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Results for “Developmental Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 271 records · Page 15Linked to original sources

bioRxiv2016

Myotome adaptability confers developmental robustness to somitic myogenesis in response to fibre number alteration.

Summary StatementHomeostatic interactions between muscle stem cells and fibres during myogenesis ensure the correct muscle size is formed independent of fibre number in zebrafish\n\nAbstractBalancing the number of stem cells and their progeny is crucial for tissue development and repair. Here we examine how muscle stem/precursor cell (MPC) numbers are tightly regulated during zebrafish somitic muscle development. MPCs expressing Pax7 are initially located in the dermomyotome (DM) external cell layer, adopt a highly stereotypical distribution and thereafter a proportion of MPCs migrate into the myotome. Regional variations in the proliferation and terminal differentiation of MPCs contribute to growth of the myotome. To probe the robustness of spatiotemporal regulation of MPCs, we compared the behaviour of wild type (wt) MPCs with those in mutant zebrafish that lack the muscle regulatory factor Myod. Myodfh261 mutants form one third fewer multinucleate fast muscle fibres than wt and show a significant expansion of the Pax7+ MPC population in the DM. Subsequently, myodfh261 mutant fibres generate more cytoplasm per nucleus, leading to recovery of muscle bulk. In addition, relative to wt siblings, there is an increased number of MPCs in myodfh261 mutants and these migrate prematurely into the myotome, differentiate and contribute to the hypertrophy of existing fibres. Thus, homeostatic reduction of the excess MPCs returns their number to normal levels, but fibre numbers remain low. The GSK3 antagonist BIO prevents MPC migration into the deep myotome, suggesting that canonical Wnt pathway activation maintains the DM in zebrafish, as in amniotes. BIO does not, however, block recovery of the myodfh261 mutant myotome, indicating that homeostasis acts on fibre intrinsic growth to maintain muscle bulk. The findings suggest the existence of a critical window for early fast fibre formation followed by a period in which homeostatic mechanisms regulate myotome growth by controlling fibre size.

developmental biology↗

bioRxiv2016

The interplay of stiffness and force anisotropies drive embryo elongation

The morphogenesis of tissues, like the deformation of an object, results from the interplay between their material properties and the mechanical forces exerted on them. Whereas the importance of mechanical forces in influencing cell behaviour is widely recognized, the importance of tissue material properties, in particular stiffness, has received much less attention. Using C. elegans as a model, we examine how both aspects contribute to embryonic elongation. Measuring the opening shape of the epidermal actin cortex after laser nano-ablation, we assess the spatiotemporal changes of actomyosin-dependent force and stiffness along the antero-posterior and dorso-ventral axis. Experimental data and analytical modelling show that myosin II-dependent force anisotropy within the lateral epidermis, and stiffness anisotropy within the fiber-reinforced dorso-ventral epidermis are critical to drive embryonic elongation. Together, our results establish a quantitative link between cortical tension, material properties and morphogenesis of an entire embryo.

developmental biology↗

bioRxiv2017

Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis

The adult mammalian kidney has a complex, highly-branched collecting duct epithelium that arises as a ureteric bud sidebranch from an epithelial tube known as the nephric duct. Subsequent branching of the ureteric bud to form the collecting duct tree is regulated by subcellular interactions between the epithelium and a population of mesenchymal cells that surround the tips of outgrowing branches. The mesenchymal cells produce glial cell-line derived neurotrophic factor (GDNF), that binds with RET receptors on the surface of the epithelial cells to stimulate several subcellular pathways in the epithelium. Such interactions are known to be a prerequisite for normal branching development, although competing theories exist for their role in morphogenesis. Here we introduce the first agent-based model of ex vivo kidney uretic branching. Through comparison with experimental data, we show that growth factor-regulated growth mechanisms can explain early epithelial cell branching, but only if epithelial cell division depends in a switch-like way on the local growth factor concentration; cell division occurring only if the driving growth factor level exceeds a threshold. We also show how a recently-developed method, \"Approximate Approximate Bayesian Computation\", can be used to infer key model parameters, and reveal the dependency between the parameters controlling a growth factor-dependent growth switch. These results are consistent with a requirement for signals controlling proliferation and chemotaxis, both of which are previously identified roles for GDNF.\n\nAuthor SummaryA number of important congenital disorders arise due to incomplete development of the mammalian kidney. Elucidating the cause of these conditions requires an understanding of the mechanisms that contribute to kidney morphogenesis. Whilst experimental work has suggested several candidate mechanisms, their importance is still not well understood. Here we develop a computational model of kidney morphogenesis at the individual cell level to compare these different hypotheses. Guided by existing experimental evidence we propose that a generic growth factor, that we term \"GDNF\", produced from the mesenchyme surrounding the epithelium, can drive a number of cellular responses. Simulations of our agent-based model reveal that diffusion of GDNF, coupled with GDNF-stimulated epithelial cell division, can generate the branching patterns seen in ex vivo kidney explant experiments. We also find that branching depends on the sensitivity of cell proliferation to changes in GDNF levels. In particular our model only generates realistic branching when there is significant variation in GDNF levels along the boundary of the epithelium, and most cells divide only if the local concentration of GDNF exceeds a threshold value. We conclude that feedback between mesenchymal cells that produce GDNF, and epithelial cells that consume it, is vital for normal kidney organogenesis.

developmental biology↗

bioRxiv2016

Rab5-mediated Yolk Endocytosis modulates Zebrafish Epiboly Biomechanics and Tissue Movements

Morphogenetic processes demand the coordinated allocation of cells and tissues to their final destination in a spatio-temporal controlled way. Identifying how these morphogenetic movements are directed and implemented is essential for understanding morphogenesis. Topographical and scalar differences in adhesion and contractility within and between cells are essential, yet, the role that membrane remodeling may play remains less clear. To clarify how surface turnover and dynamics may modulate tissue arrangements we studied epiboly in the zebrafish. During epiboly the blastoderm expands as a result of an asymmetry of mechanical tension along the embryo surface. In this scenario, we found that the membrane removal by macropinocytosis of the external yolk cell syncytial layer (E-YSL) ahead of the blastoderm is key for epiboly progression In early zebrafish embryos, the activity of the GTPase Rab5ab was essential for endocytosis, and interference in its expression exclusively in the yolk cell resulted in the reduction of yolk cell actomyosin contractility, the disruption of cortical and internal yolk flows, a disequilibrium in force balance and as a result epiboly impairment. We conclude that regulated membrane remodeling is crucial for directing cell and tissue mechanics and coordinating morphogenetic movements during epiboly.

developmental biology↗

bioRxiv2017

Multiple zebrafish atoh1 genes specify a diversity of neuronal types in the zebrafish cerebellum

The basic Helix-Loop-Helix transcription factor Atoh1 is required for the specification of multiple neuron types in the mammalian hindbrain including tegmental, precerebellar output neurons and cerebellar granule neurons. How a single proneural gene specifies so many neuron types from a single progenitor zone, the upper rhombic lip (URL), is not known. Here we use the zebrafish to explore the role of atoh1 in cerebellar neurogenesis. Using transgenic reporters we show that zebrafish atoh1c-expressing cells give rise to tegmental and granule cell populations that, together with previously described atoh1a-derived neuron populations, resemble the diversity of atoh1 derivatives observed in mammals. Using genetic mutants we find that of the three zebrafish atoh1 paralogs, atoh1c and atoh1a are required for the full complement of granule neurons in the zebrafish cerebellum. Interestingly, atoh1a and atoh1c specify non-overlapping granule populations, indicating that fish use multiple atoh1 genes to generate granule neuron diversity that is not detected in mammals. By live imaging of neurogenesis at the URL we show that atoh1c is not required for the specification of granule neuron progenitors but promotes their delamination from the URL epithelium and this process is critical for neuronal maturation. This study thus provides a better understanding of how proneural transcription factors regulate neurogenesis in the vertebrate cerebellum.\n\nSummary statementatoh1 genes specify distinct populations of tegmental and granule neurons in the zebrafish hindbrain and promote their delamination from the neuroepithelium, a process critical for neuronal maturation.

developmental biology↗

bioRxiv2017

Age-dependence and aging-dependence: The case of neuronal loss and lifespan in a C. elegans model of Parkinson’s disease

It is often assumed, but not established, that the major neurodegenerative diseases, such as Parkinsons disease, are not just age-dependent (their incidence changes with time) but actually aging-dependent (their incidence is coupled to the process that determines lifespan). To determine a dependence on the aging process requires the joint probability distribution of disease onset and lifespan. For human Parkinsons disease, such a joint distribution is not available because the disease cuts lifespan short. To acquire a joint distribution, we resorted to an established C. elegans model of Parkinsons disease in which the loss of dopaminergic neurons is not fatal. We find that lifespan is not correlated with the loss of neurons and that a lifespan-extending intervention into insulin/IGF1 signaling accelerates neuronal loss, while leaving death and neuronal loss times uncorrelated. This suggests that distinct and compartmentalized instances of the same genetically encoded insulin/IGF1 signaling machinery act independently to control neurodegeneration and lifespan in C. elegans. Although the human context might well be different, our study calls attention to maintaining a rigorous distinction between age-dependence and aging-dependence.

developmental biology↗

bioRxiv2017

Myosin II activity is not required for Drosophila tracheal branching morphogenesis

The Drosophila tracheal system consists of an interconnected network of monolayered epithelial tubes that ensures oxygen transport in the larval and adult body. During tracheal dorsal branch (DB) development, individual DBs elongate as a cluster of cells, led by tip cells at the front and trailing cells in the rear. Branch elongation is accompanied by extensive cell intercalation and cell lengthening of the trailing stalk cells. While cell intercalation is governed by Myosin II (MyoII)-dependent forces during tissue elongation in the Drosophila embryo leading to germ-band extension, it remained unclear whether MyoII plays a similar active role during tracheal branch elongation and intercalation. Here, we use a nanobody-based approach to selectively knock-down MyoII in tracheal cells. Our data shows that despite the depletion of MyoII function, tip cells migration and stalk cell intercalation (SCI) proceeds at a normal rate. Therefore, our data confirms a model in which DB elongation and SCI in the trachea occurs as a consequence of tip cell migration, which produces the necessary forces for the branching process.\n\nSummary statementBranch elongation during Drosophila tracheal development mechanistically resembles MyoII-independent collective cell migration; tensile forces resulting from tip cell migration are reduced by cell elongation and passive stalk cell intercalation.\n\nAbbreviations

developmental biology↗

bioRxiv2017

Spacer sequences separating transcription factor binding motifs set enhancer quality and strength

Only a minority of the many genomic clusters of transcription factor binding motifs (TFBM) act as transcriptional enhancers. To identify determinants of enhancer activity, we randomized the spacer sequences separating the ETS and GATA sites of the early neural enhancer of the tunicate Ciona intestinalis Otx gene. We show that spacer sequence randomization affects the level of activity of the enhancer, in part through distal effects on the affinity of the transcription factors for their binding sites. A possible mechanism is suggested by the observation that the shape of the DNA helix within the TFBM can be affected by mutation of flanking bases that modulate transcription factor affinity. Strikingly, dormant genomic clusters of ETS and GATA sites are awakened by most instances of spacer randomization, suggesting that the sequence of naturally-occurring spacers ensures the dormancy of a majority of the large reservoir of TFBM clusters present in a metazoan genome.

developmental biology↗

bioRxiv2017

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

Drosophila segmentation is a well-established paradigm for developmental pattern formation. However, the later stages of segment patterning, regulated by the \"pair-rule\" genes, are still not well understood at the systems level. Building on established genetic interactions, I construct a logical model of the Drosophila pair-rule system that takes into account the demonstrated stage-specific architecture of the pair-rule gene network. Simulation of this model can accurately recapitulate the observed spatiotemporal expression of the pair-rule genes, but only when the system is provided with dynamic \"gap\" inputs. This result suggests that dynamic shifts of pair-rule stripes are essential for segment patterning in the trunk, and provides a functional role for observed posterior-to-anterior gap domain shifts that occur during cellularisation. The model also suggests revised patterning mechanisms for the parasegment boundaries, and accounts for the even-skipped null mutant phenotype. Strikingly, a slightly modified version of the model is able to pattern segments in either simultaneous or sequential modes, depending only on initial conditions. This suggest that fundamentally similar mechanisms may underlie segmentation in short-germ and long-germ arthropods.

developmental biology↗

bioRxiv2017

The scaffolding protein Cnk Interacts with Alk to Promote Visceral Founder Cell Specification in Drosophila

In Drosophila, the receptor tyrosine kinase Alk and its ligand Jeb are required to drive founder cell (FC) specification in the visceral mesoderm (VM). Alk-signalling activates downstream MAPK/ERK- and PI3K-pathways in human and Drosophila but little is known about immediate downstream signalling events. Here we report that the scaffolding protein Cnk interacts directly with Alk via a novel c-terminal binding motif. Cnk is required for Alk-signalling as ectopic expression of the minimal interaction motif as well as loss of maternal and zygotic cnk blocks visceral FC-formation, resembling the phenotype of jeb and Alk mutants. We also show that the Cnk-interactor Aveugle/Hyphen (Ave/HYP) is critical, while the (pseudo-) kinase Ksr is not required for Alk-signalling in the developing VM. Taken together, Cnk and Ave represent the first molecules downstream of Alk whose loss genocopies the lack of visceral FC-specification of Alk and jeb mutants indicating an essential role in Alk-signalling.

developmental biology↗

bioRxiv2017

Non-viral induction of transient cell reprogramming in skeletal muscle to enhance tissue regeneration

Somatic cells can be reprogrammed to pluripotency in vivo by overexpression of defined transcription factors. While their sustained expression triggers tumorigenesis, transient reprogramming induces pluripotency-like features and proliferation only temporarily, without teratoma formation. We sought to achieve transient reprogramming within mouse skeletal muscle with a localized injection of plasmid DNA (pDNA) and hypothesized that this would enhance regeneration after severe injury. Intramuscular administration of reprogramming pDNA rapidly upregulated pluripotency (Nanog, Ecat1, Rex1) and early myogenesis genes (Pax3) in the healthy gastrocnemius of various mouse strains. Mononucleated cells expressing such markers appeared promptly in clusters among myofibers, but proliferated only transiently and did not lead to the generation of teratomas. Nanog was also upregulated in the gastrocnemius when reprogramming factors were administered 7 days after laceration of its medial head. Enhanced tissue regeneration after reprogramming was manifested by the accelerated appearance of centro-nucleated myofibers and reduced fibrosis. These results suggest that in vivo transient reprogramming may constitute a novel strategy towards the acceleration of regeneration following muscle injury, based on the induction of transiently-proliferative, pluripotent-like cells in situ. Further research to achieve clinically meaningful functional regeneration is warranted.

developmental biology↗

bioRxiv2017

Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer

Transcriptional enhancers are regions of DNA that drive gene expression at precise times, levels, and locations. While many studies have elucidated how individual enhancers can evolve, most of this work has focused on what are called \"minimal\" enhancers, the smallest DNA regions that drive expression that approximates an aspect of native gene expression. Here we explore how the Drosophila erecta even-skipped (eve) locus has evolved by testing its activity in the divergent D. melanogaster genome. We found, as has been reported previously, that the minimal D. erecta eve stripe 2 enhancer (eveS2) fails to drive appreciable expression in D. melanogaster [1]. However, we found that a large transgene carrying the entire D. erecta eve locus drives normal eve expression, including in stripe 2. We performed a functional dissection of the region upstream of the D. erecta eveS2 region and found that regulatory information outside of the minimal D. erecta eveS2 contains multiple Zelda motifs that are required for normal expression. Our results illustrate how sequences outside of minimal enhancer regions can evolve functionally through mechanisms other than changes in transcription factor binding sites that drive patterning.

developmental biology↗

bioRxiv2017

Warburg-like metabolism coordinates FGF and Wnt signaling in the vertebrate embryo

Mammalian embryos transiently exhibit aerobic glycolysis (Warburg effect), a metabolic adaptation also observed in cancer cells. The role of this particular type of metabolism during vertebrate organogenesis is currently unknown. Here, we provide evidence for spatio-temporal regulation of aerobic glycolysis in the posterior region of mouse and chicken embryos. We show that a posterior glycolytic gradient is established in response to graded transcription of glycolytic enzymes downstream of FGF signaling. We demonstrate that glycolysis controls posterior elongation of the embryonic axis by regulating cell motility in the presomitic mesoderm and by controlling specification of the paraxial mesoderm fate in the tail bud. Our results suggest that Warburg metabolism in the tail bud coordinates Wnt and FGF signaling to promote elongation of the embryonic axis.

developmental biology↗

bioRxiv2017

Cortical elasticity determines the geometry of prospective mesoderm constriction in Drosophila melanogaster

1An animal embryo begins its life as a ball of epithelial cells. In the course of development, invariably, this cellular ball will undergo a process of gastrulation to form a multilayered structure with the different germ layers designated to form organs with different shapes and functions. In the fruit fly Drosophia melanogaster, gastrulation begins with the constriction of mesodermal cells that make up a rectangular domain in the ventral part of the embryo. A remarkable aspect of this morphogenetic event is its anisotropy - the mesoderm constricts much more along one axis than along the other. In this paper we propose an explanation of this observed anisotropy. Specifically, we show that tissue contraction must be anisotropic, provided that the tissue is elastic and that the contractile domain is elongated (e.g. rectangular as opposed to square). This conclusion is generic in the sense that it does not depend on the specific values of model parameters. Since our recent study demonstrated that embryonic tissue is elastic on a developmentally relevant time-scale, it appears likely that the anisotropy of mesoderm contraction is an elastic effect. Our model makes a number of specific predictions that appear in close agreement with the available data.

developmental biology↗

bioRxiv2017

Early frameshift alleles of zebrafish tbx5a that fail to develop the heartstrings phenotype

Tbx5 is a key transcription factor for vertebrate heart and forelimb development that causes Holt-Oram syndrome when mutated in humans. The classic zebrafish mutant for tbx5a named heartstrings (hst) features recessive absence of pectoral fins and a spectrum of heart defects, most-prominently featuring the name-giving stretched heart tube. The mutation of the hst allele is a stop codon that is predicted to result in a truncated Tbx5a protein that might feature residual activity. Here, using CRISPR-Cas9 mutagenesis, we generated zebrafish strains for two new tbx5a frameshift alleles in the first coding exon: tbx5a c.21_25del and tbx5a c.22_31del, abbreviated as tbx5a{Delta}5 and tbx5a{Delta}10. Homozygous and trans-heterozygous combinations of these new tbx5a alleles cause fully penetrant loss of pectoral fins and heart defects including changes in cardiac marker expression akin to hst mutants. Nonetheless, distinct from hst mutants, homozygous and trans-heterozygous combinations of these tbx5a frameshift mutants do not readily manifest the stretched hst heart phenotype. Our observation points out the importance and value of comparing phenotypes from different classes of mutant alleles per gene.

developmental biology↗

bioRxiv2017

The differential spatiotemporal expression pattern of shelterin genes throughout lifespan

Shelterin forms the core complex of telomere proteins and plays critical roles in protecting telomeres against unwanted activation of the DNA damage response and in maintaining telomere length homeostasis. Although shelterin expression is believed to be ubiquitous for stabilization of chromosomal ends, some evidence suggests that some shelterin subunits have tissue-specific functions. However, very little is known regarding how shelterin subunit gene expression is regulated during development and aging. Using two different animal models, the mouse and zebrafish, we reveal herein that shelterin subunits exhibit distinct spatial and temporal expression patterns that do not correlate with the proliferative status of the organ systems examined. Together, this work shows that the shelterin subunits exhibit distinct spatiotemporal expression patterns, suggesting important tissue-specific functions during development throughout the lifespan.

developmental biology↗

bioRxiv2017

Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics

During tissue development, multipotent progenitors differentiate into specific cell types in characteristic spatial and temporal patterns. We address the mechanism linking progenitor identity and differentiation rate in the neural tube, where motor neuron (MN) progenitors differentiate more rapidly than other progenitors. Using single cell transcriptomics, we define the transcriptional changes associated with the transition of neural progenitors into MNs. Reconstruction of gene expression dynamics from these data indicate a pivotal role for the MN determinant Olig2 just prior to MN differentiation. Olig2 represses expression of the Notch signaling pathway effectors Hes1 and Hes5. Olig2 repression of Hes5 appears to be direct, via a conserved regulatory element within the Hes5 locus that restricts expression from MN progenitors. These findings reveal a tight coupling between the regulatory networks that control patterning and neuronal differentiation, and demonstrate how Olig2 acts as the developmental pacemaker coordinating the spatial and temporal pattern of MN generation.

developmental biology↗

bioRxiv2017

Macrophages are required to coordinate mouse digit tip regeneration

In mammals, macrophages are known to play a major role in tissue regeneration. These cells contribute to inflammation, histolysis, re-epithelialization, re-vascularization and cell proliferation. While macrophages have been shown to be essential for epimorphic regeneration in salamanders and fish, their role has not been elucidated in mammalian epimorphic regeneration. Here, using the mouse digit tip model as a mammalian model of epimorphic regeneration, we demonstrate that macrophages are essential for the regeneration process. Using cell depletion strategies, we show that regeneration is completely inhibited; bone histolysis does not occur, wound re-epithelization is inhibited and the blastema does not form. Rescue of epidermal wound closure, in the absence of macrophages, promotes blastema accumulation but not differentiation indicating that macrophage play a role in re-differentiation. Additionally, inhibition of osteoclasts and the degradation process is not sufficient to inhibit regeneration. These findings show that macrophages play an essential role in coordinating the epimorphic regenerative response in mammals.

developmental biology↗