אני רוצה להודות לסטודנטים לתואר הראשון הרבים שעבדו במעבדה שלי ותרמו להתפתחות של פרוטוקולים אלה. NAT קבל תמיכה מסקידמור-איחוד הרשת, פרויקט שהוקם עם ADVANCE NSF שולם מענק.

<ol>
	<li>Forester, R., Goldstein, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intracellular+osmoregulatory+role+of+amino+acids+and+urea+in+marine+elasmobranchs.">Intracellular osmoregulatory role of amino acids and urea in marine elasmobranchs.</a> Am. J. Physiol. 230, 925-931 (1976).</li><li>Shuttleworth, T., Shuttleworth, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Physiology of elasmobranch fishes. , 171-194 (1988).</li><li>Yancey, P. H., Clark, M. E., Hand, S. C., Bowlus, R. D., Somero, G. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Living+with+water+stress:+evolution+of+osmolyte+systems.">Living with water stress: evolution of osmolyte systems.</a> Science. 217, 1214-1222 (1982).</li><li>Ballatori, N., Villalobos, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Defining+the+molecular+and+cellular+basis+of+toxicity+using+comparative+models.">Defining the molecular and cellular basis of toxicity using comparative models.</a> Toxicl. Appl. Pharmacol. 183, 207-220 (2002).</li><li>Nieto, M. A., Patel, K., Wilkinson, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+situ+hybridization+analysis+of+chick+embryos+in+whole+mount+and+tissue+sections.">In situ hybridization analysis of chick embryos in whole mount and tissue sections.</a> Methods Cell Biol. 51, 219-235 (1996).</li><li>Jass, J. R., Walsh, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Altered+mucin+expression+in+the+gastrointestinal+tract:+a+review.">Altered mucin expression in the gastrointestinal tract: a review.</a> J Cell Mol Med. 5, 327-351 (2001).</li><li>Ballard, W. W., Mellinger, J., Lechenault, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+series+of+normal+stages+for+development+of+Scyliorhinus+canicula,+the+lesser+spotted+dogfish+(Chondrichthyes;+Scyliorhinidae).">A series of normal stages for development of Scyliorhinus canicula, the lesser spotted dogfish (Chondrichthyes; Scyliorhinidae).</a> J. Exp. Zool. 267, 318-336 (1993).</li><li>Echelard, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sonic+hedgehog,+a+member+of+a+family+of+putative+signaling+molecules,+is+implicated+in+the+regulation+of+CNS+polarity.">Sonic hedgehog, a member of a family of putative signaling molecules, is implicated in the regulation of CNS polarity.</a> Cell. 75, 1417-1430 (1993).</li><li>Riddle, R. D., Johnson, R. L., Laufer, E., Tabin, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sonic+hedgehog+mediates+the+polarizing+activity+of+the+ZPA.">Sonic hedgehog mediates the polarizing activity of the ZPA.</a> Cell. 75, 1401-1416 (1993).</li><li>Theodosiou, N. A., Hall, D. A., Jowdry, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+acid+mucin+goblet+cell+distribution+and+Hox13+expression+patterns+in+the+developing+vertebrate+digestive+tract.">Comparison of acid mucin goblet cell distribution and Hox13 expression patterns in the developing vertebrate digestive tract.</a> J. Exp. Zool. B. Mol. Dev. Evol. 308, 442-453 (2007).</li><li>Sambrook, J., Russell, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ch.+7.">Ch. 7.</a> Molecular Cloning; A Laboratory Manual. 1, 7.82 (2001).</li><li>Zhang, G., Miyamoto, M. M., Cohn, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lamprey+type+II+collagen+and+Sox9+reveal+an+ancient+origin+of+the+vertebrate+collagenous+skeleton.">Lamprey type II collagen and Sox9 reveal an ancient origin of the vertebrate collagenous skeleton.</a> Proc. Natl. Acad. Sci. U.S.A. 103, 3180-3185 (2006).</li><li>Sheehan, D. C., Hrapchak, B. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Theory and practice of histotechnology. , (1980).</li><li>Theodosiou, N. A., Simeone, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evidence+of+a+rudimentary+colon+in+the+elasmobranch,+Leucoraja+erinacea.">Evidence of a rudimentary colon in the elasmobranch, Leucoraja erinacea.</a> Dev. Genes Evol. 222, 237-243 (2012).</li><li>Filipe, M. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mucins+in+the+human+gastrointestinal+epithelium:+a+review.">Mucins in the human gastrointestinal epithelium: a review.</a> Invest. Cell Pathol. 2, 195-216 (1979).</li><li>Corfield, A. P., Wagner, S. A., Clamp, J. R., Kriaris, M. S., Hoskins, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mucin+degradation+in+the+human+colon:+production+of+sialidase,+sialate+O-acetylesterase,+N-acetylneuraminate+lyase,+arylesterase,+and+glycosulfatase+activities+by+strains+of+fecal+bacteria.">Mucin degradation in the human colon: production of sialidase, sialate O-acetylesterase, N-acetylneuraminate lyase, arylesterase, and glycosulfatase activities by strains of fecal bacteria.</a> Infect. Immun. 60, 3971-3978 (1992).</li><li>Reid, B. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow-cytometric+and+histological+progression+to+malignancy+in+Barrett's+esophagus:+prospective+endoscopic+surveillance+of+a+cohort.">Flow-cytometric and histological progression to malignancy in Barrett's esophagus: prospective endoscopic surveillance of a cohort.</a> Gastroenterology. 102, 1212-1219 (1992).</li><li>Mowry, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+staining+of+pancreatic+beta-cell+granules.+Evolution+and+present+status.">Selective staining of pancreatic beta-cell granules. Evolution and present status.</a> Arch. Pathol. Lab Med. 107, 464-468 (1983).</li><li>Roberts, D. J., Smith, D. M., Goff, D. J., Tabin, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epithelial-mesenchymal+signaling+during+the+regionalization+of+the+chick+gut.">Epithelial-mesenchymal signaling during the regionalization of the chick gut.</a> Development. 125, 2791-2801 (1998).</li></ol>

אין לי מה לחשוף.

הפרוטוקולים שהוצגו הם שיטות קלסיות לניטור ביטוי גנים וזיהוי סוגי תאים מובחנים, והותאמו לשימוש בelasmobranchs הימי. שינויים נוספים של פרוטוקולים אלה עשויים להיות נחוצים כדי להסתגל למיני elasmobranch שונים. הדאגה הנפוצה ביותר לגבי כל הר רנ&quot...

<table border="1">
 <tbody>
 <tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 <td>Comments </td>
 </tr>
 <tr>
 <td>10 x transcription buffer</td>
 <td>Roche</td>
 <td>11-465-384-001</td>
 <td></td>
 </tr>
 <tr>
 <td>DIG-RNA labeling mix</td>
 <td>Roche</td>
 <td>11-277-073-910</td>
 <td></td>
 </tr>
 <tr>
 <td>RNAse inhibitor</td>
 <td>Roche</td>
 <td>03-335-399-001</td>
 <td></td>
 </tr>
 <tr>
 <td>RNA polymerase - SP6</td>
 <td>Roche</td>
 <td>10-810-274-001</td>
 <td></td>
 </tr>
 <tr>
 <td>DNAseI, RNAse-free </td>
 <td>Roche</td>
 <td>10-776-785-001</td>
 <td></td>
 </tr>
 <tr>
 <td>Yeast RNA</td>
 <td>Invitrogen</td>
 <td>15401-029</td>
 <td></td>
 </tr>
 <tr>
 <td>CHAPS</td>
 <td>EMD-Millipore</td>
 <td>220201</td>
 <td></td>
 </tr>
 <tr>
 <td>heparin</td>
 <td>Sigma-Aldrich</td>
 <td>H4784</td>
 <td></td>
 </tr>
 <tr>
 <td>DEPC (diethyl pyrocarbonate)</td>
 <td>Research Organics</td>
 <td>2106D</td>
 <td></td>
 </tr>
 <tr>
 <td>Moria Perforated Spoon</td>
 <td>Fine Science Tools</td>
 <td>10370-17</td>
 <td></td>
 </tr>
 <tr>
 <td>Netwell inserts</td>
 <td>Electron Microscopy Sciences</td>
 <td>64713-00</td>
 <td>Netwells for use in 6-well tissue culture dishes</td>
 </tr>
 <tr>
 <td>6-well tissue culture plate</td>
 <td>Corning</td>
 <td>3516</td>
 <td></td>
 </tr>
 <tr>
 <td>Glass scintillation vials with screw-cap lids</td>
 <td>Weaton Science Products</td>
 <td>986540</td>
 <td></td>
 </tr>
 <tr>
 <td>formamide</td>
 <td>Fisher</td>
 <td>BP227500</td>
 <td></td>
 </tr>
 <tr>
 <td>Proteinase K</td>
 <td>Invitrogen</td>
 <td>59895 (AM2542)</td>
 <td></td>
 </tr>
 <tr>
 <td>NBT</td>
 <td></td>
 <td>11585029001</td>
 <td></td>
 </tr>
 <tr>
 <td>BCIP</td>
 <td>Roche</td>
 <td>11585002001</td>
 <td></td>
 </tr>
 <tr>
 <td>Hydrogen peroxide, 30%</td>
 <td>EMD</td>
 <td>HX0635-1</td>
 <td></td>
 </tr>
 <tr>
 <td>Sheep serum</td>
 <td>VWR</td>
 <td>101301-478</td>
 <td></td>
 </tr>
 <tr>
 <td>glutaraldehyde</td>
 <td>Sigma-Aldrich</td>
 <td>G5882</td>
 <td></td>
 </tr>
 <tr>
 <td>tRNA</td>
 <td>Roche</td>
 <td>10-109-541-001</td>
 <td></td>
 </tr>
 <tr>
 <td>Anti-DIG Fab Fragments</td>
 <td>Roche</td>
 <td>1137-6623</td>
 <td></td>
 </tr>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Table 3. Reagents and equipment for RNA whole mount in situ's.</td>
 </tr>
 <tr>
 <td>1% Alcian Blue 8GS, pH 2.5</td>
 <td>Electron Microscopy Sciences</td>
 <td>26323-01</td>
 <td></td>
 </tr>
 <tr>
 <td>Nuclear Fast Red</td>
 <td>Electron Microscopy Sciences</td>
 <td>26078-05</td>
 <td></td>
 </tr>
 <tr>
 <td>DPX Mountant</td>
 <td>Electron Microscopy Sciences</td>
 <td>13510</td>
 <td></td>
 </tr>
 <tr>
 <td>Paraffin (Paraplast X-tra)</td>
 <td>McCormick Scientific</td>
 <td>39503002</td>
 <td></td>
 </tr>
 <tr>
 <td>10% Formalin, NBF</td>
 <td>VWR</td>
 <td>95042-908</td>
 <td></td>
 </tr>
 <tr>
 <td>Glass scintillation vials with screw-cap lids</td>
 <td>Weaton Science Products</td>
 <td>986540</td>
 <td></td>
 </tr>
 <tr>
 <td>Stainless steal base molds</td>
 <td>Tissue-Tek</td>
 <td>4161-4165</td>
 <td>Multiple sizes available.</td>
 </tr>
 <tr>
 <td>Cassettes </td>
 <td>Tissue-Tek</td>
 <td>4170</td>
 <td></td>
 </tr>
 <tr>
 <td>Slide warmer</td>
 <td>Fisher-Scientific</td>
 <td>12-594Q</td>
 <td></td>
 </tr>
 <tr>
 <td>Tissue Embedder</td>
 <td>Leica Microsystems</td>
 <td>EG1160</td>
 <td></td>
 </tr>
 <tr>
 <td>Microtome, rotary</td>
 <td>Leica Microsystems</td>
 <td>RM2235</td>
 <td></td>
 </tr>
 <tr>
 <td>Tissue-Tek Slide Staining Set</td>
 <td>Electron Microscopy Sciences</td>
 <td>62540-01</td>
 <td></td>
 </tr>
 <tr>
 <td>Tissue-Tek 24-Slide Holder</td>
 <td>Electron Microscopy Sciences</td>
 <td>62543-06</td>
 <td></td>
 </tr>
 <tr>
 <td>Superfrost*Plus slides</td>
 <td>Fisherbrand</td>
 <td>12-550-17</td>
 <td></td>
 </tr>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Table 4. Reagents and equipment for Alcian Blue stain.</td>
 </tr>
 </tbody>
</table>

rna in situ hybridization in whole mount embryos and cell histology adapted for marine elasmobranchs

elasmobranchs הימי מוערכים מודלים של בעלי חיים למחקרים ביו וגנומית כפי שהם החוליות הפרימיטיביות ביותר שיש חסינות אדפטיבית ויש מנגנונים ייחודיים לויסות לחץ האוסמוטי 1-3. כאמן חוליות לסת החיים הפרימיטיביים ביותר עם ספיחים לזווג, elasmobranchs הוא מודל אבולוציונית חשוב, במיוחד ללימודים באבולוציה ובהתפתחות. elasmobranchs הימי יש גם שמש ללמוד טוקסיקולוגיה הימית ופיזיולוגיה של לחץ במערכת יחסים עד 4 שינויי האקלים. לפיכך, פיתוח וההתאמה של מתודולוגיות נדרשים כדי להקל ולהרחיב את השימוש בחוליות הפרימיטיביות האלה לתחומים ביולוגיים רבים. כאן אני מציג את ההסתגלות המוצלחת של כל הר רנ&quot;א כלאה באתר וטכניקות היסטולוגית ללמוד ביטוי גנים והיסטולוגיה תא בelasmobranchs. ניטור ביטוי גנים הוא כלי היכר של Biol התפתחותיתogists, ונמצא בשימוש נרחב כדי לחקור תהליכים התפתחותיים 5. כל הר רנ&quot;א כלאה באתר מאפשר להדמיה והלוקליזציה של תעתיקי גנים ספציפיים ברקמות של העובר המתפתח. דפוס הביטוי של המסר של גן יכול לספק תובנה לגבי מה תהליכים התפתחותיים והחלטות גורל תא גן יכולים לשלוט. על ידי השוואת דפוס הביטוי של גן בשלבי התפתחות שונים, תובנה ניתן להשיג בכמה תפקידים של שינויים גנטיים במהלך התפתחות. בעוד כל ההר באתר של מספק אמצעים לאיתור ביטוי גנים ברקמות, טכניקות היסטולוגית תאפשרנה זיהוי של סוגי תאים מובחנים ורקמות. כתמי היסטולוגית יש פונקציות מגוונות. כתמים כלליים משמשים כדי להדגיש מורפולוגיה של תאים, למשל hematoxylin וeosin לצביעה כללית של גרעינים וציטופלסמה, בהתאמה. כתמים אחרים יכולים לסמן תאים ספציפייםסוגים. לדוגמה, alcian כתם הכחול דיווח במאמר זה הוא בשימוש נרחב כתם קטיוני לזהות mucosaccharides. הכתמה של מערכת העיכול עם alcian כחול יכולה לזהות את חלוקת תאי גביע המייצרים mucosaccharides. שינויים במרכיבי mucosaccharide על פפטידים קצרים להבחין תאי גביע בתפקידו במסגרת מערכת העיכול 6. באמצעות כל הר RNA בשל אתרו וhistochemical שיטות בו זמנית, החלטות גורל תא יכולות להיות מקושרות לביטוי גנים ספציפיים. אמנם RNA בים וhistochemistry &quot;אתר נמצאים בשימוש נרחב על ידי חוקרים, ההסתגלות והשימוש בם בelasmobranchs הימי נפגשו הצלחה מוגבלת ומגוונת. כאן אני מציג את הפרוטוקולים שפותח עבור elasmobranchs והשתמשו על בסיס קבוע במעבדה שלי. למרות שינויים נוספים של RNA בשיטת הכלאה של אתר עשויים להיות נחוצים כדי להסתגל למינים שונים, הפרוטוקולים מתוארים כאן עמrovide נקודת התחלה חזקה עבור חוקרים המבקשים להתאים את השימוש בelasmobranchs הימי לשאלות המדעיות שלהם.

דוגמאות לכתמים כחולים alcian באזורים שונים של L. מערכת עיכול erinacea מוצגת באיור 2. mucin חומצה המכיל תאי globlet הם נראים בבירור על ידי alcian כתם הכחול לאורך מערכת העיכול. חלוקת mucins חומצה שונה באזורים השונים של מערכת העיכול, ובכך הוא משקפת הבדלים בתפקוד. mucins חומצי...

Watch this Scientific Journal Video about RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs at JoVE.com

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

על ידי שילוב של כל שיטות להר רנ&quot;א<em&gt; באתר</em&gt; הכלאה והיסטולוגיה, ביטוי גנים יכולים להיות מקושרת עם החלטות גורל תא בעובר המתפתח. שיטות אלו הותאמו לelasmobranchs הימי ולהקל על השימוש בבעלי החיים אלה כאורגניזמים מודל למחקרים ביו, רעלים והשוואתיים.

רנ&quot;א<em&gt; באתר</em&gt; הכלאה בעוברי הר שלמים והיסטולוגיה הסלולרית מותאמת לElasmobranchs הימי

Marine  elasmobranchs are valued animal models for biomedical and genomic studies as  they are the most primitive vertebrates to have adaptive immunity ...

rna-situ-hybridization-whole-mount-embryos-cell-histology-adapted-for

Research

JoVE Journal

Biology

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

12.6K Views.  Union College. על ידי שילוב של כל שיטות להר רנ"א באתר הכלאה והיסטולוגיה, ביטוי גנים יכולים להיות מקושרת עם החלטות גורל תא בעובר המתפתח. שיטות אלו הותאמו לelasmobranchs הימי ולהקל על השימוש בבעלי החיים אלה כאורגניזמים מודל למחקרים ביו, רעלים והשוואתיים.

Video: RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Double Whole Mount in situ Hybridization of Early Chick Embryos

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  gene expression in brain, neural tube, somite and heart primordia formation. This video demonstrates the different steps in 2-color whole mount in situ hybridization; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, the embryo is processed for prehybridization. The embryo is then hybridized with two different probes, one coupled to DIG, and one coupled to FITC.  Following overnight hybridization, the embryo is incubated with DIG coupled antibody. Color reaction for DIG substrate is performed, and the region of interest appears blue. The embryo is then incubated with FITC coupled antibody. The embryo is processed for color reaction with FITC, and the region of interest appears red. Finally, the embryo is fixed and processed for phtograph and sectioning. A troubleshooting guide is also presented.

This video demonstrates 2-color whole mount in situ hybridization, a method by which the spatial and temporal expression pattern of 2 different genes can be visualized in young chick embryos. This method was originally introduced by David Wilkinson, Domingos Henrique, Phil Ingham and David Ish -Horowicz.

הר שלם כפול באתרו הכלאה של עוברים צ&#39;יק מוקדם

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

Method for Whole Mount Antibody Staining in Chick

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying antibody expression in developing brain, neural tube and somite. This video demonstrates the different steps in whole-mount antibody staining using HRP conjugated secondary antibodies; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, endogenous peroxidase is inactivated; The embryo is then exposed to primary antibody. After several washes, the embryo is incubated with secondary antibody conjugated to HRP. Peroxidase activity is revealed using reaction with diaminobenzidine substrate. Finally, the embryo is fixed and processed for photography and sectioning. The advantage of this method over the use of fluorescent antibodies is that embryos can be processed for wax sectioning, thus enabling the study of antigen sites in cross section. This method was originally introduced by Jane Dodd and Tom Jessell 1.

This video demonstrates whole mount immunohistochemistry, a method by which the spatial and temporal expression pattern of an antigen can be visualized in young chick embryos. This method was originally introduced by Jane Dodd and Tom Jessell.

שיטת מכתים נוגדן שלם הר ב צ&#39;יק

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology. Here, we present a high-resolution double fluorescent in situ hybridization protocol for analyzing the precise expression pattern of a single gene and for determining the overlap of the expression domains of two genes. The protocol is a modified version of the standard in situ hybridization using alkaline phosphatase and substrates such as NBT/BCIP and Fast Red 1,2. This protocol utilizes standard digoxygenin and fluorescein labeled probes along with tyramide signal amplification (TSA) 3. The commercially available TSA kits allow flexible experimental design as fluorescence emission from green to far-red can be used in combination with various nuclear stains, such as propidium iodide, or fluorescence immunohistochemistry for proteins. TSA produces a reactive fluorescent substrate that quickly covalently binds to moieties, typically tyrosine residues, in the immediate vicinity of the labeled antisense riboprobe. The resulting staining patterns are high resolution in that subcellular localization of the mRNA can be observed using laser scanning confocal microscopy 3,4. One can observe nascent transcripts at the chromosomal loci, distinguish nuclear and cytoplasmic staining and visualize other patterns such as cortical localization of mRNA. Studies in Drosophila indicate that roughly 70% of mRNAs exhibit specific patterns of subcellular localization that frequently correlate with the function of the encoded protein 5. When combined with computer-aided reconstruction of 3D confocal datasets, our protocol allows the detailed analysis of mRNA distribution with sub-cellular resolution in whole vertebrate embryos.

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology. Here, we present a high-resolution double fluorescent in situ hybridization protocol for analyzing the precise expression pattern of a single gene and for determining the overlap of the expression domains of two genes. We include a propidium iodide nuclear counter-stain to highlight tissue organization.

דג הזברה שלמים הר ברזולוציה גבוהה פעמיים פלורסנט באתרו הכלאה

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology.  Here, we present a high-resolution double ...

Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the embryology and gross anatomy of several organisms representing various chordate taxa primarily via traditional dissections and the use of models. The final portion of the course involved an innovative approach to teaching anatomy through observation of vertebrate development employing molecular techniques in which WISH was performed on zebrafish embryos. A heterozygous fibroblast growth factor 8 a (fgf8a) mutant line, ace, was used. Due to Mendelian inheritance, ace intercrosses produced wild type, heterozygous, and homozygous ace/fgf8a mutants in a 1:2:1 ratio. RNA probes with known expression patterns in the midline and in developing anatomical structures such as the heart, somites, tailbud, myotome, and brain were used. WISH was performed using zebrafish at the 13 somite and prim-6 stages, with students performing the staining reaction in class. The study of zebrafish embryos at different stages of development gave students the ability to observe how these anatomical structures changed over ontogeny. In addition, some ace/fgf8a mutants displayed improper heart looping, and defects in somite and brain development. The students in this lab observed the normal development of various organ systems using both external anatomy as well as gene expression patterns. They also identified and described embryos displaying improper anatomical development and gene expression (i.e., putative mutants).
For instructors at institutions that do not already own the necessary equipment or where funds for lab and curricular innovation are limited, the financial cost of the reagents and apparatus may be a factor to consider, as will the time and effort required on the part of the instructor regardless of the setting. Nevertheless, we contend that the use of WISH in this type of classroom laboratory setting can provide an important link between developmental genetics and anatomy. As technology advances and the ability to study organismal development at the molecular level becomes easier, cheaper, and increasingly popular, many evolutionary biologists, ecologists, and physiologists are turning to research strategies in the field of molecular biology. Using WISH in a Comparative Vertebrate Biology laboratory classroom is one example of how molecules and anatomy can converge within a single course. This gives upper level college students the opportunity to practice modern biological research techniques, leading to a more diversified education and the promotion of future interdisciplinary scientific research.

Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

Whole mount in situ hybridization (WISH) was used in an upper level undergraduate Comparative Vertebrate Biology course in addition to vertebrate dissections. This gave students the opportunity to study gene expression patterns as well as gross anatomy, linking the study of molecular and organismal biology within one course.

שימוש הר שלם באתרו הכלאה קישור לביולוגיה מולקולרית האורגניזם

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of ...

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures are lengthy and technically demanding with multiple important steps that collectively contribute to the quality of the final result. This protocol describes in detail several key quality control steps for optimizing probe labeling and performance. Overall, our protocol provides a detailed description of the critical steps necessary to reproducibly obtain high quality results. First, we describe the generation of digoxygenin (DIG) labeled RNA probes via in vitro transcription of DNA templates generated by PCR. We describe three critical quality control assays to determine the amount, integrity and specific activity of the DIG-labeled probes. These steps are important for generating a probe of sufficient sensitivity to detect endogenous mRNAs in a whole mouse embryo. In addition, we describe methods for the fixation and storage of E8.5-E11.5 day old mouse embryos for in situ hybridization. Then, we describe detailed methods for limited proteinase K digestion of the rehydrated embryos followed by the details of the hybridization conditions, post-hybridization washes and RNase treatment to remove non-specific probe hybridization. An AP-conjugated antibody is used to visualize the labeled probe and reveal the expression pattern of the endogenous transcript. Representative results are shown from successful experiments and typical suboptimal experiments.

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

This whole mount in situ hybridization protocol discusses critical steps that ensure reproducible high quality results for gene expression studies in E8.5-E11.5 day old mouse embryos.

הר שלם<em&gt; באתר</em&gt; הכלאה של E8.5 לעוברי E11.5 עכבר

Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures ...

Detection of Viral RNA by Fluorescence in situ Hybridization (FISH)

Viruses that infect cells elicit specific changes to normal cell functions which serve to divert energy and resources for viral replication. Many aspects of host cell function are commandeered by viruses, usually by the expression of viral gene products that recruit host cell proteins and machineries. Moreover, viruses engineer specific membrane organelles or tag on to mobile vesicles and motor proteins to target regions of the cell (during de novo infection, viruses co-opt molecular motor proteins to target the nucleus; later, during virus assembly, they will hijack cellular machineries that will help in the assembly of viruses). Less is understood on how viruses, in particular those with RNA genomes, coordinate the intracellular trafficking of both protein and RNA components and how they achieve assembly of infectious particles at specific loci in the cell. The study of RNA localization began in earlier work. Developing lower eukaryotic embryos and neuronal cells provided important biological information, and also underscored the importance of RNA localization in the programming of gene expression cascades. The study in other organisms and cell systems has yielded similar important information. Viruses are obligate parasites and must utilise their host cells to replicate. Thus, it is critical to understand how RNA viruses direct their RNA genomes from the nucleus, through the nuclear pore, through the cytoplasm and on to one of its final destinations, into progeny virus particles 1.
FISH serves as a useful tool to identify changes in steady-state localization of viral RNA. When combined with immunofluorescence (IF) analysis 22, FISH/IF co-analyses will provide information on the co-localization of proteins with the viral RNA3. This analysis therefore provides a good starting point to test for RNA-protein interactions by other biochemical or biophysical tests 4,5, since co-localization by itself is not enough evidence to be certain of an interaction. In studying viral RNA localization using a method like this, abundant information has been gained on both viral and cellular RNA trafficking events 6. For instance, HIV-1 produces RNA in the nucleus of infected cells but the RNA is only translated in the cytoplasm. When one key viral protein is missing (Rev) 7, FISH of the viral RNA has revealed that the block to viral replication is due to the retention of the HIV-1 genomic RNA in the nucleus 8. 
Here, we present the method for visual analysis of viral genomic RNA in situ. The method makes use of a labelled RNA probe. This probe is designed to be complementary to the viral genomic RNA. During the in vitro synthesis of the antisense RNA probe, the ribonucleotide that is modified with digoxigenin (DIG) is included in an in vitro transcription reaction. Once the probe has hybridized to the target mRNA in cells, subsequent antibody labelling steps (Figure 1) will reveal the localization of the mRNA as well as proteins of interest when performing FISH/IF.

Detection of Viral RNA by Fluorescence in situ Hybridization FISH

A fluorescence in situ hybridization (FISH) method was developed to visually detect viral genomic RNA using fluorescence microscopy. A probe is made with specificity to the viral RNA that can then be identified using a combination of hybridization and immunofluorescence techniques. This technique offers the advantage of identifying the localization of the viral RNA or DNA at steady-state, providing information on the control of intracellular virus trafficking events.

זיהוי של רנ&quot;א נגיפי על ידי הקרינה<em&gt; באתרו</em&gt; הכלאה (דגים)

Viruses  that infect cells elicit specific changes to normal cell functions which serve  to divert energy and resources for viral replication. Many ...

Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization (FISH)

Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 protein variants encoded by the var genes.
The haploid P. falciparum genome harbors approximately 60 different var genes of which only one has been believed to be transcribed per cell at a time during the blood stage of the infection. How such mutually exclusive regulation of var gene transcription is achieved is unclear, as is the identification of individual var genes or sub-groups of var genes associated with different receptors and the consequence of differential binding on the clinical outcome of P. falciparum infections. Recently, the mutually exclusive transcription paradigm has been called into doubt by transcription assays based on individual P. falciparum transcript identification in single infected erythrocytic cells using RNA fluorescent in situ hybridization (FISH) analysis of var gene transcription by the parasite in individual nuclei of P. falciparum IE1.
Here, we present a detailed protocol for carrying out the RNA-FISH methodology for analysis of var gene transcription in single-nuclei of P. falciparum infected human erythrocytes. The method is based on the use of digoxigenin- and biotin- labeled antisense RNA probes using the TSA Plus Fluorescence Palette System2 (Perkin Elmer), microscopic analyses and freshly selected P. falciparum IE. The in situ hybridization method can be used to monitor transcription and regulation of a variety of genes expressed during the different stages of the P. falciparum life cycle and is adaptable to other malaria parasite species and other organisms and cell types.

Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization FISH

Fluorescent in situ hybridization (FISH) to identify mRNA transcripts in individual cells allows analysis of polygenic activity such as the simultaneous transcription of more than one member of the var multigene family in Plasmodium falciparum infected erythrocytes 1. The technique is adaptable and can be used on different types of genes, cells and organisms.

ניתוח של שעתוק גנים מהתא הבודד על ידי RNA פלורסנט<em&gt; באתר</em&gt; הכלאה (דגים)

Adhesion of Plasmodium falciparum infected erythrocytes (IE) to human endothelial receptors during malaria infections is mediated by expression of PfEMP1 ...

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

Assessing the expression pattern of a gene, as well as the subcellular localization properties of its transcribed RNA, are key features for understanding its biological function during development. RNA in situ hybridization (RNA-ISH) is a powerful method used for visualizing RNA distribution properties, be it at the organismal, cellular or subcellular levels 1. RNA-ISH is based on the hybridization of a labeled nucleic acid probe (e.g. antisense RNA, oligonucleotides) complementary to the sequence of an mRNA or a non-coding RNA target of interest 2. As the procedure requires primary sequence information alone to generate sequence-specific probes, it can be universally applied to a broad range of organisms and tissue specimens 3. Indeed, a number of large-scale ISH studies have been implemented to document gene expression and RNA localization dynamics in various model organisms, which has led to the establishment of important community resources 4-11. While a variety of probe labeling and detection strategies have been developed over the years, the combined usage of fluorescently-labeled detection reagents and enzymatic signal amplification steps offer significant enhancements in the sensitivity and resolution of the procedure 12. Here, we describe an optimized fluorescent in situ hybridization method (FISH) employing tyramide signal amplification (TSA) to visualize RNA expression and localization dynamics in staged Drosophila embryos. The procedure is carried out in 96-well PCR plate format, which greatly facilitates the simultaneous processing of large numbers of samples.

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

Here we describe a whole-mount fluorescent in situ hybridization (FISH) protocol for determining the expression and localization properties of RNAs expressed during embryogenesis in the fruit fly, Drosophila melanogaster.

הר כולו RNA פלורסנט<em&gt; באתר</em&gt; הכלאה של<em&gt; דרוזופילה</em&gt; עוברים

Assessing  the expression pattern of a gene, as well as the subcellular localization  properties of its transcribed RNA, are key features for ...

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made permeable. Subsequently, multiple single-stranded deoxyoligonucleotides conjugated to fluorescent dyes are used to label and visualize mRNAs. Diffraction-limited fluorescence from single mRNA molecules is quantified using a spot-detection algorithm to identify and count the number of mRNAs per cell. While the more standard quantification methods of northern blots, RT-PCR and gene expression microarrays provide information on average mRNAs in the bulk population, FISH facilitates both the counting and localization of these mRNAs in single cells at single-molecule resolution.

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

This protocol describes an experimental procedure for performing Fluorescence in situ Hybridization (FISH) for counting mRNAs in single cells at single-molecule resolution.

הדמיה וניתוח של מולקולות ה-mRNA באמצעות הקרינה<em&gt; באתרו</em&gt; הכלאה ב<em&gt; Cerevisiae Saccharomyces</em

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for ...

High Resolution Whole Mount In Situ Hybridization within Zebrafish Embryos to Study Gene Expression and Function

This article focuses on whole-mount in situ hybridization (WISH) of zebrafish embryos. The WISH technology facilitates the assessment of gene expression both in terms of tissue distribution and developmental stage. Protocols are described for the use of WISH of zebrafish embryos using antisense RNA probes labeled with digoxigenin. Probes are generated by incorporating digoxigenin-linked nucleotides through in vitro transcription of gene templates that have been cloned and linearized. The chorions of embryos harvested at defined developmental stages are removed before incubation with specific probes. Following a washing procedure to remove excess probe, embryos are incubated with anti-digoxigenin antibody conjugated with alkaline phosphatase. By employing a chromogenic substrate for alkaline phosphatase, specific gene expression can be assessed. Depending on the level of gene expression the entire procedure can be completed within 2-3 days.

High Resolution Whole Mount In Situ Hybridization within Zebrafish Embryos to Study Gene Expression and Function

The zebrafish, a small tropical fish, has become a popular model for studying gene function during vertebrate development and disease. The temporal and spatial expression of target genes can be determined by in situ hybridization. Our improved protocol allows for the detection of low abundant transcripts with low non-specific background signal.

הר שלם ברזולוציה גבוהה<em&gt; באתרו</em&gt; הכלאה בתוך עוברי דג הזברה לחקר ביטוי גנים ותפקוד

This article focuses on whole-mount in situ hybridization (WISH) of zebrafish embryos. The WISH technology facilitates the assessment of gene expression ...

רנ"א

Summary

Explore More Videos

Chapters in this video

הר שלם כפול באתרו הכלאה של עוברים צ'יק מוקדם

שיטת מכתים נוגדן שלם הר ב צ'יק

דג הזברה שלמים הר ברזולוציה גבוהה פעמיים פלורסנט באתרו הכלאה

שימוש הר שלם באתרו הכלאה קישור לביולוגיה מולקולרית האורגניזם

הר שלם

זיהוי של רנ"א נגיפי על ידי הקרינה

ניתוח של שעתוק גנים מהתא הבודד על ידי RNA פלורסנט

הר כולו RNA פלורסנט

הדמיה וניתוח של מולקולות ה-mRNA באמצעות הקרינה

הר שלם ברזולוציה גבוהה