We develop a novel method for image segmentation of 3D confocal microscopy images of emerging hematopoietic stem cells. The method is based on the theory of persistent homology and uses an optimal threshold to select the most persistent cycles in the persistence diagram. This enables the segmentation of the image’s most contrasted and representative shapes. Coupling this segmentation method with a meshing algorithm, we define a pipeline for 3D reconstruction of confocal volumes. Compared to related methods, this approach improves shape segmentation, is more ergonomic to automatize, and has fewer parameters. We apply it to the segmentation of membranes, at subcellular resolution, of cells involved in the endothelial-to-hematopoietic transition (EHT) in the zebrafish embryos.

To realize the potential of materials comprising living organisms, bioengineers require a holistic understanding of the reciprocal relationship between environmental conditions and the biochemical and biophysical processes that influence development and behaviour. Mathematical modelling has a critical part to play in managing the complexity of biological dynamical systems and attaining higher degrees of control over their trajectories and endpoints. To support the development of mycelium-based engineered living materials, this paper reviews the literature of growth models for filamentous fungi with emphasis on the connection between morphogenesis and metabolism.

All plant cells are encased by walls, which provide structural support and control their morphology. How plant cells regulate the deposition of the wall to generate complex shapes is a topic of ongoing research. Scientists have identified several model systems, the epidermal pavement cells of cotyledons and leaves being an ideal platform to study the formation of complex cell shapes. These cells indeed grow alternating protrusions and indentations resulting in jigsaw puzzle cell shapes. How and why these cells adopt such shapes has shown to be a challenging problem to solve, notably because it involves the integration of molecular and mechanical regulation together with cytoskeletal dynamics and cell wall modifications. In this review, we highlight some recent progress focusing on how these processes may be integrated at the cellular level along with recent quantitative morphometric approaches.

Most stromatolites are built by photosynthetic organisms, for which sunlight is a driving factor. We examine stromatolite morphogenesis with modelling that incorporates the growth rate of cyanobacteria (the dominant stromatolite-builder today, and presumably through much of the past), as a function of the amount of irradiance received. This function is known to be non-monotonic, with a maximum beyond which growth rate decreases. We define optimal irradiance as that which generates maximal growth, and we find fundamentally different morphologies are predicted under suboptimal and superoptimal direct irradiance. When the direct irradiance is suboptimal, narrow widely spaced columns are predicted, with sharp apices resembling conical stromatolites. When it is superoptimal, broad, closely spaced, flattened domical forms appear. Such disparate morphologies could also occur as a result of other vector-flux-dependent growth factors (e.g. currents). A differential equation is developed that describes the rate of change of the radius of curvature R at the apex of a growing stromatolite column, allowing simple simulations of the time evolution of R for model stromatolites. The term photomorphism is proposed to describe the disparate morphologies that may arise due to the effects described here (and photomorphogenesis as the process). Model results appear to explain, at least qualitatively, the morphologies of a number of stromatolites. If stromatolites are encountered on Mars, our model suggests that they are quite likely to be conical in form, owing to likely suboptimal irradiance since Mars has always received less irradiance than Earth.

During the Pleistocene in the northern part of Europe and Asia, the presence of ice sheets not only limited the range of species but also influenced landscape and thus the contemporary habitat system that determines the pattern of biodiversity. The aim of the research was to find out whether and how a lowland landscape, which formed as a result of subsequent Pleistocene glaciations (five) that in Eurasia covered various and generally successively smaller areas, affected the genetic differentiation of a species. The research was carried out in eastern Poland on the root vole Microtus oeconomus (Arvicolinae, Rodentia), a model boreal and hygrophilous species. Samples were collected from 549 vole individuals at 33 locations. Based on the analysis of 12 microsatellite loci and the 908 bp of cytochrome b sequences (mitochondrial DNA), the genetic structure of M. oeconomus in the landscape zones of the Polish Lowlands was determined. The results show that the latitudinal variability of the relief in eastern Poland (resulting from different ranges of Pleistocene ice sheets) and the related specific configuration of hydrogenic habitats are reflected in the genetic differentiation of the root vole. Therefore, it may be concluded that the history of landscape development affects the genetic structure of hydrophilic species.

Mollusc seashells grow through the local deposition and calcification of material at the shell opening by a soft and thin organ called the mantle. Through this process, a huge variety of shell structures are formed. Previous models have shown that these structural patterns can largely be understood by examining the mechanical interaction between the deformable mantle and the rigid shell aperture to which it adheres. In this paper we extend this modelling framework in two distinct directions. For one, we incorporate a mechanical feedback in the growth of the mollusc. Second, we develop an initial framework to couple the two primary and orthogonal modes of pattern formation in shells, which are termed antimarginal and commarginal ornamentation. In both cases we examine the change in shell morphology that occurs due to the different mechanical influences and evaluate the hypotheses in light of the fossil record.

City road networks have been extensively studied for their social significance or to quantify their connections and centralities, but often their geographical origin is forgotten. This work focuses on the spatial-geographical and geometrical aspects of the road network skeleton. Following previous work, a multi-scale object, the way, is constructed, based only on the local geometry at road crossings. The best method to reconstruct significant elements is investigated. The results show that this object is geographically meaningful, with many particular characteristics. A new indicator, structurality, is introduced and compared with previous indicators, on the cities of Paris and Avignon. Structurality appears to be stable over the borders of the map sample, and is able to reveal the underlying coherence of the road network. This stability can be interpreted as coming from the particular way the network developed in time, and was later preserved. This link with the historical development of the cites, which deserves to be further studied, is exemplified in the cases of Villers-sur-Mer (France) and Manaus (Brazil). The construction method, the results, and their potential meaning are discussed in detail so that they can be used in various related disciplines, such as sociology, town planning, geomatics, and physics.

The presence of permafrost in Poland north of the line indicating the maximum ice extent of the Vistulian (Weichselian) glaciation after retreat of the land-ice cap has been a subject of debate for a long time. Investigations in an area at the line of the maximum ice extent of the Pomeranian phase prove that permafrost existed, indeed, after the ice retreat. This conclusion is drawn on the basis of morphological data (the presence of oriented kettle holes), sedimentological data (the nature of the infilling of the kettle holes) and pedological data (permafrost-affected horizons in soil profiles). It appears that the permafrost mostly developed in the ice-free zone that appeared after the retreat of the land-ice cap, but it is likely that some relict permafrost that had originated earlier in front of advancing ice was also still present. The landscape of northern Poland owes its relief partly to the Late Glacial permafrost.

The morphogenesis and morphology of the marine benthic ciliate Certesia quadrinucleata collected from seawater in Nagasaki Mie Port, Japan, were investigated using microscopic observation of live and protargol-stained specimens. In terms of its morphology, the current isolate possesses diagnostic features of the genus and the species: a row of left marginal cirri, a prominent paroral membrane, 11 frontoventral cirri scattered in frontoventral area, five highly developed transverse cirri, four macronuclear nodules, five dorsal kineties and a caudally located contractile vacuole. Its morphogenesis belongs to the ‘Certesia’ subtype, and main events can be summarized as follow: (1) the oral primordium in the opisthe develops de novo in a subcortical pouch; (2) the old paroral membrane is completely replaced by the new one in the proter, but the parental adoral zone of membranelles is wholly inherited; (3) five streaks of cirral anlagen are formed in a primary mode for the proter and the opisthe, which gives rise to cirri in the pattern of 3:3:3:3:3 from left to right; (4) the leftmost frontoventral cirrus develops de novo on the cell surface in both dividers, and has no connection with the undulating membrane anlage; and (5) the anlagen for marginal cirri and dorsal kineties occur intrakinetally. Current observations confirm the separation of Certesiidae from other euplotids at the familial level.

Osteohistological characteristics of the large temnospondyl amphibian Metoposaurus diagnosticus from the Upper Triassic of Poland (Krasiejów locality) were determined using vertebral intercentra thin-sections from different regions and growth stages. The intercentra showed a trabecular structure in both the endochondral and periosteal domains. Endochondral ossification developed first, and the primary bone occurs near the periphery with a higher degree of remodelling in the centre. Periosteal bone deposition begins later; first on the ventral side, continuing laterally and finally onto the dorsal side. Periosteal growth rate was initially very rapid, and then subsequently decreased in rate. In all sections, numerous remains of calcified cartilage are visible, which may indicate a juvenile, paedomorphic or plesiomorphic character. The four histologic ontogenetic stages (HOS) of sampled vertebrae were determined based on growth marks. Most of the sampled bones belong to juvenile individuals (HOS 1 to 3), apart from one atlas and the largest anterior dorsal intercentrum, which represent the oldest described stage (HOS 4). Sharpey's fibres are preserved in ventro-lateral cortical regions, around parapophyses and on the posterior side of the neural arch.

Plants and animals have highly ordered structure both in time and in space, and one of the main questions of modern developmental biology is the transformation of genetic information into the regular structure of organism. Any multicellular plant begins its development from the universal unicellular state and acquire own species-specific structure in the course of cell divisions, cell growth and death, according to own developmental program. However the cellular mechanisms of plant development are still unknown. The aim of this work was to elaborate and verify the formalistic approach, which would allow to describe and analyze the large data of cellular architecture obtained from the real plants and to reveal the cellular mechanisms of their morphogenesis. Two multicellular embryos of Calla palustris L. (Araceae) was used as a model for the verification of our approach. The cellular architecture of the embryos was reconstructed from the stack of optical and serial sections in three dimensions and described as graphs of genealogy and space adjacency of cells. In result of the comparative analysis of these graphs, a set of regular cell types and highly conservative pattern of cell divisions during five cell generations were found. This mechanism of cellular development of the embryos could be considered as a developmental program, set of rules or grammars applied to the zygote. Also during the comparative analysis the finite plasticity in cell adjacency was described. The structural equivalence and the same morphogenetic potencies of some cells of the embryos were considered as the space-temporal symmetries. The symmetries were represented as a set of regular cell type permutations in the program of development of the embryo cellular architecture. Two groups of cell type permutations were revealed, each was composed of two elements and could be interpreted as the mirror and rotational space symmetries. The results obtained as well as the developed approach can be used in plant tissue modelling based on the real, large and complex structural data.

The anatomy of the human and other vertebrates has been well described since the days of Leonardo da Vinci and Vesalius. The causative origin of the configuration of the bones and of their shapes and forms has been addressed over the ensuing centuries by such outstanding investigators as Goethe, Von Baer, Gegenbauer, Wilhelm His and D'Arcy Thompson, who sought to apply mechanical principles to morphogenesis. However, no coherent causative model of morphogenesis has ever been presented.

This paper presents a causative model for the origin of the vertebrate skeleton, based on the premise that the body is a mosaic enlargement of self-organized patterns engrained in the membrane of the egg cell. Drawings illustrate the proposed hypothetical origin of membrane patterning and the changes in the hydrostatic equilibrium of the cytoplasm that cause topographical deformations resulting in the vertebrate body form.

The development of the tapeworm Proteocephalus torulosus (Batsch, 1786) (Cestoda: Proteocephalidae), a parasite of cyprinid fish, was studied in the intermediate host under experimental conditions. The eggs of P. torulosus were typified by a relatively small outer envelope (hyaline membrane) and a thick middle layer surrounding the oncosphere. Incubation of P. torulosus eggs at different temperatures revealed the ability of some oncospheres to survive and remain infective to the intermediate host for up to 5 weeks at 5–7°C, 12 days at 10–12°C, and 8 days at 20–22°C. Of 8 copepod species used in these experiments, complete development of larvae was observed only in Cyclops strenuus. Growth was completed in 9–12 days at 20–22°C and four weeks at 9–10°C. During development the cercomer was not observed. The infectivity of larvae from C. strenuus for the definitive hosts, cyprinid fish, was very low and only one chub of 26 fish used for feeding experiments (21 chub, Leuciscus cephalus, 3 bleak, Alburnoides bipunctatus, 1 rudd, Scardinius erythrophthalmus—all the family Cyprinidae, and 1 loach, Noemacheilus barbatulus—the family Cobitidae) became infected.

Cell-based, mathematical models helpmake sense of morphogenesis—i.e. cells organizing intoshape and pattern—by capturing cell behavior in simple, purelydescriptive models. Cell-based models then predict thetissue-level patterns the cells produce collectively. The firststep in a cell-based modeling approach is to isolatesub-processes, e.g. the patterning capabilities of one or afew cell types in cell cultures. Cell-based models can thenidentify the mechanisms responsible for patterning in vitro.This review discusses two cell culture models of morphogenesisthat have been studied using this combinedexperimental-mathematical approach: chondrogenesis (cartilagepatterning) and vasculogenesis (de novo blood vessel growth). Inboth these systems, radically different models can equallyplausibly explain the in vitro patterns. Quantitativedescriptions of cell behavior would help choose betweenalternative models. We will briefly review the experimentalmethodology (microfluidics technology and traction forcemicroscopy) used to measure responses of individual cells to theirmicro-environment, including chemical gradients, physical forcesand neighboring cells. We conclude by discussing how to includequantitative cell descriptions into a cell-based model: theCellular Potts model.

Modular organization of colonial hydroids is based on cyclic morphogenesis during growth of their body. In many thecate hydroids (Hydrozoa: Leptomedusae) the shoots of the colony consist of a few distinct elements and possess complex spatial organization. In most cases, the evolutionary sequence of morphogenetic modifications that led to present-day organization of shoots is obscure and not obvious. One of the approaches that allow getting insight into the morphogenetic evolution in colonial thecate hydroids is to analyse the spectrum of different minor morphotypes presented in the population of the certain species. In our opinion, some rare morphotypes allow understanding and reconstructing the scenario of morphogenetic evolution of species under consideration. We describe the application of such an approach for reconstruction of the morphogenetic evolution of Dynamena pumila (L.) (Sertulariidae) with some additional conclusions.

The stomatogenesis and morphology of the marine planktonic ciliate Philasterides armatalis collected from mollusc-culturing waters off the coast of Qingdao, China, were studied using a differential interference contrast microscope for observations in vivo and protargol impregnation. In terms of its infraciliature, this species possesses typical characteristics of the genus Philasterides: bipartite paroral membrane, the anterior part double-rowed and the posterior part in a zig-zag-formation, and three well-defined membranelles arranged in Paranophrys-pattern. This investigation confirms the dual origin of the buccal apparatus in the opisthe, one derived from the scutica and the other from the paroral membrane. Its stomatogenesis belongs to the ‘Philasterides’ sub-type, although it differs from its only congener P. armata, in that paroral membrane 1 gives rise to the paroral membrane and the scutica in the proter, and paroral membrane 2 forms the paroral membrane, membranelles 1 and 2 and the scutica in the opisthe. Based on stomatogenetic data, the phylogenetic positions of several genera in the suborder Philasterina are reconsidered.

Objective: Using a newly acquired archive of previously prepared material, we sought to re-examine the origin of the pulmonary vein in the human heart, aiming to determine whether it originates from the systemic venous sinus (“sinus venosus”), or appears as a new structure draining to the left atrium. In addition, we examined the temporal sequence of incorporation of the initially solitary pulmonary vein to the stage at which four venous orifices opened to the left atrium. Methods: We studied 26 normal human embryos, ranging from 3.8 mm to 112 mm crown-rump length, and representing the period from the 12th Carnegie stage to 15 weeks of gestation. Results: The pulmonary vein canalised as a solitary vessel within the mediastinal tissues so as to connect the intraparenchymal pulmonary venous networks to the heart, using the regressing dorsal mesocardium as its portal of cardiac entry. The vein was always distinct from the tributaries of the embryonic systemic venous sinus. The orifice of the solitary vein became committed to the left atrium by growth of the vestibular spine. During development, a marked disparity was seen between the temporal and morphological patterns of incorporation of the left-sided and right-sided veins into the left atrium. The pattern of the primary bifurcation was asymmetrical, a much longer tributary being formed on the left than on the right. Contact between the atrial wall and the venous tributary on the left initially produced a shelf, which became effaced with incorporation of the two left-sided veins into the atrium. Conclusions: The initial process of formation of the human pulmonary vein is very similar to that seen in animal models. The walls of the initially solitary vein in humans become incorporated by a morphologically asymmetric process so that four pulmonary veins eventually drain independently into the left atrium. Failure of incorporation on the left side may provide the substrate for congenital division of the left atrium.