This work was supported by a Howard Hughes Medical Institute Education Grant and an internal grant from the Saint Joseph's University chapter of Sigma Xi. We would also like to thank the three anonymous reviewers who helped strengthen the protocol and interpretations.

The following methodologies for the housing, care, and study of zebrafish have been approved by the Saint Joseph&#39;s University IACUC.
1. Zebrafish Housing and Care
<ol>
	<li>Obtain the subject zebrafish from a local supplier, or from wild-caught populations. Please note that housing the zebrafish is subject to IACUC guidelines and additional permits are required for housing wild-caught populations.</li>
	<li>Identify and separate zebrafish according to sex. Alternatively, skip this step or replace with a different method of separation based on the study hypothesis. 
	NOTE: Sex characteristics are difficult to determine in zebrafish, particularly in females. Refer to these guidelines10 or useful online manuals to distinguish sex.</li>
	<li>Randomly separate the populations further into the appropriate ratio of focal fish to stimulus fish. Note: Focal fish are the test subjects followed through the series of behavioral assays, and stimulus fish are the individuals that will occupy the stimulus chambers in the aggression and shoaling assays. 
	NOTE: Traditionally, between 1 and 5 stimulus fish per focal fish in shoaling assays and a 1:1 stimulus:focal fish ratio in aggression assays14,17 are used. However, the researcher needs to specifically design the study with the hypothesis in mind (i.e., should stimulus fish be kept constant to maintain consistency in focal fish behavior, or should stimulus fish be rotated between each assay to ensure proper randomization).</li>
	<li>Store all fish in zebrafish housing racks (27.5-28.5 &#176;C) under a strict 12:12 light/dark cycle. Feed all focal and stimulus fish flake food daily and brine shrimp weekly, on non-research days.</li>
	<li>Be sure that all testing is done between ZT1 and ZT5 (zeitgeber time) to avoid circadian rhythm effects26.</li>
</ol>
2. Randomization and Tank Setup
<ol>
	<li>Randomize all individuals a priori to a specific sequence of behavioral assays. Set up a consistent randomization scheme using an online random sequence generator27 or a random sequence generator from a statistical software package (R).
	<ol>
		<li>Label each assay from 1 to 3 and keep this assignment consistent. Assign a random sequence to each individual and map the sequence according to the behavioral assay label. For example, for three total assays (1 mapped to Shoaling, 2 mapped to Boldness, and 3 mapped to Aggression), a given individual may have a randomized sequence of &#39;2,3,1&#39;, which will require them to perform the specific behavioral assays in the specified sequence.</li>
	</ol>
	</li>
	<li>Set up the assay tanks (boldness, aggression, and shoaling) in the laboratory in places that minimize the possibility for adverse external stimuli and be sure to have enough room for a video camcorder to capture the entire tank. Ensure that the camcorder has enough clarity to view tank labels as well as be able to distinguish subtle behaviors of the focal fish and setup the camcorder in this position.</li>
	<li>Record all behavioral assays with the camera maintained in the same position with a full view of the specified tank to minimize unintended differences in behavioral scoring as a result of differential recordings. 
	NOTE: Avoid placing tanks in heavy trafficked areas and by doors as movement and sound will affect zebrafish behavior.</li>
	<li>Establish unique JWatcher protocols24 for scoring each behavioral assay. Refer to the JWatcher manual to learn how to create focal master files to assign behaviors to keystrokes and focal analysis files to summarize data collected. 
	NOTE: JWatcher is behavioral scoring software that allows for reliable and repeatable customized behavioral scoring24.</li>
	<li>Define a labeling scheme to track the date, fish number, and assay number for all behavioral assays (e.g., &#39;F5-B-123115&#39; implying Fish 5, Boldness assay, on December 31st, 2015) and label the outside of the tank with tape in view and in focus of the camera. Keep and record this information in a lab notebook for quick reference and future quality control.</li>
	<li>Set up an acclimation tank that will be used between all assays as well as directly after the individuals are removed from the housing rack. 
	NOTE: The acclimation tanks and terminal tanks are small aquariums (40 cm x 20 cm x 25 cm) with gravel and a filter that closely resemble the housing rack.</li>
	<li>After the assays are all completed, transfer the individual into a separate terminal tank that will serve as the final destination tank for all used focal individuals. Use a tank that is large enough to house a group of individuals for the remainder of their lives (e.g., 25 gallon). 
	NOTE: It is very important to maintain consistent and similar water temperatures and conditions across all tanks. This includes housing, acclimation, and all testing tanks.</li>
</ol>
3. Conducting the Aggression Assay
<ol>
	<li>Conduct the aggression assay in a 19 L rectangular tank measuring 30 cm x 15 cm x 10 cm. Outfit the tank in external opaque partitions surrounding three sides of the aggression tank, leaving the front exposed for viewing, to reduce undesirable outside stimuli. Divide the tank with external markings into four equal rectangular quadrants and fix a mirror permanently (with silicone caulk) within the lower left quadrant, inclined at 22.5&#176; forming a right triangle against the far left side of the tank.</li>
	<li>Ensure that the temperature of the water in the acclimation tank and aggression tank is within 2 &#176;C of the housing rack. To do so, have fresh, aged water pre-warmed to 27.5-28.5 &#176;C ready to add to the aggression tank. Please note that it is important to change the water in between each assay to eliminate unwarranted olfactory cues.</li>
	<li>Transfer, by cupping, a focal fish from the housing rack to a separate acclimation tank where it will acclimate for 10 min. 
	NOTE: It is important to reduce stimulus introduced to the fish through improper handling. Transfer individuals as previously described27.
	<ol>
		<li>Specifically, manually and carefully place a small, transparent plastic cup into the tank of interest. Without disrupting the fish as much as transferring by using a net, slowly scoop up the fish into the cup.</li>
	</ol>
	</li>
	<li>Ensure that the video camcorder is ready to record by confirming that the aggression assay tank (see step 3.1) is in focus and immediately before transferring the individual into the aggression tank, press record on the device. Transfer focal fish via cupping from acclimation tank to aggression tank. 
	NOTE: It is important to record prior to the fish entering the aggression tank to track the exact time of entry.</li>
	<li>Record the aggression tank for 10 min and 30 sec and then cup the focal fish from the aggression tank back into the acclimation tank.</li>
	<li>When watching the recording, wait 30 sec after the fish has been introduced to the tank as an additional acclimation period before scoring behaviors.</li>
	<li>Using the JWatcher scoring system defined for aggressive behaviors, quantify the following behaviors for 10 min: Time spent near mirror, number of mirror approaches, number of darts, number of attempted bites (opening mouth in direction of mirror), and number of lateral displays (dorsal, pectoral, anal, and caudal fin erection)9.</li>
	<li>Score a single aggression assay at least twice, until the assay is scored with high agreement between iterations.</li>
</ol>
4. Conducting the Boldness Assay
<ol>
	<li>Conduct the boldness assay in a small 1.5 L trapezoidal tank, measuring 15 cm tall x 26.5 cm top x 22.5 cm bottom x 6 cm width. Wrap opaque paper around all sides of the tank but leave the front exposed for viewing. Place a single, thin piece of tape external to the tank to demarcate the top from the bottom portion of the tank.</li>
	<li>Ensure that the temperature of the water in the boldness tank is within 2 &#176;C of the housing rack (see step 3.2)</li>
	<li>Transfer the focal fish from the housing rack to the acclimation tank (see step 3.3) and let acclimate for 10 min.</li>
	<li>Ensure that the camcorder is ready to record the boldness assay and, once ready to transfer the focal fish, press record on the device. Transfer the focal fish from the acclimation tank to the boldness tank and record for 8 min and 30 sec.</li>
	<li>When watching the recording, allow for an additional 30 sec acclimation period after the fish is introduced to the tank before scoring.</li>
	<li>Using JWatcher software, quantify boldness behaviors for 8 min. Specifically, quantify the following behaviors: Time near surface, latency to enter upper portion, number of transitions into the upper portion, and number of erratic movements (darts)29.</li>
	<li>Score a single boldness assay at least twice, until the assay is scored with high agreement between iterations.</li>
</ol>
5. Conducting the Shoaling Assay
<ol>
	<li>Conduct the shoaling assay in a 76 L tank that has three compartments divided by two glass dividers sealed with silicone caulk (the resulting three compartments consist of two stimulus zones and one focal compartment). Externally, mark two preference zones designated 6.35 cm from each of the stimulus zones&#39; glass divider, indicative of two body lengths30. Apply opaque partitions externally around three sides of the shoaling tank, but leave the front exposed for viewing. 
	NOTE: This preference zone can be customized to test for specific hypotheses for different sized species.</li>
	<li>Depending on the nature of the study, select stimulus shoals to acclimate for at least 12 hr before testing and remain in the shoaling tank throughout the course of the experiment. 
	NOTE: Stimulus shoals are collections of individual fish that are used to assess how the focal fish behaves in the presence or absence of these shoals. Different stimulus shoal combinations can be selected to test a number of diverse shoaling hypotheses. Be sure that the stimulus shoals are rotated between each stimulus zone to avoid side bias and are also allowed to acclimate for at least 12 hr before testing.</li>
	<li>Transfer the focal fish into the acclimation tank as previously described (see step 3.3)</li>
	<li>Transfer, by cupping, the focal fish from the intermediate acclimation tank to the central compartment in the shoaling tank.</li>
	<li>Allow for a 10 min acclimation period before a 10 min live-scoring observation period. Alternatively, record the shoaling assays and score later using JWatcher. Fish are determined to be shoaling when they are within the preference zone in the chamber housing the target shoal.</li>
	<li>Quantify time spent in each preference zone and time spent in the center volume.</li>
	<li>As an additional descriptive measure, calculate &#39;strength of shoaling&#39; (SoS). Assign a value between -1 and +1 where the magnitude describes how often an individual fish shoals.</li>
	<li>Calculate the ratio of time spent shoaling divided by the area of the shoaling zones and subtract the ratio of time spent not shoaling and the area of the non-shoaling zones. Place this quantity over the sum of time spent in each zone divided by the volume of each zone individually. More information about this calculation can be found in a previous study14.</li>
</ol>
6. Data Quality Control
<ol>
	<li>Analyze data using traditional data analysis tools31-32.</li>
	<li>Test for homogeneity of variance using nonparametric Levene&#39;s test for all behaviors. If a behavior is non-homogeneous perform a log-transformation33.</li>
	<li>Confirm that there are no sequence effects (i.e., that the randomization order did not affect the individuals&#39; behavior) using a Kruskal-Wallis ANOVA on the homogeneous data34.</li>
	<li>Confirm that there are no side biases for the shoaling assay by creating univariate general linear models on SoS indices with side as a fixed factor35. 
	NOTE: If there are little to no issues with the data, downstream analyses can be conducted. If there are issues, reconcile with additional transformations, rationalize with biologically plausible explanations, and/or increase sample sizes.</li>
</ol>
7. Analyze Data
<ol>
	<li>Calculate two-tailed Spearman rank correlations36 for all behaviors separately within the boldness and aggression assays.</li>
	<li>Calculate intraclass correlation coefficients (ICC) as a two-way mixed model with consistency for behavioral assays that were conducted more than one time for a given individual36. In this setting, the ICC is a measurement of how consistently a fish behaved in a given assay measured more than one time.</li>
	<li>Preprocess boldness and aggression behaviors by centering and norming all behaviors to prepare for input to a principal components analysis (PCA)25. 
	NOTE: Preprocessing the measurements by centering and norming is a vital step. Without this preprocessing step behaviors that occur with more frequency and more variably will excessively influence the interpretations of the extracted components. The process of centering and norming will remove this bias.</li>
	<li>Perform a PCA with a correlation matrix to determine if boldness and aggression are linked together as a behavioral syndrome. Interpret behavioral loadings of each component significant at &#62;0.6. See Budaev 201024 for a comprehensive guide for reporting PCA for behavioral studies. A scree plot will be informative on which eigenvectors should be kept for interpretation.</li>
	<li>Using statistical software package such as R or SPSS31,32, extract scores for each component for each individual. The scores represent how much the given individual&#39;s behavior can be explained by the particular component.</li>
	<li>Calculate Spearman rank correlations between factor regression scores and the strength of shoaling36. 
	NOTE: A behavioral syndrome is considered present if boldness and aggression behaviors load on the same component or, if any component with significant interpretable loadings correlates with strength of shoaling. Also, note that strength of shoaling is not included in the PCA to allow for better interpretations of the more complex behavioral quantifications (boldness and aggression). The PCA will orthogonally collapse boldness and aggression features into eigenvectors to maximize the amount of variation explained and is well suited for these complex measurements. Interpreting the resulting eigenvectors and regressing our strength of shoaling measurements on each of them gives a much more intuitive interpretation of how each of the complex behaviors (boldness and aggression) relate to a more well-defined binary shoaling measurement (i.e., the fish is shoaling or not shoaling).</li>
</ol>

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M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Behavioural+differences+between+individuals+and+two+populations+of+stickleback+(Gasterosteus+aculeatus).">Behavioural differences between individuals and two populations of stickleback (Gasterosteus aculeatus).</a> J Evolution Biol. 18 (2), 464-473 (2005).</li><li>Wilson, A. D. M., Godin, J. -. G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Boldness+and+behavioral+syndromes+in+the+bluegill+sunfish,+Lepomis+macrochirus.">Boldness and behavioral syndromes in the bluegill sunfish, Lepomis macrochirus.</a> Behav Ecol. 20 (2), 231-237 (2009).</li><li>Brodin, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Behavioral+syndrome+over+the+boundaries+of+life--carryovers+from+larvae+to+adult+damselfly.">Behavioral syndrome over the boundaries of life--carryovers from larvae to adult damselfly.</a> Behav Ecol. 20 (1), 30-37 (2008).</li><li>Noldus, L. P., Spink, A. J., Tegelenbosch, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=EthoVision:+a+versatile+video+tracking+system+for+automation+of+behavioral+experiments.">EthoVision: a versatile video tracking system for automation of behavioral experiments.</a> Behav Res Methods Instrum Comput. 33 (3), 398-414 (2001).</li><li>Cote, J., Fogarty, S., Weinersmith, K., Brodin, T., Sih, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Personality+traits+and+dispersal+tendency+in+the+invasive+mosquitofish+(Gambusia+affinis).">Personality traits and dispersal tendency in the invasive mosquitofish (Gambusia affinis).</a> Proc R Soc B. 277 (1687), 1571-1579 (2010).</li><li>Fraser, D. F., Gilliam, J. F., Daley, M. J., Le, A. N., Skalski, G. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Explaining+leptokurtic+movement+distributions:+intrapopulation+variation+in+boldness+and+exploration.">Explaining leptokurtic movement distributions: intrapopulation variation in boldness and exploration.</a> Am Nat. 158 (2), 124-135 (2001).</li><li>Dingemanse, N. J., Wright, J., Kazem, A. J. N., Thomas, D. K., Hickling, R., Dawnay, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Behavioural+syndromes+differ+predictably+between+12+populations+of+three-spined+stickleback.">Behavioural syndromes differ predictably between 12 populations of three-spined stickleback.</a> J Anim Ecol. 76 (6), 1128-1138 (2007).</li></ol>

The authors (GW and SPM) have no competing financial interests or conflicts of interest.

The protocol will determine if there are consistent associations in boldness, aggression, and shoaling behaviors in zebrafish. If there are consistent associations in a given population between any of these behaviors, then a behavioral syndrome is present. By studying a population&#39;s natural behavioral syndrome, researchers can have a more complete understanding of its behavioral dynamic, population structure, and possibly evolutionary history3. Furthermore, manipulating the environment that affects these b...

There is a growing body of literature investigating the associations between distinct behaviors within individual animals from a given population. These associations are termed behavioral syndromes, and the measurements typically include boldness, aggression, exploratory behavior, and sociability1-5. Behavioral syndromes are valuable for both direct and indirect reasons. Directly, knowledge of behavioral syndromes can provide a more complete view of evolutionary theory, population structure, and population dynamics3. Indirectly, knowledge regarding behavioral associations may inform fields that quantify behavior such as pharmacology6 , toxicology7, behavioral genetics8,9, and endocrinology10. Because of these direct and indirect benefits, an increased knowledge of behavioral syndromes is especially valuable in commonly used model organisms such as the zebrafish. Studies using zebrafish are found in a variety of disciplines, including the analysis of behavioral syndromes11-13. To advance knowledge in behavioral syndrome research, and because other disciplines also use behavioral measurements for hypothesis testing, reliable and succinct descriptions of behavior are required for valid analyses and interpretations and standardized protocols will facilitate inter-study comparisons within species. Our protocol was developed to measure a boldness-aggression-shoaling behavioral syndrome in a population of lab-reared zebrafish14. However, the basis of the protocol (tracking individual fish, ensuring proper randomization, and appropriate analyses) can be easily modified for a variety of alternative behavioral measures. Additionally, boldness, aggression, or shoaling assays can be run individually for the testing of distinct hypotheses. Therefore, while it is our goal to describe how to conduct a behavioral syndrome study and the protocol for successful individual level behavioral measurement, each facet of this procedure can stand alone.
The literature on behavioral syndromes spans several taxonomic groups, from arthropods to humans4 and, in order to measure a behavioral syndrome, at least two behavioral contexts must be quantified. Unfortunately, there is often little consistency in the assays that are used to quantify the behavioral measurement across the axes of behavior. For example, in fish, boldness may be measured using T-maze assays, open-field assays, or introduction of a novel or foreign stimulus15. Aggression studies in fish might involve dyad interactions, video stimulus assays, or clay model assays12,16,17. Likewise, analysis of shoaling behavior, which typically involves the measurement of shoalmate preference, may be performed in different types of tanks, with different methods to determine association time21-23. In this protocol a specific subset of the overall behavioral assay repertoire is presented. Specifically, this protocol presents a methodology to track individuals through boldness, aggression, and shoaling assays in a way that facilitates comparisons within individuals to determine whether the comparisons are consistent across all individuals within a population. We have performed this protocol with zebrafish and convict cichlids (Amatitlania nigrofasciata) in previous studies14,18, and it will work with any similarly sized freshwater fish.
Boldness assays are conducted in a 1.5 L trapezoidal tank that has a horizontal line delineating equal sized areas in the upper and lower portions of the tank. Quantified behaviors include the number of transitions by the test fish between the upper and lower portion of the tank, the time spent in each portion, the number of darts, and the latency to enter the upper portion. The aggression assay is performed in a 19L rectangular tank that includes a 3 inch x 5 inch mirror inclined at about 22&#176; situated in the lower left corner of the tank19. Quantified behaviors include the total amount of time spent by the target fish interacting with the mirror20, along with specific aggressive indicators &#8211; number of bites, lateral displays, darts between the test fish and its reflection. For these specific indicators, bites are defined as quick lunges toward the mirror with an open mouth, lateral displays are defined as the flaring of lateral, pectoral, anal and dorsal fins in the direction of the mirror, and darts are any erratic movements that are not directed toward the mirror. Lastly, the shoaling assay quantifies the behavior of a test fish in center chamber of a tri-chambered tank. The side chambers of the tank are either empty, or contain a &#34;target shoal&#34; of fish, and the time the test fish spends near each side chamber is measured21-23. A single composite score, referred to as Strength of Shoaling (SoS), is calculated for each individual test fish, specific to the stimuli, and can be used in downstream analyses14. All behaviors are scored by a single viewer, or multiple viewers using free behavioral quantification software known as JWatcher24.
Testing the presence of a behavioral syndrome is primarily a statistical endeavor, and it is advisable to follow the guidelines as presented by Budeav 201025. Specifically, it is recommended to perform a principal components analysis (PCA) on centered and normed data in which the inputs are the vectors of an individual&#39;s behaviors in assays with multiple behavioral measurements (i.e., boldness and aggression). The PCA, performed on a correlation matrix, reduces the dimensionality of the behavioral measurements, and thus extracts the most important knowledge that explains a majority of the variation. The extracted components can then be interpreted based on high factor loadings for the individual behavior of interest and regression scores can be extracted for each individual on the basis of the explanatory components. These regression scores can then be compared to the SoS measurement and other various non-behavioral measurements such as fish size or sex.
This workflow has been implemented in a study of zebrafish behavioral syndromes in which a sex specific behavioral syndrome that exists between boldness and shoaling14 was discovered. In this situation, bolder zebrafish males are more likely to associate with a larger, more aggressive species (D. albolineatus), but this association is lost in females. This workflow was also implemented in a study of juvenile convict cichlid kin (Amatitlania nigrofasciata)18 in which a behavioral syndrome was not discovered, potentially indicating behavioral plasticity of the species. Therefore, the following protocol is presented with a goal of delineating the nature of three specific assays (boldness, aggression, and shoaling) in the framework of studying an individual level behavioral syndrome.

<table border="0" cellpadding="0" cellspacing="0" width="783">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:352px;">Zebrafish Rack System</td>
			<td style="width:224px;">Aquaneering Inc</td>
			<td style="width:119px;">Cat. # ZS550</td>
			<td style="width:88px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pet Valu Tropical Fish Food, 224.0g</td>
			<td>Pet Valu</td>
			<td>Cat. # 31700</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Premium Grade Brine Shrimp Eggs, 16 oz</td>
			<td>Brine Shrimp Direct</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1.5 L Trapezoidal Tank</td>
			<td>Pentair Aquatic Ecosystems</td>
			<td>Cat. # itsts-a</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">19L rectangular tank</td>
			<td>That Fish Place</td>
			<td align="right">211932</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">76L rectangular tank</td>
			<td>That Fish Place</td>
			<td align="right">212180</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hitachi KP-D20A CCD Camera</td>
			<td>Prescott&#39;s, Inc.</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nikon AF Nikkor 35-105mm f/305~4.5s MACRO lens</td>
			<td>Nikon Corporation</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">ArtMinds Square Mirror, Value Pack 3&#34;x3&#34;</td>
			<td>Michaels</td>
			<td>Cat. # 10334162</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Jwatcher</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SPSS Statistics Base</td>
			<td>IBM</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">R</td>
			<td>The R Foundation</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

boldness, aggression, and shoaling assays for zebrafish behavioral syndromes

A behavioral syndrome exists when specific behaviors interact under different contexts. Zebrafish have been test subjects in recent studies and it is important to standardize protocols to ensure proper analyses and interpretations. In our previous studies, we have measured boldness by monitoring a series of behaviors (time near surface, latency in transitions, number of transitions, and darts) in a 1.5 L trapezoidal tank. Likewise, we quantified aggression by observing bites, lateral displays, darts, and time near an inclined mirror in a rectangular 19 L tank. By dividing a 76 L tank into thirds, we also examined shoaling preferences. The shoaling assay is a highly customizable assay and can be tailored for specific hypotheses. However, protocols for this assay also must be standardized, yet flexible enough for customization. In previous studies, end chambers were either empty, contained 5 or 10 zebrafish, or 5 pearl danios (D. albolineatus). In the following manuscript, we present a detailed protocol and representative data that accompany successful applications of the protocol, which will allow for replication of behavioral syndrome experiments.

Depending on the nature of the study, and specific protocol employed, several distinct results are possible in a behavioral syndromes experiment. The following tables and figures, where indicated, are adapted from our previous study published in the journal Behavioural Processes14 and the journal Zebrafish17. When the proposal (as described above) is carried out in its entirety, two sets of results, &#39;within assay correlations&#39; and &#39;between assay correlati...

Watch this Scientific Journal Video about Boldness, Aggression, and Shoaling Assays for Zebrafish Behavioral Syndromes at JoVE.com

Boldness, Aggression, and Shoaling Assays for Zebrafish Behavioral Syndromes

This manuscript describes the setup, implementation, and analysis of boldness, aggression, and shoaling in zebrafish and testing for the presence of a behavioral syndrome. A standardized approach for behavioral quantification will allow for easier comparison across studies. Modifications to this protocol are possible as each assay can be run individually.

A behavioral syndrome exists when specific behaviors interact under different contexts. Zebrafish have been test subjects in recent studies and it is ...

boldness-aggression-shoaling-assays-for-zebrafish-behavioral

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10.2K Views.  Saint Joseph’s University. This manuscript describes the setup, implementation, and analysis of boldness, aggression, and shoaling in zebrafish and testing for the presence of a behavioral syndrome. A standardized approach for behavioral quantification will allow for easier comparison across studies. Modifications to this protocol are possible as each assay can be run individually.

Video: Boldness, Aggression, and Shoaling Assays for Zebrafish Behavioral Syndromes

Intra-Operative Behavioral Tasks in Awake Humans Undergoing Deep Brain Stimulation Surgery

Deep brain stimulation (DBS) is a surgical procedure that directs chronic, high frequency electrical stimulation to specific targets in the brain through implanted electrodes. Deep brain stimulation was first implemented as a therapeutic modality by Benabid et al. in the late 1980s, when he used this technique to stimulate the ventral intermediate nucleus of the thalamus for the treatment of tremor 1. Currently, the procedure is used to treat patients who fail to respond adequately to medical management for diseases such as Parkinson's, dystonia, and essential tremor. The efficacy of this procedure for the treatment of Parkinson's disease has been demonstrated in well-powered, randomized controlled trials 2. Presently, the U.S. Food and Drug Administration has approved DBS as a treatment for patients with medically refractory essential tremor, Parkinson's disease, and dystonia. Additionally, DBS is currently being evaluated for the treatment of other psychiatric and neurological disorders, such as obsessive compulsive disorder, major depressive disorder, and epilepsy. 
DBS has not only been shown to help people by improving their quality of life, it also provides researchers with the unique opportunity to study and understand the human brain. Microelectrode recordings are routinely performed during DBS surgery in order to enhance the precision of anatomical targeting. Firing patterns of individual neurons can therefore be recorded while the subject performs a behavioral task. Early studies using these data focused on descriptive aspects, including firing and burst rates, and frequency modulation 3. More recent studies have focused on cognitive aspects of behavior in relation to neuronal activity 4,5. This article will provide a description of the intra-operative methods used to perform behavioral tasks and record neuronal data with awake patients during DBS cases. Our exposition of the process of acquiring electrophysiological data will illuminate the current scope and limitations of intra-operative human experiments.

Deep brain stimulation surgery offers a unique opportunity to examine information encoding in the awake human brain. This article will describe intra-operative methods used to perform cognitive and behavioral tasks while simultaneously acquiring physiological data such as EMG, single-unit neuronal activity and/or local field potentials.

Deep brain stimulation (DBS) is a surgical procedure that directs chronic, high frequency electrical stimulation to specific targets in the brain through ...

Using Visual and Narrative Methods to Achieve Fair Process in Clinical Care

The Institute of Medicine has targeted patient-centeredness as an important area of quality improvement. A major dimension of patient-centeredness is respect for patient's values, preferences, and expressed needs. Yet specific approaches to gaining this understanding and translating it to quality care in the clinical setting are lacking. From a patient perspective quality is not a simple concept but is best understood in terms of five dimensions: technical outcomes; decision-making efficiency; amenities and convenience; information and emotional support; and overall patient satisfaction. Failure to consider quality from this five-pronged perspective results in a focus on medical outcomes, without considering the processes central to quality from the patient's perspective and vital to achieving good outcomes. In this paper, we argue for applying the concept of fair process in clinical settings. Fair process involves using a collaborative approach to exploring diagnostic issues and treatments with patients, explaining the rationale for decisions, setting expectations about roles and responsibilities, and implementing a core plan and ongoing evaluation. Fair process opens the door to bringing patient expertise into the clinical setting and the work of developing health care goals and strategies. This paper provides a step by step illustration of an innovative visual approach, called photovoice or photo-elicitation, to achieve fair process in clinical work with acquired brain injury survivors and others living with chronic health conditions. Applying this visual tool and methodology in the clinical setting will enhance patient-provider communication; engage patients as partners in identifying challenges, strengths, goals, and strategies; and support evaluation of progress over time. Asking patients to bring visuals of their lives into the clinical interaction can help to illuminate gaps in clinical knowledge, forge better therapeutic relationships with patients living with chronic conditions such as brain injury, and identify patient-centered goals and possibilities for healing. The process illustrated here can be used by clinicians, (primary care physicians, rehabilitation therapists, neurologists, neuropsychologists, psychologists, and others) working with people living with chronic conditions such as acquired brain injury, mental illness, physical disabilities, HIV/AIDS, substance abuse, or post-traumatic stress, and by leaders of support groups for the types of patients described above and their family members or caregivers.

This paper illustrates an innovative visual approach (photovoice or photo-elicitation) to achieve fair process in clinical care for patients living with chronic health conditions, illuminate gaps in clinical knowledge, forge better therapeutic relationships, and identify patient-centered goals and possibilities for healing.

The Institute of Medicine has targeted patient-centeredness as an important area of quality improvement. A major dimension of patient-centeredness is ...

Biomarkers in an Animal Model for Revealing Neural, Hematologic, and Behavioral Correlates of PTSD

Identification of biomarkers representing the evolution of the pathophysiology of Post Traumatic Stress Disorder (PTSD) is vitally important, not only for objective diagnosis but also for the evaluation of therapeutic efficacy and resilience to trauma. Ongoing research is directed at identifying molecular biomarkers for PTSD, including traumatic stress induced proteins, transcriptomes, genomic variances and genetic modulators, using biologic samples from subjects' blood, saliva, urine, and postmortem brain tissues. However, the correlation of these biomarker molecules in peripheral or postmortem samples to altered brain functions associated with psychiatric symptoms in PTSD remains unresolved. Here, we present an animal model of PTSD in which both peripheral blood and central brain biomarkers, as well as behavioral phenotype, can be collected and measured, thus providing the needed correlation of the central biomarkers of PTSD, which are mechanistic and pathognomonic but cannot be collected from people, with the peripheral biomarkers and behavioral phenotypes, which can.
Our animal model of PTSD employs restraint and tail shocks repeated for three continuous days - the inescapable tail-shock model (ITS) in rats. This ITS model mimics the pathophysiology of PTSD 17, 7, 4, 10. We and others have verified that the ITS model induces behavioral and neurobiological alterations similar to those found in PTSD subjects 17, 7, 10, 9. Specifically, these stressed rats exhibit (1) a delayed and exaggerated startle response appearing several days after stressor cessation, which given the compressed time scale of the rat's life compared to a humans, corresponds to the one to three months delay of symptoms in PTSD patients (DSM-IV-TR PTSD Criterian D/E 13), (2) enhanced plasma corticosterone (CORT) for several days, indicating compromise of the hypothalamopituitary axis (HPA), and (3) retarded body weight gain after stressor cessation, indicating dysfunction of metabolic regulation.
The experimental paradigms employed for this model are: (1) a learned helplessness paradigm in the rat assayed by measurement of acoustic startle response (ASR) and a charting of body mass; (2) microdissection of the rat brain into regions and nuclei; (3) enzyme-linked immunosorbent assay (ELISA) for blood levels of CORT; (4) a gene expression microarray plus related bioinformatics tools 18. This microarray, dubbed rMNChip, focuses on mitochondrial and mitochondria-related nuclear genes in the rat so as to specifically address the neuronal bioenergetics hypothesized to be involved in PTSD.

We describe a rat model of post traumatic stress disorder (PTSD) that reveals the persistent alterations in neuroendocrine function and the delayed long-term, exaggerated fear response, characteristic of PTSD patients. The animal model and methods described here are useful for correlating biomarkers in brain nuclei, which are mechanistic but cannot be measured in patients, with biomarkers in peripheral white blood cells, which can.

Identification of biomarkers representing the evolution of the pathophysiology of Post Traumatic Stress Disorder (PTSD) is vitally important, not only for ...

Eye Tracking Young Children with Autism

The rise of accessible commercial eye-tracking systems has fueled a rapid increase in their use in psychological and psychiatric research. By providing a direct, detailed and objective measure of gaze behavior, eye-tracking has become a valuable tool for examining abnormal perceptual strategies in clinical populations and has been used to identify disorder-specific characteristics1, promote early identification2, and inform treatment3. In particular, investigators of autism spectrum disorders (ASD) have benefited from integrating eye-tracking into their research paradigms4-7. Eye-tracking has largely been used in these studies to reveal mechanisms underlying impaired task performance8 and abnormal brain functioning9, particularly during the processing of social information1,10-11. While older children and adults with ASD comprise the preponderance of research in this area, eye-tracking may be especially useful for studying young children with the disorder as it offers a non-invasive tool for assessing and quantifying early-emerging developmental abnormalities2,12-13. Implementing eye-tracking with young children with ASD, however, is associated with a number of unique challenges, including issues with compliant behavior resulting from specific task demands and disorder-related psychosocial considerations. In this protocol, we detail methodological considerations for optimizing research design, data acquisition and psychometric analysis while eye-tracking young children with ASD. The provided recommendations are also designed to be more broadly applicable for eye-tracking children with other developmental disabilities. By offering guidelines for best practices in these areas based upon lessons derived from our own work, we hope to help other investigators make sound research design and analysis choices while avoiding common pitfalls that can compromise data acquisition while eye-tracking young children with ASD or other developmental difficulties.

Eye tracking has long been used to study gaze patterns in typically-developing individuals, but recent technological advancements have made its use with clinical populations, including autism, more feasible. While eye-tracking young children with autism can offer insight into early symptom manifestations, it involves methodological challenges. Suggestions for best practices are provided.

The rise of accessible commercial eye-tracking systems has fueled a rapid increase in their use in psychological and psychiatric research. By providing a ...

Processing of Primary Brain Tumor Tissue for Stem Cell Assays and Flow Sorting

Brain tumors are typically comprised of morphologically diverse cells that express a variety of neural lineage markers. Only a relatively small fraction of cells in the tumor with stem cell properties, termed brain tumor initiating cells (BTICs), possess an ability to differentiate along multiple lineages, self-renew, and initiate tumors in vivo. We applied culture conditions originally used for normal neural stem cells (NSCs) to a variety of human brain tumors and found that this culture method specifically selects for stem-like populations. Serum-free medium (NSC) allows for the maintenance of an undifferentiated stem cell state, and the addition of bFGF and EGF allows for the proliferation of multi-potent, self-renewing, and expandable tumorspheres.
To further characterize each tumor's BTIC population, we evaluate cell surface markers by flow cytometry. We may also sort populations of interest for more specific characterization. Self-renewal assays are performed on single BTICs sorted into 96 well plates; the formation of tumorspheres following incubation at 37 &deg;C indicates the presence of a stem or progenitor cell. Multiple cell numbers of a particular population can also be sorted in different wells for limiting dilution analysis, to analyze self-renewal capacity. We can also study differential gene expression within a particular cell population by using single cell RT-PCR.
The following protocols describe our procedures for the dissociation and culturing of primary human samples to enrich for BTIC populations, as well as the dissociation of tumorspheres. Also included are protocols for staining for flow cytometry analysis or sorting, self-renewal assays, and single cell RT-PCR.

The identification of brain tumor initiating cells (BTICs), the rare cells within a heterogeneous tumor possessing stem cell properties, provides new insights into human brain tumor pathogenesis. We have refined specific culture conditions to enrich for BTICs, and we routinely use flow cytometry to further enrich these populations. Self-renewal assays and transcript analysis by single cell RT-PCR can subsequently be performed on these isolated cells.

Brain tumors are typically comprised of morphologically diverse cells that express a variety of neural lineage markers. Only a relatively small fraction ...

Screening for Melanoma Modifiers using a Zebrafish Autochthonous Tumor Model

Genomic studies of human cancers have yielded a wealth of information about genes that are altered in tumors1,2,3. A challenge arising from these studies is that many genes are altered, and it can be difficult to distinguish genetic alterations that drove tumorigenesis from that those arose incidentally during transformation. To draw this distinction it is beneficial to have an assay that can quantitatively measure the effect of an altered gene on tumor initiation and other processes that enable tumors to persist and disseminate. Here we present a rapid means to screen large numbers of candidate melanoma modifiers in zebrafish using an autochthonous tumor model4 that encompasses steps required for melanoma initiation and maintenance. A key reagent in this assay is the miniCoopR vector, which couples a wild-type copy of the mitfa melanocyte specification factor to a Gateway recombination cassette into which candidate melanoma genes can be recombined5. The miniCoopR vector has a mitfa rescuing minigene which contains the promoter, open reading frame and 3'-untranslated region of the wild-type mitfa gene. It allows us to make constructs using full-length open reading frames of candidate melanoma modifiers. These individual clones can then be injected into single cell Tg(mitfa:BRAFV600E);p53(lf);mitfa(lf)zebrafish embryos. The miniCoopR vector gets integrated by Tol2-mediated transgenesis6 and rescues melanocytes. Because they are physically coupled to the mitfa rescuing minigene, candidate genes are expressed in rescued melanocytes, some of which will transform and develop into tumors. The effect of a candidate gene on melanoma initiation and melanoma cell properties can be measured using melanoma-free survival curves, invasion assays, antibody staining and transplantation assays.

A rapid way to screen for melanoma modifiers using a zebrafish autochthonous tumor model is presented. It takes advantage of the miniCoopR vector which allows for expression of candidate melanoma genes in melanocytes. A method to obtain melanoma-free survival curves, an invasion assay, a protocol for antibody staining of scale melanocytes and a melanoma transplantation assay are described.

Genomic studies of  human cancers have yielded a wealth of information about genes that are altered  in tumors1,2,3. A challenge arising from these ...

Adaptation of Semiautomated Circulating Tumor Cell (CTC) Assays for Clinical and Preclinical Research Applications

The majority of cancer-related deaths occur subsequent to the development of metastatic disease. This highly lethal disease stage is associated with the presence of circulating tumor cells (CTCs). These rare cells have been demonstrated to be of clinical significance in metastatic breast, prostate, and colorectal cancers. The current gold standard in clinical CTC detection and enumeration is the FDA-cleared CellSearch system (CSS). This manuscript outlines the standard protocol utilized by this platform as well as two&#160;additional adapted protocols that describe the detailed process of user-defined marker optimization for protein characterization of patient CTCs and a comparable protocol for CTC capture in very low volumes of blood, using standard CSS reagents, for studying in vivo preclinical mouse models of metastasis. In addition, differences in CTC quality between healthy donor blood spiked with cells from tissue culture versus patient blood samples are highlighted. Finally, several commonly discrepant items that can lead to CTC misclassification errors are outlined. Taken together, these protocols will provide a useful resource for users of this platform interested in preclinical and clinical research pertaining to metastasis and CTCs.

Adaptation of Semiautomated Circulating Tumor Cell CTC Assays for Clinical and Preclinical Research Applications

Circulating tumor cells (CTCs) are prognostic in several metastatic cancers. This manuscript describes the gold standard CellSearch system (CSS) CTC enumeration platform and highlights common misclassification errors. In addition, two&#160;adapted protocols are described for user-defined marker characterization of CTCs and CTC enumeration in preclinical mouse models of metastasis using this technology.

The majority of cancer-related deaths occur subsequent to the development of metastatic disease. This highly lethal disease stage is associated with the ...

A Novel in vivo Gene Transfer Technique and in vitro Cell Based Assays for the Study of Bone Loss in Musculoskeletal Disorders

Differentiation and activation of osteoclasts play a key role in the development of musculoskeletal diseases as these cells are primarily involved in bone resorption. Osteoclasts can be generated in vitro from monocyte/macrophage precursor cells in the presence of certain cytokines, which promote survival and differentiation. Here, both in vivo and in vitro techniques are demonstrated, which allow scientists to study different cytokine contributions towards osteoclast differentiation, signaling, and activation. The minicircle DNA delivery gene transfer system provides an alternative method to establish an osteoporosis-related model is particularly useful to study the efficacy of various pharmacological inhibitors in vivo. Similarly, in vitro culturing protocols for producing osteoclasts from human precursor cells in the presence of specific cytokines enables scientists to study osteoclastogenesis in human cells for translational applications. Combined, these techniques have the potential to accelerate drug discovery efforts for osteoclast-specific targeted therapeutics, which may benefit millions of osteoporosis and arthritis patients worldwide.

A Novel in vivo Gene Transfer Technique and in vitro Cell Based Assays for the Study of Bone Loss in Musculoskeletal Disorders

Differentiation of precursor cells into osteoclasts is regulated by cytokines and growth factors. Here, a novel gene transfer technique for differentiation of osteoclasts in vivo and cell culture protocols for differentiating precursor cells into osteoclasts in vitro as a method to study the effects of cytokines on osteoclastogenesis are described.

Differentiation and activation of osteoclasts play a key role in the development of musculoskeletal diseases as these cells are primarily involved in bone ...

A Novel Model of Mild Traumatic Brain Injury for Juvenile Rats

Despite growing evidence that childhood represents a major risk period for mild traumatic brain injury (mTBI) from sports-related concussions, motor vehicle accidents, and falls, a reliable animal model of mTBI had previously not been developed for this important aspect of development. The modified weight-drop technique employs a glancing impact to the head of a freely moving rodent transmitting acceleration, deceleration, and rotational forces upon the brain. When applied to juvenile rats, this modified weight-drop technique induced clinically relevant behavioural outcomes that were representative of post-concussion symptomology. The technique is a rapidly applied procedure with an extremely low mortality rate, rendering it ideal for high-throughput studies of therapeutics. In addition, because the procedure involves a mild injury to a closed head, it can easily be used for studies of repetitive brain injury. Owing to the simplistic nature of this technique, and the clinically relevant biomechanics of the injury pathophysiology, the modified weight-drop technique provides researchers with a reliable model of mTBI that can be used in a wide variety of behavioural, molecular, and genetic studies.

The modified weight-drop technique is an easy, cost-effective procedure used for the induction of mild traumatic brain injury in juvenile rats. This novel technique produces clinically relevant symptomology that will advance the study of mild traumatic brain injury (mTBI) and concussion.

Despite growing evidence that childhood represents a major risk period for mild traumatic brain injury (mTBI) from sports-related concussions, motor ...

Real-time Cytotoxicity Assays in Human Whole Blood

A live cell-based whole blood cytotoxicity assay (WCA) that allows access to temporal information of the overall cell cytotoxicity is developed with high-throughput cell positioning technology. The targeted tumor cell populations are first preprogrammed to immobilization into an array format, and labeled with green fluorescent cytosolic dyes. Following the cell array formation, antibody drugs are added in combination with human whole blood. Propidium iodide (PI) is then added to assess cell death. The cell array is analyzed with an automatic imaging system. While cytosolic dye labels the targeted tumor cell populations, PI labels the dead tumor cell populations. Thus, the percentage of target cancer cell killing can be quantified by calculating the number of surviving targeted cells to the number of dead targeted cells. With this method, researchers are able to access time-dependent and dose-dependent cell cytotoxicity information. Remarkably, no hazardous radiochemicals are used. The WCA presented here has been tested with lymphoma, leukemia, and solid tumor cell lines. Therefore, WCA allows researchers to assess drug efficacy in a highly relevant ex&#160;vivo condition.

The whole blood cytotoxicity assay (WCA) is a cytotoxicity assay developed by incorporating high-throughput cell positioning technology with fluorescence microscopy and automated image processing. Here, we describe how lymphoma cells treated with an anti-CD20 antibody can be analyzed real-time in human whole blood to provide quantitative cellular cytotoxicity analysis.

A live cell-based whole blood cytotoxicity assay (WCA) that allows access to temporal information of the overall cell cytotoxicity is developed with ...