Dataset: Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project)

Name: Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project)
Published: 2022-12-19
Keywords: microfluidics, chemotaxis, infection dynamics, oceans

Final no updates expectedDOI: 10.26008/1912/bco-dmo.885574.1Version 1 (2022-12-19)Dataset Type:model resultsDataset Type:experimentalDataset Type:model resultsDataset Type:experimental

Co-Principal Investigator: Sheri Floge (Wake Forest University)

Co-Principal Investigator: Jeffrey Guasto (Tufts University)

Scientist, Contact: Richard J. Henshaw (ETH-Zurich)

BCO-DMO Data Manager: Sawyer Newman (Woods Hole Oceanographic Institution)

Project: Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux (VIC)

Abstract

This data set summarises the chemotactic response of a model marine bacteria (Vibrio alginolyticus YM4 wild-type) to filtered exudates of the cyanobacteria Synechococcus sp WH8102. Two filtrate sets were collected, each spanning 6 time points (named T1 -> T6), with the initial assays split into 4 biological replicates (named A,B,C,D). The two treatments were: 1) A control treatment (named "Control", or shortened to "C") 2) A phage-infected treatment (named "Phage", or shortened to "P"), wher...

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File(s)	Type	Description	Action
Filtrate_Chemotaxis.zip (19.29 GB)	ZIP Archive (ZIP)		Download

Supplemental File(s)	Type	Description	Action
Filtrate_Chemotaxis_Analysis.zip (8.95 KB)	ZIP Archive (ZIP)	This file package contains MatLab functions within .m files. Each file contains more description of usage, input, and output in the header of each m-file. Below is a brief description of the purpose of each function. --- "Chemotaxis_Analysis.m" contains setup and parameters, you should only need to change numbers/details here. --- "cntrd.m" contains function: cntrd(im,mx,sz,interactive) PURPOSE: calculates the centroid of bright spots to sub-pixel accuracy. Inspired by Grier & Crocker's feature for IDL, but greatly simplified and optimized for matlab. --- pkfnd.m contains function: pkfnd(im,th,sz) PURPOSE: finds local maxima in an image to pixel level accuracy. This provides a rough guess of particle centers to be used by cntrd.m. Inspired by the lmx subroutine of Grier and Crocker's feature.pro --- "bpass.m" contains function: bpass(image_array,lnoise,lobject,threshold) PURPOSE: Implements a real-space bandpass filter that suppresses pixel noise and long-wavelength image variations while retaining information of a characteristic size. ---	Download

Files

Filename: Filtrate_Chemotaxis.zip (19.29 GB)
Type: ZIP Archive (ZIP)
Description:

Download

Supplemental Files

Filename: Filtrate_Chemotaxis_Analysis.zip (8.95 KB)
Type: ZIP Archive (ZIP)
Description: This file package contains MatLab functions within .m files. Each file contains more description of usage, input, and output in the header of each m-file. Below is a brief description of the purpose of each function. --- "Chemotaxis_Analysis.m" contains setup and parameters, you should only need to change numbers/details here. --- "cntrd.m" contains function: cntrd(im,mx,sz,interactive) PURPOSE: calculates the centroid of bright spots to sub-pixel accuracy. Inspired by Grier & Crocker's feature for IDL, but greatly simplified and optimized for matlab. --- pkfnd.m contains function: pkfnd(im,th,sz) PURPOSE: finds local maxima in an image to pixel level accuracy. This provides a rough guess of particle centers to be used by cntrd.m. Inspired by the lmx subroutine of Grier and Crocker's feature.pro --- "bpass.m" contains function: bpass(image_array,lnoise,lobject,threshold) PURPOSE: Implements a real-space bandpass filter that suppresses pixel noise and long-wavelength image variations while retaining information of a characteristic size. ---

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The data in this data set is organized as follows:

Accumulation Curves: The final processed data for each time point (T1-6), each replicate (A-D) with the average and SEM values tabled.

Filtrates_T#R: Where # is the time point number (1-6) and R the replicate (A-D). Each folder contains:

1) Three Excel sheets corresponding to the raw cell counts for each biological replicate (each with 3 repeats)

2) A supplemental folder containing a cell array with the full bacteria positions for each time point for each replicate (.mat format)

The chemotaxis data was collected by Dr. Richard J. Henshaw of Tufts University (Boston, MA, USA) from 3rd December 2020 to 8th October 2021. Queries about this dataset should be directed to rhenshaw@ethz.ch.

Related Datasets

Floge, S., Guasto, J., Henshaw, R. J. (2023) Chemotaxis of Vibrio alginolyticus towards live phage-infected/control Synechococcus cells (VIC project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-10-17 http://lod.bco-dmo.org/id/dataset/913619

Related Publications

Methods

Dehkharghani, A., Waisbord, N., Dunkel, J., & Guasto, J. S. (2019). Bacterial scattering in microfluidic crystal flows reveals giant active Taylor–Aris dispersion. Proceedings of the National Academy of Sciences, 116(23), 11119–11124. https://doi.org/10.1073/pnas.1819613116

Methods

Howard-Varona, C., Roux, S., Bowen, B. P., Silva, L. P., Lau, R., Schwenck, S. M., Schwartz, S., Woyke, T., Northen, T., Sullivan, M. B., & Floge, S. A. (2022). Protist impacts on marine cyanovirocell metabolism. ISME Communications, 2(1). https://doi.org/10.1038/s43705-022-00169-6

Methods

Stehnach, M. R., Waisbord, N., Walkama, D. M., & Guasto, J. S. (2021). Viscophobic turning dictates microalgae transport in viscosity gradients. Nature Physics, 17(8), 926–930. https://doi.org/10.1038/s41567-021-01247-7

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Dataset: Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project)

Final no updates expectedDOI: 10.26008/1912/bco-dmo.885574.1Version 1 (2022-12-19)Dataset Type:model resultsDataset Type:experimentalDataset Type:model resultsDataset Type:experimental

Co-Principal Investigator: Sheri Floge (Wake Forest University)

Co-Principal Investigator: Jeffrey Guasto (Tufts University)

Scientist, Contact: Richard J. Henshaw (ETH-Zurich)

BCO-DMO Data Manager: Sawyer Newman (Woods Hole Oceanographic Institution)

Project: Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux (VIC)

Abstract

Cite Dataset

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Downloads

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Citations

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File(s)	Type	Description	Action
Filtrate_Chemotaxis.zip (19.29 GB)	ZIP Archive (ZIP)		Download

Supplemental File(s)	Type	Description	Action
Filtrate_Chemotaxis_Analysis.zip (8.95 KB)	ZIP Archive (ZIP)	This file package contains MatLab functions within .m files. Each file contains more description of usage, input, and output in the header of each m-file. Below is a brief description of the purpose of each function. --- "Chemotaxis_Analysis.m" contains setup and parameters, you should only need to change numbers/details here. --- "cntrd.m" contains function: cntrd(im,mx,sz,interactive) PURPOSE: calculates the centroid of bright spots to sub-pixel accuracy. Inspired by Grier & Crocker's feature for IDL, but greatly simplified and optimized for matlab. --- pkfnd.m contains function: pkfnd(im,th,sz) PURPOSE: finds local maxima in an image to pixel level accuracy. This provides a rough guess of particle centers to be used by cntrd.m. Inspired by the lmx subroutine of Grier and Crocker's feature.pro --- "bpass.m" contains function: bpass(image_array,lnoise,lobject,threshold) PURPOSE: Implements a real-space bandpass filter that suppresses pixel noise and long-wavelength image variations while retaining information of a characteristic size. ---	Download

Files

Filename: Filtrate_Chemotaxis.zip (19.29 GB)
Type: ZIP Archive (ZIP)
Description:

Download

Supplemental Files

Download

The data in this data set is organized as follows:

Accumulation Curves: The final processed data for each time point (T1-6), each replicate (A-D) with the average and SEM values tabled.

Filtrates_T#R: Where # is the time point number (1-6) and R the replicate (A-D). Each folder contains:

1) Three Excel sheets corresponding to the raw cell counts for each biological replicate (each with 3 repeats)

2) A supplemental folder containing a cell array with the full bacteria positions for each time point for each replicate (.mat format)

Related Datasets

Related Publications

Methods

Dataset: Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project)

Co-Principal Investigator: Sheri Floge (Wake Forest University)

Co-Principal Investigator: Jeffrey Guasto (Tufts University)

Scientist, Contact: Richard J. Henshaw (ETH-Zurich)

BCO-DMO Data Manager: Sawyer Newman (Woods Hole Oceanographic Institution)

Project: Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux (VIC)

Abstract

Metadata

XXX

XX

X

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: Chemotaxis of Vibrio alginolyticus to control/phage-infected Synechococcus exudates from 2020-2021 (VIC project)

Co-Principal Investigator: Sheri Floge (Wake Forest University)

Co-Principal Investigator: Jeffrey Guasto (Tufts University)

Scientist, Contact: Richard J. Henshaw (ETH-Zurich)

BCO-DMO Data Manager: Sawyer Newman (Woods Hole Oceanographic Institution)

Project: Collaborative Research: Viral induced chemotaxis mediating cross-trophic microbial interactions and carbon flux (VIC)

Abstract

Metadata

XXX

XX

X

Files

Supplemental Files

Related Datasets

Related Publications