Abstract:
The dataset is comprised of photos that have tracking lines connecting each individual's starting and final locations for each time bin. There are photos tracking the movement of each individual for 1) the entire hour fifty-minute trial, 2)1 second before stimulus, 3)1 second during stimulus, 4) 1 second after stimulus and 5) the ten-minute intervals between stimuli. The data file also contains a video of each of the hour and fifty-minute trials. Summarizing the data is an Excel file with columns displaying the distance and speed of each individual's movement for each time bin (ten-minute interval, 1 second prestimulus, 1 second during stimulus, 1 second poststimulus).
Suggested Citation:
Ranges, Kristen and Martin Grosell. 2021. Quantification of larval zebrafish (Danio rerio) startle responses to auditory stimuli. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/ZAEWYYPQ
Data Parameters and Units:
Zebrafish were exposed for 24-hr in 1% HEWAF. Three trials were performed: 7 days post fertilization, 9 days, and 11 days. On each trial day, 3 runs were conducted. The data is organized in separate folders by trial (trail#- date-days post fertilization), then further by folders for individual runs (trial #-run #). The datasheets derived from the software are the only Excel files in each subfolder. The other files are videos and images taken throughout the runs, organized and named by time point within the trial. There is also a separate file, “Imaging”, which contains 20-second videos, taken after various runs, that will be used to measure heart rate. The data is organized in an Excel format in the ZebraLab software. The abbreviations in the columns from left to right are as follows: Datatype- the measurement the software was tracking; Location- the individual number; Animal- animal name (blank); Aname- well name; Areaid- identification of sample area (irrelevant); Timebinid- identification of timebin number (always 2, irrelevant); Pn- numbering of sampling time period; Start- sampling time period start (from start of trial, not 24-h time); End- sampling time period end (measured from start of trial, not 24-h);Start reason- how the samples will be sorted (chronolog); End reason- the stimuli administered (sound); Stdate- start date of trial; Sttime- start time of trial (24-h time); Algostatus- not recorded; Stimuli_start- irrelevant (records as 0); Stimuli_stop- irrelevant (records as 0); Stimuli_frquency- not recorded; Stimuli_color- not recorded; Stimuli_name- not recorded; Entct- each time the animal enters the area (area meaning the sampling area of the well)- number count; Inact- inactivity count (1 count=when fish is entering this speed class)- number count; Inadur- total duration spent in inactivity- seconds; Inadist- total distance covered by the animal in inactivity- mm; Smlct- small movement count- number count; Smldur- total duration spent by the animal in small movement- seconds; Smldist- total distance covered by the animal in small movement- mm; Larct- large movement count- number count; Lardur- total duration spent by the animal in large movements- seconds; Lardist- total distance covered by the animal in large movements- mm; Emptyct- number of times during which no object/animal is detected in the location (could be due to total inactivity so that animal is not detected)- number count; Emptydur- time during which no object/animal is detected in the location- seconds. The rest of the columns are parameters for the software, not data.
Two Excel files are part of the dataset R6.x804.000:0052, “8, 10, 12, days post fertilization response trials.” The first is entitled “G213_Suppplemental” which includes water chemistry and details of sampling collection times, and the second is labelled “ALS data_G213” which contains analysis of crude oil samples sent for analysis. Additional methodological details are also included.
Excel file 1: “Ranges_SupplementalData_G213”
Tab 1: “Water Quality Monitoring” This sheet includes water quality data. C1, C2, C3 refer to the names of replicate control beakers. E1, E2, E3 refer to the names of replicate exposure beakers. Initial refers to the period right after exposure medium preparation/exposure start. 24h refers to the period 24 hours after exposure medium preparation/exposure start.
Tab 2: “Water Accommodated Fraction Prep” This sheet includes dates, times, and composition of WAF preparation.
Tab 3: “Analytical Sample Inventory” This sheet contains dates, times, and sample names. E tank ID refers to exposure beakers and C refers to control beakers. Initial refers to the period right after exposure medium preparation/exposure start. 24h refers to the period 24 hours after exposure medium preparation/exposure start. The analyses from these samples are included in document “ALS data_G213”
Excel file 2: “Ranges_ALSdata_G213”
Tab 1: “SUM 50 PAH” includes concentrations of each measured PAH that comprises the SUM 50 PAH measurement.
Tab 2: “Additional PAH” measurements analyzed in the sample but not included in the SUM 50 PAH calculation.
Tab 3: “BTEXX” measurements of Benzene, Toluene, Ethylbenzene, and Xylenes.
ND in this Excel sheet means “not detectable,” meaning that the level of this PAH is zero or below the detection limit in ALS analyses.
All concentrations reported are in the units of micrograms per liter.
Sampling corresponding to Trial 1:
G213-F0307-003: taken day 7, 24h after initial exposure, compilation of exposure medium from exposure beakers
Sampling corresponding to Trial 2:
G213-F0308-005 : taken day 8, initial exposure, compilation of exposure medium from control beakers
G213-F0308-007 : taken day 8, initial exposure, compilation of exposure medium from exposure beakers
G213-F0309-009 : taken day 9, 24h after initial exposure, compilation of exposure medium from exposure beakers
Sampling corresponding to Trial 3:
G213-F0310-011: taken day 10, initial exposure, compilation of exposure medium from exposure beakers
G213-F0311-013: taken day 11, 24h after initial exposure, compilation of exposure medium from exposure beakers
Methods:
Data was collected from the ZebraLab software, followed by manual imaging.
HEWAF (high energy water accommodated fraction) crude oil methodology: Source oil collected from the Deepwater Horizon spill (sample ID: A0076T) was used to prepare a high-energy water accommodated fraction (HEWAF) of crude oil by mixing 1gram of oil per liter of freshwater at low speed for 30 seconds in a Waring CB 15 blender (Torrington, CT). The blended oil and freshwater mixture was immediately transferred to a glass separatory funnel, allowed to settle for 1 hour, and the lower 90% was drained and retained as the 100% WAF. This WAF was then diluted with control freshwater to make a 1% source oil exposure treatment. Water samples were collected in 250 milliliter amber bottles at the beginning and end of the 24-hour exposure to quantify sum PAHs (polycyclic aromatic hydrocarbons). Samples were shipped overnight on ice to ALS Environmental (Kelso, WA) for gas chromatography/mass spectrometry-selective ion monitoring. Zebrafish were then introduced to either control freshwater beakers or the 1% exposure medium.
View Metadata