Modern Developmental Biology Research Articles

Historic obstacles and emerging opportunities in the field of developmental metabolism - lessons from Heidelberg.

The field of developmental metabolism is experiencing a technological revolution that is opening entirely new fields of inquiry. Advances in metabolomics, small-molecule sensors, single-cell RNA sequencing and computational modeling present new opportunities for exploring cell-specific and tissue-specific metabolic networks, interorgan metabolic communication, and gene-by-metabolite interactions in time and space. Together, these advances not only present a means by which developmental biologists can tackle questions that have challenged the field for centuries, but also present young scientists with opportunities to define new areas of inquiry. These emerging frontiers of developmental metabolism were at the center of a highly interactive 2023 EMBO workshop 'Developmental metabolism: flows of energy, matter, and information'. Here, we summarize key discussions from this forum, emphasizing modern developmental biology's challenges and opportunities.

Devo-Aging: Intersections Between Development and Aging

There are two fundamental questions in developmental biology. How does a single fertilized cell give rise to a whole body? and how does this body later produce progeny? Synchronization of these embryonic and postembryonic developments ensures continuity of life from one generation to the next. An enormous amount of work has been done to unravel the molecular mechanisms behind these processes, but more recently, modern developmental biology has been expanded to study development in wider contexts, including regeneration, environment, disease, and even aging. However, we have just started to understand how the mechanisms that govern development also regulate aging. This review discusses examples of signaling pathways involved in development to elucidate how their regulation influences healthspan and lifespan. Therefore, a better knowledge of developmental signaling pathways stresses the possibility of using them as innovative biomarkers and targets for aging and age-related diseases.

Genetic Mechanisms of the Early Development of the Telencephalon, a Unique Segment of the Vertebrate Central Nervous System, as Reflecting Its Emergence and Evolution

The emergence of the telencephalon as a forebrain part with a complex structure is one of the most important aromorphoses in vertebrate evolution. The telencephalon developed and improved in evolution to allow higher nervous activity forms observed in animals and humans. A telencephalic anlage is separated at the earliest stages of vertebrate ontogenesis, when the anterior part of the neural tube differentiates into three cerebral vesicles: the prozencephalon as an anlage of the future forebrain, the mesencephalon as the future midbrain, and the rhombencephalon as the future hindbrain. The forebrain further differentiates to form the telencephalon and the diencephalon. The development of brain structures and regions is modulated by the expression of certain regulatory genes, which code for transcription factors and signaling molecules. Problems of the evolutionary origin and ontogenesis of the telencephalon are still poorly understood at the molecular level, although they are among central problems of modern developmental biology. Recent studies of the evolutionary mechanisms responsible for the emergence of the telencephalon in vertebrates have paid much attention to cyclostomes (lampreys and hagfishes) as the most evolutionarily ancient vertebrate groups and Tunicata (ascidians) and Cephalochordata (lancelets) as the closest relatives of vertebrates. Cyclostomes are of particular interest because they were the first in evolution to have the telencephalon as a separate morphological structure and because they might preserve the expression patterns and regulatory mechanisms characteristic of vertebrate ancestors. The review summarizes and analyzes the data accumulated in recent years from studies of the genetic mechanisms of early telencephalon development in lower vertebrates and searches for telencephalon homologs in two vertebrate-related chordate groups, Cephalochordata and Tunicata.

Use of the industrial X-ray computed microtomography to address scientific questions in developmental biology

X-ray computed microtomography (microCT) that allows to extract quantitative 3D information about various objects is already a well-established and widely used industrial technique for non-destructive testing, materials characterization and dimensional metrology. On the other hand, modern developmental biology requires both qualitative and quantitative three-dimensional information about the studied objects, which is not provided by conventional 2D imaging methods. In addition, the complexity of biological structures often requires a more comprehensive methodology to compare shapes and sizes. Our approach is to connect these two worlds, i.e. to apply procedures and analysis routinely used or developed for industrial computed tomography to address scientific questions in developmental biology. This approach, which is based on the long-term experience of the CEITEC BUT Brno micro/nanoCT research team on both, industrial and scientific application of X-ray microCT, brings new possibilities in imaging, data processing and evaluation of 3D biological models. Here we present 3D structures that were analysed by different approaches on the selected examples from developmental biology. In addition, quantitative analysis usually used in industry were applied to segmented 3D models e.g. wall thickness analysis of facial cartilage, shape comparisons of nasal capsules, automatic quantification of the cells in the salamander limb etc. A complete procedure consisting of staining, microCT measurement and subsequent data processing is discussed.

Breakthroughs and challenges of modern developmental biology and reproductive medicine.

In recent decades we have witnessed unprecedented progress in the field of the developmental biology of mammals. Building on 20th century discoveries, we have managed to increase our understanding of the molecular and cellular mechanisms governing early mammalian embryogenesis and link them to other biological questions, such as stem cells, regeneration, cancer, or tissue and organ formation. Consequently, it has also led to a creation of a completely new branch of reproductive medicine, i.e. assisted reproductive technology (ART). In this Special Issue of The International Journal of Developmental Biology (Int. J. Dev. Biol.) we wished to review state-of-the-art research regarding early mammalian development, from fertilization up to the implantation stage, and discuss its potential meaning for practical applications, including ART. As an introduction to the issue we present a compilation of short essays written by the most renowned scientists in the field, working both in basic and clinical research. The essays are dedicated to the greatest breakthroughs and challenges of 21st century developmental biology and reproductive medicine.

Development of Methods and Techniques to Visualize Mechanical Tension in Embryos Using Genetically Encoded Fluorescent Mechanosensors

Lately, the growing body of quantitative data has provided evidence of the importance of mechanical forces in embryogenesis. The study of spatial and temporal distribution of mechanical tension in the course of embryogenesis is one of the most important problems of modern developmental biology. Development of genetically encoded fluorescent mechanosensors allowed their application in an intravital study of mechanical tension in developing embryos via noninvasive techniques. The possibility of applying fluorescent mechanosensors based on vinculin and C-cadherin to visualize mechanical tension in tissues of Gallus and Xenopus embryos was studied. The methods to express and detect these proteins, as well as process the resulting images, were elaborated. The best results were obtained using Xenopus embryos and the vinculin-based mechanosensor.

Microfluidics Approaches in Modern Developmental Biology

Modern automated microsystems based on microhydrodynamic (microfluidic) technologies— labs on chips—make it possible to solve various basic and applied research problems. In the last 15 years, the development of these approaches in application to the problems of modern quantitative (systems) development biology has been observed. In this field, high-throughput experiments aimed at accumulating ample quantitative data for their subsequent computer analysis are important. In this review, the main directions in the development and application of microfluidics approaches for solving problems of modern developmental biology using the classical model object, Drosophila embryo, as an example is discussed. Microfluidic systems provide an opportunity to perform experiments that can hardly be performed using other approaches. These systems allow automated, rapid, reliable, and proper placing of many live embryos on a substrate for their simultaneous confocal scanning, sorting them, or injecting them with various agents. Such systems make it possible, in particular, to create controlled gradients of microenvironmental parameters along a series of developing embryos or even to introduce discontinuity in parameters within the microenvironment of one embryo, so that the head half is under other conditions compared to the tail half (at continuous scanning). These approaches are used both in basic research of the functions of gene ensembles that control early development, including the problems of resistance of early patterns to disturbances, and in test systems for screening chemical agents on developing embryos. The problems of integration of microfluidic devices in systems for automated performance of experiments simultaneously on many developing embryos under conditions of their continuous scanning using modern fluorescence microscopy instruments will be discussed. The methods and approaches developed for Drosophila are also applicable to other model objects, even mammalian embryos.

Integration of a faculty's ongoing research into an undergraduate laboratory teaching class in developmental biology

Traditional developmental biology laboratory classes have utilized a number of different model organisms to allow students to be exposed to diverse biological phenomena in developing organisms. This traditional approach has mainly focused on the diverse morphological and anatomical descriptions of the developing organisms. However, modern developmental biology is focusing more on conserved genetic networks which are responsible for generating conserved body patterns in developing organisms. Therefore, it is necessary to develop a new pedagogical tool to educate undergraduate biology students in the laboratory class of developmental biology with the genetic principles which are responsible for generating and controlling the developing body patterns. A new undergraduate laboratory class for developmental biology was developed in order to offer students the opportunity to explore a wide range of experimental procedures, also incorporating the instructor's on-going research. Thereby the course can serve as a bridge between research and education by combining both into a single theme. The course design involves a sequence of exercises which can be easily adapted to the faculty's ongoing research. This style of laboratory coursework could be a transitional form between a regular laboratory course and a discovery-based laboratory course. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(2):141-150, 2018.

Cancer as a disorder of patterning information: computational and biophysical perspectives on the cancer problem

The current paradigm views cancer as arising clonally from degradation of genetic information in single cells. A complementary perspective, originating at the dawn of modern developmental biology, is that cancer is the result of system disorder of algorithms that normally orchestrate individual cell activities toward specific anatomical structures and away from tumorigenesis. A view of cancer as disease of geometry focuses on the pathways that allow cells to cooperate to build and maintain large-scale anatomical patterning. Cancer may result when cells stop maintaining higher-order structures and reduce the boundary of their computational selves to single-cell level, reverting to unicellular lifestyle in which the rest of the organism is merely part of the environment at the expense of which all living things survive. While this view has been widely discussed, little progress has been made in providing quantitative, mechanistic framework within which this perspective's specific and unique implications for treatment strategies can be tested and biomedically exploited. Here, we highlight two recent areas of progress which may facilitate much-needed progress on the cancer problem. First, we review the roles that endogenous bioelectrical networks, operating across many tissues in vivo, play as medium of information processing in tumor suppression, progression, and reprogramming. Second, we provide primer to the development of computational theory and tools for quantifying the information and causal control structures in cancer and other complex biological systems. Rigorous mathematical formalisms now exist to measure and analyze the extent to which a whole is more than the sum of its parts, applications of which could lead to new strategies for cancer reprogramming. Here, we review the basic landscape of these related subfields, and sketch specific ways in which synthesis of novel integrative biophysics and mathematical analysis may contribute to novel ways to understand and address cancer in vivo.

Tokindo S. Okada.

Tokindo S. Okada.

Evolution of the hominoid scapula and its implications for earliest hominid locomotion.

The higher primate scapula has been subject to many explanations of the putative "adaptive value" of its individual traits. However, the shift from the bone's position in above branch quadrupeds to its more posterolateral position in recent hominoids obviously required fundamental changes to its general form. We hypothesize that most features argued to be individually adaptive are more likely secondary consequences of changes in its fundamental bauplan, a view more consistent with modern developmental biology. We tested this hypothesis with scapular metrics and angles from a broad anthropoid sample. Our results support our hypothesis. Contrary to earlier predictions, vertebral border length differs little relative to body size in anthropoids, inferior angle position primarily reflects mediolateral scapular breadth, and supraspinous and infraspinous fossa sizes largely reflect scapular spine orientation. Suspensory taxa have cranially oriented glenoids, whereas slow clamberers and humans do not. Australopithecus most closely resembles the latter. Most scapular features can be explained by only two primary changes: (1) reduction in mediolateral breadth and (2) change in the glenoid position relative to the vertebral border with increased reliance on suspension, which led to a more cranially angled scapular spine. Virtually all other scapular traits appear to be byproducts of these two changes. Based on fossil morphology, hominids1 were derived from a last common ancestor primarily adapted for clambering and not for suspension. Scapular form in early hominids such as Australopithecus is therefore primitive and largely reflects the genus's general clambering heritage.

Mechanical Behavior of Cells within a Cell-Based Model of Wheat Leaf Growth.

Understanding the principles and mechanisms of cell growth coordination in plant tissue remains an outstanding challenge for modern developmental biology. Cell-based modeling is a widely used technique for studying the geometric and topological features of plant tissue morphology during growth. We developed a quasi-one-dimensional model of unidirectional growth of a tissue layer in a linear leaf blade that takes cell autonomous growth mode into account. The model allows for fitting of the visible cell length using the experimental cell length distribution along the longitudinal axis of a wheat leaf epidermis. Additionally, it describes changes in turgor and osmotic pressures for each cell in the growing tissue. Our numerical experiments show that the pressures in the cell change over the cell cycle, and in symplastically growing tissue, they vary from cell to cell and strongly depend on the leaf growing zone to which the cells belong. Therefore, we believe that the mechanical signals generated by pressures are important to consider in simulations of tissue growth as possible targets for molecular genetic regulators of individual cell growth.

Rudolf Weber (1922-2015): a driving force in the transition of developmental biology into a molecular and cellular science.

Prof. Dr. Rudolf Heinrich Weber passed away on December 23, 2015, at the high age of 93 years. Succeeding Fritz Baltzer and Fritz Erich Lehmann, he became the third in a line of outstanding developmental biologists at the University of Bern, Switzerland. Throughout his career, he helped shape modern developmental biology by introducing and promoting biochemical and molecular techniques. RudolfWeber was born in Basel, Switzerland, on September 27, 1922. He studied biology in Basel and obtained his PhD in 1949 under the supervision of Adolf Portmann. His thesis (Weber 1949) had a developmental topic (Transitory closures of distant sensory organs during the embryonic period in amniotes; translated from German), yet its character was descriptive and comparative, quite in line with Portmann’s tradition of comparative morphology and evolutionary biology. Weber later admitted that he was never quite happy with his thesis, as his main interest had always been to understand the mechanisms that drive development. He was convinced that this could not be achieved solely bymorphological descriptions and comparisons, but that experiments and in particular chemical and biochemical methods had to be used as well. After his graduation, Weber worked and acquired experiences in different fields, countries, and institutions, in particular at the University of Uppsala (Sweden), the Division de Malarialogia in Maracay (Venezuela), the Swiss Tropical Institute in Basel, and the Carlsberg Laboratories in Copenhagen (Denmark). A turning point in his career was 1954, when he accepted an assistant position offered by Fritz Erich Lehmann at the Zoological Institute of the University of Bern. This institution was to remain his academic home until his retirement in 1988. In 1954, Lehmann had just succeeded Fritz Baltzer as institute director, and both of them were world-renowned specialists of developmental physiology (Entwicklungsphysiologie), the term used for the research field of developmental biology at the time. A native of Bern, Baltzer had studied with Theodor Boveri in Wurzburg (Germany) and with Hans Spemann in Freiburg im Breisgau (Germany). These experiences had influenced him, once he was appointed professor in Bern, to study the roles of chromosomal and cytoplasmic determinants in various systems, including sea urchins (Baltzer 1910), the worm Bonellia (Baltzer 1928), and amphibians (newts) (Baltzer 1922; Baltzer 1952). His work was driven by the urge to integrate information from * Daniel Schumperli daniel.schuemperli@izb.unibe.ch

Managing variation in the investigation of organismal development: problems and opportunities.

This paper aims to clarify the consequences of new scientific and philosophical approaches for the practical-theoretical framework of modern developmental biology. I highlight normal development, and the instructive-permissive distinction, as key parts of this framework which shape how variation is conceptualised and managed. Furthermore, I establish the different dimensions of biological variation: the units, temporality and mode of variation. Using the analytical frame established by this, I interpret a selection of examples as challenges to the instructive-permissive distinction. These examples include the phenomena of developmental plasticity and transdifferentiation, the role of the microbiome in development, and new methodological approaches to standardisation and the assessment of causes. Furthermore, I argue that investigations into organismal development should investigate the effects of a wider range of kinds of variation including variation in the units, modes and temporalities of development. I close by examining various possible opportunities for producing and using normal development free of the assumptions of the instructive-permissive distinction. These opportunities are afforded by recent developments, which include new ways of producing standards incorporating more natural variation and being based on function rather than structure, and the ability to produce, store, and process large quantities of data.

Blastocyst genotyping for quality control of mouse mutant archives: an ethical and economical approach.

With the advent of modern developmental biology and molecular genetics, the scientific community has generated thousands of newly genetically altered strains of laboratory mice with the aim of elucidating gene function. To this end, a large group of Institutions which form the International Mouse Phenotyping Consortium is generating and phenotyping a knockout mouse strain for each of the ~20,000 protein-coding genes using the mutant ES cell resource produced by the International Knockout Mouse Consortium. These strains are made available to the research community via public repositories, mostly as cryopreserved sperm or embryos. To ensure the quality of this frozen resource there is a requirement that for each strain the frozen sperm/embryos are proven able to produce viable mutant progeny, before the live animal resource is removed from cages. Given the current requirement to generate live pups to demonstrate their mutant genotype, this quality control check necessitates the use and generation of many animals and requires considerable time, cage space, technical and economic resources. Here, we describe a simple and efficient method of genotyping pre-implantation stage blastocysts with significant ethical and economic advantages especially beneficial for current and future large-scale mouse mutagenesis projects.

Abstracting the principles of development using imaging and modeling.

Here we look at modern developmental biology with a focus on the relationship between different approaches of investigation. We argue that direct imaging is a powerful approach not only for obtaining descriptive information but also for model generation and testing that lead to mechanistic insights. Modeling, on the other hand, conceptualizes imaging data and provides guidance to perturbations. The inquiry progresses most efficiently when a trinity of approaches—quantitative imaging (measurement), modeling (theory) and perturbation (test)—are pursued in concert, but not when one approach is dominant. Using recent studies of the zebrafish system, we show how this combination has effectively advanced classic topics in developmental biology compared to a perturbation-centric approach. Finally, we show that interdisciplinary expertise and perhaps specialization are necessary for carrying out a systematic approach, and discuss the technical hurdles.

Quantitative high dynamic range beam profiling for fluorescence microscopy.

Modern developmental biology relies on optically sectioning fluorescence microscope techniques to produce non-destructive in vivo images of developing specimens at high resolution in three dimensions. As optimal performance of these techniques is reliant on the three-dimensional (3D) intensity profile of the illumination employed, the ability to directly record and analyze these profiles is of great use to the fluorescence microscopist or instrument builder. Though excitation beam profiles can be measured indirectly using a sample of fluorescent beads and recording the emission along the microscope detection path, we demonstrate an alternative approach where a miniature camera sensor is used directly within the illumination beam. Measurements taken using our approach are solely concerned with the illumination optics as the detection optics are not involved. We present a miniature beam profiling device and high dynamic range flux reconstruction algorithm that together are capable of accurately reproducing quantitative 3D flux maps over a large focal volume. Performance of this beam profiling system is verified within an optical test bench and demonstrated for fluorescence microscopy by profiling the low NA illumination beam of a single plane illumination microscope. The generality and success of this approach showcases a widely flexible beam amplitude diagnostic tool for use within the life sciences.

It's time to exploit your favorite quirky organism with new technologies.

We live in a competitive world where, at any given moment, our peers might achieve the very discoveries we hope to make with our own research. This reality creates butterflies in the stomachs of those who are engaged in risky experiments. Any hesitation or setback, even momentary, can make you feel that by the time you are in a position to pursue your own direction, every novelty will already have been discovered. But don't worry, for many years to come there will be plenty of biology waiting to be investigated with many questions we haven't yet thought of asking. I think that the most important field in biology today is developmental biology. During development, it is thought that each event or structure is consequential to a preceding event or structure and that the layering of subsequent processes ultimately brings the phenotype into being. This process is also studied by those in the field we now call epigenetics, which, I believe, is modern developmental biology armed with state‐of‐the art genomics tools and systems bioinformatics. I want to know how a fertilized egg with one genome can give rise to a dazzling variety of cell types in which all genomes are the same as that of the egg, …

A generic classification-based method for segmentation of nuclei in 3D images of early embryos

BackgroundStudying how individual cells spatially and temporally organize within the embryo is a fundamental issue in modern developmental biology to better understand the first stages of embryogenesis. In order to perform high-throughput analyses in three-dimensional microscopic images, it is essential to be able to automatically segment, classify and track cell nuclei. Many 3D/4D segmentation and tracking algorithms have been reported in the literature. Most of them are specific to particular models or acquisition systems and often require the fine tuning of parameters.ResultsWe present a new automatic algorithm to segment and simultaneously classify cell nuclei in 3D/4D images. Segmentation relies on training samples that are interactively provided by the user and on an iterative thresholding process. This algorithm can correctly segment nuclei even when they are touching, and remains effective under temporal and spatial intensity variations. The segmentation is coupled to a classification of nuclei according to cell cycle phases, allowing biologists to quantify the effect of genetic perturbations and drug treatments. Robust 3D geometrical shape descriptors are used as training features for classification. Segmentation and classification results of three complete datasets are presented. In our working dataset of the Caenorhabditis elegans embryo, only 21 nuclei out of 3,585 were not detected, the overall F-score for segmentation reached 0.99, and more than 95% of the nuclei were classified in the correct cell cycle phase. No merging of nuclei was found.ConclusionWe developed a novel generic algorithm for segmentation and classification in 3D images. The method, referred to as Adaptive Generic Iterative Thresholding Algorithm (AGITA), is freely available as an ImageJ plug-in.

Construction of a Self-Consistent Landscape for Multistable Gene Regulatory Circuits

Cell fate decisions during embryonic development and tumorigenesis pose a major research challenge in modern developmental and cancer biology. Cell fate decisions between different phenotypes (e.g. epithelial, mesenchymal and epithelial/mesenchymal hybrids) are regulated by multistable gene circuits that give rise to the coexistence of several stable states (phenotypes). Internal and external noise play crucial role in determining the transitions between and the relative stability of the coexisting phenotypes. The deterministic dynamics of these circuits is not derivable from a potential. Yet, motivated by Waddington Epigenetic Landscape, many rely on the notion of effective potential to describe cell fate determination in the presence of noise. Here, we present a construction of a self-consistent landscape (effective potential, W = -ln(probability)), utilizing the Eikonal equation approach (WKB approximation of the corresponding Fokker Planck equation) for the cases of white noise and shot noise. The approach is based on utilizing the method of characteristics in a special way, which is illustrated for the concrete examples of the bistable and tristable double inhibition circuits. We also deviced a numerical method to efficiently calculate the contour of the potential and the optimal path for the transitions from one stable state to another. We tested the method on the bistable and tristable double inhibition circuits, and we showed that the constructed landscape agrees very well with the numerical simulation of the stochastic equations. We expect this method to be valuable to a wide range of multistable gene circuits.