Reassessment of the Basis of Cell Size Control Based on Analysis of Cell-to-Cell Variability

Abstract

Image acquisition and analysisAll images analysed here are taken from our previous publication [1]. High resolution images were used to obtain cell segmentation at different resolutions by binning pixels (Figs. 2,3, S1). This allowed us to study the effect of the segmentation error. In these cases, we applied the following new semi-automated algorithm to the images acquired at the best z-plane. We first drew manually an approximate cell axis that connected the two cell tips (A and B, see Fig. S7A). The AB distance was a first estimation L of the cell length. A first estimation of the cell radius was calculated as follows. From the middle point M of the AB segment, we derived an intensity profile along the direction orthogonal to the axis (towards both lateral borders of the cell, red dashed line in Fig. S7A). The steepest gradient of this signal identified the border of the cell, i.e. the cell radius. We repeated this gradient procedure using neighbouring points of M (at a distance k·dx, with k=-3, -2, … , +2, +3, and where dx is the pixel size). The average of all these values gave our first estimation of the radius. We then shortened the segment AB by this amount from both ends. This defined the new segment A'B'. We divided this segment into n equal parts (n=0.5·L/dx) by placing n-1 internal points. The gradient procedure we used for the middle point M was then applied to all these points and to the two extremal points A' and B'. This identified the lateral borders of the cells. The symmetry axis of the resulting lateral borders was taken to be the new symmetry axis of the cell (segment CD). From both extreme points C and D, we derived the intensity profile along the different radial directions (from 0 to 180 degrees, steps of 2 degrees, purple dashed line in Fig. S7B). Ideally, the distance of the cell border to the CD segment should always have been equal to R for every point from C to D. However, cell irregularity and imaging defects altered this width. Therefore, after calculating the width from a point xi, if the difference between this width and the width from the previous point xi-1 was bigger than a given threshold (0.1 μm), we set the width equal to the width from xi-1. The final result was a set of points that described the cell border. From these points we derived the cell length as the maximal distance between two points of the set (Fig. S7C). The cell radius was defined as the average of its value at different positions along the CD segment, i.e. excluding the two cell tips (Fig. S7C). Surface area and volume were then calculated using simple geometrical equations. As

Modeling homeostasis mechanisms that set the target cell size

“…Another recent study also showed that growing budding yeast and primary mammalian cells beyond a certain size leads to impaired cell-cycle progression, and the authors attribute this to cytoplasmic dilution or a reduced DNA to cytoplasm ratio, although in these cases the cells were grown substantially beyond their normal range 27 . Overall, the findings reported here are consistent with many experimental observations, including the recent single-cell tracking of several mammalian cell types, where the authors showed that size added in a cell-cycle duration is independent of the newborn size as per the adder model 23 , 46 .…”

Strongly oversized fission yeast cells lack any size control and tend to grow linearly rather than bilinearly

“…During the last couple of years, there have been many, many new results published on both individual cellular growth and population‐level size homeostasis and the connections between these two aspects (Allard et al, 2018; Barber, Amir, & Murray, 2020; Cantwell & Nurse, 2019; Facchetti, Knapp, Chang, & Howard, 2019; Facchetti et al, 2019; Hannebelle et al, 2020; Nordholt, van Heerden, & Bruggeman, 2020; Opalko et al, 2019; Patterson et al, 2019; Pickering et al, 2019; Si et al, 2019; Vuaridel‐Thurre, Vuaridel, Dhar, & McKinney, 2020; Xie & Skotheim, 2020; Zatulovskiy & Skotheim, 2020; Zatulovskiy, Zhang, Berenson, Topacio, & Skotheim, 2020). The model organisms studied vary from unicellular prokaryotes via yeasts to animal cells; moreover, modern techniques have even made possible to examine mammalian cells in tissues in vivo.…”

Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells

“…S8) and should not be ignored when calculating volume or representing cells in 3D. For the same reason, recent extrusion approaches to measure cell volume and surface area have already started to use techniques that take variations of cell width along the length of the cell into account [64][65][66] . Pomegranate differs from these methods in that it uses the topological skeleton rather than a straight central axis for extrusion.…”