Three-dimensional Morphogenesis Research Articles

Three-Dimensional Morphogenesis in Canine Gut-on-a-Chip Using Intestinal Organoids Derived from Inflammatory Bowel Disease Patients.

Canine intestines possess similarities in anatomy, microbiology, and physiology to those of humans, and dogs naturally develop spontaneous intestinal disorders similar to humans. Overcoming the inherent limitation of three-dimensional (3D) organoids in accessing the apical surface of the intestinal epithelium has led to the generation of two-dimensional (2D) monolayer cultures, which expose the accessible luminal surface using cells derived from the organoids. The integration of these organoids and organoid-derived monolayer cultures into a microfluidic Gut-on-a-Chip system has further evolved the technology, allowing for the development of more physiologically relevant dynamic in vitro intestinal models. In this study, we present a protocol for generating 3D morphogenesis of canine intestinal epithelium using primary intestinal tissue samples obtained from dogs affected by inflammatory bowel disease (IBD). We also outline a protocol for generating and maintaining 2D monolayer cultures and intestine-on-a-chip systems using cells derived from the 3D intestinal organoids. The protocols presented in this study serve as a foundational framework for establishing a microfluidic Gut-on-a-Chip system specifically designed for canines. By laying the groundwork for this innovative approach, we aim to expand the application of these techniques in biomedical and translational research, aligning with the principles of the One Health Initiative. By utilizing this approach, we can develop more physiologically relevant dynamic in vitro models for studying intestinal physiology in both dogs and humans. This has significant implications for biomedical and pharmaceutical applications, as it can aid in the development of more effective treatments for intestinal diseases in both species.

Three-dimensional morphogenesis of epithelial tubes

Three-dimensional morphogenesis of epithelial tubes

Three-dimensional morphological analysis of the human spleen and its surrounding organs during the early fetal period.

The spleen has variations in its morphology and is considered to acquire a defined shape in the third month of gestation. However, few studies have investigated spleen development during the first 3 months of fetal life. This study aimed to determine the three-dimensional (3D) morphogenesis of the spleen during the third month of gestation. In this study, 30 fetal specimens (crown-rump length [CRL]: 22-103 mm) were subjected to magnetic resonance imaging analysis. We manually segmented the spleen, stomach, and adrenal gland, reconstructed 3D models, and analyzed the volume and shape of these organs. The results showed that the variation in spleen size was large compared to that in other organs. Spleen morphology was classified into six types based on the number of splenic surfaces as follows: two-faced, three-faced, four-faced, five-faced, ovoid, and irregular. Two-faced spleens were only observed in small specimens, whereas three- and four-faced spleens were observed in larger specimens. We also revealed that the number of fetal splenic surfaces increased as CRL enlarged. Additionally, 3D models indicated that some specimens formed their splenic surfaces without contact with the adjacent organs. This suggested that the splenic surface may be caused not only by pressure from the faced organs but also by an intrinsic program. This study may provide a better understanding of the normal development of the spleen during the early fetal period, and may potentially assist future studies in investigating congenital morphological anomalies of the spleen.

Issue Cover (February 2023)

Front cover: Cover image: see T. Kanahashi et al., ‘Three-dimensional morphogenesis of the human diaphragm during the late embryonic and early fetal period: Analysis using T1-weighted and diffusion tensor imaging’, this issue.

Tentorium cerebelli formation during human embryonic and early fetal development.

The morphologies of the fetal tentorium cerebelli (TC) and brain influence each other during development. This study aimed to analyze and more comprehensively understand the three-dimensional morphogenesis of the TC and fetal brain. We examined magnetic resonance imaging from 64 embryonic and fetal specimens (crown-rump length range, 9.2-225 mm). During the embryonic period, the lateral folds of the TC elongated to traverse the middle part of the midbrain. The TC and falx cerebri appeared separated, and no invaginations at the parieto-occipital region were observed. In the early fetal period, the cerebrum covered approximately half of the midbrain. The separation of the dural limiting layer at the parieto-occipital region widened from the posterior cerebrum to the cranial cerebellum. The lateral folds of the TC were spread between its tip, continuous with the falx cerebri, and its base plane, located between the midbrain and rostral hindbrain. Differences in the TC components' growth directions gradually diminished as the cerebrum covered the midbrain. We observed rotation of the TC at its median section according to its growth, which ceased in the middle fetal period. The brainstem and cerebellum extended inferiorly via differential growth, with the cerebrum covering them superiorly. The morphology of the TC curved to conform to the cerebellar and cerebral surfaces. Our present study suggests that factors affecting TC morphology differ between the early and middle fetal periods. Present data provided a more comprehensive view of TC formation according to developmental stage.

Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming

Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.

Three-dimensional morphogenesis of the human diaphragm during the late embryonic and early fetal period: Analysis using T1-weighted and diffusion tensor imaging.

A precise understanding of human diaphragm development is essential in fetal medicine. To our knowledge, no previous study has attempted a three-dimensional (3-D) analysis and evaluation of diaphragmatic morphogenesis and development from the embryonic to the early fetal period. This study aimed to evaluate the morphogenesis and fibrous architecture of the developing human diaphragm during the late embryonic and early fetal periods. Fifty-seven human embryos and fetuses (crown-rump length [CRL]=8-88 mm) preserved at the Congenital Anomaly Research Center of Kyoto University and Shimane University were analyzed. 3-D morphogenesis and fiber orientation of the diaphragm were assessed using phase-contrast X-ray computed tomography, T1-weighted magnetic resonance imaging (T1W MRI), and diffusion tensor imaging (DTI). T1W MR images and DTI scans were obtained using a 7-T MR system. The diaphragm was completely closed at Carnegie stage (CS) 20 and gradually developed a dome-like shape. The diaphragm was already in contact with the heart and liver ventrally in the earliest CS16 specimen observed, and the adrenal glands dorsally at CS19 or later. In the fetal period, the diaphragm contacted the gastric fundus in samples with a CRL ≥41 mm, and the spleen in samples with a CRL ≥70 mm. The relative position of the diaphragm with reference to the vertebrae changed rapidly from CS16 to CS19. The most cranial point of the diaphragm was located between the 4th and 8th thoracic vertebrae, regardless of fetal growth, in samples with a CRL of ≥16 mm. Diaphragmatic thickness was nearly uniform (0.15-0.2 mm) across samples with a CRL of 8-41 mm. The sternal, costal, lumbar parts, and the area surrounding the esophageal hiatus thickened with growth in samples with a CRL of ≥46 mm. The thickness at the center of the diaphragm and the left and right hemidiaphragmatic domes did not increase with growth. Tractography showed that the fiber orientation of the sternal, costal, and lumbar parts became more distinct as growth progressed in CS19 or later. All fibers in the costal and lumbar regions ran toward the left and right hemidiaphragmatic domes, except for those running to the caval opening and esophageal hiatus. The fiber orientation patterns from the right and left crura surrounding the esophageal hiatus were classified into three types. Distinct fiber directions between the costal and sternal and between the costal and lumbar diaphragmatic parts were observable in samples with a CRL of ≥46 mm. Anterior costal and sternal fibers ran toward the center. Fiber tracts around the center and the left and right hemidiaphragmatic domes; between the costal and lumbar orientations; and between the costal and sternal orientations showed a tendency for decreasing fractional anisotropy values with fetal growth and showed less density than other areas. In conclusion, we used 3-D thickness assessment and DTI tractography to identify qualitative changes in the muscular and tendonous regions of the diaphragm during the embryonic and early fetal periods. This study provides information on normal human diaphragm development for the progression of fetal medicine and furthering the understanding of congenital anomalies.

Method for estimating the area expansion rate distribution of epithelial cell sheets in three-dimensional morphogenesis

Method for estimating the area expansion rate distribution of epithelial cell sheets in three-dimensional morphogenesis

Epithelial-Mesenchymal Transition Drives Three-Dimensional Morphogenesis in Mammalian Early Development.

From fertilization to onset of gastrulation, a mammalian embryo goes through several rounds of cellular morphogenesis resembling phenomena of epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET), collectively referred to as EMTs. How these EMT events play a role in shaping the three-dimensional (3-D) architecture of the developing embryo is not well-understood. In this review, we present a model in which cellular morphogenesis, represented primarily by dynamic changes in its epithelialization status, is the driving force of embryonic 3-D organization. This is achieved through the integration of three key components of mammalian early development, the pluripotency regulation, morphogenetic signaling, and biomechanical force anisotropy. Although cells in an early embryo do not exhibit full mesenchymal characteristics, our model underscores the importance of investigating molecular regulation of epithelial cell polarity and partial EMT/MET in understanding mammalian early development.

Heterogeneous induction of an invasive phenotype in prostate cancer cells by coculturing with patient-derived fibroblasts.

Prostate cancer (PCa) cells frequently invade the surrounding stroma, leading to heterogeneous formation of structural atypia. The surrounding stroma contains multiple functionally diverse populations of fibroblasts that trigger numerous changes in PCa cells including motility. Thus, we hypothesized that direct or indirect contact of PCa cells with fibroblasts determines an invasive phenotype in PCa cells. We investigated the effects of 10 different patient-derived fibroblast lines on the three-dimensional (3D) morphogenesis of PCa cells growing on a viscous substrate in vitro. When grown alone, all 10 patient-derived fibroblast lines clumped on the viscous substrate, whereas the human androgen-sensitive PCa cell line LNCaP did not. Cocultures of LNCaP cells with seven of the patient-derived fibroblast lines (PrSC, pcPrF-M5, pcPrF-M7, pcPrF-M23, pcPrF-M24, pcPrF-M28, and pcPrF-M31) formed a thick fibroblast layer that resembled human prostate stromal structures. In contrast, cocultures of LNCaP cells with the remaining three fibroblast lines (NPF-M13, pcPrF-M10, and pcPrF-M26) did not form a thick fibroblast layer. Of the seven fibroblast lines that caused thick layer formation, four patient-derived fibroblast lines (PrSC, pcPrF-M5, pcPrF-M28, and pcPrF-M31) induced an invasive phenotype in LNCaP cells with a cord-like infiltrating growth pattern, whereas the other three fibroblast lines (pcPrF-M7, pcPrF-M23, and pcPrF-M24) induced no or a very weak invasive phenotype. Using cell culture inserts, none of the four patient-derived fibroblast lines that induced an invasive phenotype (PrSC, pcPrF-M5, pcPrF-M28, and pcPrF-M31) affected CDH1 mRNA expression in LNCaP cells; yet, two patient-derived fibroblast lines (pcPrF-M5 and pcPrF-M28) increased CDH2 mRNA expression in LNCaP cells, whereas the other two fibroblast lines (PrSC and pcPrF-M31) did not. These results suggest that the existence of multiple functionally diverse populations of fibroblasts in PCa tissue may be responsible for the diversity in PCa cell invasion, leading to heterogeneous formation of structural atypia.

Abstract 3983: Direct contact of heterogeneous fibroblasts with cancer cells regulates the invasive phenotype of prostate cancer cells

Abstract In the tumor microenvironment of prostate cancer (PCa), cancer cells frequently invade the surrounding stroma in the way of single cell migration (SCM) or collective cell migration (CCM). This phenomenon can be responsible for the heterogeneous formation of structural atypia such as Gleason pattern. Generally, PCa cells undergo a phenotypic change which is called the epithelial-to-mesenchymal transition (EMT), e.g., downregulation of epithelial cell-cell adhesion molecules such as E-cadherin and gain of mesenchymal morphology and motility. The surrounding stroma is mainly composed of fibroblasts and extracellular matrix (ECM). We hypothesize that direct contact-mediated interactions at the interface between PCa cells and fibroblasts/ECM can trigger numerous changes in PCa cells including morphology and motility. In this study, we investigated the roles of fibroblasts in the three-dimensional (3D) morphogenesis of PCa cells on a viscous substrate. To examine the effects of fibroblasts on the 3D morphogenesis of PCa cells on Matrigel, we mixed human PCa cell line LNCaP cells with commercially available normal human prostate stromal cells (PrSC) or nine primary cultures of prostate fibroblasts (pcPrFs and NPFs) isolated from patients with PCa and bladder cancer. The 3D morphogenesis of LNCaP cells mixed with fibroblasts on Matrigel was confirmed by E-cadherin immunohistochemical staining. All ten fibroblasts alone were aggregated on Matrigel, whereas LNCaP cells alone were not. LNCaP cells mixed with six fibroblasts (PrSC, pcPrF-M5, pcPrF-M23, pcPrF-M24, pcPrF-M28, and pcPrF-M31) formed a deep crater-like hole on Matrigel. In the 3D structure, the upper and lower tiers were composed of LNCaP cells and fibroblasts, respectively. Of note, direct contact of four fibroblasts (NPF-M13, pcPrF-M7, pcPrF-M10, and pcPrF-M26) with LNCaP cells decreased the aggregation of fibroblasts on Matrigel. Five of six fibroblasts (PrSC, pcPrF-M5, pcPrF-M23, pcPrF-M28, and pcPrF-M31) induced SCM of LNCaP cells, while only one fibroblasts (pcPrF-M24) induced CCM. In the scratch assay, the cell motility of CCM-inducing fibroblasts was slower than that of SCM-inducing fibroblasts. Expression pattern of primary cilia in SCM-inducing fibroblasts was changed by mixing with LNCaP cells, whereas that in CCM-inducing fibroblasts was not. PCa is quite interesting because of the multi-focal and heterologous progression of primary tumors. The heterogeneous stromal compartment in PCa tissues contains multiple populations of fibroblasts that are associated with morphology and motility of PCa cells. Here our results showed that direct contact of heterogeneous fibroblasts with PCa cells on Matrigel regulated the invasive phenotype of PCa cells such as SCM and CCM. Impairing the malignant phenotype of fibroblasts in PCa tissues, e.g., differentiation therapy targeting tumor stroma, may abrogate PCa cell invasion. Citation Format: Kenichiro Ishii, Yasuhisa Nakagawa, Taku Shirai, Masako Ichishi, Masaya Fujiwara, Daisuke Kato, Chise Matsuda, Yoshifumi Hirokawa, Yoshiki Sugimura, Masaki Inagaki, Masatoshi Watanabe. Direct contact of heterogeneous fibroblasts with cancer cells regulates the invasive phenotype of prostate cancer cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3983.

The impact of using three-dimensional digital models of human embryos in the biomedical curriculum

BackgroundKnowledge of embryonic development is essential to understand the positioning of organs in the human body. Unfortunately, (bio)medical students have to struggle with textbooks that use static, two-dimensional (2D) schematics to grasp the intricate three-dimensional (3D) morphogenesis of the developing human body. To facilitate embryology education on an understandable and scientific level, a 3D Atlas of Human Embryology (3D Atlas) was created (Science, 2016), encompassing 14 interactive 3D-PDFs of various stages of human embryonic development (freely available from http://www.3datlasofhumanembryology.com). This study examined whether the use of the 3D atlas has added educational value and improves the students learning experience. MethodsThe 3D atlas was introduced and integrated in lectures and practical classes of an existing embryology course at our university for first year biomedical students. By means of a questionnaire the use of the 3D atlas was evaluated. The outcomes in written examinations was compared between cohorts that followed the course before and after integration of the 3D atlas. ResultsOur results showed that the 3D Atlas significantly improves students’ understanding of human embryology, reflected in significant higher test scores for new students. Furthermore, the 3D atlas also significantly improved repeaters’ test scores. ConclusionsThe results indicate that the3D Atlas of Human Embryology facilitates students’ learning experience as a resource to support embryology lectures. Students appreciated the use of the 3D atlas in practical classes and liked its interactive aspect. Interestingly, the students also appreciated the physical hand-painted embryological models that were used in addition to the digital 3D atlas during practical classes. The 3D Atlas of Human Embryology has proven to be a valuable resource in addition to the existing resources to teach the intricate developmental processes of human embryology, especially in a blended learning curriculum.

Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.

The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.

A Three-Dimensional Organoid Culture Model to Assess the Influence of Chemicals on Morphogenetic Fusion.

Embryologic development involves cell differentiation and organization events that are unique to each tissue and organ and are susceptible to developmental toxicants. Animal models are the gold standard for identifying putative teratogens, but the limited throughput of developmental toxicological studies in animals coupled with the limited concordance between animal and human teratogenicity motivates a different approach. In vitro organoid models can mimic the three-dimensional (3D) morphogenesis of developing tissues and can thus be useful tools for studying developmental toxicology. Common themes during development like the involvement of epithelial-mesenchymal transition and tissue fusion present an opportunity to develop in vitro organoid models that capture key morphogenesis events that occur in the embryo. We previously described organoids composed of human stem and progenitor cells that recapitulated the cellular features of palate fusion, and here we further characterized the model by examining pharmacological inhibitors targeting known palatogenesis and epithelial morphogenesis pathways as well as 12 cleft palate teratogens identified from rodent models. Organoid survival was dependent on signaling through EGF, IGF, HGF, and FGF pathways, and organoid fusion was disrupted by inhibition of BMP signaling. We observed concordance between the effects of EGF, FGF, and BMP inhibitors on organoid fusion and epithelial cell migration in vitro, suggesting that organoid fusion is dependent on epithelial morphogenesis. Three of the 12 putative cleft palate teratogens studied here (theophylline, triamcinolone, and valproic acid) significantly disrupted in vitro organoid fusion, while tributyltin chloride and all-trans retinoic acid were cytotoxic to fusing organoids. The study herein demonstrates the utility of the in vitro fusion assay for identifying chemicals that disrupt human organoid morphogenesis in a scalable format amenable to toxicology screening.

Two-stage patterning dynamics in conifer cotyledon whorl morphogenesis.

Conifer embryos, unlike those of monocots or dicots, have variable numbers of cotyledons, even within the same species. Cotyledons form in a single whorl on a dome-shaped embryo. The closely spaced cotyledons are not found outside this ring, indicating a radial control on where they can form. Polar transport of the hormone auxin affects outgrowth of distinct cotyledons, but not the radial aspect of the whorl or the within-whorl spacing between cotyledons. A quantitative model of plant growth regulator patterning is needed to understand the dynamics of this complex morphogenetic process. A two-stage reaction-diffusion model is developed for the spatial patterning of growth regulators on the embryo surface, with a radial pattern (P1) constraining the shorter-wavelength cotyledon pattern (P2) to a whorl. These patterns drive three-dimensional (3-D) morphogenesis by catalysing local surface growth. Growth driven by P2 generates single whorls across the experimentally observed range of two to 11 cotyledons, as well as the circularly symmetric response to auxin transport interference. These computations are the first corroboration of earlier theoretical proposals for hierarchical control of whorl formation. The model generates the linear relationship between cotyledon number and embryo diameter observed experimentally. This accounts for normal integer cotyledon number selection, as well as the less common cotyledon fusings and splittings observed experimentally. Flattening of the embryo during development may affect the upward outgrowth angle of the cotyledons. Cotyledon morphogenesis is more complex geometrically in conifers than in angiosperms, involving 2-D patterning which deforms a surface in three dimensions. This work develops a quantitative framework for understanding the growth and patterning dynamics involved in conifer cotyledon development, and applies more generally to the morphogenesis of whorls with many primordia.

ANGUSTIFOLIA contributes to the regulation of three-dimensional morphogenesis in the liverwort Marchantia polymorpha.

Arabidopsis thaliana mutants deficient in ANGUSTIFOLIA (AN) exhibit several phenotypes at the sporophyte stage, such as narrow and thicker leaves, trichomes with two branches, and twisted fruits. It is thought that these phenotypes are caused by abnormal arrangement of cortical microtubules (MTs). AN homologs are present in the genomes of diverse land plants, including the basal land plant Marchantia polymorpha, and their molecular functions have been shown to be evolutionarily conserved in terms of the ability to complement the A. thaliana an-1 mutation. However, the roles of ANs in bryophytes, the life cycle of which includes a dominant haploid gametophyte generation, remain unknown. Here, we have examined the roles of AN homologs in the model bryophyte M. polymorpha (MpAN). Mpan knockout mutants showed abnormal twisted thalli and suppressed thallus growth along the growth axis. Under weak blue light conditions, elongated thallus growth was observed in wild-type plants, whereas it was suppressed in the mutants. Moreover, disordered cortical MT orientations were observed. Our findings suggest that MpAN contributes to three-dimensional morphogenesis by regulating cortical MT arrangement in the gametophytes of bryophytes.

Reconstructing 3D deformation dynamics for curved epithelial sheet morphogenesis from positional data of sparsely-labeled cells

Quantifying global tissue deformation patterns is essential for understanding how organ-specific morphology is generated during development and regeneration. However, due to imaging difficulties and complex morphology, little is known about deformation dynamics for most vertebrate organs such as the brain and heart. To better understand these dynamics, we propose a method to precisely reconstruct global deformation patterns for three-dimensional morphogenesis of curved epithelial sheets using positional data from labeled cells representing only 1–10% of the entire tissue with limited resolution. By combining differential-geometrical and Bayesian frameworks, the method is applicable to any morphology described with arbitrary coordinates, and ensures the feasibility of analyzing many vertebrate organs. Application to data from chick forebrain morphogenesis demonstrates that our method provides not only a quantitative description of tissue deformation dynamics but also predictions of the mechanisms that determine organ-specific morphology, which could form the basis for the multi-scale understanding of organ morphogenesis.

Directing three-dimensional multicellular morphogenesis by self-organization of vascular mesenchymal cells in hyaluronic acid hydrogels

BackgroundPhysical scaffolds are useful for supporting cells to form three-dimensional (3D) tissue. However, it is non-trivial to develop a scheme that can robustly guide cells to self-organize into a tissue with the desired 3D spatial structures. To achieve this goal, the rational regulation of cellular self-organization in 3D extracellular matrix (ECM) such as hydrogel is needed.ResultsIn this study, we integrated the Turing reaction–diffusion mechanism with the self-organization process of cells and produced multicellular 3D structures with the desired configurations in a rational manner. By optimizing the components of the hydrogel and applying exogenous morphogens, a variety of multicellular 3D architectures composed of multipotent vascular mesenchymal cells (VMCs) were formed inside hyaluronic acid (HA) hydrogels. These 3D architectures could mimic the features of trabecular bones and multicellular nodules. Based on the Turing reaction–diffusion instability of morphogens and cells, a theoretical model was proposed to predict the variations observed in 3D multicellular structures in response to exogenous factors. It enabled the feasibility to obtain diverse types of 3D multicellular structures by addition of Noggin and/or BMP2.ConclusionsThe morphological consistency between the simulation prediction and experimental results probably revealed a Turing-type mechanism underlying the 3D self-organization of VMCs in HA hydrogels. Our study has provided new ways to create a variety of self-organized 3D multicellular architectures for regenerating biomaterial and tissues in a Turing mechanism-based approach.

A living mesoscopic cellular automaton made of skin scales.

In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here we show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. We analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern. Using numerical simulations and mathematical derivation, we identify how a discrete von Neumann cellular automaton emerges from a continuous Turing reaction-diffusion system. Skin thickness variation generated by three-dimensional morphogenesis of skin scales causes the underlying reaction-diffusion dynamics to separate into microscopic and mesoscopic spatial scales, the latter generating a cellular automaton. Our study indicates that cellular automata are not merely abstract computational systems, but can directly correspond to processes generated by biological evolution.

Morphogenesis of the middle ear ossicles and spatial relationships with the external and inner ears during the embryonic period.

We describe the three-dimensional morphogenesis of the middle ear ossicles (MEOs) according to Carnegie stage (CS) in human embryos. Seventeen samples including 33 MEOs from CS18 to 23 were selected from the Kyoto Collection. The primordia of the MEOs and related structures were histologically observed and three-dimensionally reconstructed from digital images. The timing of chondrogenesis was variable among structures. The stapes was recognizable as a vague condensation of the mesenchymal cells in all samples from CS18, whereas the malleus and incus were recognizable at CS19. Chondrogenesis of all MEOs was evident in all samples after CS21. The chondrocranium was recognizable in all samples by CS18, and the perichondrium border of the auricular cartilage and otic capsule was distinct in all samples at CS23. At CS19, the MEOs were positioned in the anterior to posterior direction, following the order malleus, incus, stapes, which adjusted gradually during development. The MEOs connected in all samples after CS22. The stapes was located close to the vestibular part of the inner ear, although the basal part was not differentiated into the "footplate" form, even at CS23. The handles of the malleus were close to the tubotympanic recess at CS23, but were distant from the external auditory meatus. Determining the timeline of the formation of MEOs and connection of the external and inner ears can be informative for understanding hearing loss caused by failure of this connection. These data may provide a useful standard for morphogenesis, and will contribute to distinguishing between normal and abnormal MEO development. Anat Rec, 299:1325-1337, 2016. © 2016 Wiley Periodicals, Inc.