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Complex morphologies of biogenic crystals emerge from anisotropic growth of symmetry-related facets

Citation

Avrahami, Emanuel; Houben, Lothar; Aram, Lior; Gal, Assaf (2022), Complex morphologies of biogenic crystals emerge from anisotropic growth of symmetry-related facets, Dryad, Dataset, https://doi.org/10.5061/dryad.zcrjdfndp

Abstract

Directing crystal growth into complex morphologies is challenging, as crystals tend to adopt thermodynamically stable morphologies. Yet, many organisms form crystals with intricate morphologies, as exemplified by coccoliths, microscopic calcite crystal-arrays produced by unicellular algae. The complex morphologies of the coccolith crystals were hypothesized to materialize from numerous crystallographic facets, stabilized by fine-tuned interactions between organic molecules and the growing crystals. Using state-of-the-art electron tomography, we examined multiple stages of coccolith development in 3D. We found that the crystals are expressing only one set of symmetry-related crystallographic facets, which grow differentially to yield highly anisotropic shapes. Morphological chirality arises from positioning the crystals along specific edges of these same facets. Our findings show that manipulations of growth kinetics can yield complex crystalline morphologies.

Usage Notes

Data for 'Complex morphologies of biogenic crystals emerge from anisotropic growth of symmetry related facets':

Zipped folder 1: "Data" (22.42 GB)

1. Sub-folder '1_Reconstructions_crystal stages 1-5': containing files of the reconstructed volumes of the five different coccolith growth stages  discussed throughout the main text, denoted as stages 1-5. 
Apart from 'stage 3' which was acquired in BF-STEM mode with a microprobe, all other data was acquired using a nanoprobe, collected in HAADF-STEM mode. Data collected on Tecnai G2 F20 S/TEM microscope, at room temperature conditions.
Files in .rec format.

2. Sub-folder '2_Reconstructions_repeated tilt': containing files of the reconstructed volumes of coccolith used as control to determine preservation of crystals after a rpeated tilt series, as presented in SI Figure 7. 
Data collected on Tecnai G2 F20 S/TEM microscope, at room teperature, operation in HAADF-STEM mode and using a nanoprobe.  File in .rec format. 

3. Sub-folder '3_Reconstruction_plunge frozen coccolith': containing files of the reconstructed volume of the coccolith used as control to determine preservation of crystal structure in cryogenic conditions, as presented in SI Figure 3. 
This coccolith was plunge frozen in liquid ethane immediately after extraction, and was not exposed to NaHClO. Data collected on Titan Krios G3i S/TEM microscope, at cryogenic conditions, operation in HAADF-STEM mode and using a nanoprobe.  File in .rec format. 

4. Sub-folder '4_Segmentations': containing segmentations files (3D visualizations) of reconstructed volumes of the coccolith growth stages discussed throughout the main text, denoted as stages 1-5 (associated with the supplied reconstructions in sub-folder 1. See ''1_Reconstructions_crystal stages 1-5'').
V units are colored orange, R units are colored blue. Data generated on Amira software. Files in .am format.

5. Sub-folder '5_SEM images hypotonic solutions': containing SEM images of ICCs extracted into different hypotonic solutions, used for quantification of overall structural preservation, as presented in SI Figure 2. 
In each solution conditions, 50 random coccoliths were imaged, and divided into one of three groups - 'good condition', 'partially deformed' and 'deformed'. Data collected on Sigma 500 SEM, at room temperature. Files in .tif format.

6. Sub-folder '6_volume renderings': containing files of whole volume renderings (3D visualization based on automatically-generated 3D pixels, relying on the image's data histogram) of the coccoliths presented in Figure 2 and in SI Figure 3.
Data generated on Amira software. Files in .am format.

Softwares required to open files:

"*.rec" and "*.mrc" files, which are the reconstructed volumes, can be opened with the free ImageJ software, using the Slicer plugin.
"*.am" files, which are the label and surface files, were generated by Amira for 3D visualization. They can be opened by Amira or any other compatible sofwares.

Zipped folder 2: "movies" (129 MB)

This folder contains five movies of the tomograms and rendered volumes of all crystal growth stages (denoted as 'stages i-v'). In each movie, four segmented units are shown (two R-units, in blue, and two V-units, in orange). All movies are at a resolution of 1398x930 pixels. Files in .avi format.

Funding

Israel Science Foundation, Award: 697/19