This work was supported by National Institute of Health Grants EY0081 and 5T32UY07145 and by the Knights Templar Eye Foundation. Jason Rihel is a Bristol-Squibb Fellow of the Life Sciences Research Foundation.

This protocol outlines the steps to perform the Visual-Motor Response of zebrafish larvae to light increments and decrements in your own lab. Zebrafish are a great model system for behavioral studies. They are easy to maintain, they have large clutch sizes, and they develop quickly. For example, the eyes of zebrafish larvae are responsive to light by day 3 of development and at which time they exhibit a startle response. 

Part 1: Plating individual fish into a 96 well plate
<ol>
<li>Grow WT larvae under a dark/light cycle at 28&deg;C until at least 4 days post fertilization (dpf). Our typical light:dark cycle is 14 hours of lights ON starting at 9:00AM, and 10 hours of lights OFF, starting at 11:00 PM. For the best behavioral results, avoid overcrowding; we usually keep no more than 50 larvae in a single petri dish. </li>
<li>After 4 dpf, the zebrafish are ready to be transferred into a 96-well plate. To give the larvae more swimming room, we typically use a 96-well plate with a large well-size of 650 &micro;l; however, standard 96-well plates work just fine. Using a plastic transfer pipet, gently transfer one larva per well. </li>
<li>After transferring fish into the wells, fill out each well with enough fish water such that the water surface is nearly flush to the top of the wells. Either overfilling or underfilling the well can cause optical problems for the recording camera. Also, take care not to introduce bubbles into the wells. </li>
</ol>
Part 2: Survey of the recording apparatus
For this part of the protocol, please refer to the film to identify components and to familiarize yourself with our set up of the recording apparatus.
<ol>
<li>Inside the recording chamber is a well defined place to position the 96-well plate.</li>
<li>The camera is positioned in the back and is focused on the plate using mirrors off the box. The angle of these mirrors can be adjusted by turning the screws that hold the mirrors in place. </li>
<li>The recording chamber is illuminated from the bottom by infrared LEDs. This allows the camera to see the fish even in the dark. The larvae cannot detect IR light, so this constant IR illumination does not affect the experiment. White LEDs also illuminate the recording chamber from below. They are controlled separately from the IR lights. Illuminating the chamber with white light from above or from the sides is certainly possible; however, in those cases, care must be taken to avoid strong glares off the water surface that may interfere with the camera.</li>
<li>For experiments that last longer than a couple of hours, fill the chamber with gently running water to help maintain a constant temperature for the experimental duration. One way to accomplish a constant flow of water is to pump water from a reservoir by a small aquarium pump that is heated to 28&deg; with a typical underwater aquarium heater.</li>
<li>To minimize stray vibration from the room, the entire recording unit should sit atop a heavy balance table.</li>
</ol>
Part 3: Alignment of the 96-well plate with the computer grid of the video-tracking
<ol>
<li>Place the 96-well plate containing the fish into the recording chamber.</li>
<li>When using a water bath, slowly place the plate in the water, giving the water level a chance to adjust without spilling onto the plate. Alternatively, shut off the water flow, add the plate, and then resume the flow. Also, be sure to use a spring or a rubber band to hold the 96-well plate in place.</li>
<li>In the Viewpoint Videotrack software, check that all the larvae of your experiment are visible on the computer screen. Using the controls of the software, align the grid of the video-tracking software with the wells of your plate such that each fish is within a square of the grid. The tracking computer will be calculating the movement separately for each of these boxes, so if you misalign the computer grid some of the fish movements may be lost. Or even worse: two adjacent fish will occupy the same area and be counted as one fish. This step is very important for all your recordings.</li>
<li>After the alignment, program the timing for when the lights should go on and off. We typically allow 3 hours of light or dark adaptation in the box both to obtain a baseline activity level, but also to give the larvae an opportunity to calm down following the pipetting and handling. After the baseline, we then alternate with 30 minutes of lights ON followed by 30 minutes of lights OFF, and repeat several times.</li>
<li>Next, close the door of the recording chamber and start recording.</li>
<li>In practice, we record the activity of each fish per second, but the Viewpoint software in fact records the frame by frame data (refer to the film for a demonstration of the data collection). Setting the threshold value for minimum pixel change per frame will depend somewhat on your particular camera and light setup. For our setup, we typically use a threshold of 4 pixels; that is, if fewer than 4 pixels are changing, it is considered background. If more than 4 pixels are moving, it indicates the fish is moving. We empirically determined that this cutoff detects nearly all the larval swim and turn movements.</li>
<li>Even though the recording boxes isolate the larvae fairly well, turn OFF the light in the room and take care to minimize interruptions with mechanical noise such as closing and opening doors in the room, having a dance party, or doing your exercise routines.</li>
</ol>
Part 4: Analyzing the data
<ol>
<li>After the experiment is completed, transfer the data collected into an excel sheet or into your favorite analysis suite.</li>
<li>The attached excel sheet is an example of what the data may look like: it contains the time in seconds from the start of the experiment and the activity of each larva per seconds for all the fish throughout the entire experiment (See supplementary file&nbsp;Example Data&nbsp;in the Files section of this page).</li>
<li>Figure&nbsp;1 shows an example of the activity of a single larva. Figure&nbsp;2 is a representative trace of the average of 40 WT zebrafish larvae. The averaged ON and OFF responses are prominent and consistent. <img src="/files/ftp_upload/old/923_2008_9_26_9/923_Figure-02.png" alt="Figure 1" width="569" height="398" /> Figure 1: Activity of a single fish. The activity of a single WT fish at 5 dpf in response to alternating periods of 30 minutes light ON and OFF. The ON responses are indicated by black arrows and the OFF responses with red arrows. <img src="/files/ftp_upload/old/923_2008_9_26_11/923_Figure-03.png" alt="Figure 2" width="577" height="387" /> Figure 2: Average activity of 40 fish. The average activity of 40 WT fish at 5 dpf in response to alternating periods of 30 minutes light ON and OFF. The averaged ON (black arrows) and OFF (red arrows) responses are prominent and consistent.</li>
</ol>
5. Representative Results
Figure 3 is a schematic outline of the experimental outline used in all of our experiments. <img src="/files/ftp_upload/old/923_2008_9_26_12/923_Figure-04.png" alt="Figure 3" width="530" height="479" /> Figure 3. Experimental design of the Visual Motor Response (VMR) test. A) Individual fish are placed in a 96-well plate in a recording chamber. The activity of each fish is measured per second. B) Fish are given a period of dark or light adaptation to settle them and to obtain a baseline activity level. Periods of 30 minutes lights ON and lights OFF are introduced consecutively for a total of 3 hours. This diagram was adapted from Prober et al., 2006.
What do the Visual-Motor Response graphs look like? We measured the ON and OFF responses of WT fish to light increments and decrements. To confirm that these responses were dependent on eye function, we measured the activity of chk mutants, which do not develop any eyes. Figure&nbsp;4 shows the average activity obtained from WT animals as well as the chk mutants. <img src="/files/ftp_upload/old/923_2008_9_26_13/923_Figure-05.png" alt="Figure 4" width="489" height="212" /> Figure 4: WT fish have clear ON and OFF responses that are mediated by the lateral eyes. The locomotor behavior of zebrafish larvae at 5 dpf in response to 30 minutes of light ON and 30 minutes of light OFF is recorded per second. Each trace represents an average of 480 responses from 120 individual WT (blue trace) or chk mutant larvae (orange trace) recorded over 3 experiments. The chk mutants do not significantly increase their activity to either light increments or decrements and have a low baseline level of activity. This figure was adapted from Emran et al., 2007.
Visual-Motor Responses from the nrc mutant fish. The nrc mutant was thought to be completely blind based on the OKR test. In the nrc mutant, the photoreceptor terminals do not form properly and the On visual pathway is severely compromised 1. Retinal ganglion cell recordings from these mutant fish revealed that they exhibit predominantly OFF-type ganglion cell responses, some abnormal ON-OFF, but no pure On-type responses 2.
Using the VMR test we showed that the nrc mutant has a normal OFF-response and a delayed and sluggish ON-response (see Figure 5). Thus, the nrc mutant is not completely blind as previously thought 2. <img src="/files/ftp_upload/old/923_2008_9_26_14/923_Figure-06.png" alt="Figure 5" width="591" height="244" /> Figure 5: Nrc mutats increase their activity in response to changes in light intensities. Behavioral responses to light ON and OFF from WT and nrc mutant larvae at 5 dpf. Each trace represents an average of 480 responses from 120 individual fish from each genotype. The average locomotor behavior of nrc mutants (pink traces) is slightly reduced as compared to WT fish (blue traces) but remains vigorous following the light OFF stimulus. Note the slow rise time in the nrc mutant response to light ON compared to light ON response of the WT fish.

<ol>
	<li>Allwardt, A. B., Lall, B. A., Brockerhoff, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Synapse+formation+is+arrested+in+retinal+photoreceptors+of+the+zebrafish+nrc+mutant.">Synapse formation is arrested in retinal photoreceptors of the zebrafish nrc mutant.</a> J Neurosci. 21, 2330-2330 (2001).</li><li>Emran, F., Rihel, J., Adolph, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=OFF+ganglion+cells+cannot+drive+the+optokinetic+reflex+in+zebrafish.">OFF ganglion cells cannot drive the optokinetic reflex in zebrafish.</a> Proceedings of the National Academy of Sciences of the United States of America. 104, 19126-19126 (2007).</li><li>Prober, D. A., Rihel, J., Onah, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hypocretin/orexin+overexpression+induces+an+insomnia-like+phenotype+in+zebrafish.">Hypocretin/orexin overexpression induces an insomnia-like phenotype in zebrafish.</a> J Neurosci. 26, 13400-13400 (2006).</li><li>Westerfield, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The zebrafish book: a guide for the laboratory use of zebrafish. , (2000).</li></ol>

The experimental procedures we show in the film are all representative of WT fish. However, these experiments can be done analogously on mutant fish as well (see representative result section). We suggest to plate WT fish and mutant fish on the same plate in a checker board outline for optimal control purposes.
When using mutant fish on the same plate as WT fish make sure that you write down what type of fish was plated in each well. Here is a suggestion on how to keep track of the fish plate...

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Microplate devices</td>
<td>Tool</td>
<td>Whatman</td>
<td>7701-1651</td>
<td>&nbsp;</td>
<tr>
<td>Transfer pipetes</td>
<td>Tool</td>
<td>VWR</td>
<td>202205</td>
<td>&nbsp;</td>
<tr>
<td>Fish water</td>
<td>Reagent</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>refer to reference #4</td>
</tr>
<tr>
<td>Recording chambers (Zebrabox)</td>
<td>Tool</td>
<td>Viewpoint Lifesciences</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Videotrack Software</td>
<td>Tool</td>
<td>Viewpoint Lifesciences</td>
<td>&nbsp;</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

a behavioral assay to measure responsiveness of zebrafish to changes in light intensities 

The optokinetic reflex (OKR) is a basic visual reflex exhibited by most vertebrates and plays an important role in stabilizing the eye relative to the visual scene. However, the OKR requires that an animal detect moving stripes and it is possible that fish that fail to exhibit an OKR may not be completely blind. One zebrafish mutant, the no optokinetic response c (nrc) has no OKR under any light conditions tested and was reported to be completely blind. Previously, we have shown that OFF-ganglion cell activity can be recorded in these mutants. To determine whether mutant fish with no OKR such as the nrc mutant can detect simple light increments and decrements we developed the visual motor behavioral assay (VMR). In this assay, single zebrafish larvae are placed in each well of a 96-well plate allowing the simultaneous monitoring of larvae using an automated video-tracking system. The locomotor responses of each larva to 30 minutes light ON and 30 minutes light OFF were recorded and quantified. WT fish have a brief spike of motor activity upon lights ON, known as the startle response, followed by return to lower-than baseline activity, called a freeze. WT fish also sharply increase their locomotor activity immediately following lights OFF and only gradually (over several minutes) return to baseline locomotor activity. The nrc mutants respond similarly to light OFF as WT fish, but exhibit a slight reduction in their average activity as compared to WT fish. Motor activity in response to light ON in nrc mutants is delayed and sluggish. There is a slow rise time of the nrc mutant response to light ON as compared to WT light ON response. The results indicate that nrc fish are not completely blind. Because teleosts can detect light through non-retinal tissues, we confirmed that the immediate behavioral responses to light-intensity changes require intact eyes by using the chokh (chk) mutants, which completely lack eyes from the earliest stages of development. In our VMR assay, the chk mutants exhibit no startle response to either light ON or OFF, showing that the lateral eyes mediate this behavior. The VMR assay described here complements the well-established OKR assay, which does not test the ability of zebrafish larvae to respond to changes in light intensities. Additionally, the automation of the VMR assay lends itself to high-throughput screening for defects in light-intensity driven visual responses.

Watch this Scientific Journal Video about A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities at JoVE.com

A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities

We developed the Visual-Motor Response to quantitate the motor output of larval zebrafish in response to light increments and decrements. We also examined zebrafish vision mutants, including the no optokinetic response (nrc) mutants, which were thought to be completely blind when tested by another vision assay, the optokinetic reflex.

A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities 

The optokinetic reflex (OKR) is a basic visual reflex exhibited by most vertebrates and plays an important role in stabilizing the eye relative to the ...

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JoVE Journal

Biology

16.3K Views.  Harvard. Abbiamo sviluppato il Visual-Motor risposta per quantificare la potenza del motore di zebrafish larvale in risposta alla luce incrementi e decrementi. Abbiamo anche esaminato visione zebrafish mutanti, tra cui la non optocinetico risposta (NRC) mutanti, che si pensava essere completamente cieco quando testato da un altro saggio di visione, il riflesso optocinetica.

Video: A Behavioral Assay to Measure Responsiveness of Zebrafish to Changes in Light Intensities

Chromatin Immunoprecipitation (ChIP) to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

In response to a variety of extracellular ligands, the STAT (signal transducer and activator of transcription) transcription factors are rapidly recruited from their latent state in the cytoplasm to cell surface receptors where they are activated by phosphorylation at a single tyrosine residue1. They then dimerize and translocate to the nucleus to drive the transcription of target genes, affecting growth, differentiation, homeostasis and the immune response. Not surprisingly, given their widespread involvement in normal cell processes, dysregulation of STAT function contributes to human disease, particularly to cancers2 and autoimmune diseases3. It is well established that transcription is regulated by alterations to the chromatin template4,5. These alterations include the activities of ATP-dependent complexes, as well as covalent histone modifications and DNA methylation6. Because STAT activation of gene expression is both rapid and transient, it requires specific mechanisms for modulating the chromatin template at STAT-dependent gene loci. To define these mechanisms, we characterize the histone modifications and the enzymatic activities that generate them at gene loci that respond to STAT signaling. This protocol describes chromatin immunoprecipitation, a method that is valuable for the study of STAT signaling to chromatin in activated gene expression.

Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

This protocol describes how chromatin immunoprecipitation (ChIP) is used to study the dynamic alterations to the chromatin template that regulate transcription induced by a signal transduction pathway.

In response to a variety of extracellular ligands, the STAT (signal transducer and activator of transcription) transcription factors are rapidly recruited ...

Intravenous Microinjections of Zebrafish Larvae to Study Acute Kidney Injury

In this video article we describe a zebrafish model of AKI using gentamicin as the nephrotoxicant.  The technique consists of intravenous microinjections on 2 dpf zebrafish. This technique represents an efficient and rapid method to deliver soluble substances into the bloodstream of zebrafish larvae, allowing for the injection of 15-20 fish per hour. In addition to AKI studies, this microinjection technique can also be used for other types of experimental studies such as angiography.  We provide a detailed protocol of the technique from equipment required to visual measures of decreased kidney function. In addition, we also demonstrate the process of fixation, whole mount immunohistochemistry with a kidney tubule marker, plastic embedding and sectioning of the larval zebrafish. We demonstrate that zebrafish larvae injected with gentamicin show morphological features consistent with AKI: edema, loss of cell polarity in proximal tubular epithelial cells, and morphological disruption of the tubule.

We describe a technique of microinjecting the aminoglycoside, gentamicin, into 2 days post-fetilization (dpf) zebrafish larvae to induce acute kidney injury (AKI). We also describe a method for whole mount immunohistochemistry, plastic embedding and sectioning of zebrafish larvae to visualize the AKI mediated damage.

In this video article we describe a zebrafish model of AKI using gentamicin as the nephrotoxicant.  The technique consists of intravenous microinjections ...

Laser Ablation of the Zebrafish Pronephros to Study Renal Epithelial Regeneration

Acute kidney injury (AKI) is characterized by high mortality rates from deterioration of renal function over a period of hours or days that culminates in renal failure1. AKI can be caused by a number of factors including ischemia, drug-based toxicity, or obstructive injury1. This results in an inability to maintain fluid and electrolyte homeostasis. While AKI has been observed for decades, effective clinical therapies have yet to be developed. Intriguingly, some patients with AKI recover renal functions over time, a mysterious phenomenon that has been only rudimentally characterized1,2. Research using mammalian models of AKI has shown that ischemic or nephrotoxin-injured kidneys experience epithelial cell death in nephron tubules1,2, the functional units of the kidney that are made up of a series of specialized regions (segments) of epithelial cell types3. Within nephrons, epithelial cell death is highest in proximal tubule cells. There is evidence that suggests cell destruction is followed by dedifferentiation, proliferation, and migration of surrounding epithelial cells, which can regenerate the nephron entirely1,2. However, there are many unanswered questions about the mechanisms of renal epithelial regeneration, ranging from the signals that modulate these events to reasons for the wide variation of abilities among humans to regenerate injured kidneys.
The larval zebrafish provides an excellent model to study kidney epithelial regeneration as its pronephric kidney is comprised of nephrons that are conserved with higher vertebrates including mammals4,5. The nephrons of zebrafish larvae can be visualized with fluorescence techniques because of the relative transparency of the young zebrafish6. This provides a unique opportunity to image cell and molecular changes in real-time, in contrast to mammalian models where nephrons are inaccessible because the kidneys are structurally complex systems internalized within the animal. Recent studies have employed the aminoglycoside gentamicin as a toxic causative agent for study of AKI and subsequent renal failure: gentamicin and other antibiotics have been shown to cause AKI in humans, and researchers have formulated methods to use this agent to trigger kidney damage in zebrafish7,8. However, the effects of aminoglycoside toxicity in zebrafish larvae are catastrophic and lethal, which presents a difficulty when studying epithelial regeneration and function over time. Our method presents the use of targeted cell ablation as a novel tool for the study of epithelial injury in zebrafish. Laser ablation gives researchers the ability to induce cell death in a limited population of cells. Varying areas of cells can be targeted based on morphological location, function, or even expression of a particular cellular phenotype. Thus, laser ablation will increase the specificity of what researchers can study, and can be a powerful new approach to shed light on the mechanisms of renal epithelial regeneration. This protocol can be broadly applied to target cell populations in other organs in the zebrafish embryo to study injury and regeneration in any number of contexts of interest.

Acute kidney injury (AKI) in humans is a common clinical problem caused by damage to the epithelial cells that comprise kidney nephrons, and AKI is associated with high mortality rates of 50-70%1. Following epithelial cell destruction, nephrons have a limited ability to regenerate, though the mechanisms and limitations that guide this phenomenon remain poorly understood. In this video article, we describe our technique for targeted laser ablation of kidney nephron cells in the zebrafish embryo kidney, or pronephros. Our new method can be used to complement nephrotoxicity-induced models of AKI and gain a high-resolution understanding of the cell and molecular alterations that are associated with epithelial regeneration in the kidney nephron.

Acute kidney injury (AKI) is characterized by high mortality rates from deterioration of renal function over a period of hours or days that culminates in ...

Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

Fluorescent in situ hybridization using DNA probes on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA FISH) represents the most direct way to visualize the location of gene loci, chromosomal sub-regions or entire territories in individual cells. This type of analysis provides insight into the global architecture of the nucleus as well as the behavior of specific genomic loci and regions within the nuclear space. Immunofluorescence, on the other hand, permits the detection of nuclear proteins (modified histones, histone variants and modifiers, transcription machinery and factors, nuclear sub-compartments, etc). The major challenge in combining immunofluorescence and 3D DNA FISH is, on the one hand to preserve the epitope detected by the antibody as well as the 3D architecture of the nucleus, and on the other hand, to allow the penetration of the DNA probe to detect gene loci or chromosome territories 1-5. Here we provide a protocol that combines visualization of chromatin modifications with genomic loci in 3D preserved nuclei.

Here we describe a protocol for simultaneous detection of histone modifications by immunofluorescence and DNA sequences by DNA FISH followed by 3D microscopy and analyses (3D immuno-DNA FISH).

Fluorescent in situ hybridization using DNA probes  on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA  FISH) represents the ...

Analysis of Apoptosis in Zebrafish Embryos by Whole-mount Immunofluorescence to Detect Activated Caspase 3

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis in zebrafish embryos. The whole-mount analysis provides spatial information in regard to tissue specificity of apoptosing cells, although sectioning and/or colabeling is ultimately required to pinpoint the exact cell types undergoing apoptosis. The whole-mount Casp3 assay is optimized for analysis of fixed embryos between the 4-cell stage and 32 hr-post-fertilization and is useful for a number of applications, including analysis of zebrafish mutants and morphants, overexpression of mutant and wild-type mRNAs, and exposure to chemicals. Compared to acridine orange staining, which can identify apoptotic cells in live embryos in a matter of hours, Casp3 and TUNEL assays take considerably longer to complete (2-4 days). However, because of the dynamic nature of apoptotic cell formation and clearance, analysis of fixed embryos ensures accurate comparison of apoptotic cells across multiple samples at specific time points. We have also found the Casp3 assay to be superior to analysis of apoptotic cells by the whole-mount TUNEL assay in regard to cost and reliability. Overall, the Casp3 assay represents a robust, highly reproducible assay in which to analyze apoptotic cells in early zebrafish embryos.

Certain genetic perturbations or exposure to toxins can disrupt normal developmental processes leading to death of specific cell types. The analysis of activated Caspase 3 by whole-mount immunofluorescence in zebrafish embryos reveals stage- and tissue-specific localization of cells specifically undergoing apoptosis.

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis ...

In vitro Methylation Assay to Study Protein Arginine Methylation

Protein arginine methylation is one of the most abundant post-translational modifications in the nucleus. Protein arginine methylation can be identified and/or determined via proteomic approaches, and/or immunoblotting with methyl-arginine specific antibodies. However, these techniques sometimes can be misleading and often provide false positive results. Most importantly, these techniques cannot provide direct evidence in support of the PRMT substrate specificity. In vitro methylation assays, on the other hand, are useful biochemical assays, which are sensitive, and consistently reveal if the identified proteins are indeed PRMT substrates. A typical in vitro methylation assay includes purified, active PRMTs, purified substrate and a radioisotope labeled methyl donor (S-adenosyl-L-[methyl-3H] methionine). Here we describe a step-by-step protocol to isolate catalytically active PRMT1, a ubiquitously expressed PRMT family member. The methyl transferase activities of the purified PRMT1 were later tested on Ras-GTPase activating protein binding protein 1 (G3BP1), a known PRMT substrate, in the presence of S-adenosyl-L-[methyl-3H] methionine as the methyl donor. This protocol can be employed not only for establishing the methylation status of novel physiological PRMT1 substrates, but also for understanding the basic mechanism of protein arginine methylation.

In vitro Methylation Assay to Study Protein Arginine Methylation

Protein arginine methylation, catalyzed by a class of enzymes viz., protein arginine methyl transferases (PRMTs), is the process of enzymatic addition of methyl group(s) to arginines within proteins. The in vitro methylation assay is the most dependable tool for assessing the methylation status of known or novel PRMT substrates.

Protein arginine methylation is one of the most abundant post-translational modifications in the nucleus. Protein arginine methylation can be identified ...

Quantitative Immunofluorescence Assay to Measure the Variation in Protein Levels at Centrosomes

Centrosomes are small but important organelles that serve as the poles of mitotic spindle to maintain genomic integrity or assemble primary cilia to facilitate sensory functions in cells. The level of a protein may be regulated differently at centrosomes than at other .cellular locations, and the variation in the centrosomal level of several proteins at different points of the cell cycle appears to be crucial for the proper regulation of centriole assembly. We developed a quantitative fluorescence microscopy assay that measures relative changes in the level of a protein at centrosomes in fixed cells from different samples, such as at different phases of the cell cycle or after treatment with various reagents. The principle of this assay lies in measuring the background corrected fluorescent intensity corresponding to a protein at a small region, and normalize that measurement against the same for another protein that does not vary under the chosen experimental condition. Utilizing this assay in combination with BrdU pulse and chase strategy to study unperturbed cell cycles, we have quantitatively validated our recent observation that the centrosomal pool of VDAC3 is regulated at centrosomes during the cell cycle, likely by proteasome-mediated degradation specifically at centrosomes.

Here, a novel quantitative fluorescence assay is developed to measure changes in the level of a protein specifically at centrosomes by normalizing that protein&#8217;s fluorescence intensity to that of an appropriate internal standard.

Centrosomes are small but important organelles that serve as the poles of mitotic spindle to maintain genomic integrity or assemble primary cilia to ...

Method for the Assessment of Effects of a Range of Wavelengths and Intensities of Red/near-infrared Light Therapy on Oxidative Stress In Vitro

Red/near-infrared light therapy (R/NIR-LT), delivered by laser or light emitting diode (LED), improves functional and morphological outcomes in a range of central nervous system injuries in vivo, possibly by reducing oxidative stress. However, effects of R/NIR-LT on oxidative stress have been shown to vary depending on wavelength or intensity of irradiation. Studies comparing treatment parameters are lacking, due to absence of commercially available devices that deliver multiple wavelengths or intensities, suitable for high through-put in vitro optimization studies. This protocol describes a technique for delivery of light at a range of wavelengths and intensities to optimize therapeutic doses required for a given injury model. We hypothesized that a method of delivering light, in which wavelength and intensity parameters could easily be altered, could facilitate determination of an optimal dose of R/NIR-LT for reducing reactive oxygen species (ROS) in vitro.
Non-coherent Xenon light was filtered through narrow-band interference filters to deliver varying wavelengths (center wavelengths of 440, 550, 670 and 810nm) and fluences (8.5 x 10-3 to 3.8 x 10-1 J/cm2) of light to cultured cells. Light output from the apparatus was calibrated to emit therapeutically relevant, equal quantal doses of light at each wavelength. Reactive species were detected in glutamate stressed cells treated with the light, using DCFH-DA and H2O2 sensitive fluorescent dyes.&#160;
We successfully delivered light at a range of physiologically and therapeutically relevant wavelengths and intensities, to cultured cells exposed to glutamate as a model of CNS injury. While the fluences of R/NIR-LT used in the current study did not exert an effect on ROS generated by the cultured cells, the method of light delivery is applicable to other systems including isolated mitochondria or more physiologically relevant organotypic slice culture models, and could be used to assess effects on a range of outcome measures of oxidative metabolism.

Method for the Assessment of Effects of a Range of Wavelengths and Intensities of Red/near-infrared Light Therapy on Oxidative Stress In Vitro

Non-coherent Xenon light was passed through narrow-band interference and neutral density filters to deliver light of varying wavelength and intensity to cultured cells. This protocol was used to assess the effects of red/near-infrared light therapy on production of reactive species in vitro: no effects were observed using the tested parameters.

Red/near-infrared light therapy (R/NIR-LT), delivered by laser or light emitting diode (LED), improves functional and morphological outcomes in a range of ...

Use of the Ramsay Assay to Measure Fluid Secretion and Ion Flux Rates in the Drosophila melanogaster Malpighian Tubule

Modulation of renal epithelial ion transport allows organisms to maintain ionic and osmotic homeostasis in the face of varying external conditions. The Drosophila&#160;melanogaster Malpighian (renal) tubule offers an unparalleled opportunity to study the molecular mechanisms of epithelial ion transport, due to the powerful genetics of this organism and the accessibility of its renal tubules to physiological study. Here, we describe the use of the Ramsay assay to measure fluid secretion rates from isolated fly renal tubules, with the use of ion-specific electrodes to measure sodium and potassium concentrations in the secreted fluid. This assay allows study of transepithelial fluid and ion fluxes of ~20 tubules at a time, without the need to transfer the secreted fluid to a separate apparatus to measure ion concentrations. Genetically distinct tubules can be analyzed to assess the role of specific genes in transport processes. Additionally, the bathing saline can be modified to examine the effects of its chemical characteristics, or drugs or hormones added. In summary, this technique allows the molecular characterization of basic mechanisms of epithelial ion transport in the Drosophila tubule, as well as regulation of these transport mechanisms.

Use of the Ramsay Assay to Measure Fluid Secretion and Ion Flux Rates in the Drosophila melanogaster Malpighian Tubule

This protocol describes the use of the Ramsay assay to measure fluid secretion rates from isolated Malpighian (renal) tubules from Drosophila melanogaster. In addition, the use of ion-specific electrodes to measure sodium and potassium concentrations in the secreted fluid, allowing calculation of transepithelial ion flux, is described.

Modulation of renal epithelial ion transport allows organisms to maintain ionic and osmotic homeostasis in the face of varying external conditions. The ...

In Vitro Assay to Measure Phosphatidylethanolamine Methyltransferase Activity

Phosphatidylethanolamine methyltransferases are biosynthetic enzymes that catalyze the transfer of one or more methyl group(s) from S-adenosyl-L-methionine onto phosphatidylethanolamine, monomethyl-phosphatidylethanolamine, or dimethyl-phosphatidylethanolamine to give either monomethyl-phosphatidylethanolamine, dimethyl-phosphatidylethanolamine or phosphatidylcholine. These enzymes are ubiquitous in animal cells, fungi, and are also found in approximately 10% of bacteria. They fulfill various important functions in cell physiology beyond their direct role in lipid metabolism such as in insulin resistance, diabetes, atherosclerosis, cell growth, or virulence. The present manuscript reports on a simple cell-free enzymatic assay that measures the transfer of tritiated methyl group(s) from S-[Methyl-3H]adenosyl-L-methionine onto phosphatidylethanolamine using whole cell extracts as an enzyme source. The resulting methylated forms of phosphatidylethanolamine are hydrophobic and thus, can be separated from water soluble S-[Methyl-3H]adenosyl-L-methionine by organic extraction. This assay can potentially be applied to any other cell types and used to test inhibitors/drugs specific to a phosphatidylethanolamine methyltransferase of interest without the need to purify the enzyme.

In Vitro Assay to Measure Phosphatidylethanolamine Methyltransferase Activity

The present report describes an in vitro enzymatic assay to measure phosphatidylethanolamine methyltransferase activity using Leishmania cell extracts. This assay is based on the transfer of a radioactive methyl group from S-[Methyl-3H]adenosyl-L-methionine onto endogenous phosphatidylethanolamine.