Nous remercions Sergei Demin et Tatyana Karamysheva pour leur aide dans la préparation des chromosomes et FISH sur Anopheles. Nous remercions également David Severson de nous donner Aedes et Culex ADN génomique des clones BAC et Melissa Wade pour éditer le texte. Ce travail a été soutenu par deux subventions du National Institutes of Health: 1R21 AI88035-01 à Maria V. Sharakhova et AI094289 1R21-01 à Igor V. Sharakhov.

<ol>
	<li>Sharakhov, I. V., Sharakhova, M. V., Verrity, J. F., Abbington, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Chromosome Mapping Research Developments. , (2008).</li><li>Holt, R. A., 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=The+genome+sequence+of+the+malaria+mosquito+Anopheles+gambiae.">The genome sequence of the malaria mosquito Anopheles gambiae.</a> Science. 298, 129-149 (2002).</li><li>Sharakhova, M. V., 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=Update+of+the+Anopheles+gambiae+PEST+genome+assembly.">Update of the Anopheles gambiae PEST genome assembly.</a> Genome biology. 8, R5 (2007).</li><li>Campos, J., Andrade, C. F., Recco-Pimentel, S. 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+technique+for+preparing+polytene+chromosomes+from+Aedes+aegypti+(Diptera,+Culicinae).">A technique for preparing polytene chromosomes from Aedes aegypti (Diptera, Culicinae).</a> Memorias do Instituto Oswaldo Cruz. 98, 387-390 (2003).</li><li>Campos, J., Andrade, C. F., Recco-Pimentel, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Malpighian+tubule+polytene+chromosomes+of+Culex+quinquefasciatus+(Diptera,+Culicinae).">Malpighian tubule polytene chromosomes of Culex quinquefasciatus (Diptera, Culicinae).</a> Memorias do Instituto Oswaldo Cruz. 98, 383-386 (2003).</li><li>McAbee, R. D., Christiansen, J. A., Cornel, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+detailed+larval+salivary+gland+polytene+chromosome+photomap+for+Culex+quinquefasciatus+(Diptera:+Culicidae)+from+Johannesburg,+South+Africa.">A detailed larval salivary gland polytene chromosome photomap for Culex quinquefasciatus (Diptera: Culicidae) from Johannesburg, South Africa.</a> J. Med. Entomol. 44, 229-237 (2007).</li><li>Nene, V., 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=Genome+sequence+of+Aedes+aegypti,+a+major+arbovirus+vector.">Genome sequence of Aedes aegypti, a major arbovirus vector.</a> Science. 316, 1718-1723 (2007).</li><li>Arensburger, P., 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=Sequencing+of+Culex+quinquefasciatus+establishes+a+platform+for+mosquito+comparative+genomics.">Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.</a> Science. 330, 86-88 (2010).</li><li>Sharakhova, M. V., 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=Imaginal+discs--a+new+source+of+chromosomes+for+genome+mapping+of+the+yellow+fever+mosquito+Aedes+aegypti.">Imaginal discs--a new source of chromosomes for genome mapping of the yellow fever mosquito Aedes aegypti.</a> PLoS neglected tropical diseases. 5, e1335 (2011).</li><li>Brown, S. E., 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=Toward+a+physical+map+of+Aedes+aegypti.">Toward a physical map of Aedes aegypti.</a> Insect Mol. Biol. 4, 161-167 (1995).</li><li>Steiniger, G. E., Mukherjee, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insect+chromosome+banding:+technique+for+G-+and+Q-banding+pattern+in+the+mosquito+Aedes+albopictus.">Insect chromosome banding: technique for G- and Q-banding pattern in the mosquito Aedes albopictus.</a> Can. J. Genet. Cytol. 17, 241-244 (1975).</li><li>Garimberti, E., Tosi, S., Bridger, J. M., Volpi, E. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Fluorescence in situ hybridization (FISH). , (2010).</li><li>Scott, J. A., Brogdon, W. G., Collins, F. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+single+specimens+of+the+Anopheles+gambiae+complex+by+the+polymerase+chain+reaction.">Identification of single specimens of the Anopheles gambiae complex by the polymerase chain reaction.</a> The American journal of tropical medicine and hygiene. 49, 520-529 (1993).</li><li>Trifonov, V. A., Vorobyeva, N. N., Rens, W., Leiehr, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Fluorescence in situ hybridization (FISH). , (2009).</li><li>Collins, F. H., 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=A+ribosomal+RNA+gene+probe+differentiates+member+species+of+the+Anopheles+gambiae+complex.">A ribosomal RNA gene probe differentiates member species of the Anopheles gambiae complex.</a> The American journal of tropical medicine and hygiene. 37, 37-41 (1987).</li><li>Kumar, A., Rai, K. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromosomal+localization+and+copy+number+of+18S+28S+ribosomal+RNA+genes+in+evolutionary+diverse+mosquitoes+(Diptera,+Culicidae).">Chromosomal localization and copy number of 18S+28S ribosomal RNA genes in evolutionary diverse mosquitoes (Diptera, Culicidae).</a> Hereditas. 113, 277-289 (1990).</li><li>Brown, S. E., Knudson, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FISH+landmarks+for+Aedes+aegypti+chromosomes.">FISH landmarks for Aedes aegypti chromosomes.</a> Insect Mol. Biol. 6, 197-202 (1997).</li><li>Brown, S. E., Severson, D. W., Smith, L. A., Knudson, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integration+of+the+Aedes+aegypti+mosquito+genetic+linkage+and+physical+maps.">Integration of the Aedes aegypti mosquito genetic linkage and physical maps.</a> Genetics. 157, 1299-1305 (2001).</li></ol>

Aucun conflit d&#39;intérêt déclaré.

Non fluorescent hybridation in situ sur chromosomes mitotiques de moustiques a été réalisée pour la première fois en 1990 par A. Kumar et K. Rai 17. Dans cette étude, 18S et 28S des gènes d&#39;ADN ribosomal, cloné dans un plasmide ensemble, ont été placés sur les chromosomes de 20 espèces de moustiques. La sonde d&#39;ADN a été marqué radioactivement et hybridés aux chromosomes de ganglions du cerveau. Parmi les trois genres de moustiques, une technique FISH a été développé uniquement pour les chromosomes mitotiques de la lignée cellulaire d&#39;Ae. aegypti 10,18,19 et n&#39;a jamais été effectuée sur les chromosomes mitotiques de moustiques vivants. Récemment, nous avons développé une technique simple et robuste pour l&#39;obtention des préparations chromosomiques de haute qualité des ID des 4 e stade larvaire 9. Cette méthode permet à un nombre élevé de chromosomes à obtenir dans une diapositive et peut être utilisé universellement pour toutes les espèces de moustiques. La nécessité d&#39;utiliser sta seule larve, nymphe ou adulte neges de moustiques, pour la préparation des lames est probablement la seule limite de la méthode. La méthode FISH standard de 12 a été optimisé pour l&#39;utilisation de la génomique clone BAC et l&#39;IGS ADNr comme sondes pour les chromosomes mitotiques de Aedes, Culex, Anopheles et. En plus de ces applications spécifiques, les protocoles FISH décrites ici peuvent également être utilisés à d&#39;autres fins. Le protocole FISH avancé, qui utilise C 0 t fractions d&#39;ADN pour bloquer l&#39;hybridation non spécifique, peut également être appliquée pour l&#39;hybridation de clones BAC ou d&#39;autres fragments d&#39;ADN grandes régions hétérochromatiques d&#39;Anopheles. Régions hétérochromatiques sont enrichis en éléments transposables et répète autres, et les sondes de ces régions produisent normalement solide expérience sur les 3 chromosomes. Utilisation non marquées C 0 fractions d&#39;ADN t aidera à réduire l&#39;hybridation non spécifique de la sonde aux chromosomes. La version simple de la pr POISSONotocole peut être utilisé pour n&#39;importe quel ADNr ou des sondes d&#39;ADN répétitives sur les chromosomes mitotiques de moustiques et d&#39;autres insectes. En outre, il peut également être appliquée pour l&#39;hybridation de l&#39;ADN clone BAC en espèces à faible teneur en ADN répétitif dans les régions euchromatiques comme Anopheles ou la drosophile. Le protocole proposé ici permettra d&#39;obtenir très-finis assemblées du génome chromosomique base pour les moustiques et peut être largement utilisé pour des applications cytogénétiques différents autres groupes d&#39;insectes.

<table border="1"><tbody><tr><td> Nom du réactif / Equipement </td><td> Entreprise </td><td> Numéro de catalogue </td><td> Commentaires </td></tr><tr><td> Stéréomicroscope Leica MZ6 </td><td> Leica </td><td> VA-OM-E194-354 </td><td> Un stéréomicroscope différente peut être utilisée </td></tr><tr><td> Microscope Olympus CX41 phase de </td><td> Olympe </td><td> CX41 </td><td> Un microscope de phase différent peut être utilisé </td></tr><tr><td> Olympus BX61 microscope à fluorescence </td><td> Olympe </td><td> BX61 </td><td> Un microscope fluorescent différent peut être utilisé </td></tr><tr><td> Faites glisser ThermoBrite dénaturation / hybridation système </td><td> Abbott Molecular </td><td> 30-144110 </td><td> Sert de bloc de chauffage et une chambre humide </td></tr><tr><td> Aiguilles à dissection </td><td> ScienceTools Beaux- </td><td> 10130-10</td><td></td></tr><tr><td> Porte-aiguilles </td><td> Outils Fine Science </td><td> 26018-17 </td><td></td></tr><tr><td> Ciseaux à dissection </td><td> Outils Fine Science </td><td> 15000-03 </td><td></td></tr><tr><td> 75x25 à double dépoli micro glisse </td><td> Corning </td><td> 2949-75x25 </td><td></td></tr><tr><td> 22x22 lamelles de microscope mm </td><td> Fisher Scientific </td><td> 12-544-10 </td><td></td></tr><tr><td> Parafilm </td><td> Fisher Scientific </td><td> 13-374-10 </td><td></td></tr><tr><td> Rubber Cement </td><td> Fisher Scientific </td><td> 50-949-105 </td><td></td></tr><tr><td> L&#39;acide acétique </td><td> Fisher Scientific </td><td> A491-212 </td><td></td></tr><tr><td> Alcool 200 Proof </td><td> Decon Laboratories </td><td> 2701 </td><td></td></tr><tr><td> L&#39;acide propionique </td><td> Sigma-ALDRich </td><td> 402907 </td><td></td></tr><tr><td> Acide chlorhydrique </td><td> Fisher Scientific </td><td> A144-500 </td><td></td></tr><tr><td> Citrate de sodium dihydraté </td><td> Fisher Scientific </td><td> S279-500 </td><td></td></tr><tr><td> Trihydrate d&#39;acétate de sodium </td><td> Fisher Scientific </td><td> BP334-500 </td><td></td></tr><tr><td> Le chlorure de potassium </td><td> Fisher Scientific </td><td> BP366-500 </td><td></td></tr><tr><td> EDTA </td><td> Fisher Scientific </td><td> S311-500 </td><td></td></tr><tr><td> Tris base </td><td> Fisher Scientific </td><td> BP152-1 </td><td></td></tr><tr><td> 10x PBS </td><td> Invitrogen </td><td> P5493 </td><td></td></tr><tr><td> 10% FBN (formol tamponné neutre) </td><td> Sigma-Aldrich </td><td> HT501128 </td><td></td></tr><tr><td> Formamide 99% </td><td> Fisher Scientific </td><td> BP227500 </td><td></td></tr><tr><td> Sel de sodium de sulfate de dextrane </td><td> Sigma-Aldrich </td><td> D8906 </td><td></td></tr><tr><td> 20x tampon SSC </td><td> Invitrogen </td><td> AM9765 </td><td></td></tr><tr><td> 1 mM YOYO-1 d&#39;iodure (491/509) solution </td><td> Invitrogen </td><td> Y3601 </td><td></td></tr><tr><td> Prolongez Antifade réactif de Gold </td><td> Invitrogen </td><td> <a href="http://products.invitrogen.com/ivgn/en/US/adirect/invitrogen?cmd=catProductDetail&amp;productID=P36930" target="_blank">P36930</a> </td><td></td></tr><tr><td> dATP, dCTP, dGTP, dTTP </td><td> Fermentas </td><td> R0141, R0151, R0161, R0171 </td><td></td></tr><tr><td> Cy3-dUTP, Cy5-dUTP </td><td> GE Healthcare </td><td> PA53022, PA55022 </td><td></td></tr><tr><td> BSA </td><td> Sigma-Aldrich </td><td> A3294 </td><td></td></tr><tr><td> ADN polymérase I </td><td> Fermentas </td><td> EP0041 </td><td></td></tr><tr><td> DNase I </td><td> Fermentas </td><td> EN0521 </td><td></td></tr><tr><td> S1 nucléase </td><td> Fermentas </td><td> EN0321 </td><td></td></tr><tr><td> Taq DNA Polymerase </td><td> Invitrogen </td><td> 18038-042 </td><td></td></tr><tr><td> RNase </td><td> Sigma-Aldrich </td><td> 9001-99-4 </td><td></td></tr><tr><td> Pepsine </td><td> USB </td><td> 9001-75-6 </td><td></td></tr><tr><td> ADN de sperme de saumon </td><td> Sigma-Aldrich </td><td> D7656 </td><td></td></tr><tr><td> Nonidet-P40 (NP40) </td><td> US Biological </td><td> NC9375914 </td><td></td></tr><tr><td> Sang Qiagen et Maxikit culture cellulaire </td><td> Qiagen </td><td> 13362 </td><td></td></tr><tr><td> Kit Qiagen construire de grands </td><td> Qiagen </td><td> 12462 </td&gt; <td></td></tr></tbody></table>

fluorescent in situ hybridization on mitotic chromosomes of mosquitoes

Hybridation fluorescente in situ (FISH) est une technique couramment utilisée par de nombreux laboratoires pour déterminer la position chromosomique de sondes d&#39;ADN et d&#39;ARN. Une application importante de cette méthode est le développement de la haute qualité des cartes physiques utiles pour améliorer les assemblages génome pour divers organismes. La tendance naturelle des bandes des chromosomes polytènes et mitotique fournit des indications pour la commande précise et l&#39;orientation des supercontigs génomiques. Parmi les trois genres de moustiques anophèles, à savoir, Aedes, et Culex, une technique bien établie basée sur la cartographie de chromosomes a été développé uniquement pour les Anopheles, dont les membres possèdent des chromosomes polytènes lisibles 1. En raison de travaux de cartographie du génome, 88% de l&#39;An. gambiae génome a été placé à des postes précis du chromosome 2,3. Deux genres de moustiques du genre Aedes, autres et Culex, ont mal polytenized b chromosomesarce que la surreprésentation significative des éléments transposables dans leurs génomes 4, 5, 6. Seulement 31 et 9% des supercontings génomiques ont été attribués sans ordre ou l&#39;orientation des chromosomes de Ae. aegypti 7 et Cx. quinquefasciatus 8, respectivement. Préparation des chromosomes mitotiques pour ces deux espèces avaient déjà été limitée aux ganglions du cerveau et des lignées cellulaires. Toutefois, des lames de chromosomes préparés à partir des ganglions du cerveau de moustiques contiennent généralement un faible nombre de plaques métaphasiques 9. En outre, même si une technique FISH a été développé pour les chromosomes mitotiques provenant d&#39;une lignée cellulaire d&#39;Ae. aegypti 10, l&#39;accumulation de multiples réarrangements chromosomiques dans les chromosomes de lignées cellulaires 11 rend inutiles pour la cartographie du génome. Nous décrivons ici une technique simple et robuste pour obtenir de haute qualité des préparations de chromosomes mitotiques de disques imaginaux (ID) de 4 e stade larvaire qui cPeut être utilisé pour les trois genres de moustiques. Un protocole standard de 12 FISH est optimisé pour l&#39;utilisation de clones BAC de l&#39;ADN génomique comme une sonde sur les chromosomes mitotiques de Ae. aegypti et Culex. quinquefasciatus, et d&#39;utiliser un espaceur intergénique (IGS) de l&#39;ADN ribosomique (ADNr) comme sonde sur un. chromosomes gambiae. Outre la cartographie physique, la technique développée peut être appliquée à la cytogénétique populations et la taxonomie des chromosomes / systématique de moustiques ou d&#39;autres insectes et les groupes.

Watch this Scientific Journal Video about Fluorescent in situ Hybridization on Mitotic Chromosomes of Mosquitoes at JoVE.com

Fluorescent in situ Hybridization on Mitotic Chromosomes of Mosquitoes

Parmi les trois genres de moustiques, à savoir<em&gt; Anopheles,</em&gt;<em&gt; Aedes</em&gt;, Et<em&gt; Culex</em&gt;, Physiques techniques de cartographie du génome ont été mis en place uniquement pour les<em&gt; Anopheles</em&gt;, Dont les membres possèdent des chromosomes polytènes lisibles. Pour les genres de<em&gt; Aedes</em&gt; Et<em&gt; Culex</em&gt; Cependant, la cartographie cytogénétique reste difficile en raison de la mauvaise qualité des chromosomes polytènes. Nous présentons ici un protocole universel pour obtenir de haute qualité des préparations de chromosomes mitotiques et un protocole FISH optimisé pour les trois genres de moustiques.

Fluorescent<em&gt; In situ</emHybridation&gt; sur les chromosomes mitotiques de moustiques

Fluorescent in situ hybridization (FISH) is a technique routinely used by many laboratories to determine the chromosomal position of DNA and RNA probes. ...

fluorescent-in-situ-hybridization-on-mitotic-chromosomes-of-mosquitoes

Research

JoVE Journal

Immunology and Infection

Fluorescent in situ Hybridization on Mitotic Chromosomes of Mosquitoes

25.6K vues.  Virginia Tech. Parmi les trois genres de moustiques, à savoir Anopheles, Aedes, Et Culex, Physiques techniques de cartographie du génome ont été mis en place uniquement pour les Anopheles, Dont les membres possèdent des chromosomes polytènes lisibles. Pour les genres de Aedes Et Culex Cependant, la cartographie cytogénétique reste difficile en raison de la mauvaise qualité des chromosomes ...

Vidéo: Fluorescent in situ Hybridization on Mitotic Chromosomes of Mosquitoes

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in situ hybridization (FISH) for rapid culture-independent detection of Salmonella spp. Cell-charged tapes can also be placed face-down on selective agar for solid-phase enrichment prior to detection. Alternatively, low-volume liquid enrichments (liquid surface miniculture) can be performed on the surface of the tape in non-selective broth, followed by FISH and analysis via flow cytometry. To begin, sterile adhesive tape is brought into contact with fresh produce, gentle pressure is applied, and the tape is removed, physically extracting microbes present on these surfaces. Tapes are mounted sticky-side up onto glass microscope slides and the sampled cells are fixed with 10% formalin (30 min) and dehydrated using a graded ethanol series (50, 80, and 95%; 3 min each concentration). Next, cell-charged tapes are spotted with buffer containing a Salmonella-targeted DNA probe cocktail and hybridized for 15 - 30 min at 55&deg;C, followed by a brief rinse in a washing buffer to remove unbound probe. Adherent, FISH-labeled cells are then counterstained with the DNA dye 4',6-diamidino-2-phenylindole (DAPI) and results are viewed using fluorescence microscopy. For solid-phase enrichment, cell-charged tapes are placed face-down on a suitable selective agar surface and incubated to allow in situ growth of Salmonella microcolonies, followed by FISH and microscopy as described above. For liquid surface miniculture, cell-charged tapes are placed sticky side up and a silicone perfusion chamber is applied so that the tape and microscope slide form the bottom of a water-tight chamber into which a small volume (&le; 500 &mu;L) of Trypticase Soy Broth (TSB) is introduced. The inlet ports are sealed and the chambers are incubated at 35 - 37&deg;C, allowing growth-based amplification of tape-extracted microbes. Following incubation, inlet ports are unsealed, cells are detached and mixed with vigorous back and forth pipetting, harvested via centrifugation and fixed in 10% neutral buffered formalin. Finally, samples are hybridized and examined via flow cytometry to reveal the presence of Salmonella spp. As described here, our "tape-FISH" approach can provide simple and rapid sampling and detection of Salmonella on tomato surfaces. We have also used this approach for sampling other types of fresh produce, including spinach and jalape&ntilde;o peppers.

Combination of Adhesive-tape-based Sampling and Fluorescence in situ Hybridization for Rapid Detection of Salmonella on Fresh Produce

This protocol describes a simple adhesive-tape-based approach for sampling of tomato and other fresh produce surfaces, followed by rapid whole cell detection of Salmonella using fluorescence in situ hybridization (FISH).

Combinaison de adhésif à base de bandes d&#39;échantillonnage et de fluorescence In situ</emHybridation> pour la détection rapide des Salmonella Sur les produits frais

This protocol describes a simple approach for adhesive-tape-based sampling of tomato and other fresh produce surfaces, followed by on-tape fluorescence in ...

Recherche

Immunologie et infection

Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization (LNA flow-FISH): a Method for Bacterial Small RNA Detection

Fluorescence in situ hybridization (FISH) is a powerful technique that is used to detect and localize specific nucleic acid sequences in the cellular environment. In order to increase throughput, FISH can be combined with flow cytometry (flow-FISH) to enable the detection of targeted nucleic acid sequences in thousands of individual cells. As a result, flow-FISH offers a distinct advantage over lysate/ensemble-based nucleic acid detection methods because each cell is treated as an independent observation, thereby permitting stronger statistical and variance analyses. These attributes have prompted the use of FISH and flow-FISH methods in a number of different applications and the utility of these methods has been successfully demonstrated in telomere length determination1,2, cellular identification and gene expression3,4, monitoring viral multiplication in infected cells5, and bacterial community analysis and enumeration6.
Traditionally, the specificity of FISH and flow-FISH methods has been imparted by DNA oligonucleotide probes. Recently however, the replacement of DNA oligonucleotide probes with nucleic acid analogs as FISH and flow-FISH probes has increased both the sensitivity and specificity of each technique due to the higher melting temperatures (Tm) of these analogs for natural nucleic acids7,8. Locked nucleic acid (LNA) probes are a type of nucleic acid analog that contain LNA nucleotides spiked throughout a DNA or RNA sequence9,10. When coupled with flow-FISH, LNA probes have previously been shown to outperform conventional DNA probes7,11 and have been successfully used to detect eukaryotic mRNA12 and viral RNA in mammalian cells5.
Here we expand this capability and describe a LNA flow-FISH method which permits the specific detection of RNA in bacterial cells (Figure 1). Specifically, we are interested in the detection of small non-coding regulatory RNA (sRNA) which have garnered considerable interest in the past few years as they have been found to serve as key regulatory elements in many critical cellular processes13. However, there are limited tools to study sRNAs and the challenges of detecting sRNA in bacterial cells is due in part to the relatively small size (typically 50-300 nucleotides in length) and low abundance of sRNA molecules as well as the general difficulty in working with smaller biological cells with varying cellular membranes. In this method, we describe fixation and permeabilzation conditions that preserve the structure of bacterial cells and permit the penetration of LNA probes as well as signal amplification steps which enable the specific detection of low abundance sRNA (Figure 2).

Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization LNA flow-FISH: a Method for Bacterial Small RNA Detection

A novel high-throughput method is described that enables the detection and relative quantitation of small RNA and mRNA expression from single bacterial cells using locked nucleic acid probes and flow cytometry-fluorescence in situ hybridization.

Verrouillé flux Nucleic Acid cytométrie de fluorescence In situ</emHybridation> (LNA flux FISH): une méthode d&#39;bactérienne détection de l&#39;ARN petits

Fluorescence in situ hybridization (FISH) is a powerful technique that is used to detect and localize specific nucleic acid sequences in the cellular ...

Hybridization in situ of Salivary Glands, Ovaries, and Embryos of Vector Mosquitoes

Mosquitoes are vectors for a diverse set of pathogens including arboviruses, protozoan parasites and nematodes. Investigation of transcripts and gene regulators that are expressed in tissues in which the mosquito host and pathogen interact, and in organs involved in reproduction are of great interest for strategies to reduce mosquito-borne disease transmission and disrupt egg development. A number of tools have been employed to study and validate the temporal and tissue-specific regulation of gene expression. Here, we describe protocols that have been developed to obtain spatial information, which enhances our understanding of where specific genes are expressed and their products accumulate. The protocol described has been used to validate expression and determine accumulation patterns of transcripts in tissues related to mosquito-borne pathogen transmission, such as female salivary glands, as well as subcellular compartments of ovaries and embryos, which relate to mosquito reproduction and development. 
 The following procedures represent an optimized methodology that improves the efficiency of various steps in the protocol without loss of target-specific hybridization signals. Guidelines for RNA probe preparation, dissection of soft tissues and the general procedure for fixation and hybridization are described in Part A, while steps specific for the collection, fixation, pre-hybridization and hybridization of mosquito embryos are detailed in Part B.

Hybridization in situ of Salivary Glands, Ovaries, and Embryos of Vector Mosquitoes

Temporal and spatial gene expression analyses have a crucial role in functional genomics. Whole-mount hybridization in situ is useful for determining the localization of transcripts within tissues and subcellular compartments. Here we outline a hybridization in situ protocol with modifications for specific target tissues in mosquitoes.

Hybridation<em&gt; In situ</em&gt; Des glandes salivaires, des ovaires et des embryons de moustiques vecteurs

Mosquitoes are vectors for a diverse set of pathogens including arboviruses, protozoan parasites and nematodes.  Investigation of transcripts and gene ...

Using Fluorescent Proteins to Visualize and Quantitate Chlamydia Vacuole Growth Dynamics in Living Cells

The obligate intracellular bacterium Chlamydia elicits a great burden on global public health. C.&#160;trachomatis is the leading bacterial cause of sexually transmitted infection and also the primary cause of preventable blindness in the world. An essential determinant for successful infection of host cells by Chlamydia is the bacterium's ability to manipulate host cell signaling from within a novel, vacuolar compartment called the inclusion. From within the inclusion, Chlamydia acquire nutrients required for their 2-3 day developmental growth, and they additionally secrete a panel of effector proteins onto the cytosolic face of the vacuole membrane and into the host cytosol. Gaps in our understanding of Chlamydia biology, however, present significant challenges for visualizing and analyzing this intracellular compartment. Recently, a reverse-imaging strategy for visualizing the inclusion using GFP expressing host cells was described. This approach rationally exploits the intrinsic impermeability of the inclusion membrane to large molecules such as GFP. In this work, we describe how GFP- or mCherry-expressing host cells are generated for subsequent visualization of chlamydial inclusions. Furthermore, this method is shown to effectively substitute for costly antibody-based enumeration methods, can be used in tandem with other fluorescent labels, such as GFP-expressing Chlamydia, and can be exploited to derive key quantitative data about inclusion membrane growth from a range of Chlamydia species and strains.

Using Fluorescent Proteins to Visualize and Quantitate Chlamydia Vacuole Growth Dynamics in Living Cells

A live cell fluorescent protein based method for illuminating cellular vacuoles (inclusions) containing Chlamydia is described. This strategy enables rapid, automated determination of Chlamydia infectivity in samples and can be used to quantitatively investigate inclusion growth dynamics.

Utilisation de protéines fluorescentes de visualiser et de quantifier<em&gt; Chlamydia</em&gt; Vacuole la dynamique de croissance dans les cellules vivantes

The obligate intracellular bacterium Chlamydia elicits a great burden on global public health. C.&#160;trachomatis is the leading bacterial cause of ...

2D and 3D Chromosome Painting in Malaria Mosquitoes

Fluorescent in situ hybridization (FISH) of whole arm chromosome probes is a robust technique for mapping genomic regions of interest, detecting chromosomal rearrangements, and studying three-dimensional (3D) organization of chromosomes in the cell nucleus. The advent of laser capture microdissection (LCM) and whole genome amplification (WGA) allows obtaining large quantities of DNA from single cells. The increased sensitivity of WGA kits prompted us to develop chromosome paints and to use them for exploring chromosome organization and evolution in non-model organisms. Here, we present a simple method for isolating and amplifying the euchromatic segments of single polytene chromosome arms from ovarian nurse cells of the African malaria mosquito Anopheles gambiae. This procedure provides an efficient platform for obtaining chromosome paints, while reducing the overall risk of introducing foreign DNA to the sample. The use of WGA allows for several rounds of re-amplification, resulting in high quantities of DNA that can be utilized for multiple experiments, including 2D and 3D FISH. We demonstrated that the developed chromosome paints can be successfully used to establish the correspondence between euchromatic portions of polytene and mitotic chromosome arms in An. gambiae. Overall, the union of LCM and single-chromosome WGA provides an efficient tool for creating significant amounts of target DNA for future cytogenetic and genomic studies.

Chromosome painting is a useful method for studying organization of the cell nucleus and evolution of the karyotype. Here, we demonstrate an approach to isolate and amplify specific regions of interest from single polytene chromosomes that are subsequently used for two- and three-dimensional fluorescent in situ hybridization (FISH).

Peinture chromosomique 2D et 3D chez les moustiques du paludisme

Fluorescent in situ hybridization (FISH) of whole arm chromosome probes is a robust technique for mapping genomic regions of interest, detecting ...

Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells

Mechanistic insight arrives from careful study and quantification of specific RNAs and proteins. The relative locations of these biomolecules throughout the cell at specific times can be captured with fluorescence in situ hybridization (FISH) and immunofluorescence (IF). During lytic herpesvirus infection, the virus hijacks the host cell to preferentially express viral genes, causing changes in cell morphology and behavior of biomolecules. Lytic activities are centered in nuclear factories, termed viral replication compartments, which are discernable only with FISH and IF. Here we describe an adaptable protocol of RNA FISH and IF techniques for Kaposi's sarcoma-associated herpesvirus (KSHV)-infected cells, both adherent and in suspension. The method includes steps for the development of specific anti-sense oligonucleotides, double RNA FISH, RNA FISH with IF, and quantitative calculations of fluorescence intensities. This protocol has been successfully applied to multiple cell types, uninfected cells, latent cells, lytic cells, time-courses, and cells treated with inhibitors to analyze the spatiotemporal activities of specific RNAs and proteins from both the human host and KSHV.

Quantitative Fluorescence In Situ Hybridization FISH and Immunofluorescence IF of Specific Gene Products in KSHV-Infected Cells

We describe a protocol utilizing fluorescence in situ hybridization (FISH) to visualize multiple herpesviral RNAs within lytically infected human cells, either in suspension or adherent. This protocol includes quantification of fluorescence producing a nucleocytoplasmic ratio and can be extended for simultaneous visualization of host and viral proteins with immunofluorescence (IF).

Fluorescence quantitative In Situ Hybridization (FISH) et Immunofluorescence (IF) de produits génétiques spécifiques dans les cellules infectées par le KSHV

Mechanistic insight arrives from careful study and quantification of specific RNAs and proteins. The relative locations of these biomolecules throughout ...

Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization

Candida albicans is a fungal component of the gut microbiota in humans and many other mammals. Although C. albicans does not cause symptoms in most colonized hosts, the commensal reservoir does serve as a repository for infectious disease, and the presence of high fungal titers in the gut is associated with inflammatory bowel disease. Here, we describe a method to visualize C. albicans cell morphology and localization in a mouse model of stable gastrointestinal colonization. Colonization is established using a single dose of C. albicans in animals that have been treated with oral antibiotics. Segments of gut tissue are fixed in a manner that preserves the architecture of luminal contents (microorganisms and mucus) as well as the host mucosa. Finally, fluorescent in situ hybridization is performed using probes against fungal rRNA to stain for C. albicans and hyphae. A key advantage of this protocol is that it allows for simultaneous observation of C. albicans cell morphology and its spatial association with host structures during gastrointestinal colonization.

Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization

The purpose of this protocol is to visualize Candida albicans cell shape and localization in the mammalian gastrointestinal tract.

Visualisation de Candida albicans dans le tractus gastro-intestinal murine utilisant l'hybridation fluorescente in Situ

Candida albicans is a fungal component of the gut microbiota in humans and many other mammals. Although C. albicans does not cause symptoms in most ...

Vector Competence Analyses on Aedes aegypti Mosquitoes using Zika Virus

The procedures presented describe a generalized methodology to infect Aedes aegypti mosquitoes with Zika virus under laboratory conditions to determine the rate of infection, disseminated infection, and potential transmission of the virus in the mosquito population in question. These procedures are widely utilized with various modifications in vector competence evaluations globally. They are important in determining the potential role that a given mosquito (i.e., species, population, individual) may play in the transmission of a given agent.

Vector Competence Analyses on Aedes aegypti Mosquitoes using Zika Virus

The presented protocol can determine the vector competence of Aedes aegypti mosquito populations for a given virus, such as Zika, in a containment setting.

Analyses de compétence vectorielle sur les moustiques Aedes aegypti utilisant le virus Zika

The procedures presented describe a generalized methodology to infect Aedes aegypti mosquitoes with Zika virus under laboratory conditions to determine ...

Propagation of the Microsporidian Parasite Edhazardia aedis in Aedes aegypti Mosquitoes

Edhazardia aedis is a microsporidian parasite of Aedes aegypti mosquitoes, a disease vector that transmits multiple arboviruses which cause millions of disease cases each year. E. aedis causes mortality and reduced reproductive fitness in the mosquito vector and has been explored for its potential as a biocontrol agent. The protocol we present for culturing E. aedis is based on its natural infection cycle, which involves both horizontal and vertical transmission at different life stages of the mosquito host. Ae. aegypti mosquitoes are exposed to spores in the larval stage. These infected larvae then mature into adults and transmit the parasite vertically to their offspring. Infected offspring are then used as a source of spores for future horizontal transmission. Culturing E. aedis can be challenging to the uninitiated given the complexities of the parasite&#8217;s life cycle, and this protocol provides detailed guidance and visual aids for clarification.

Propagation of the Microsporidian Parasite Edhazardia aedis in Aedes aegypti Mosquitoes

A protocol to culture the microsporidian parasite Edhazardia aedis. The parasite is passaged from one generation of Aedes aegypti mosquitoes to the next via horizontal transfer at the larval stage followed by vertical transmission at the adult stage. Live sporoplasms survive long-term in infected eggs.

Propagation du parasite microsporidien Edhazardia aedis chez les moustiques Aedes aegypti

Edhazardia aedis is a microsporidian parasite of Aedes aegypti mosquitoes, a disease vector that transmits multiple arboviruses which cause millions of ...

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

This manuscript provides a protocol for in situ hybridization chain reaction (HCR) coupled with immunofluorescence to visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in cell line&#160;and three-dimensional (3D) cultures of human airway epithelium. The method allows highly specific and sensitive visualization of viral RNA by relying on HCR initiated by probe localization. Split-initiator probes help amplify the signal by fluorescently labeled amplifiers, resulting in negligible background fluorescence in confocal microscopy. Labeling amplifiers with different fluorescent dyes facilitates the simultaneous recognition of various targets. This, in turn, allows the mapping of the infection in tissues to better understand viral pathogenesis and replication at the single-cell level. Coupling this method with immunofluorescence may facilitate better understanding of host-virus interactions, including alternation of the host epigenome and immune response pathways. Owing to sensitive and specific HCR technology, this protocol can also be used as a diagnostic tool. It is also important to remember that the technique may be modified easily to enable detection of any RNA, including non-coding RNAs and RNA viruses that may emerge in the future.

Here, we describe a simple method that combines RNA fluorescence in situ&#160;hybridization (RNA-FISH) with immunofluorescence to visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. This protocol may increase understanding of the molecular characteristics of SARS-CoV-2 RNA-host interactions at a single-cell level.

Visualisation du SARS-CoV-2 à l’aide de l’hybridation in situ par immuno-ARN-fluorescence

This manuscript provides a protocol for in situ hybridization chain reaction (HCR) coupled with immunofluorescence to visualize severe acute respiratory ...