Onco-Breastomics: An Eco-Evo-Devo Holistic Approach.

Known as a diverse collection of neoplastic diseases, breast cancer (BC) can be hyperbolically characterized as a dynamic pseudo-organ, a living organism able to build a complex, open, hierarchically organized, self-sustainable, and self-renewable tumor system, a population, a species, a local community, a biocenosis, or an evolving dynamical ecosystem (i.e., immune or metabolic ecosystem) that emphasizes both developmental continuity and spatio-temporal change. Moreover, a cancer cell community, also known as an oncobiota, has been described as non-sexually reproducing species, as well as a migratory or invasive species that expresses intelligent behavior, or an endangered or parasite species that fights to survive, to optimize its features inside the host's ecosystem, or that is able to exploit or to disrupt its host circadian cycle for improving the own proliferation and spreading. BC tumorigenesis has also been compared with the early embryo and placenta development that may suggest new strategies for research and therapy. Furthermore, BC has also been characterized as an environmental disease or as an ecological disorder. Many mechanisms of cancer progression have been explained by principles of ecology, developmental biology, and evolutionary paradigms. Many authors have discussed ecological, developmental, and evolutionary strategies for more successful anti-cancer therapies, or for understanding the ecological, developmental, and evolutionary bases of BC exploitable vulnerabilities. Herein, we used the integrated framework of three well known ecological theories: the Bronfenbrenner's theory of human development, the Vannote's River Continuum Concept (RCC), and the Ecological Evolutionary Developmental Biology (Eco-Evo-Devo) theory, to explain and understand several eco-evo-devo-based principles that govern BC progression. Multi-omics fields, taken together as onco-breastomics, offer better opportunities to integrate, analyze, and interpret large amounts of complex heterogeneous data, such as various and big-omics data obtained by multiple investigative modalities, for understanding the eco-evo-devo-based principles that drive BC progression and treatment. These integrative eco-evo-devo theories can help clinicians better diagnose and treat BC, for example, by using non-invasive biomarkers in liquid-biopsies that have emerged from integrated omics-based data that accurately reflect the biomolecular landscape of the primary tumor in order to avoid mutilating preventive surgery, like bilateral mastectomy. From the perspective of preventive, personalized, and participatory medicine, these hypotheses may help patients to think about this disease as a process governed by natural rules, to understand the possible causes of the disease, and to gain control on their own health.

Establishment of an in vitro culture system to study the developmental biology of Onchocerca volvulus with implications for anti-Onchocerca drug discovery and screening.

BACKGROUND: Infections with Onchocerca volvulus nematodes remain a threat in Sub-Saharan Africa after three decades of ivermectin mass drug administration. Despite this effort, there is still an urgent need for understanding the parasite biology especially the mating behaviour and nodule formation as well as the development of more potent drugs that can clear the developmental (L3, L4, L5) and adult stages of the parasite and inhibit parasite reproduction and behaviour. METHODOLOGY/PRINCIPAL FINDINGS: Prior to culture, freshly harvested O. volvulus L3 larvae from dissected Simulium damnosum flies were purified by centrifugation using a 30% Percoll solution to eliminate fly tissue debris and contaminants. Parasites were cultured in both cell-free and cell-based co-culture systems and monitored daily by microscopic visual inspection. Exhausted culture medium was replenished every 2-3 days. The cell-free culture system (DMEM supplemented with 10% NCS) supported the viability and motility of O. volvulus larvae for up to 84 days, while the co-culture system (DMEM supplemented with 10% FBS and seeded on LLC-MK2 feeder cells) extended worm survival for up to 315 days. Co-culture systems alone promoted two consecutive parasite moults (L3 to L4 and L4 to L5) with highest moulting rates (69.2±30%) observed in DMEM supplemented with 10% FBS and seeded on LLC-MK2 feeder cells, while no moult was observed in DMEM supplemented with 10% NCS and seeded on LEC feeder cells. In DMEM supplemented with 10% FBS and seeded on LLC-MK2 feeder cells, O. volvulus adult male worms attached to the vulva region of adult female worms and may have mated in vitro. Apparent early initiation of nodulogenesis was observed in both DMEM supplemented with 10% FBS and seeded on LLC-MK2 and DMEM supplemented with 10% NCS and seeded on LLC-MK2 systems. CONCLUSIONS/SIGNIFICANCE: The present study describes an in vitro system in which O. volvulus L3 larvae can be maintained in culture leading to the development of adult stages. Thus, this in vitro system may provide a platform to investigate mating behaviour and early stage of nodulogenesis of O. volvulus adult worms that can be used as additional targets for macrofilaricidal drug screening.

Why we should use topological data analysis in ageing: Towards defining the "topological shape of ageing".

Living systems are subject to the arrow of time; from birth, they undergo complex transformations (self-organization) in a constant battle for survival, but inevitably ageing and disease trap them to death. Can ageing be understood and eventually reversed? What tools can be employed to further our understanding of ageing? The present article is an invitation for biologists and clinicians to consider key conceptual ideas and computational tools (known to mathematicians and physicists), which potentially may help dissect some of the underlying processes of ageing and disease. Specifically, we first discuss how to classify and analyse complex systems, as well as highlight critical theoretical difficulties that make complex systems hard to study. Subsequently, we introduce Topological Data Analysis - a novel Big Data tool - which may help in the study of complex systems since it extracts knowledge from data in a holistic approach via topological considerations. These conceptual ideas and tools are discussed in a relatively informal way to pave future discussions and collaborations between mathematicians and biologists studying ageing.

Developmental biology of dispersed pollen grains.

Professor Panchanan Maheshwari served as Professor and Head of the Department of Botany, University of Delhi, from 1950 to 1966 and built an internationally reputed School of integrated plant embryology. Studies carried out during and after Maheshwari's period from this School have enormously advanced our knowledge of the structural, developmental and functional aspects of embryological processes. This review covers studies carried out at the Delhi School on the developmental biology of dispersed pollen grains which operate from pollen dispersal from the anthers until pollen tubes discharge the male gametes in the embryo sac for fertilization. These events include pollen viability and vigour, pollen germination and pollen tube growth, structural details of the pistil relevant to pollen function, pollination and pollen-pistil interaction.

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing.

The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.

The Early Ediacaran Caveasphaera Foreshadows the Evolutionary Origin of Animal-like Embryology.

The Ediacaran Weng'an Biota (Doushantuo Formation, 609 Ma old) is a rich microfossil assemblage that preserves biological structure to a subcellular level of fidelity and encompasses a range of developmental stages [1]. However, the animal embryo interpretation of the main components of the biota has been the subject of controversy [2, 3]. Here, we describe the development of Caveasphaera, which varies in morphology from lensoid to a hollow spheroidal cage [4] to a solid spheroid [5] but has largely evaded description and interpretation. Caveasphaera is demonstrably cellular and develops within an envelope by cell division and migration, first defining the spheroidal perimeter via anastomosing cell masses that thicken and ingress as strands of cells that detach and subsequently aggregate in a polar region. Concomitantly, the overall diameter increases as does the volume of the cell mass, but after an initial phase of reductive palinotomy, the volume of individual cells remains the same through development. The process of cell ingression, detachment, and polar aggregation is analogous to gastrulation; together with evidence of functional cell adhesion and development within an envelope, this is suggestive of a holozoan affinity. Parental investment in the embryonic development of Caveasphaera and co-occurring Tianzhushania and Spiralicellula, as well as delayed onset of later development, may reflect an adaptation to the heterogeneous nature of the early Ediacaran nearshore marine environments in which early animals evolved.

Cortical organoids: why all this hype?

The development of organoids derived from human pluripotent stem cells heralded a new area in studying human organ development and pathology outside of the human body. Triggered by the seminal work of pioneers in the field such as Yoshiki Sasai or Hans Clevers, organoid research has become one of the most rapidly developing fields in cell biology. The potential applications are manifold reaching from developmental studies to tissue regeneration and drug screening. In this review, we will concentrate on brain organoids of cortical identity. We will describe the 'state of the art' in generating cortical organoids and discuss potential applications. Finally, we will provide future perspectives including suggestions how further innovations can broaden the application of brain organoids.

The not-so-long history of zebrafish research in Israel.

The zebrafish has become a model of choice in fundamental and applied life sciences and is widely used in various fields of biomedical research as a human disease model for cancer, metabolic and neurodegenerative diseases, and regenerative medicine. The transparency of the zebrafish embryo allows real-time visualization of the development and morphogenesis of practically all of its tissues and organs. Zebrafish are amenable to genetic manipulation, for which innovative genetic and molecular techniques are constantly being introduced. These include the study of gene function and regulation using gene knockdown, knockout and knock-in, as well as transgenesis and tissue-specific genetic perturbations. Complementing this genetic toolbox, the zebrafish exhibits measurable behavioral and hormonal responses already at the larval stages, providing a viable vertebrate animal model for high-throughput drug screening and chemical genetics. With the available tools of the genomic era and the abundance of disease-associated human genes yet to be explored, the zebrafish model is becoming the preferred choice in many studies. Its advantages and potential are being increasingly recognized within the Israeli scientific community, and its use as a model system for basic and applied science has expanded in Israel in recent years. Since the first zebrafish-focused laboratory was introduced at Tel Aviv University 16 years ago, seven more zebrafish-centric research groups have been established, along with more than two dozen academic research groups and three bio-medical companies that are now utilizing this model.

Neural organoids for disease phenotyping, drug screening and developmental biology studies.

Human induced pluripotent stem cells (hiPSCs) can theoretically yield limitless supplies of cells fated to any cell type that comprise the human organism, making them a new tool by which to potentially overcome caveats in current biomedical research. In vitro derivation of central nervous system (CNS) cell types has the potential to provide material for drug discovery and validation, safety and toxicity assays, cell replacement therapy and the elucidation of previously unknown disease mechanisms. However, current two-dimensional (2D) CNS differentiation protocols do not faithfully recapitulate the spatial organization of heterogeneous tissue, nor the cell-cell interactions, cell-extracellular matrix interactions, or specific physiological functions generated within complex tissue such as the brain. In an effort to overcome 2D protocol limitations, there have been advancements in deriving highly complicated 3D neural organoid structures. Herein we provide a synopsis of the derivation and application of neural organoids and discuss recent advancements and remaining challenges on the full potential of this novel technological platform.

The Yin and Yang of Wnt/Ryk axon guidance in development and regeneration.

In the developing embryo, nascent axons navigate towards their specific targets to establish the intricate network of axonal connections linking neurons within the mature nervous system. Molecular navigational systems comprising repulsive and attractive guidance cues form chemotactic gradients along the pathway of the exploring growth cone. Axon-bound receptors detect these gradients and determine the trajectory of the migrating growth cone. In contrast to their benevolent role in the developing nervous system, repulsive guidance receptors are detrimental to the axon's ability to regenerate after injury in the adult. In this review we explore the essential and beneficial role played by the chemorepulsive Wnt receptor, Ryk/Derailed in axon navigation in the embryonic nervous system (the Yin function). Specifically, we focus on the role of Wnt5a/Rykmediated guidance in the establishment of two major axon tracts in the mammalian central nervous system, the corticospinal tract and the corpus callosum. Recent studies have also identified Ryk as a major suppressor of axonal regeneration after spinal cord injury. Thus, we also discuss this opposing aspect of Ryk function in axonal regeneration where its activity is a major impediment to axon regrowth (the Yang function).

Nuclease-mediated genome editing: At the front-line of functional genomics technology.

Genome editing with engineered endonucleases is rapidly becoming a staple method in developmental biology studies. Engineered nucleases permit random or designed genomic modification at precise loci through the stimulation of endogenous double-strand break repair. Homology-directed repair following targeted DNA damage is mediated by co-introduction of a custom repair template, allowing the derivation of knock-out and knock-in alleles in animal models previously refractory to classic gene targeting procedures. Currently there are three main types of customizable site-specific nucleases delineated by the source mechanism of DNA binding that guides nuclease activity to a genomic target: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Among these genome engineering tools, characteristics such as the ease of design and construction, mechanism of inducing DNA damage, and DNA sequence specificity all differ, making their application complementary. By understanding the advantages and disadvantages of each method, one may make the best choice for their particular purpose.

Comparative developmental biology of the uterus: insights into mechanisms and developmental disruption.

The uterus is an essential organ for reproduction in mammals that derives from the Müllerian duct. Despite the importance of the uterus for the fertility and health of women and their offspring, relatively little is known about the hormonal, cellular and molecular mechanisms that regulate development of the Müllerian duct and uterus. This review aims to summarize the hormonal, cellular and molecular mechanisms and pathways governing development of the Müllerian duct and uterus as well as highlight developmental programming effects of endocrine disruptor compounds. Organogenesis, morphogenesis, and functional differentiation of the uterus are complex, multifactorial processes. Disruption of uterine development in the fetus and neonate by genetic defects and exposure to endocrine disruptor compounds can cause infertility and cancer in the adult and their offspring via developmental programming. Clear conservation of some factors and pathways are observed between species; therefore, comparative biology is useful to identify candidate genes and pathways underlying congenital abnormalities in humans.

Molecular foundations of reproductive lethality in Arabidopsis thaliana.

The SeedGenes database (www.seedgenes.org) contains information on more than 400 genes required for embryo development in Arabidopsis. Many of these EMBRYO-DEFECTIVE (EMB) genes encode proteins with an essential function required throughout the life cycle. This raises a fundamental question. Why does elimination of an essential gene in Arabidopsis often result in embryo lethality rather than gametophyte lethality? In other words, how do mutant (emb) gametophytes survive and participate in fertilization when an essential cellular function is disrupted? Furthermore, why do some mutant embryos proceed further in development than others? To address these questions, we first established a curated dataset of genes required for gametophyte development in Arabidopsis based on information extracted from the literature. This provided a basis for comparison with EMB genes obtained from the SeedGenes dataset. We also identified genes that exhibited both embryo and gametophyte defects when disrupted by a loss-of-function mutation. We then evaluated the relationship between mutant phenotype, gene redundancy, mutant allele strength, gene expression pattern, protein function, and intracellular protein localization to determine what factors influence the phenotypes of lethal mutants in Arabidopsis. After removing cases where continued development potentially resulted from gene redundancy or residual function of a weak mutant allele, we identified numerous examples of viable mutant (emb) gametophytes that required further explanation. We propose that the presence of gene products derived from transcription in diploid (heterozygous) sporocytes often enables mutant gametophytes to survive the loss of an essential gene in Arabidopsis. Whether gene disruption results in embryo or gametophyte lethality therefore depends in part on the ability of residual, parental gene products to support gametophyte development. We also highlight here 70 preglobular embryo mutants with a zygotic pattern of inheritance, which provide valuable insights into the maternal-to-zygotic transition in Arabidopsis and the timing of paternal gene activation during embryo development.

The control of developmental phase transitions in plants.

Plant development progresses through distinct phases: vegetative growth, followed by a reproductive phase and eventually seed set and senescence. The transitions between these phases are controlled by distinct genetic circuits that integrate endogenous and environmental cues. In recent years, however, it has become evident that the genetic networks that underlie these phase transitions share some common factors. Here, we review recent advances in the field of plant phase transitions, highlighting the role of two microRNAs - miR156 and miR172 - and their respective targets during these transitions. In addition, we discuss the evolutionary conservation of the functions of these miRNAs in regulating the control of plant developmental phase transitions.

B12 in fetal development.

Vitamin B12 (cobalamin) is necessary for development of the fetus and child. Pregnant women who are vegetarian or vegan, have Crohn's or celiac disease, or have undergone gastric bypass surgery are at increased risk of B12 deficiency. Low serum levels of B12 have been linked to negative impacts in cognitive, motor, and growth outcomes. Low cobalamin levels also may be related to depression in adults. Some studies indicate that B12 supplementation may improve outcomes in children, although more research is needed in this area. Overall, the mechanisms of B12 action in development remain unclear. Further studies in this area to elucidate the pathways of cobalamin influence on development, as well as to prevent B12 deficiency in pregnant women and children are indicated.

The serotonergic system in fish.

Neurons using serotonin (5-HT) as neurotransmitter and/or modulator have been identified in the central nervous system in representatives from all vertebrate clades, including jawless, cartilaginous and ray-finned fishes. The aim of this review is to summarize our current knowledge about the anatomical organization of the central serotonergic system in fishes. Furthermore, selected key functions of 5-HT will be described. The main focus will be the adult brain of teleosts, in particular zebrafish, which is increasingly used as a model organism. It is used to answer not only genetic and developmental biology questions, but also issues concerning physiology, behavior and the underlying neuronal networks. The many evolutionary conserved features of zebrafish combined with the ever increasing number of genetic tools and its practical advantages promise great possibilities to increase our understanding of the serotonergic system. Further, comparative studies including several vertebrate species will provide us with interesting insights into the evolution of this important neurotransmitter system.

Stem cells: general information and perspectives

We are now in the middle of stem cell war. Each country is trying to invest a large amount of funds into stem cell research. This is due to a potentiality of stem cells. Stem cells are capable of proliferating in an undifferentiated manner and are able to differentiate into a desired cell lineage under certain conditions. These abilities make stem cells an appealing source for cell replacement therapies (regenerative medicine), the study of developmental biology and drug/toxin screening. In addition to embryonic and adult stem cells, induced pluripotent stem (iPS) cells has been recently generated through reprogramming from adult tissue cells such as fibroblasts. This technique has opened up new avenues to generate patient- and disease-specific pluripotent stem cells. Human iPS cells may be useful for gaining valuable insight into the pathophysiology of disease, as well as for discovering for new prognostic biomarkers and drug screening. Moreover, the iPS cell technology may play a major role in immune-matched clinical application in the future. In this chapter, we introduce general characteristics of various stem cells, clinical application of stem cells and future perspectives.

Holism and life manifestations: molecular and space-time biology.

Appeals of philosophers to look for new concepts in sciences are being met with a weak response. Limited attention is paid to the relation between synthetic and analytic approach in solving problems of biology. An attempt is presented to open a discussion on a possible role of holism. The term "life manifestations" is used in accordance with phenomenology. Multicellular creatures maintain milieu intérieur to keep an aqueous milieu intracellulair in order to transform the energy of nutrients into the form utilizable for driving cellular life manifestations. Milieu intérieur enables to integrate this kind of manifestations into life manifestations of the whole multicellular creatures. The integration depends on a uniqueness and uniformity of the genome of cells, on their mutual recognition and adherence. The processes of ontogenetic development represent the natural mode of integration of cellular life manifestations. Functional systems of multicellular creatures are being established by organization of integrable cells using a wide range of developmental processes. Starting from the zygote division the new being displays all properties of a whole creature, although its life manifestations vary. Therefore, the whole organism is not only more than its parts, as supposed by holism, but also more than developmental stages of its life manifestations. Implicitly, the units of whole multicellular creature are rather molecular and developmental events than the cells per se. Holism, taking in mind the existence of molecular and space-time biology, could become a guide in looking for a new mode of the combination of analytical and synthetic reasoning in biology.

The developmental biology of birth defect

Knowledge of developmental biology is essential for clinicians who seek to develop a rational approach to the diagnostic evaluation of patients with birth defects. After an accurate diagnosis, a clinician can make predictions about prognosis, recommend management options, and provide an indication of recurrence risk for the parents and relatives. In this paper, we first review the basic mechanisms of embryological development and clinical dysmorphology. We then review cellular and molecular mechanisms in development and related congenital anomalies. Developmental anomalies have a major impact on public health. Genetic counseling and prenatal diagnosis, with the option to continue or to terminate a pregnancy, are important for helping families faced with the risk of a serious congenital anomaly in their offspring. Moreover, primary prevention of birth defects, for example, supplementation of prenatal folic acid and prevention of consumption of alcohol which has teratogenic effects, can be accomplished using developmental biology knowledge.