Joint modeling of cell and nuclear shape variation

Modeling cell shape variation is critical to our understanding of cell biology. Previous work has demonstrated the utility of nonrigid image registration methods for the construction of nonparametric nuclear shape models in which pairwise deformation distances are measured between all shapes and are embedded into a low-dimensional shape space. Using these methods, we explore the relationship between cell shape and nuclear shape. We find that these are frequently dependent on each other and use this as the motivation for the development of combined cell and nuclear shape space models, extending nonparametric cell representations to multiple-component three-dimensional cellular shapes and identifying modes of joint shape variation. We learn a first-order dynamics model to predict cell and nuclear shapes, given shapes at a previous time point. We use this to determine the effects of endogenous protein tags or drugs on the shape dynamics of cell lines and show that tagged C1QBP reduces the correlation between cell and nuclear shape. To reduce the computational cost of learning these models, we demonstrate the ability to reconstruct shape spaces using a fraction of computed pairwise distances. The open-source tools provide a powerful basis for future studies of the molecular basis of cell organization.     

Microtubules control nuclear shape and gene expression during early stages of hematopoietic differentiation

Hematopoietic stem and progenitor cells (HSPC) can differentiate into all hematopoietic lineages to support hematopoiesis. Cells from the myeloid and lymphoid lineages fulfill distinct functions with specific shapes and intra‐cellular architectures. The role of cytokines in the regulation of HSPC differentiation has been intensively studied but our understanding of the potential contribution of inner cell architecture is relatively poor. Here, we show that large invaginations are generated by microtubule constraints on the swelling nucleus of human HSPC during early commitment toward the myeloid lineage. These invaginations are associated with a local reduction of lamin B density, local loss of heterochromatin H3K9me3 and H3K27me3 marks, and changes in expression of specific hematopoietic genes. This establishes the role of microtubules in defining the unique lobulated nuclear shape observed in myeloid progenitor cells and suggests that this shape is important to establish the gene expression profile specific to this hematopoietic lineage. It opens new perspectives on the implications of microtubule‐generated forces, in the early commitment to the myeloid lineage.     

Patient-specific acetabular shape modelling: comparison among sphere,ellipsoid and conchoid parameterisations

The shape of the human acetabular cup was commonly represented as a hemisphere, but different geometries and patient-specific shapes have been recently proposed in the literature. Our aim was to test the limits of the sphericity assumption by comparing three different parameterisations, namely the sphere, the ellipsoid and the rotational conchoid. Models of hip surfaces, reconstructed from CT scans taken from Caucasian race cadavers and patients, were automatically processed to extract the acetabular surface. Two separate analyses were carried out on the overall acetabular shape, including both the acetabular fossa and the lunate surface (case A) and acetabular cup represented by the lunate surface only (case B). Nonlinear gradient-based and evolutionary computation approaches were implemented for the fitting process. Minor differences from the three idealised geometries were detected (median values of the fitting errors < 1 mm). Nonetheless, the sphere fitting was found to be statistically different from both the ellipsoid (p < 2.50e ? 10) and the conchoid (p < 1.07e ? 09), whereas no statistical difference was detected between the ellipsoid and the conchoid for case A. Significance of the difference between ellipsoid and sphere (p < 4.55e ? 12) and between conchoid and sphere (p < 1.93e ? 11) was found for case B as well. Interestingly, for case B statistical difference was detected between the ellipsoid and the conchoid. In conclusion, we synthesise that the morphology of the overall acetabular cup can be parameterised both with an ellipsoid shape and with a conchoid shape as well with superior quality than the simple sphere. Differently, if one considers just the lunate surface, better fitting results are expected when using the ellipsoid.     

The evolution of egg shape in birds: selection during the incubation period

A recent broad comparative study suggested that factors during egg formation – in particular ‘flight efficiency’, which explained only 4% of the interspecific variation – are the main forces of selection on the evolution of egg shape in birds. As an alternative, we tested whether selection during the incubation period might also influence egg shape in two taxa with a wide range of egg shapes, the alcids (Alcidae) and the penguins (Spheniscidae). To do this, we analysed data from 30 species of these two distantly related but ecologically similar bird families with egg shapes ranging from nearly spherical to the most pyriform eggs found in birds. The shape of pyriform eggs, in particular, has previously proven difficult to quantify. Using three egg‐shape indices – pointedness, polar‐asymmetry and elongation – that accurately describe the shapes of all birds’ eggs, we examined the effects of egg size, chick developmental mode, clutch size and incubation site on egg shape. Linear models that include only these factors explained 70–85% of the variation in these egg‐shape indices, with incubation site consistently explaining > 60% of the variation in shape. The five species of alcids and penguins that produce the most pyriform eggs all incubate in an upright posture on flat or sloping substrates, whereas species that incubate in a cup nest have more spherical eggs. We suggest that breeding sites and incubation posture influence the ability of parents to manipulate egg position, and thus selection acting during incubation may influence egg‐shape variation across birds as a whole.     

Misinformative characters and phylogeny shape

The discrepancy between theoretical and observed distributions of tree shapes in recent surveys of phylogeny estimates has lead to investigations of possible biological and methodological causes. I investigated whether the phylogenetic quality of characters is related to the tree shape on which they evolve. Simulated evolution revealed shape-related tendencies for characters to indicate correct cladistic relationships; these differences were measured by examining the characters directly, without deriving any phylogeny estimates. Tree stemminess indices correlated strongly with character quality when characters evolved either speciationally or phyletically. Tree balance was a significant correlate of character quality under speciational evolution but not under phyletic evolution. These results help explain the findings of other simulation studies. With additional study of the behavior of evolving characters and their interaction with phylogenetic methods, we might be able to increase the accuracy of tree estimation and compensate for potential biases related to shape. These results give further reason for caution in trusting phylogeny estimates.     

Schmidt-Lanterman clefts: a morphometric study in human sural nerve

In the human sural nerve, large myelinated fibers contained 35 Schmidt-Lanterman (SL) clefts per mm, and small myelinated fibers contained only eight SL clefts per mm. The incidence of SL clefts is linearly related to myelin thickness. The SL clefts extended over 13 micron in large and over 9 micron in small fibers, the total extent of the SL region amounting to nearly 50% of internodal length in large and to 6% in small fibers. In the SL region, the fiber diameter was 6% larger than outside this region, and the axon was 17% smaller in large and 28% smaller in small fibers. The paranodal-nodal region occupied less than 2% of internodal length in large fibers and 6.5% in small fibers; in the nodal region the axon diameter was reduced by 40-50%.     

Bacterial shape

In free-living eubacteria an external shell of peptidoglycan opposes internal hydrostatic pressure and prevents membrane rupture and death. At the same time, this wall imposes on each cell a shape. Because shape is both stable and heritable, as is the ability of many organisms to execute defined morphological transformations, cells must actively choose from among a large repertoire of available shapes. How they do so has been debated for decades, but recently experiment has begun to catch up with theory. Two discoveries are particularly informative. First, specific protein assemblies, nucleated by FtsZ, MreB or Mbl, appear to act as internal scaffolds that influence cell shape, perhaps by correctly localizing synthetic enzymes. Second, defects in cell shape are correlated with the presence of inappropriately placed, metabolically inert patches of peptidoglycan. When combined with what we know about mutants affecting cellular morphology, these observations suggest that bacteria may fabricate specific shapes by directing the synthesis of two kinds of cell wall: a long-lived, rigid framework that defines overall topology, and a metabolically plastic peptidoglycan whose shape is directed by internal scaffolds.     

An application of mathematical morphology to analysis of the size and shape of nuclei in tissue sections of non-Hodgkin's lymphoma

Using principles from the theory of mathematical morphology, a semiautomatic analysis of the size and shape of cell nuclei on tissue sections was carried out on a Leitz Texture Analysis System (Leitz-TAS). The four parameters proposed here are more discriminatory than conventional shape evaluation by the form factor (FF), which is based on the ratio of perimeter squared to area. The parameters quantified, respectively, nuclear elongation (ND), narrow (R1) and wide (R2) irregularities, and the distribution of R1 and R2 along the nuclear contour (ID). The properties of these parameters were tested nucleus-by-nucleus on 24 nuclear models. The methodology was then illustrated by a study of lymph node nuclei in non-Hodgkin's lymphoma (NHL). Prior to analysis, 45 lymphomas were classified into five categories of nuclear size and shape according to the International Working Formulation (IWF). Two hundred nuclei were measured on each lymph node section. Statistical interpretation was based upon an analysis of the nuclear surface area on sections and upon the mean values of R1, R2, and ND, the standard deviations of R1 and R2, and the percentage of cleaved nuclei detected by ID. The mean value of R2 discriminated best between the two sets of populations with regular and irregular nuclear contours, respectively. Parameters R1, ND, and ID permitted the distinction of certain NHL cases among populations with irregular nuclei. Nuclear invaginations decreased in depth as the nuclear area became greater. The median surface area was well correlated to the IWF, and the skewness coefficient (third statistical moment of the nuclear surface area distribution) was related to the number of nuclear size or shape subpopulations.     

Heritability of bulb shape in some north European onion varieties

Heritabilities for shape index (the ratio of bulb height to diameter), based on parent—offspring regressions, were calculated for north European onion cultivars and inbred lines derived from them. Heritability estimates of 0·46 and 0·47 respectively were obtained for the two groups, S₀ parent bulbs giving S₁ progenies, and S₁ parent bulbs giving S₂ progenies. Within each offspring progeny, the regression of bulb shape index on log_e bulb weight was significant. The regressions were used to estimate the mean shape indices of the progenies at the same mean bulb weight as their parents, and a series of ‘corrected’ progeny shape means thus obtained. Recalculation of the heritabilities using these ‘corrected’ progeny means gave increased estimates (0·78 and 0·84). By using this regression approach, the breeder can achieve high heritabilities when selecting for a specific mean shape index.     

Cell shape regulates collagen type I expression in human tendon fibroblasts

Understanding the relationship between cell shape and cellular function is important for study of cell biology in general and for regulation of cell phenotype in tissue engineering in particular. In this study, microcontact printing technique was used to create cell-adhesive rectangular and circular islands. The rectangular islands had three aspect ratios: 19.6, 4.9, and 2.2, respectively, whereas circular islands had a diameter of 50 microm. Both rectangular and circular islands had the same area of 1960 microm(2). In culture, we found that human tendon fibroblasts (HTFs) assumed the shapes of these islands. Quantitative immunofluorescence measurement showed that more elongated cells expressed higher collagen type I than did less stretched cells even though cell spreading area was the same. This suggests that HTFs, which assume an elongated shape in vivo, have optimal morphology in terms of expression of collagen type I, which is a major component of normal tendons. Using immunohistochemistry along with cell traction force microscopy (CTFM), we further found that these HTFs with different shapes exhibited variations in actin cytoskeletal structure, spatial arrangement of focal adhesions, and spatial distribution and magnitude of cell traction forces. The changes in the actin cytoskeletal structure, focal adhesion distributions, and traction forces in cells with different shapes may be responsible for altered collagen expression, as they are known to be involved in cellular mechanotransduction.