Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast
Data files
May 15, 2025 version files 69.07 GB
-
Data_for_revision_comments_hydrodynamic_flows_-_Copy.7z
197.77 MB
-
Fig_1_all_data.7z
102.81 MB
-
Fig_2_all_data.7z
8.26 GB
-
Fig_3_all_data.7z
59.63 GB
-
Fig_4_all_data.7z
872.07 MB
-
README.md
10.94 KB
Abstract
The ecological and evolutionary success of multicellular lineages stems substantially from their increased size relative to unicellular ancestors. However, large size poses biophysical challenges, especially regarding nutrient transport to all cells: these constraints are typically overcome through multicellular innovations. Here we show that an emergent biophysical mechanism --- spontaneous fluid flows arising from metabolically generated density gradients --- can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This demonstrates how simple physical mechanisms can act as a `biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations.
[https://doi.org/10.5061/dryad.0000000dx](https://doi.org/10.5061/dryad.0000000dx)
Description of the data and file structure
The data uploaded here was collected to evaluate fluid flows surrounding and growth rates for different-sized clusters of snowflake yeast.
All data comes with associated notes in the files which describe the frame rate at which movies were collected along with scale bars for the spatial calibration of the movies and images.
The data is mostly time series(images) collected via microscopy and particle tracks (CSVs) which are analysed using mosaic particle tracker in open source image processing software image J
Each folder uploaded corresponds to a figure in the manuscript titled "Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast"
Files and variables
Particle Track CSVs : All particle Track CSVs uploaded for this submission contain 5 columns
All particle track data was collected at 1FPS hence the time column is seconds. Since there are different magnifications for different experiments I have provided the x and y coordinates in pixels and each folder in which the perticular csv is found will contain a specified magnification.
Index : Trajectory ID : Frame(Time) : X coordinate (Pixels) : Y coordinate (Pixels)
File: Fig1_all_data.7z
Description: Data corresponding to figure 1 includes
CEN.PK Growth on Agar : This folder contains time lapse images of colonies of CEN.PK (single cell yeast) growing on YEPD medium supplemented with 2% Agar. The frames are collected every 10 minutes and the scale is 75 pixels per mm. Each sub folder contians replicates of the same experiment.
G11 Growth on Agar : This folder contains time lapse images of single clusters of Snowflake yeast growing on YEPD medium supplemented with 2% Agar. The frames are collected every 10 minutes and the scale is 75 pixels per mm. Each sub folder contians replicates of the same experiment.
G11 Growth in water : This folder contains time lapse images of single clusters of snowflake yeast growing in YEPD medium prepared in water. The frames are collected every 10 minutes and the scale is 75 pixels per mm. Each sub folder contians replicates of the same experiment.
Color code Data : This folder contains two folders, one containing a time lapse of single clusters of Snowflake yeast growing on YPD supplemented with 2% Agar and one containing a time lapse of single Snowflake yeast growing in YEPD prepared in water.
All frames have been thresholded and binarized on open source software FIJI. To Generate the figure 1B we generated a temporal color code of each time series, which were then cropped and placed next to each other to highlight the difference in growth form between the two conditions.
SEM image: This folder contains two scanning electron microscope images of a snowflake yeast cluster, one at a low magnification where the whole cluster can be seen and one at a higher magnification so as to see the surface of the individual cells that make up the cluster.
Top and size view growth time lapses : This folder contains three replicates of snowflake yeast clusters growing imaged in the Top (x-y) plane and the Side (x-z) plane. It also contains a CSV of the mean volume growth of the three replicates over time.
File: Data_for_revision_comments_hydrodynamic_flows.7z
Description: Data corresponding to fig S7 includes
Agar_2%_10minint : This folder contains 2 folders with time lapse images of single clusters of snowflake yeast growing on YPD medium supplemented with 2% Agar.The frames are collected every 10 minutes and scale bar is provided
Ethyl_2%_10minint : This folder contains 4 folders with time lapse images of single clusters of snowflake yeast growing on YPD medium supplemented with 2% 5-Hydroxy Ethyl Cellulose. The frames are collected every 10 minutes and scale bar is provided
Agar_top_particle_tracks : CSV file of particle tracks in the Agar medium in the presence of a single snowflake yeast cluster.
Ethyl_top_particle_tracks : CSV file of particle tracks in the 5-Hydroxy Ethyl Cellulose medium in the presence of a single snowflake yeast cluster.
Ethyl_Agar_top_analysed : CSV file containing area vs time of single snowflake yeast cluster growing on top of 2% Agar and 2% 5-Hydroxy Ethyl Cellulose (area in mm^2)
Scale 1mm : image of a scale bar taken at the magnification used for collecting the data provided in the folder.
File: Fig_2_all_data.7z
Description: Data corresponding to Figure 2 includes
flow field time series : This folder contains
Particle Tracks : This folder contains CSV files of particle tracks corresponding to different time points across 8 hours, measured for a single snowflake yeast cluster.
Videos : This folder contains video files of measured flow fields corresponding to different time points across 8 hours, measured for a single snowflake yeast cluster.
flowVelTimeGrowth : CSV files of analysed velocity of flow field across time for 8 hours
File: Fig_3_all_data.7z
Description: Data corresponding to Figure 3 includes
Nutritional Scaling : This folder contains 4 folders corresponding to different concentrations of glucose supplemented into PBS, in which flow field measurements were made(0.0002 - 2% glucose). Each folder is named by its corresponding glucose concentration; there are movies of the measured flow field in that condition. Frame rate is 1FPS and scale calibration is 2048 pixels is 1330 um. Further it contains another folder called “All Particle Tracks” with all CSV files for particle tracks from the movies.
Broken flakes : This folder contains 2 folders one with a time series of the flow field measurements made on snowflake yeast clusters that were broken off of larger snowflake yeast clusters.Frame rate is 1FPS and scale calibration is 2048 pixels is 1330 um.
The second folder contains CSV files for all particle tracks from the aforementioned movies.
CEN.PK colony flows : This folder contains a single movie of measured flow fields around a colony of CEN.PK (single cell yeast) and CSV files of the associated particle tracks.
Flip experiment : this folder contains data corresponding to the figure 3A which further includes two folders labeled bot and top.
Bot corresponds to flow field measured on the bottom of an individual cluster adhered to the bottom of the PDMS chamber. Here the individual snowfalke yeast cluster was adhered to the bottom of the PDMS chamber and the orientation of the flow field was measured using PIV at the bottom of the cluster (indicated in figure 3A)
Top corresponds to flow field measured on the bottom of an individual cluster adhered to the top of the petri dish. Here the individual snowfalke yeast cluster that was adhered to the bottom of the PDMS chamber has been fliped along with the chamber itself such that not the individual snowflake yeast cluster is adhere to the top of the PDMS chamber. The orientation of the flow field was measured using PIV at the bottom of the cluster (indicated in figure 3A)
anaerobic ancestor colony flows : This folder contains two further folders which contain replicates of the same experiments. The experiment is measuring the flow fields in a colony of the anaerobic ancestor of the evolutionary line. Along with the time series there are associated CSVs of the particle tracks.
Media MSD stuff : This folder contains further 5 folders. 4 of the 5 folders are different media conditions in which flow field measurements are made. Each folder is named by its associated media condition and contains movies of the flow field measurements made. The 5th folder contains CSV files of all the particle tracks for all media conditions.
Size scaling data : this folder contains two additional folders of two independent experiments on flow field measurements across different sized snowflake yeast clusters. Within each sub folder there are time series, bright field images (to measure size) and particle tracks. There is also a CSV of the size MSD relationship. For folder two the scale bar is also provided along with another note on details of the experiment.
For folder 1 : scale is : 1539 pixels/mm
areas for clusters in folder 1 are in um^2 and radii for clusters in folder 1 are in um (this relevant in the size MSD relationship csv)
For folder 2 scale is : 398 pixels/mm
areas for clusters in folder 1 are in um^2 and radii for clusters in folder 1 are in um (this relevant in the size MSD relationship csv)
File: Fig_4_all_data.7z
Description: Data corresponding to Figure 4 includes
Two cluster flow field top view : This folder contains data for the flow field between two snowflake yeast clusters imaged in the x-y plane. Within this folder there are subfolders :
Original : This folder contains the non-processed time series of the flow field measured in the x-y plane between two snowflake yeast clusters.
Cropped and centered : This folder contains the processed(cropped and centered)time series of the flow field measured in the x-y plane between two snowflake yeast clusters. This was done purely for aesthetic reasons and does not change the data.
There are two additional files :
“Streamlines” is an image of the cropped and centered time series processed with flow trace on imageJ
“Velocity Profile between two clusters” is a CSV of the velocity profile along the mid plane connecting the two clusters.
vertical_twocluster_cropped : This folder contains data for the flow field between two snowflake yeast clusters imaged in the x-z plane.Within this folder there are subfolders :
Original : This folder contains the non-processed time series of the flow field measured in the x-z plane between two snowflake yeast clusters.
Streamlines : This folder contains a time series of the same data as available in Original but processed with flow trace on ImageJ.
Code/software
For visualizing the time series data and tracking particles in the time series data we recommend using image J an open source image viewing software. Analysis code is provided along with the data
Code description :
msds.m : This code computes the MSDs and velocity of the provided racer particle data. This data is collected by tracing particles using the mosaic particle tracker in Image J.
Shape detector : this code calculates the area of individual snowflake yeast clusters as they grow.
Access information
Other publicly accessible locations of the data:
- n/a
Data was derived from the following sources:
- n/a
All data was collected using optical microscopy or scanning electron microscopy