Name: assessment of zebrafish lens nucleus localization and sutural integrity
Uploaded: 2019-05-06T14:00:00
Description: Watch this Scientific Journal Video about Assessment of Zebrafish Lens Nucleus Localization and Sutural Integrity at JoVE.com

We would like to acknowledge our funding source: NIH R01 EY05661 to J.E.H, Ines Gehring for assisting with generating the aqp0a/b double mutants and zebrafish husbandry, Dr Daniel Dranow for discussions leading to generation of the transgenics, Dr Bruce Blumberg and Dr Ken Cho&#8217;s labs for use of their dissecting microscopes, and Dr Megan Smith for help with statistical analysis.

The animal protocols used in this study adhere to the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and have been approved by the Institutional Animal Care and Use Committee (IACUC) of University of California, Irvine.

1. Zebrafish Husbandry and Euthanasia
<ol>
	<li>Raise and maintain zebrafish (AB strain) under standard laboratory conditions12. Raise embryos in embryo medium (EM)12. Add 0.003% PTU to EM from 2...

<ol>
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Analysis of zebrafish lens morphology is the initial step in understanding phenotypes in mutants, or the effects of pharmacological interventions aimed at studying biology of the ocular lens. We outline methods to analyze lens sutures, cortical fiber cell morphology and aspects of the lens nucleus. These approaches are a combination of in vitro and in vivo (compared in Table 1). The in vitro methods allow for greater detail of the outer cortical cell morphology, as well as acce...

The zebrafish is an excellent model for studying lens development and physiology due to the anatomical similarities to mammalian lenses, relative ease of genetic and pharmacological manipulation, speed of embryonic eye development, small size and transparency at early stages allowing for in vivo imaging. The methods described here were developed to analyze zebrafish lens morphology at embryonic and adult stages with a focus on sutural integrity, cortical membrane morphology in vitro and in vivo, and location of lens nuclear position along the anterior-posterior axis ex vivo. These methods serve as a starting point for functional studies of lens development and physiology, as well as reverse genetic screens for lens phenotypes in zebrafish.
Imaging zebrafish lens morphology
Aquaporin 0 (AQP0) is the most abundant lens membrane protein and is critical for both, lens development and clarity, due to multiple essential functions in mammals. Zebrafish have two Aqp0s (Aqp0a and Aqp0b) and we have developed methods to analyze loss of their functions in both embryonic and adult lenses. Our studies reveal that aqp0a-/- mutants develop anterior polar opacity due to instability of the anterior suture, and aqp0a/b double mutants develop nuclear opacity1. AQP0 has been shown to play roles in water transport2, adhesion3,4, cytoskeletal anchoring5 and generation of the refractive index gradient6, but these studies have largely been performed in vitro. The zebrafish provides a unique opportunity to study how loss of function, or perturbed function of Aqp0a or Aqp0b would affect morphology and function in a living lens. To assess lens cell morphology and sutural integrity during development, we modified existing in vitro immunohistochemical methods7 for use in embryonic and adult lenses, and generated transgenics to monitor this process in vivo.
Immunohistochemical analysis of plasma membrane structure and sutural integrity was performed in whole fixed embryos and adult lenses. Zebrafish lenses are extremely small (lens diameter is ~100 &#181;m in embryos and up to 1 mm in adults) compared with their mammalian counterparts and have point sutures8, which are infrequently captured in cryosections. Thus, whole lenses are essential for analyzing sutural integrity. For in vivo analysis of anterior suture formation, and imaging of precise lens cell architecture, we generated transgenics expressing mApple specifically labeling lens membranes.
Advantages of live imaging of lens membrane transgenics include: 1) avoiding fixation artifacts, 2) studying dynamic morphological changes in time-lapse movies, and 3) enabling longitudinal studies in which earlier events can be correlated with later phenotypes. Pigmentation of the iris normally prevents clear imaging of the lens periphery. Addition of 1-phenyl 2-thiourea (PTU) before the primordia-5 (prim-5) stage9 prevents melanogenesis and eye pigmentation up to around 4 days postfertilization (dpf). However, after 4 dpf, the lens periphery is obscured in vivo, particularly at older stages. Furthermore, the density of the lens itself obscures imaging of its posterior pole. Therefore, to study morphology of the lens periphery, or the posterior suture, after 4 dpf, lenses need to be excised and fixed.
Transgenic zebrafish lines have been used to analyze embryonic lens membrane structure in vivo10. The Q01 transgenic expresses a cyan fluorescent protein fused to a membrane targeting sequence, Gap43, driven by the EF1&#945; promoter and a hexamer of the DF4 pax6 enhancer element ubiquitously in lens fiber cells11. Q01 does have extra-lenticular expression, including amacrine cells in the retina, which adds background signal if the primary interest is the lens. We developed a novel transgenic line that expresses a membrane-tethered mApple specifically in the lens, with the aim of avoiding any extra-lenticular signal.
Lens nucleus localization
We discovered that the lens nucleus moves from an initial anterior location in larval zebrafish to a central location in the anterior-posterior axis in adult lenses. This shift in the position of the high refractive index lens nucleus is thought to be a requirement for normal development of zebrafish lens optics1. Our methods allow quantification of lens nuclear centralization in relation to the lens radius. Using this method, we showed that Aqp0a is required for lens nuclear centralization1, and this simple method can be applied to other studies of the development and physiology of the lens and its optical properties in the zebrafish model.

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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">1-phenyl-2-thiourea (PTU)</td>
			<td style="width:196px;">Sigma</td>
			<td style="width:118px;">P7629</td>
			<td style="width:258px;">CAUTION &#8211; very toxic</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:310px;">4% Paraformaldehyde aqueous solution</td>
			<td style="width:196px;">Electron Microscopy Sciences</td>
			<td style="width:118px;">RT 157-4</td>
			<td>CAUTION &#8211; health hazard, combustible</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Confocal microscope</td>
			<td style="width:196px;">Nikon</td>
			<td style="width:118px;">Eclipse Ti-E</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Cryostat</td>
			<td style="width:196px;">Leica</td>
			<td style="width:118px;">CM3050S</td>
			<td style="width:258px;">Objective and chamber temperature set to -21&#730;C</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">DAPI</td>
			<td style="width:196px;">Invitrogen</td>
			<td style="width:118px;">D1306</td>
			<td>CAUTION &#8211; irritating to eyes and skin</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Dimethyl Sulfoxide (DMSO)</td>
			<td style="width:196px;">Fisher Scientific</td>
			<td style="width:118px;">D128</td>
			<td style="width:258px;">CAUTION &#8211; combustible, penetrates skin&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Disposable base mold</td>
			<td style="width:196px;">VWR Scientific</td>
			<td style="width:118px;">15154-631</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Disposable Pasteur glass pipets</td>
			<td style="width:196px;">Fisherbrand</td>
			<td style="width:118px;">13-678-20A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Dumont # 5 forceps</td>
			<td style="width:196px;">Dumont &#38; Fils</td>
			<td style="width:118px;"></td>
			<td>Keep forceps sharpened</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Ethyl 3-aminobenzoate methanesulfonate salt (Tricaine)</td>
			<td style="width:196px;">Sigma-Aldrich</td>
			<td style="width:118px;">A5040</td>
			<td>CAUTION - toxic</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Glass bottom microwell dish (35mm petri dish, 14mm microwell, #1.5 coverglass)</td>
			<td style="width:196px;">MatTek Corporation</td>
			<td style="width:118px;">P35G-1.5-14-C</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Glycerol</td>
			<td style="width:196px;">Sigma</td>
			<td style="width:118px;">G2025</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">hu&#946;B1cry:mAppleCAAX DNA construct</td>
			<td style="width:196px;">Addgene</td>
			<td style="width:118px;">ID:122451</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">ImageJ</td>
			<td style="width:196px;">Wayne Rasband, NIH</td>
			<td style="width:118px;">v1.51n</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Low Melt Agarose (LMA)</td>
			<td style="width:196px;">Apex</td>
			<td style="width:118px;">902-36-6</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">NIS-Elements</td>
			<td style="width:196px;">Nikon</td>
			<td style="width:118px;">V 4.5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">NIS-Elements AR software</td>
			<td style="width:196px;">Nikon</td>
			<td style="width:118px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Olympus&#160; with a model 2.1.1.183 controller</td>
			<td style="width:196px;">Olympus Corp</td>
			<td style="width:118px;">DP70</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Olympus microscope&#160;</td>
			<td style="width:196px;">Olympus Corp</td>
			<td style="width:118px;">SZX12</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Phalloidin-Alexa Flour 546</td>
			<td style="width:196px;">Thermo Fisher</td>
			<td style="width:118px;">A22283</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Phenol Red indicator (1% w/v)</td>
			<td style="width:196px;">Ricca Chemical Company</td>
			<td style="width:118px;">5725-16</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Phosphate buffered saline (PBS)</td>
			<td style="width:196px;">Fisher Scientific</td>
			<td style="width:118px;">BP399</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Photoshop</td>
			<td style="width:196px;">Adobe</td>
			<td style="width:118px;">CS5 v12.0</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Photoshop software</td>
			<td style="width:196px;">Adobe</td>
			<td style="width:118px;">CS5 v12.0</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plan Apo 60x/1.2 WD objective</td>
			<td style="width:196px;">Nikon</td>
			<td style="width:118px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Power source</td>
			<td style="width:196px;">Wild Heerbrugg</td>
			<td style="width:118px;">MTr 22</td>
			<td>Or equivalent power source&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Slide warmer model No. 26020FS</td>
			<td style="width:196px;">Fisher Scientific</td>
			<td style="width:118px;">12-594</td>
			<td></td>
		</tr>
		<tr height="83">
			<td height="83" style="height:83px;width:310px;">Sodium Hydroxide beads</td>
			<td style="width:196px;">Fisher Scientific</td>
			<td style="width:118px;">S612-3</td>
			<td style="width:258px;">CAUTION - corrosive/irritating to eyes and skin, target organ - respiratory system, corrosive to metals</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Superfrost/Plus microscope slide</td>
			<td style="width:196px;">Fisher Scientific</td>
			<td style="width:118px;">12-550-15</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Sylgard 184 silicone Dow Corning</td>
			<td style="width:196px;">World Prevision Instruments</td>
			<td style="width:118px;">SYLG184</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Tissue-Tek O.C.T. Compound</td>
			<td style="width:196px;">Sakura Finetek</td>
			<td style="width:118px;">4583</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Triton X-100 BioXtra</td>
			<td style="width:196px;">Sigma</td>
			<td style="width:118px;">T9284</td>
			<td style="width:258px;">CAUTION &#8211; Toxic, hazardous to aquatic environment, corrosive</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Vannas micro-dissection scissors</td>
			<td style="width:196px;">Ted Pella Inc</td>
			<td style="width:118px;">1346</td>
			<td>Sharp/sharp straight tips</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:310px;">Vectashield antifade mouting medium</td>
			<td style="width:196px;">Vector laboratories</td>
			<td style="width:118px;">H-1000</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:310px;">Wheat Germ Agglutinin (WGA)-Alexa Flour-594</td>
			<td style="width:196px;">Life Technologies</td>
			<td style="width:118px;">W11262</td>
			<td></td>
		</tr>
	</tbody>
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assessment of zebrafish lens nucleus localization and sutural integrity

The zebrafish is uniquely suited to genetic manipulation and in vivo imaging, making it an increasingly popular model for reverse genetic studies and for generation of transgenics for in vivo imaging. These unique capabilities make the zebrafish an ideal platform to study ocular lens development and physiology. Our recent findings that an Aquaporin-0, Aqp0a, is required for stability of the anterior lens suture, as well as for the shift of the lens nucleus to the lens center with age led us to develop tools especially suited to analyzing the properties of zebrafish lenses. Here we outline detailed methods for lens dissection that can be applied to both larval and adult lenses, to prepare them for histological analysis, immunohistochemistry and imaging. We focus on analysis of lens suture integrity and cortical cell morphology and compare data generated from dissected lenses with data obtained from in vivo imaging of lens morphology made possible by a novel transgenic zebrafish line with a genetically encoded fluorescent marker. Analysis of dissected lenses perpendicular to their optical axis allows quantification of the relative position of the lens nucleus along the anterior-posterior axis. Movement of the lens nucleus from an initial anterior position to the center is required for normal lens optics in adult zebrafish. Thus, a quantitative measure of lens nuclear position directly correlates with its optical properties.

Adult zebrafish eye anatomy closely resembles that of mammals (Figure 1A). Despite some differences between zebrafish and mammalian eyes, such as having a ciliary zone instead of a ciliary body17, differences in optical properties18, and differences in morphogenesis during embryonic development19, the zebrafish eye is an excellent model for studying eye development and understanding ophth...

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Assessment of Zebrafish Lens Nucleus Localization and Sutural Integrity

These protocols were developed to analyze cortical lens morphology, structural integrity of the zebrafish lens sutures in fixed and live lenses and to measure the position of the zebrafish lens nucleus along the anterior-posterior axis.

The zebrafish is uniquely suited to genetic manipulation and in vivo imaging, making it an increasingly popular model for reverse genetic studies and for ...

Our protocols provide a starting point for functional studies of lens development and physiology and for reverse genetic screening of lens phenotypes in zebrafish. Our protocols bridge in vitro and in vivo analyses of zebrafish lens membrane morphology and provide a new and straightforward method for quantifying the development of zebrafish lens optics. Analyzing zebrafish lens morphology and optics leads to insights into mechanisms controlling lens development, normal physiology, and pathophysiology.These insights can in turn lead to an ability to delay or prevent cataract. There have been no reports in species other than zebrafish of asymmetrically localized lens nuclei. Identifying lens sutures is critical for correctly orienting the lens to measure nucleus localization.After confirmation of sufficient sedation with Tricaine, use microdissection scissors to immediately excise both eyes from either an adult or a larval zebrafish and place both eyes into a 35-millimeter custom-made Petri dish with a silicone dissection mold filled with PBS. To harvest the lens from an adult zebrafish, place the eye posterior side up and insert forceps at a less than 45-degree angle through the optic disc. Use dissection scissors to make two or three radial incisions through the retina and sclera from the optic disc to the ciliary zone in the immobilized eye and peel back the retina and sclera like flower petals.Invert the eye, cornea-side up, and use the flat side of the scissors to immobilize the lens indirectly via manipulation of the sclera and cornea by using forceps to pull away the retina and attached tissues, then carefully trim away any excess tissue from the lens. For larval zebrafish lens harvest, place a larval eye posterior side up onto the flat part of a silicone dish of PBS and use a sharpened tungsten needle to make radial cuts through the retina and sclera while immobilizing the eye with another needle or forceps, then gently scoop the lens from the dissociated eye with the blunt side of a custom-made tungsten-wire needle and carefully pull away the attached tissue. To measure the anterior-posterior axis lens nucleus localization, orient the freshly-excised lenses axially in PBS in a 35-millimeter dish with a cover glass bottom with the poles and sutures oriented parallel to the plane of focus.To identify the lens nucleus, look for a difference in the refractive index, which usually occurs at the interface of the lens cortex and lens nucleus. If lens sutures are not apparent, a slight lick with forceps to the lens capsule reveals the sutures and the lens nucleus, helping orient the lens for the measurement. Place the dish on the stage of a dissection microscope equipped with a camera and image the lenses with the lens nucleus in focus under brightfield illumination or with differential interference contrast optics.Image a micrometer under the same magnification for calibration and click Live View. Click Snapshot to obtain an image and save the image as a TIFF file. To calibrate the acquired lens images, in an appropriate image-processing software program, select the straight line tool and draw a line of known length on the micrometer image.Click Analyze and Set Scale and enter the known distance and units, then select Global calibration and click OK.To measure the distance from the center of the lens nucleus to the anterior pole, identify the location of the lens suture and use the straight line tool to draw a line across the imaged center of the lens nucleus in an axial orientation. The center of this line is the center of the lens nucleus. Draw another line from this point to the anterior pole of the lens and select Measure in the Analyze menu to measure the distance.Draw another line from the anterior pole to the posterior pole and measure this distance as the lens diameter, then copy these lengths from the Results window to a spreadsheet and calculate the normalized localization of the lens nucleus with respect to the lens radius. By three days post-fertilization, anterior sutures form at the anterior pole and the striking convergence of cells is clearly visualized by phalloidin staining of the narrow fiber cell membranes in fixed embryos. Stronger broad-fiber cell labeling in lens membrane localized mApple transgenic allows live visualization of membrane subdomains but lacks the sutural convergence.Posterior sutures can be visualized both in vitro and in vivo at three days post-fertilization. In an equatorial plane, phalloidin strongly labels the outer cortical fiber cells, revealing a flattened hexagonal shape. Phalloidin is excluded from the compacted lens nucleus and wild type and mutant lens look indistinguishable.The strong labeling of broad fiber cells in lens membrane-localized mApple mosaics transgenics reveal disruptions in cell volume within the mutant lens. As transgene expression is not limited by permeability, some mosaics reveal lens nucleus labeling. In wild type animals, the lens nucleus starts closer to the anterior lens pole during the early stages of development before centralizing during adulthood.Expression of green-tagged proteins in a transgenic host in which the cell membranes fluoresce red allows simultaneous protein localization as well as assessment of fiber cell morphology in vivo. Zebrafish are especially well suited for in vivo studies. Using the tools described here, we can probe lens mechanisms, largely studied in vitro, in an in vivo system.

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Research

JoVE Journal

Biology

Lens Transplantation in Zebrafish and its Application in the Analysis of Eye Mutants

The lens plays an important role in the development of the optic cup[1,2]. Using the zebrafish as a model organism, questions regarding lens development can be addressed. The zebrafish is useful for genetic studies due to several advantageous characteristics, including small size, high fecundity, short lifecycle, and ease of care. Lens development occurs rapidly in zebrafish. By 72 hpf, the zebrafish lens is functionally mature [3]. Abundant genetic and molecular resources are available to support research in zebrafish. In addition, the similarity of the zebrafish eye to those of other vertebrates provides basis for its use as an excellent animal model of human defects[4-7]. Several zebrafish mutants exhibit lens abnormalities, including high levels of cell death, which in some cases leads to a complete degeneration of lens tissues [8]. To determine whether lens abnormalities are due to intrinsic causes or to defective interactions with the surrounding tissues, transplantation of a mutant lens into a wild-type eye is performed. Using fire-polished metal needles, mutant or wild-type lenses are carefully dissected from the donor animal, and transferred into the host. To distinguish wild-type and mutant tissues, a transgenic line is used as the donor. This line expresses membrane-bound GFP in all tissues, including the lens. This transplantation technique is an essential tool in the studies of zebrafish lens mutants.

Lens development involves interactions with other tissues. Several zebrafish eye mutants are characterized by an abnormally small lens size. Here we demonstrate a lens transplantation experiment to determine whether this phenotype is due to intrinsic causes or defective interactions with tissues that surround the lens.

The lens plays an important role in the development of the optic cup[1,2]. Using the zebrafish as a model organism, questions regarding lens development ...

Heterokaryon Technique for Analysis of Cell Type-specific Localization

A significant number of proteins are regulated by subcellular trafficking or nucleocytolasmic shuttling. These proteins display a diverse array of cellular functions including nuclear import/export of RNA and protein, transcriptional regulation, and apoptosis. Interestingly, major cellular reorganizations including cell division, differentiation and transformation, often involve such activities3,4,8,10. The detailed study of these proteins and their respective regulatory mechanisms can be challenging as the stimulation for these localization changes can be elusive, and the movements themselves can be quite dynamic and difficult to track. Studies involving cellular oncogenesis, for example, continue to benefit from understanding pathways and protein activities that differ between normal primary cells and transformed cells6,7,11,12. As many proteins show altered localization during transformation or as a result of transformation, methods to efficiently characterize these proteins and the pathways in which they participate stand to improve the understanding of oncogenesis and open new areas for drug targeting.
Here we present a method for the analysis of protein trafficking and shuttling activity between primary and transformed mammalian cells. This method combines the generation of heterokaryon fusions with fluorescence microscopy to provide a flexible protocol that can be used to detect steady-state or dynamic protein localizations. As shown in Figure 1, two separate cell types are transiently transfected with plasmid constructs bearing a fluoroprotein gene attached to the gene of interest. After expression, the cells are fused using polyethylene glycol, and protein localizations may then be imaged using a variety of methods. The protocol presented here is a fundamental approach to which specialized techniques may be added.

A flexible and efficient method for the characterization of cell type-specific protein localization and nucleocytoplasmic shuttling is described. This heterokaryon approach uses fluorescently-labeled fusion proteins to image protein localizations after cell fusion. The protocol is amenable to steady-state localizations or more dynamic determinations based on live cell imaging.

A significant number of proteins are regulated by subcellular trafficking or nucleocytolasmic shuttling.  These proteins display a diverse array of ...

In vivo Electroporation of Morpholinos into the Adult Zebrafish Retina

Many devastating inherited eye diseases result in progressive and irreversible blindness because humans cannot regenerate dying or diseased retinal neurons. In contrast, the adult zebrafish retina possesses the robust ability to spontaneously regenerate any neuronal class that is lost in a variety of different retinal damage models, including retinal puncture, chemical ablation, concentrated high temperature, and intense light treatment 1-8. Our lab extensively characterized regeneration of photoreceptors following constant intense light treatment and inner retinal neurons after intravitreal ouabain injection 2, 5, 9. In all cases, resident M&uuml;ller glia re-enter the cell cycle to produce neuronal progenitors, which continue to proliferate and migrate to the proper retinal layer, where they differentiate into the deficient neurons. 
	We characterized five different stages during regeneration of the light-damaged retina that were highlighted by specific cellular responses. We identified several differentially expressed genes at each stage of retinal regeneration by mRNA microarray analysis 10. Many of these genes are also critical for ocular development. To test the role of each candidate gene/protein during retinal regeneration, we needed to develop a method to conditionally limit the expression of a candidate protein only at times during regeneration of the adult retina. 
	Morpholino oligos are widely used to study loss of function of specific proteins during the development of zebrafish, Xenopus, chick, mouse, and tumors in human xenografts 11-14. These modified oligos basepair with complementary RNA sequence to either block the splicing or translation of the target RNA. Morpholinos are stable in the cell and can eliminate or "knockdown" protein expression for three to five days 12. 
	Here, we describe a method to efficiently knockdown target protein expression in the adult zebrafish retina. This method employs lissamine-tagged antisense morpholinos that are injected into the vitreous of the adult zebrafish eye. Using electrode forceps, the morpholino is then electroporated into all the cell types of the dorsal and central retina. Lissamine provides the charge on the morpholino for electroporation and can be visualized to assess the presence of the morpholino in the retinal cells. 
	Conditional knockdown in the retina can be used to examine the role of specific proteins at different times during regeneration. Additionally, this approach can be used to study the role of specific proteins in the undamaged retina, in such processes as visual transduction and visual processing in second order neurons.

In vivo Electroporation of Morpholinos into the Adult Zebrafish Retina

A method to conditionally knockdown a target protein&#x2019;s expression in the adult zebrafish retina is described, which involves intravitreally injecting antisense morpholinos and electroporating them into the retina. The resulting protein is knocked down for several days, which allows testing the protein&#x2019;s role in the regenerating or intact retina.

Many devastating inherited eye diseases result in progressive and irreversible blindness because humans cannot regenerate dying or diseased retinal ...

In vivo Electroporation of Morpholinos into the Regenerating Adult Zebrafish Tail Fin

Certain species of urodeles and teleost fish can regenerate their tissues. Zebrafish have become a widely used model to study the spontaneous regeneration of adult tissues, such as the heart1, retina2, spinal cord3, optic nerve4, sensory hair cells5, and fins6.
The zebrafish fin is a relatively simple appendage that is easily manipulated to study multiple stages in epimorphic regeneration. Classically, fin regeneration was characterized by three distinct stages: wound healing, blastema formation, and fin outgrowth. After amputating part of the fin, the surrounding epithelium proliferates and migrates over the wound. At 33 &deg;C, this process occurs within six hours post-amputation (hpa, Figure 1B)6,7. Next, underlying cells from different lineages (ex. bone, blood, glia, fibroblast) re-enter the cell cycle to form a proliferative blastema, while the overlying epidermis continues to proliferate (Figure 1D)8. Outgrowth occurs as cells proximal to the blastema re-differentiate into their respective lineages to form new tissue (Figure 1E)8. Depending on the level of the amputation, full regeneration is completed in a week to a month.
The expression of a large number of gene families, including wnt, hox, fgf, msx, retinoic acid, shh, notch, bmp, and activin-betaA genes, is up-regulated during specific stages of fin regeneration9-16. However, the roles of these genes and their encoded proteins during regeneration have been difficult to assess, unless a specific inhibitor for the protein exists13, a temperature-sensitive mutant exists or a transgenic animal (either overexpressing the wild-type protein or a dominant-negative protein) was generated7,12. We developed a reverse genetic technique to quickly and easily test the function of any gene during fin regeneration.
Morpholino oligonucleotides are widely used to study loss of specific proteins during zebrafish, Xenopus, chick, and mouse development17-19. Morpholinos basepair with a complementary RNA sequence to either block pre-mRNA splicing or mRNA translation. We describe a method to efficiently introduce fluorescein-tagged antisense morpholinos into regenerating zebrafish fins to knockdown expression of the target protein. The morpholino is micro-injected into each blastema of the regenerating zebrafish tail fin and electroporated into the surrounding cells. Fluorescein provides the charge to electroporate the morpholino and to visualize the morpholino in the fin tissue.
This protocol permits conditional protein knockdown to examine the role of specific proteins during regenerative fin outgrowth. In the Discussion, we describe how this approach can be adapted to study the role of specific proteins during wound healing or blastema formation, as well as a potential marker of cell migration during blastema formation.

In vivo Electroporation of Morpholinos into the Regenerating Adult Zebrafish Tail Fin

We describe a method to conditionally knockdown the expression of a target protein during adult zebrafish fin regeneration. This technique involves micro-injecting and electroporating antisense oligonucleotide morpholinos into fin tissue, which allows testing the protein&#x2019;s role in various stages of fin regeneration, including wound healing, blastema formation, and regenerative outgrowth.

Certain species of urodeles and teleost fish can regenerate their tissues. Zebrafish have become a widely used model to study the spontaneous regeneration ...

Nano-fEM: Protein Localization Using Photo-activated Localization Microscopy and Electron Microscopy

Mapping the distribution of proteins is essential for understanding the function of proteins in a cell. Fluorescence microscopy is extensively used for protein localization, but subcellular context is often absent in fluorescence images. Immuno-electron microscopy, on the other hand, can localize proteins, but the technique is limited by a lack of compatible antibodies, poor preservation of morphology and because most antigens are not exposed to the specimen surface. Correlative approaches can acquire the fluorescence image from a whole cell first, either from immuno-fluorescence or genetically tagged proteins. The sample is then fixed and embedded for electron microscopy, and the images are correlated 1-3. However, the low-resolution fluorescence image and the lack of fiducial markers preclude the precise localization of proteins. 
Alternatively, fluorescence imaging can be done after preserving the specimen in plastic. In this approach, the block is sectioned, and fluorescence images and electron micrographs of the same section are correlated 4-7. However, the diffraction limit of light in the correlated image obscures the locations of individual molecules, and the fluorescence often extends beyond the boundary of the cell. 
Nano-resolution fluorescence electron microscopy (nano-fEM) is designed to localize proteins at nano-scale by imaging the same sections using photo-activated localization microscopy (PALM) and electron microscopy. PALM overcomes the diffraction limit by imaging individual fluorescent proteins and subsequently mapping the centroid of each fluorescent spot 8-10. 
We outline the nano-fEM technique in five steps. First, the sample is fixed and embedded using conditions that preserve the fluorescence of tagged proteins. Second, the resin blocks are sectioned into ultrathin segments (70-80 nm) that are mounted on a cover glass. Third, fluorescence is imaged in these sections using the Zeiss PALM microscope. Fourth, electron dense structures are imaged in these same sections using a scanning electron microscope. Fifth, the fluorescence and electron micrographs are aligned using gold particles as fiducial markers. In summary, the subcellular localization of fluorescently tagged proteins can be determined at nanometer resolution in approximately one week.

We describe a method to localize fluorescently tagged proteins in electron micrographs. Fluorescence is first localized using photo-activated localization microscopy on ultrathin sections. These images are then aligned to electron micrographs of the same section.

Mapping the distribution of proteins is essential for understanding the function of proteins in a cell. Fluorescence microscopy is extensively used for ...

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

Long interspersed nuclear element-1 (Line-1 or L1) accounts for approximately 17% of the DNA present in the human genome. While the majority of L1s are inactive due to 5' truncations, ~80-100 of these elements remain retrotransposition competent and propagate to different locations throughout the genome via RNA intermediates. While older L1s are believed to target AT rich regions of the genome, the chromosomal targets of newer, more active L1s remain poorly defined. Here we describe fluorescence in situ hybridization (FISH) methodology that can be used to track patterns of L1 insertion and rates of ectopic L1 incorporation at the single nucleus level. In these experiments, fluorescein isothiocyanate/cyanine-3 (FITC/CY3) labeled neomycin probes were employed to track L1 retrotransposition in vitro in HepG2 cells stably expressing ectopic L1. This methodology prevents errors in the estimation of rates of retrotransposition posed by toxicity and account for the occurrence of multiple insertions into a single nucleus.

Here we employ FISH methodology to track LINE-1 retrotransposition at the single nuclei level in chromosome spreads of HepG2 cell lines stably expressing synthetic LINE-1.

Long interspersed nuclear element-1 (Line-1 or L1) accounts for approximately 17% of the DNA present in the human genome. While the majority of L1s are ...

Nephrotoxin Microinjection in Zebrafish to Model Acute Kidney Injury

The kidneys are susceptible to harm from exposure to chemicals they filter from the bloodstream. This can lead to organ injury associated with a rapid decline in renal function and development of the clinical syndrome known as acute kidney injury (AKI). Pharmacological agents used to treat medical circumstances ranging from bacterial infection to cancer, when administered individually or in combination with other drugs, can initiate AKI. Zebrafish are a useful animal model to study the chemical effects on renal function in vivo, as they form an embryonic kidney comprised of nephron functional units that are conserved with higher vertebrates, including humans. Further, zebrafish can be utilized to perform genetic and chemical screens, which provide opportunities to elucidate the cellular and molecular facets of AKI and develop therapeutic strategies such as the identification of nephroprotective molecules. Here, we demonstrate how microinjection into the zebrafish embryo can be utilized as a paradigm for nephrotoxin studies.

Renal injuries incurred from nephrotoxins, which include drugs ranging from antibiotics to chemotherapeutics, can result in complex disorders whose pathogenesis remains incompletely understood. This protocol demonstrates how zebrafish can be used for disease modeling of these conditions, which can be applied to the identification of renoprotective measures.

The kidneys are susceptible to harm from exposure to chemicals they filter from the bloodstream. This can lead to organ injury associated with a rapid ...

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

The presence of ribonucleotides in nuclear DNA has been shown to be a source of genomic instability. The extent of ribonucleotide incorporation can be assessed by alkaline hydrolysis and gel electrophoresis as RNA is highly susceptible to hydrolysis in alkaline conditions. This, in combination with Southern blot analysis can be used to determine the location and strand into which the ribonucleotides have been incorporated. However, this procedure is only semi-quantitative and may not be sensitive enough to detect small changes in ribonucleotide content, although strand-specific Southern blot probing improves the sensitivity. As a measure of one of the most striking biological consequences of ribonucleotides in DNA, spontaneous mutagenesis can be analyzed using a forward mutation assay. Using appropriate reporter genes, rare mutations that results in the loss of function can be selected and overall and specific mutation rates can be measured by combining data from fluctuation experiments with DNA sequencing of the reporter gene. The fluctuation assay is applicable to examine a wide variety of mutagenic processes in specific genetic background or growth conditions.

Ribonucleotides are among the most abundant non-canonical nucleotides incorporated into the genome during eukaryotic nuclear DNA replication. If not properly removed, ribonucleotides can cause DNA damage and mutagenesis. Here, we present two experimental approaches that are used to assess the abundance of ribonucleotide incorporation into DNA and its mutagenic effects.

The presence of ribonucleotides in nuclear DNA has been shown to be a source of genomic instability. The extent of ribonucleotide incorporation can be ...

Dissecting Mechanoenzymatic Properties of Processive Myosins with Ultrafast Force-Clamp Spectroscopy

Ultrafast force-clamp spectroscopy (UFFCS) is a single molecule technique based on laser tweezers that allows the investigation of the chemomechanics of both conventional and unconventional myosins under load with unprecedented time resolution. In particular, the possibility to probe myosin motors under constant force right after the actin-myosin bond formation, together with the high rate of the force feedback (200 kHz), has shown UFFCS to be a valuable tool to study the load dependence of fast dynamics such as the myosin working stroke. Moreover, UFFCS enables the study of how processive and non-processive myosin-actin interactions are influenced by the intensity and direction of the applied force.
By following this protocol, it will be possible to perform ultrafast force-clamp experiments on processive myosin-5 motors and on a variety of unconventional myosins. By some adjustments, the protocol could also be easily extended to the study of other classes of processive motors such as kinesins and dyneins. The protocol includes all the necessary steps, from the setup of the experimental apparatus to sample preparation, calibration procedures, data acquisition and analysis.

Presented here is a comprehensive protocol to perform ultrafast force-clamp experiments on processive myosin-5 motors, which could be easily extended to the study of other classes of processive motors. The protocol details all the necessary steps, from the setup of the experimental apparatus to sample preparation, data acquisition and analysis.

Ultrafast force-clamp spectroscopy (UFFCS) is a single molecule technique based on laser tweezers that allows the investigation of the chemomechanics of ...

Assessment of Gut Barrier Integrity in Mice Using Fluorescein-Isothiocyanate-Labeled Dextran

Gut barrier integrity is a hallmark of intestinal health. While gut barrier integrity can be assessed using indirect markers such as the measurement of plasma inflammatory markers and bacterial translocation to the spleen and lymph nodes, the gold standard directly quantifies the ability of selected molecules to traverse the gut mucosal layer toward systemic circulation. This article uses a non-invasive, cost-effective, and low-burden technique to quantify and follow in real time the intestinal permeability in mice using fluorescein-isothiocyanate-labeled dextran (FITC-dextran). Prior to oral supplementation with FITC-dextran, the mice are fasted. They are then gavaged with FITC-dextran diluted in phosphate-buffered saline (PBS). One hour after the gavage, the mice are subjected to general anesthesia using isoflurane, and the in vivo fluorescence is visualized in an imaging chamber. This technique aims to assess residual fluorescence in the abdominal cavity and the hepatic uptake, which is suggestive of portal migration of the fluorescent probe. Blood and stool samples are collected 4 h after oral gavage, and the mice are sacrificed. Plasma and fecal samples diluted in PBS are then plated, and the fluorescence is recorded. The concentration of FITC-dextran is then calculated using a standard curve. In previous research, in vivo imaging has shown that fluorescence rapidly spreads to the liver in mice with a weaker gut barrier induced by a low-fiber diet, while in mice supplemented with fiber to strengthen the gut barrier, the fluorescent signal is retained mostly in the gastrointestinal tract. In addition, in this study, control mice had elevated plasma fluorescence and reduced fluorescence in the stool, while inversely, inulin-supplemented mice had higher levels of fluorescence signals in the gut and low levels in the plasma. In summary, this protocol provides qualitative and quantitative measurements of intestinal permeability as a marker for gut health.

In the present study, fluorescein-isothiocyanate-labeled (FITC) dextran is administered to mice via oral gavage to evaluate intestinal permeability both in vivo and in plasma and fecal samples. As gut barrier function is affected in many disease processes, this direct and quantitative assay can be used in diverse research areas.

Gut barrier integrity is a hallmark of intestinal health. While gut barrier integrity can be assessed using indirect markers such as the measurement of ...