-over for unmodified genomes.

Mosaic animals have provided the platform for many fundamental discoveries in developmental biology, cell biology, and other fields. Techniques to produce mosaic animals by mitotic recombination have been extensively developed in Drosophila melanogaster but are less common for other laboratory organisms. Here, we report mosaic analysis by gRNA-induced crossing-over (MAGIC), a new technique for generating mosaic animals based on DNA double-strand breaks produced by CRISPR/Cas9. MAGIC efficiently produces mosaic clones in both somatic tissues and the germline of Drosophila. Further, by developing a MAGIC toolkit for 1 chromosome arm, we demonstrate the method's application in characterizing gene function in neural development and in generating fluorescently marked clones in wild-derived Drosophila strains. Eliminating the need to introduce recombinase-recognition sites into the genome, this simple and versatile system simplifies mosaic analysis in Drosophila and can in principle be applied in any organism that is compatible with CRISPR/Cas9.

What Is Lost in the Weismann Barrier?

The Weismann barrier has long been regarded as a basic tenet of biology. However, upon close examination of its historical origins and August Weismann’s own writings, questions arise as to whether such a status is warranted. As scientific research has advanced, the persistence of the concept of the barrier has left us with the same dichotomies Weismann contended with over 100 years ago: germ or soma, gene or environment, hard or soft inheritance. These dichotomies distract from the more important questions we need to address going forward. In this review, we will examine the theories that have shaped Weismann’s thinking, how the concept of the Weismann barrier emerged, and the limitations that it carries. We will contrast the principles underlying the barrier with recent and less recent findings in developmental biology and transgenerational epigenetic inheritance that have profoundly eroded the oppositional view of germline vs. soma. Discarding the barrier allows us to examine the interactive processes and their response to environmental context that generate germ cells in the first place, determine the entirety of what is inherited through them, and set the trajectory for the health status of the progeny they bear.

Materials control of the epigenetics underlying cell plasticity

The dynamic epigenetic landscape directs gene expression patterns that dictate cellular form and function, and drive the assembly of cells into tissues. The high degree of plasticity in the epigenetic landscape of mammalian cells is directed by materials, which provide the context in which cells receive and integrate multivariate signals to programme the chromatin state towards specific functional outcomes. In this Review, we explore how materials guide the cellular epigenetic landscape and discuss how engineered materials target cell plasticity, particularly through dynamic changes in histone methylation and acetylation. After discussing findings in developmental biology and cancer research that link materials parameters to chromatin state, we highlight how cell culture materials that control ligand presentation, mechanics, topography and geometry have shown how materials cues and context influence chromatin state through mechanotransduction. Finally, we describe how tissue fabrication can control cellular plasticity to drive meaningful biological activities that may facilitate the assembly of cells and tissues into functional architectures. The dynamic epigenetic landscape directs gene expression patterns that regulate cellular form and function. Designer cell culture materials have shed light on how materials cues influence cellular plasticity through the epigenome and directed tissue-fabrication approaches that drive biological activities.

One of the most significant discoveries in Developmental Biology from an Indian laboratory - Iqbal A. Niazi and the role of retinoids in limb regeneration.

In this short commentary, we reflect upon the fascinating paper by I.A. Niazi entitled "Background to work on retinoids and amphibian limb regeneration: Studies on anuran tadpoles - a retrospect." originally published in J. Biosciences (1996), and herein reproduced with the kind permission of the author and the Journal of Biosciences. It is fitting that this landmark publication is included in this India-related Special Issue of the Int. J. Dev. Biol., because it sketches the background to what is arguably one of the two most significant discoveries in Developmental Biology to come from an Indian laboratory. Besides being of intrinsic interest, it spawned an entire area of research, one that deals with the role of retinoids in morphogenesis and development generally.

Two-step Approach to Explore Early- and Late-stages of Organ Formation in the Avian Model: The Thymus and Parathyroid Glands Organogenesis Paradigm.

The avian embryo, as an experimental model, has been of utmost importance for seminal discoveries in developmental biology. Among several approaches, the formation of quail-chicken chimeras and the use of the chorioallantoic membrane (CAM) to sustain the development of ectopic tissues date back to the last century. Nowadays, the combination of these classical techniques with recent in vitro methodologies offers novel prospects to further explore organ formation. Here we describe a two-step approach to study early- and late-stages of organogenesis. Briefly, the embryonic region containing the presumptive territory of the organ is isolated from quail embryos and grown in vitro in an organotypic system (up to 48 h). Cultured tissues are subsequently grafted onto the CAM of a chicken embryo. After 10 days of in ovo development, fully formed organs are obtained from grafted tissues. This method also allows the modulation of signaling pathways by the regular administration of pharmacological agents and tissue genetic manipulation throughout in vitro and in ovo developmental steps. Additionally, developing tissues can be collected at any time-window to analyze their gene-expression profile (using quantitative PCR (qPCR), microarrays, etc.) and morphology (assessed with conventional histology and immunochemistry). The described experimental procedure can be used as a tool to follow organ formation outside the avian embryo, from the early stages of organogenesis to fully formed and functional organs.

A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice.

Lineage tracing experiments define the origin, fate and behavior of cells in a specific tissue or organism. This technique has been successfully applied for many decades, revealing seminal findings in developmental biology. More recently, it was adopted by stem cell biologists to identify and track different stem cell populations with minimal experimental intervention. The recent developments in mouse genetics, the availability of a large number of mouse strains, and the advancements in fluorescent microscopy allow the straightforward design of powerful lineage tracing systems for various tissues with basic expertise, using commercially available tools. We have recently taken advantage of this powerful methodology to explore the origin and fate of stem cells at the ocular surface using R26R-Confetti mouse. This model offers a multi-color genetic system, for the expression of 4 fluorescent genes in a random manner. Here we describe the principles of this methodology and provide an adaptable protocol for designing lineage tracing experiments; specifically for the corneal epithelium as well as for other tissues.

A Method for Lineage Tracing of Corneal Cells Using Multi-color Fluorescent Reporter Mice

Lineage tracing experiments define the origin, fate and behavior of cells in a specific tissue or organism. This technique has been successfully applied for many decades, revealing seminal findings in developmental biology. More recently, it was adopted by stem cell biologists to identify and track different stem cell populations with minimal experimental intervention. The recent developments in mouse genetics, the availability of a large number of mouse strains, and the advancements in fluorescent microscopy allow the straightforward design of powerful lineage tracing systems for various tissues with basic expertise, using commercially available tools. We have recently taken advantage of this powerful methodology to explore the origin and fate of stem cells at the ocular surface using R26R-Confetti mouse. This model offers a multi-color genetic system, for the expression of 4 fluorescent genes in a random manner. Here we describe the principles of this methodology and provide an adaptable protocol for designing lineage tracing experiments; specifically for the corneal epithelium as well as for other tissues.

Budgett's frog (Lepidobatrachus laevis): A new amphibian embryo for developmental biology

The large size and rapid development of amphibian embryos has facilitated ground-breaking discoveries in developmental biology. Here, we describe the embryogenesis of the Budgett's frog (Lepidobatrachus laevis), an unusual species with eggs that are over twice the diameter of laboratory Xenopus, and embryos that can tolerate higher temperatures to develop into a tadpole four times more rapidly. In addition to detailing their early development, we demonstrate that, like Xenopus, these embryos are amenable to explant culture assays and can express exogenous transcripts in a tissue-specific manner. Moreover, the steep developmental trajectory and large scale of Lepidobatrachus make it exceptionally well-suited for morphogenesis research. For example, the developing organs of the Budgett's frog are massive compared to those of most model species, and are composed of larger individual cells, thereby affording increased subcellular resolution of early vertebrate organogenesis. Furthermore, we found that complete limb regeneration, which typically requires months to achieve in most vertebrate models, occurs in a matter of days in the Budgett's tadpole, which substantially accelerates the pace of experimentation. Thus, the unusual combination of the greater size and speed of the Budgett's frog model provides inimitable advantages for developmental studies—and a novel inroad to address the mechanisms of spatiotemporal scaling during evolution.

The role of mathematical models in understanding pattern formation in developmental biology.

In a Wall Street Journal article published on April 5, 2013, E. O. Wilson attempted to make the case that biologists do not really need to learn any mathematics-whenever they run into difficulty with numerical issues, they can find a technician (aka mathematician) to help them out of their difficulty. He formalizes this in Wilsons Principle No. 1: "It is far easier for scientists to acquire needed collaboration from mathematicians and statisticians than it is for mathematicians and statisticians to find scientists able to make use of their equations." This reflects a complete misunderstanding of the role of mathematics in all sciences throughout history. To Wilson, mathematics is mere number crunching, but as Galileo said long ago, "The laws of Nature are written in the language of mathematics[Formula: see text] the symbols are triangles, circles and other geometrical figures, without whose help it is impossible to comprehend a single word." Mathematics has moved beyond the geometry-based model of Galileo's time, and in a rebuttal to Wilson, E. Frenkel has pointed out the role of mathematics in synthesizing the general principles in science (Both point and counter-point are available in Wilson and Frenkel in Notices Am Math Soc 60(7):837-838, 2013). We will take this a step further and show how mathematics has been used to make new and experimentally verified discoveries in developmental biology and how mathematics is essential for understanding a problem that has puzzled experimentalists for decades-that of how organisms can scale in size. Mathematical analysis alone cannot "solve" these problems since the validation lies at the molecular level, but conversely, a growing number of questions in biology cannot be solved without mathematical analysis and modeling. Herein, we discuss a few examples of the productive intercourse between mathematics and biology.

Ardipithecusand Early Human Evolution in Light of Twenty-First-Century Developmental Biology

One specimen of Ardipithecus ramidus, ARA-VP-6/500, is the earliest and also among the most complete fossil hominids ever recovered. Although it took more than a decade to extract, prepare, and analyze (along with a number of other less-complete specimens), the thoroughness of its recovery and preparation has yielded surprising revelations about its environment as well as new knowledge about the divergence of our earliest human ancestors from the last common ancestor they shared with chimpanzees. Decades of groundbreaking discoveries in developmental biology have also transformed our understanding of the evolutionary process itself, especially the need to view the significance of adult anatomical structures holistically. Today, no such structure can be reasonably understood without direct reference to its likely mode of morphogenesis. The twenty-first-century convergence of these two special sources of information requires a radical revision of how our early hominid forebears set the stage for our own sub...

Fibroblast growth factor receptors: multifactorial-contributors to tumor initiation and progression.

Fibroblast growth factor receptors (FGFRs), encoded by four genes (FGFR1, FGFR2, FGFR3, and FGFR4) are tightly associated with many biological processes such as organ development, cell proliferation and migration. Studies over the past decades have validated the pivotal roles FGFRs play in tumorigenesis due to the regulation of diverse tumorigenesis-related processes, including cell survival, proliferation, inflammation, metastasis and angiogenesis. Interestingly, FGFR mutations in somatic cells leading to tumorigenesis and those in germ cells leading to developmental disorders are identical, suggesting that FGFR mutations result in different diseases due to their spatio-temporal expression. Thus, discoveries in developmental biology may also be applicable to cancer. FGFRs regulate the expression and/or the activity of a myriad of molecules (e.g. matrix metalloproteinases (MMPs) and Snail) that are tightly linked to tumorigenesis by four main signaling pathways (RAS-MAPK, PI3K-AKT, PLCγ-PIP2, and STAT), as well as other minor branches. Epigenetic and genetic alteration of FGFR genes, including DNA methylation, histone remodeling, microRNA regulation, single nucleotide polymorphisms (SNPs), gene missense mutations, amplification, and fusion of FGFRs with other genes, which result in gain or loss of FGFR function, have been identified in many types of cancer. In this review, we focus in particular on recent advances in the relationship between FGFR disorders and tumorigenesis.

The Ethical Implications of Organism-Environment Interdependency

Modern ethical perspectives toward the environment often emphasize the connection of humans to a broader biotic community. The full intimacy of this connectedness, however, is only now being revealed as scientific findings in developmental biology and genetics provide new insights into the importance of environmental interaction for the development of organisms. These insights are reshaping our understanding of how organism-environment interaction contributes to both consistency and variation in organism development, and leading to a new perspective whereby an “organism” is not solely viewed as the adaptive product of evolutionary selection to an external environment over generations, but as continuously being constructed through systems of interactions that link an organism’s characteristics developmentally to the physical and social influences it experiences during life. This newfound emphasis on “interaction” leads to an interdependency whereby any change to an “environment” impacts the interacting “organism(s),” and an alteration to the “organism” eventually affects its “environment.” The causal reciprocity embedded within this organism-environment interdependency holds implications for our moral obligations to environments, given their compulsory role in shaping all organisms including ourselves. * Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA 93407; e–mail: slema@calpoly.edu. Lema’s research focuses on understanding the physiological and genetic mechanisms underlying the phenotypic responses of organisms to changing environments, the effects of chemical pollutants on hormone signaling, and the incorporation of phenotypic plasticity into new approaches for animal conservation. The author thanks Kenneth Wilson, Kristin Hardy, and two anonymous referees, Peter Miller and Holmes Rolston, III, for their helpful comments and suggestions on this manuscript. 1 See, for example, Don E. Marietta, Jr., “The Interrelationship of Ecological Science and Environ -mental Ethics,”

Morpholinos: Studying gene function in the chick

The use of morpholinos for perturbing gene function in the chick, Gallus gallus, has led to many important discoveries in developmental biology. This technology makes use of in vivo electroporation, which allows gain and loss of function in a temporally, and spatially controlled manner. Using this method, morpholinos can be transfected into embryonic tissues from early to late developmental stages. In this article, we describe the methods currently used in our laboratory to knock down gene function using morpholinos in vivo. We also detail how morpholinos are used to provide consistency of the results, and describe two protocols to visualise the morpholino after electroporation. In addition, we provide guidance on avoiding potential pitfalls, and suggestions for troubleshooting solutions. These revised techniques provide a practical starting point for investigating gene function in the chick.

Bridging Structure and Process in Developmental Biology through New Imaging Technologies

Many unexpected discoveries in developmental biology have depended on advancement of imaging technologies to visualize developmental processes as they unfold across multiple spatial and temporal scales. This essay surveys the recent advances in imaging, highlighting emerging capabilities with an eye toward those poised to have the greatest impact on developmental biology.

Imaging and examination strategies of normal male and female sex development and anatomy

Over recent years a variety of new details on the developmental biology of sexual differentiation has been discovered. Moreover, important advances have been made in imaging and examination strategies for urogenital organs, and these have added new knowledge to our understanding of the 'normal' anatomy of the sexes. Both aspects contribute to the comprehension of phenotypic sex development, but they are not commonly presented in the same context. This will be attempted in this chapter, which aims to link discoveries in developmental biology to anatomical details shown by modern examination techniques. A review of the literature concerning the link between sexual development and imaging of urogenital organs was performed. Genes, proteins and pathways related to sexual differentiation were related to some organotypic features revealed by clinical examination techniques. Early 'organotypic' patterns can be identified in prostatic, urethral and genital development and followed into postnatal life. New imaging and endoscopy techniques allow for detailed descriptive anatomical studies, hopefully resulting in a broader understanding of sex development and a better genotype-phenotype correlation in defined disorders. Clinical description relying on imaging techniques should be related to knowledge of the genetic and endocrine factors influencing sex development in a specific and stepwise manner.

CGMP kinase and food-related behaviours

The repeated incorporation of common gene activities and pathways into diverse behavioural and environmental contexts throughout evolution is similar to findings in developmental biology showing that principle regulators have been co-opted to generate novel patterns [1]. Nevertheless, such genetic systems must be flexible enough to generate adaptive phenotypes in the midst of unique environmental and developmental constraints. For the foraging gene which encodes a cGMP dependent protein kinase (PKG), variation in gene activity has been associated with distinct alleles within populations in some species (e.g. D. melanogaster) and developmental transitions over the lifecycle of single individuals in others (e.g. honeybees [2] and ants). Here we show that the foraging gene in Drosophila also plays a role in behavioural plasticity within the lifetime of the individual. foraging affects food-related locomotion, food intake, responses to food deprivation, energy homeostasis, sucrose responsiveness [3] and learning. Recent immunohistochemical analysis of for expression combined with behaviour genetic analysis enables us to begin to draw parallels between PKG function in invetebrates and mammals.

Disruption of the somitic molecular clock causes abnormal vertebral segmentation

Somites are the precursors of the vertebral column. They segment from the presomitic mesoderm (PSM) that is caudally located and newly generated from the tailbud. Somites form in synchrony on either side of the embryonic midline in a reiterative manner. A molecular clock that operates in the PSM drives this reiterative process. Genetic manipulation in mouse, chick and zebrafish has revealed that the molecular clock controls the activity of the Notch and WNT signaling pathways in the PSM. Disruption of the molecular clock impacts on somite formation causing abnormal vertebral segmentation (AVS). A number of dysmorphic syndromes manifest AVS defects. Interaction between developmental biologists and clinicians has lead to groundbreaking research in this area with the identification that spondylocostal dysostosis (SCD) is caused by mutation in Delta-like 3 (DLL3), Mesoderm posterior 2 (MESP2), and Lunatic fringe (LFNG); three genes that are components of the Notch signaling pathway. This review describes our current understanding of the somitic molecular clock and highlights how key findings in developmental biology can impact on clinical practice.