Ringraziamo Sergei Demin e Tatyana Karamysheva per il loro aiuto nella preparazione dei cromosomi e FISH su Anopheles. Ringraziamo anche David Severson per averci fornito Aedes e Culex DNA genomico cloni BAC e Melissa Wade per la modifica del testo. Questo lavoro è stato sostenuto da due sovvenzioni dal National Institutes of Health: 1R21 AI88035-01 a Maria V. Sharakhova e 1R21 AI094289-01 a 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>

Nessun conflitto di interessi dichiarati.

Non fluorescente ibridazione in situ su cromosomi mitotici di zanzare è stata eseguita per la prima volta nel 1990 da A. e K. Kumar Rai 17. In questo studio, 18S e 28S DNA geni ribosomali, clonato nel plasmide insieme uno, sono stati collocati i cromosomi di 20 specie di zanzare. La sonda di DNA è stato marcato radioattivamente e ibridizzati ai cromosomi gangli cerebrali. Tra i tre generi di zanzare, una tecnica FISH è stato sviluppato solo per i cromosomi mitotici dalla linea cellulare di Ae. aegypti 10,18,19 e non è mai stata eseguita su cromosomi mitotici dalle zanzare dal vivo. Recentemente, abbiamo messo a punto una tecnica semplice ed affidabile per ottenere alta qualità di preparazioni cromosomiche da ID di larve di 4 ° instar 9. Questo metodo permette un elevato numero di cromosomi da ottenere in una diapositiva e può essere usato universalmente per tutte le specie di zanzare. La necessità di usare sta solo larve non, pupa o adultoGES di zanzare, per la preparazione del vetrino è probabilmente l&#39;unica limitazione del metodo. Il metodo FISH standard a 12 è stato ottimizzato per l&#39;utilizzo di genomica BAC clone e IGS rDNA come sonde per i cromosomi mitotici di Aedes, Culex e Anopheles. In aggiunta a queste specifiche applicazioni, i protocolli FISH qui descritte possono anche essere utilizzati per altri scopi. Il protocollo FISH avanzata, che utilizza C 0 t frazioni di DNA per bloccare ibridazione non specifica, può essere applicato anche per l&#39;ibridazione di cloni BAC o qualsiasi altri frammenti di DNA grandi regioni eterocromatiche di Anopheles. Regioni eterocromatiche si arricchiscono di elementi trasponibili e ripete le altre, e le sonde di queste regioni producono normalmente forte background sui cromosomi 3. Utilizzo senza etichette C 0 frazioni di DNA t contribuirà a ridurre l&#39;ibridazione non specifica della sonda ai cromosomi. La versione semplice della FISH protocol può essere utilizzato per qualsiasi rDNA o sonde di DNA ripetute sui cromosomi mitotici di zanzare e altri insetti. Inoltre, può anche essere applicato per la ibridazione di DNA clone BAC in specie con basso contenuto di DNA ripetitivo in regioni eucromatiche come Anopheles o Drosophila. Il protocollo qui proposto contribuirà ad ottenere altamente cromosoma finiti a base di gruppi di genoma per le zanzare e può essere ampiamente utilizzato per applicazioni diverse citogenetici in altri gruppi di insetti.

<table border="1"><tbody><tr><td> Nome del reagente / attrezzature </td><td> Azienda </td><td> Numero di catalogo </td><td> Commenti </td></tr><tr><td> MZ6 stereomicroscopio Leica </td><td> Leica </td><td> VA-OM-E194-354 </td><td> Uno stereomicroscopio diverso può essere utilizzato </td></tr><tr><td> Olympus CX41 fase microscopio </td><td> Olimpo </td><td> CX41 </td><td> Un microscopio diversa fase può essere utilizzata </td></tr><tr><td> Olympus BX61 microscopio a fluorescenza </td><td> Olimpo </td><td> BX61 </td><td> Un microscopio fluorescente differente può essere utilizzata </td></tr><tr><td> Thermobrite Diapositiva Denaturazione / ibridazione di sistema </td><td> Abbott Molecular </td><td> 30-144110 </td><td> Serve come un blocco di riscaldamento e camera umida </td></tr><tr><td> Aghi di dissezione </td><td> ScienceTools Belle </td><td> 10130-10</td><td></td></tr><tr><td> Needle titolari </td><td> Strumenti Scienza Belle </td><td> 26018-17 </td><td></td></tr><tr><td> Forbici per dissezione </td><td> Strumenti Scienza Belle </td><td> 15000-03 </td><td></td></tr><tr><td> 75x25 satinato doppia micro scivola </td><td> Corning </td><td> 2949-75x25 </td><td></td></tr><tr><td> Coprioggetto 22x22 millimetri microscopio </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> Mastice </td><td> Fisher Scientific </td><td> 50-949-105 </td><td></td></tr><tr><td> Acido acetico </td><td> Fisher Scientific </td><td> A491-212 </td><td></td></tr><tr><td> Alcohol 200 Proof </td><td> Decon Laboratories </td><td> 2701 </td><td></td></tr><tr><td> L&#39;acido propionico </td><td> Sigma-Aldrich </td><td> 402907 </td><td></td></tr><tr><td> Acido cloridrico </td><td> Fisher Scientific </td><td> A144-500 </td><td></td></tr><tr><td> Sodio citrato diidrato </td><td> Fisher Scientific </td><td> S279-500 </td><td></td></tr><tr><td> Sodio acetato triidrato </td><td> Fisher Scientific </td><td> BP334-500 </td><td></td></tr><tr><td> Cloruro di potassio </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 di 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% NBF (formalina tamponata neutra) </td><td> Sigma-Aldrich </td><td> HT501128 </td><td></td></tr><tr><td> 99% formammide </td><td> Fisher Scientific </td><td> BP227500 </td><td></td></tr><tr><td> Destrano solfato sale sodico </td><td> Sigma-Aldrich </td><td> D8906 </td><td></td></tr><tr><td> 20x tampone SSC </td><td> Invitrogen </td><td> AM9765 </td><td></td></tr><tr><td> 1 mM YOYO-1 ioduro (491/509) Soluzione </td><td> Invitrogen </td><td> Y3601 </td><td></td></tr><tr><td> Antifade Prolong reagente Oro </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> DNA polimerasi I </td><td> Fermentas </td><td> EP0041 </td><td></td></tr><tr><td> DNasi I </td><td> Fermentas </td><td> EN0521 </td><td></td></tr><tr><td> S1 nucleasi </td><td> Fermentas </td><td> EN0321 </td><td></td></tr><tr><td> Taq DNA polimerasi </td><td> Invitrogen </td><td> 18038-042 </td><td></td></tr><tr><td> RNasi </td><td> Sigma-Aldrich </td><td> 9001-99-4 </td><td></td></tr><tr><td> Pepsina </td><td> USB </td><td> 9001-75-6 </td><td></td></tr><tr><td> DNA di sperma di salmone </td><td> Sigma-Aldrich </td><td> D7656 </td><td></td></tr><tr><td> Nonidet-P40 (NP40) </td><td> US biologica </td><td> NC9375914 </td><td></td></tr><tr><td> Qiagen Sangue e Cultura Maxikit cellulare </td><td> Qiagen </td><td> 13362 </td><td></td></tr><tr><td> Kit Qiagen Construct Grande </td><td> Qiagen </td><td> 12462 </td&gt; <td></td></tr></tbody></table>

fluorescent in situ hybridization on mitotic chromosomes of mosquitoes

Ibridazione in situ fluorescente (FISH) è una tecnica normalmente utilizzata da molti laboratori per determinare la posizione cromosomica di sonde di DNA e RNA. Una importante applicazione di questo metodo è lo sviluppo di mappe fisiche alta qualità utili per migliorare le assemblee genoma di vari organismi. Il modello naturale strisce di cromosomi politenici mitotico e fornisce una guida per l&#39;ordine preciso e l&#39;orientamento delle supercontigs genomici. Tra i tre generi, vale a dire zanzara Anopheles, Aedes e Culex, una consolidata cromosoma base tecnica di mappatura è stata sviluppata solo per Anopheles, i cui membri possiedono cromosomi politenici leggibili 1. Come risultato di sforzi mappatura del genoma, 88% di An. gambiae genoma è stato collocato in posizioni precise cromosoma 2,3. Due generi di zanzare Aedes e altri, Culex, sono scarsamente polytenized b cromosomiecause di sovrarappresentazione significativo di elementi trasponibili nei loro genomi 4, 5, 6. Solo il 31 e il 9% delle supercontings genomici sono stati assegnati senza ordine o l&#39;orientamento di cromosomi di Ae. aegypti 7 e Cx. quinquefasciatus 8, rispettivamente. Preparazione cromosoma mitotico per queste due specie precedentemente limitato a gangli cervello e linee cellulari. Tuttavia, i vetrini preparati cromosoma dai gangli cerebrali di zanzare di solito contengono un basso numero di piastre in metafase 9. Inoltre, sebbene una tecnica FISH è stata sviluppata per i cromosomi mitotici da una linea cellulare di Ae. aegypti 10, l&#39;accumulo di più riarrangiamenti cromosomici nei cromosomi 11 linee cellulari li rende inutili per la mappatura del genoma. Qui si descrive una tecnica semplice ed affidabile per ottenere alta qualità di preparazioni cromosomiche mitotiche da dischi immaginali (ID) di larve di 4 ° instar che cun essere utilizzato per tutti i tre generi di zanzare. Un protocollo FISH standard 12 è ottimizzato per l&#39;utilizzo di cloni BAC di DNA genomico come una sonda su cromosomi mitotici di Ae. aegypti e Cx. quinquefasciatus, e utilizzando un distanziatore intergenica (IGS) regione del DNA ribosomiale (rDNA) come sonda sul An. cromosomi gambiae. Oltre alla mappatura fisica, la tecnica sviluppata può essere applicata a citogenetica popolazione e la tassonomia cromosoma / sistematica di zanzare ed altri insetti gruppi.

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

Tra i tre generi di zanzare, vale a dire<em&gt; Anopheles,</em&gt;<em&gt; Aedes</em&gt;, E<em&gt; Culex</em&gt;, Fisici tecniche di mappatura del genoma sono stati stabiliti solo per<em&gt; Anopheles</em&gt;, I cui membri possiedono leggibili cromosomi politenici. Per la generi di<em&gt; Aedes</em&gt; E<em&gt; Culex</em&gt;, Tuttavia, la mappatura citogenetica rimane difficile a causa della scarsa qualità dei cromosomi politenici. Qui vi presentiamo un protocollo universale per ottenere alta qualità di preparazioni di cromosomi mitotici ed un protocollo FISH ottimizzato per tutti e tre i generi di zanzare.

Fluorescente<em&gt; In situ</emIbridazione&gt; su cromosomi mitotici di zanzare

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 Views.  Virginia Tech. Tra i tre generi di zanzare, vale a dire Anopheles, Aedes, E Culex, Fisici tecniche di mappatura del genoma sono stati stabiliti solo per Anopheles, I cui membri possiedono leggibili cromosomi politenici. Per la generi di Aedes E Culex, Tuttavia, la mappatura citogenetica rimane difficile a causa della scarsa qualità dei cromosomi politenici. Qui vi presentiamo un protocollo univers...

Video: 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).

Combinazione di nastro adesivo a base di campionamento e di fluorescenza In situ</emIbridazione> per il rilevamento rapido di Salmonella Su prodotti freschi

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

Ricerca

Immunologia e infezioni

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.

Chiuso flusso degli acidi nucleici Citometria fluorescenza In situ Ibridazione (LNA flow-FISH): un metodo per la rilevazione dei batteri piccoli RNA

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.

Ibridazione<em&gt; In situ</em&gt; Delle ghiandole salivari, ovaie, e gli embrioni di Vector zanzare

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.

Utilizzo di proteine ​​fluorescenti per visualizzare e Quantificazione<em&gt; Chlamydia</em&gt; Vacuolo crescita dinamica in cellule viventi

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).

Pittura cromosoma 2D e 3D nelle zanzare della malaria

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).

Quantitative Fluorescence In Situ Hybridization (FISH) e Immunofluorescence (IF) di prodotti genici specifici nelle cellule infette da 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.

Visualizzazione degli albicani Candida nel tratto gastrointestinale Murine utilizzando l'ibridazione 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.

Analisi di competenza vettoriale sulle zanzare Aedes aegypti utilizzando il 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.

Propagazione del parassita microsporidiano Edhazardia aedis nelle zanzare 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.

Visualizzazione di SARS-CoV-2 utilizzando l'ibridazione immuno RNA-fluorescenza in situ

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