Name: ground state depletion super-resolution imaging in mammalian cells
Uploaded: 2017-11-05T08:30:00
Description: Watch this Scientific Journal Video about Ground State Depletion Super-resolution Imaging in Mammalian Cells at JoVE.com

Questo lavoro è stato supportato da una sovvenzione AHA a r.e.d. (15SDG25560035). Gli autori si desidera ringraziare Dr. Fernando Santana per l'uso del suo microscopio 3D Leica SR GSD e Dr. Johannes Hell per gentilmente fornire l'anticorpo FP1.

1. lavaggio vetrini coprioggetti <ol><li>il giorno prima dell'elaborazione del campione, pulire #1.5 vetrini coprioggetti di sonicating in una soluzione 1 M di KOH per 1 h. Questa operazione rimuove qualsiasi fluorescente contaminanti che possono essere presenti sui coprioggetti.
	<ol><li>Risciacquare accuratamente il KOH da lamelle con acqua deionizzata.</li>
		<li>Una volta puliti in KOH, conservare i coprioggetti in etanolo al 70% fino all'uso.</li>
	</ol></li></ol> 2. Lamell...

<ol>
	<li>Willig, K. I., Rizzoli, S. O., Westphal, V., Jahn, R., Hell, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=STED+microscopy+reveals+that+synaptotagmin+remains+clustered+after+synaptic+vesicle+exocytosis.">STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis.</a> Nature. 440 (7086), 935-939 (2006).</li><li>Gustafsson, M. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nonlinear+structured-illumination+microscopy:+wide-field+fluorescence+imaging+with+theoretically+unlimited+resolution.">Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution.</a> Proc Natl Acad Sci U S A. 102 (37), 13081-13086 (2005).</li><li>Betzig, 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=Imaging+intracellular+fluorescent+proteins+at+nanometer+resolution.">Imaging intracellular fluorescent proteins at nanometer resolution.</a> Science. 313 (5793), 1642-1645 (2006).</li><li>Hell, S. W., Kroug, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ground-state-depletion+fluorscence+microscopy:+A+concept+for+breaking+the+diffraction+resolution+limit.">Ground-state-depletion fluorscence microscopy: A concept for breaking the diffraction resolution limit.</a> JAppl Phys B. 60 (5), 495-497 (1995).</li><li>Bretschneider, S., Eggeling, C., Hell, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Breaking+the+diffraction+barrier+in+fluorescence+microscopy+by+optical+shelving.">Breaking the diffraction barrier in fluorescence microscopy by optical shelving.</a> Phys Rev Lett. 98 (21), 218103 (2007).</li><li>Flynn, J. M., Santana, L. F., Melov, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+cell+transcriptional+profiling+of+adult+mouse+cardiomyocytes.">Single cell transcriptional profiling of adult mouse cardiomyocytes.</a> J Vis Exp. (58), e3302 (2011).</li><li>Davare, M. A., Horne, M. C., Hell, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+phosphatase+2A+is+associated+with+class+C+L-type+calcium+channels+(Cav1.2)+and+antagonizes+channel+phosphorylation+by+cAMP-dependent+protein+kinase.">Protein phosphatase 2A is associated with class C L-type calcium channels (Cav1.2) and antagonizes channel phosphorylation by cAMP-dependent protein kinase.</a> J Biol Chem. 275 (50), 39710-39717 (2000).</li><li>Dempsey, G. T., Vaughan, J. C., Chen, K. H., Bates, M., Zhuang, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+fluorophores+for+optimal+performance+in+localization-based+super-resolution+imaging.">Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging.</a> Nat Methods. 8 (12), 1027-1036 (2011).</li><li>Chozinski, T. J., Gagnon, L. A., Vaughan, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Twinkle,+twinkle+little+star:+photoswitchable+fluorophores+for+super-resolution+imaging.">Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging.</a> FEBS Lett. 588 (19), 3603-3612 (2014).</li><li>Dempsey, G. T., 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=Photoswitching+mechanism+of+cyanine+dyes.">Photoswitching mechanism of cyanine dyes.</a> J Am Chem Soc. 131 (51), 18192-18193 (2009).</li><li>Nahidiazar, L., Agronskaia, A. V., Broertjes, J., van den Broek, B., Jalink, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimizing+Imaging+Conditions+for+Demanding+Multi-Color+Super+Resolution+Localization+Microscopy.">Optimizing Imaging Conditions for Demanding Multi-Color Super Resolution Localization Microscopy.</a> PLoS One. 11 (7), e0158884 (2016).</li><li>Ovesny, M., Krizek, P., Borkovec, J., Svindrych, Z., Hagen, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ThunderSTORM:+a+comprehensive+ImageJ+plug-in+for+PALM+and+STORM+data+analysis+and+super-resolution+imaging.">ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging.</a> Bioinformatics. 30 (16), 2389-2390 (2014).</li><li>Veeraraghavan, R., Gourdie, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stochastic+optical+reconstruction+microscopy-based+relative+localization+analysis+(STORM-RLA)+for+quantitative+nanoscale+assessment+of+spatial+protein+organization.">Stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA) for quantitative nanoscale assessment of spatial protein organization.</a> Mol Biol Cell. 27 (22), 3583-3590 (2016).</li><li>Ries, J., Kaplan, C., Platonova, E., Eghlidi, H., Ewers, 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+simple,+versatile+method+for+GFP-based+super-resolution+microscopy+via+nanobodies.">A simple, versatile method for GFP-based super-resolution microscopy via nanobodies.</a> Nat Methods. 9 (6), 582-584 (2012).</li><li>Dixon, R. 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=Graded+Ca2+/calmodulin-dependent+coupling+of+voltage-gated+CaV1.2+channels.">Graded Ca2+/calmodulin-dependent coupling of voltage-gated CaV1.2 channels.</a> Elife. 4, (2015).</li><li>Annibale, P., Vanni, S., Scarselli, M., Rothlisberger, U., Radenovic, A. <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+clustering+artifacts+in+photoactivated+localization+microscopy.">Identification of clustering artifacts in photoactivated localization microscopy.</a> Nat Methods. 8 (7), 527-528 (2011).</li><li>Nan, X., 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=Single-molecule+superresolution+imaging+allows+quantitative+analysis+of+RAF+multimer+formation+and+signaling.">Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling.</a> Proc Natl Acad Sci U S A. 110 (46), 18519-18524 (2013).</li><li>Fricke, F., Beaudouin, J., Eils, R., Heilemann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=One,+two+or+three?+Probing+the+stoichiometry+of+membrane+proteins+by+single-molecule+localization+microscopy.">One, two or three? Probing the stoichiometry of membrane proteins by single-molecule localization microscopy.</a> Sci Rep. 5, 14072 (2015).</li></ol>

La recente esplosione di tecnologie che permettono la formazione immagine oltre il limite di diffrazione hanno offerto nuove finestre nella complessità della cellula di mammiferi segnalazione nello spazio e nel tempo. Queste tecnologie includono tempesta, STED, PALM, GSD, SIM e le loro varianti (ad es., dSTORM, FPALM). L'ingegnosità degli scienziati dietro queste tecniche ha permesso di eludere i limiti imposti dalle leggi della fisica che regolano la diffrazione della luce. Nonostante questo risultato enorme,...

Le reazioni cellulari di segnalazione traducono cambiando ambienti interni ed esterni per avviare una risposta cellulare. Esse regolano tutti gli aspetti della fisiologia umana, che serve da base per l'ormone e rilascio di neurotrasmettitori, il battito cardiaco, visione, fertilizzazione e funzione conoscitiva. Rottura di queste cascate di segnalazione può avere gravi conseguenze sotto forma di condizioni patologiche tra cui cancro, morbo di Parkinson e di Alzheimer. Per decenni, gli investigatori biologici e medici sono utilizzati con successo le proteine fluorescenti, sonde e biosensori accoppiati con microscopia di fluorescenza come i principali strumenti per comprendere l'organizzazione spaziale e temporale preciso di questi cellulari segnali.
I punti di forza di tecniche ottiche quali epifluorescenza, confocale, o microscopia a fluorescenza (TIRF) riflessione interna totale sono loro sensibilità, velocità e compatibilità con live cell imaging, mentre la maggiore limitazione è loro diffrazione limitata risoluzione, strutture di significato o complessi di proteine inferiori a 200-250 nm non possono essere risolto. Con lo sviluppo teorico e pratico di deterministico super-risoluzione (per esempio, microscopia di svuotamento stimolato dell'emissione (STED1), strutturato microscopia di illuminazione (SIM2) o stocastici super-risoluzione (ad es. , deplezione di fotoattivazione localizzazione microscopia (PALM3), o stato fondamentale (GSD4,5)), risoluzione assiale e laterale in microscopia a fluorescenza è stata estesa oltre la barriera di diffrazione, all'ordine di decine di nanometri. Così, gli investigatori hanno ora la possibilità senza precedenti per visualizzare e comprendere come organizzazione e dinamica di proteine si traduce in funzione al livello vicino-molecolare.
Microscopia di svuotamento di stato fondamentale seguita da ritorno di singola molecola (GSDIM), o semplicemente GSD come è noto, aggira il limite di diffrazione riducendo il numero di emettere simultaneamente fluorofori4,5. Luce laser ad alta energia è usata per eccitare l'esempio fluorophore-etichettati, bombardando gli elettroni con fotoni e aumentando la probabilità saranno sottoposte a un 'spin-flip' e inserire il tripletto o 'buio-stato' stato eccitato4. Questo impoverisce efficacemente lo stato di terra, da qui il nome «suolo lo svuotamento dello stato». In stato di tripletto, fluorofori non emettono fotoni e il campione appare dimmer. Tuttavia, questi fluorofori casualmente ritorno allo stato di terra e possono passare attraverso diversi fotoni che emettono le transizioni di stato eccitato a terra prima di ritornare allo stato di tripletto. Con meno fluorofori che emettono in un dato momento, fotone scoppi emessa da singoli fluorophores diventare spazialmente e temporalmente distinte dai vicini fluorofori. La raffica di fotoni possa essere in forma con una funzione gaussiana, il centroide calcolato che corrisponde alla posizione del fluoroforo con una precisione di localizzazione che dipenda l'apertura numerica (NA) della lente, la lunghezza d'onda della luce utilizzata per eccitazione e fondamentalmente, il numero di fotoni emessi al fluoroforo. Una limitazione di GSD è che, poiché solo un sottoinsieme dei fluorofori emette attivamente in qualsiasi momento, migliaia di immagini dovrà essere raccolti nel corso di alcuni minuti per costruire una mappa di localizzazione completa. Il tempo di acquisizione lungo combinato con il requisito di laser ad alta potenza, significa che la GSD è più adatto a piuttosto che campioni dal vivo.
Questo articolo descrive la preparazione di campioni fissati per formazione immagine di microscopia di Super-risoluzione della membrana e del reticolo endoplasmatico (ER)-proteine residenti (per un elenco dei materiali di consumo necessari e reagenti Vedi Tabella materiali). Esempi di come questo protocollo può essere facilmente adattato per quantificare la dimensione e il grado di clustering di L-tipo scanalature tensione-gated Ca2 + (Cav1.2) nel sarcolemma dei miociti cardiaci, o usato per prevedere la distribuzione cellulare dell'ER, sono dimostrati. Comprendere la distribuzione e l'organizzazione di questi componenti cellulari è criticamente importante per capire l'iniziazione, traduzione e, infine, la funzione di molte Ca2 +-cascate di segnalazione dipendente. Ad esempio, Cav1.2 canali sono fondamentalmente importante per accoppiamento, mentre il ricevitore-mediata Ca2 + rilascio dall'ER è forse la più onnipresente cascata di segnalazione in cellule di mammifero eccitazione-contrazione.

<table>
	<tbody>
		<tr>
			<td>KOH</td>
			<td>Thermo Scientific</td>
			<td>P250-500</td>
			<td>To clean coverglass</td>
		</tr>
		<tr>
			<td>#1.5 coverglass 18 x 18 mm</td>
			<td>Marienfeld Superior</td>
			<td>0107032)</td>
			<td>To grow/process/image cells</td>
		</tr>
		<tr>
			<td>10X PBS</td>
			<td>Thermo Scientific</td>
			<td>BP3994</td>
			<td>Dilute to 1X with de-ionized water</td>
		</tr>
		<tr>
			<td>Poly-L-Lysine</td>
			<td>Sigma</td>
			<td>P4832</td>
			<td>Aids with cell adhesion to cover glass</td>
		</tr>
		<tr>
			<td>laminin</td>
			<td>Sigma</td>
			<td>114956-81-9</td>
			<td>Aids with cell adhesion to cover glass</td>
		</tr>
		<tr>
			<td>Medium 199</td>
			<td>Thermo Scientific</td>
			<td>11150-059</td>
			<td>Ventricular myocyte culture media</td>
		</tr>
		<tr>
			<td>DMEM 11995</td>
			<td>Gibco</td>
			<td>11995</td>
			<td>Cell culture media</td>
		</tr>
		<tr>
			<td>Fetal bovine Serum (FBS)</td>
			<td>Thermo Scientific</td>
			<td>10437028</td>
			<td>Media supplement</td>
		</tr>
		<tr>
			<td>Penicillin/streptomycin</td>
			<td>Sigma</td>
			<td>P4333</td>
			<td>Media supplement</td>
		</tr>
		<tr>
			<td>0.05% trypsin-EDTA</td>
			<td>Corning</td>
			<td>25-052-CL</td>
			<td>Cell culture solution</td>
		</tr>
		<tr>
			<td>Lipofectamine 2000</td>
			<td>Invitrogen</td>
			<td>11668-019</td>
			<td>Transient transfection reagent</td>
		</tr>
		<tr>
			<td>Ca2+-free PBS</td>
			<td>Gibco</td>
			<td>1419-144</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>100 % Methanol</td>
			<td>Thermo Fisher Scientific</td>
			<td>A414-4</td>
			<td>Cell Fixation</td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Electron Microscopy Sciences</td>
			<td>15710</td>
			<td>Cell Fixation</td>
		</tr>
		<tr>
			<td>Glutaraldehyde</td>
			<td>Sigma Aldrich</td>
			<td>SLBR6504V</td>
			<td>Cell Fixation</td>
		</tr>
		<tr>
			<td>SEAblock</td>
			<td>Thermo Scientific</td>
			<td>37527</td>
			<td>BSA or other blocking solution alternatives exist</td>
		</tr>
		<tr>
			<td>Triton-X 100</td>
			<td>Sigma</td>
			<td>T8787</td>
			<td>Detergent to permeabilize cells</td>
		</tr>
		<tr>
			<td>Rabbit anti-CaV1.2 (FP1)</td>
			<td>Gift</td>
			<td>N/A</td>
			<td>Commercial anti-CaV1.2 antibodies exist such as Alomone Labs Rb anti-CaV1.2 (ACC-003)</td>
		</tr>
		<tr>
			<td>Mouse monoclonal anti-RFP</td>
			<td>Rockland Inc.</td>
			<td>200-301-379</td>
			<td>Primary antibody</td>
		</tr>
		<tr>
			<td>Alexa Fluor 647 donket anti-rabbit IgG (H+L)</td>
			<td>Invitrogen (Thermo Scientific)</td>
			<td>A31573</td>
			<td>Secondary antibody</td>
		</tr>
		<tr>
			<td>Alexa Fluor 568 goat anti-mouse IgG (H+L)</td>
			<td>Invitrogen (Thermo Scientific)</td>
			<td>A11031</td>
			<td>Secondary antibody</td>
		</tr>
		<tr>
			<td>Sodium azide</td>
			<td>Sigma</td>
			<td>S2002</td>
			<td>Prevents microbial growth for long term storage of samples</td>
		</tr>
		<tr>
			<td>Catalase</td>
			<td>Sigma</td>
			<td>C40</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>Glucose oxidase</td>
			<td>Sigma</td>
			<td>G2133</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Sigma</td>
			<td>T6066</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>beta-Mercaptoethylamin hydrochloride</td>
			<td>Fisher</td>
			<td>BP2664100</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>&#946;-mercaptoethanol</td>
			<td>Sigma</td>
			<td>63689</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Fisher</td>
			<td>S271-3</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>Dextrose</td>
			<td>Fisher</td>
			<td>D14-212</td>
			<td>Photoswitching buffer ingredient</td>
		</tr>
		<tr>
			<td>Glass Depression slides</td>
			<td>Neolab</td>
			<td>1 &#8211; 6293</td>
			<td>To mount samples</td>
		</tr>
		<tr>
			<td>Twinsil</td>
			<td>Picodent</td>
			<td>13001000</td>
			<td>To seal coverglass</td>
		</tr>
		<tr>
			<td>sec61&#946;-mCherry plasmid</td>
			<td>Addgene</td>
			<td>49155</td>
			<td></td>
		</tr>
		<tr>
			<td>Leica SR GSD 3D microscope</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Washing block solution</td>
			<td></td>
			<td></td>
			<td>20 % SEAblock in PBS</td>
		</tr>
		<tr>
			<td>Primary antibody incubation solution</td>
			<td></td>
			<td></td>
			<td>0.5 % Triton-X100, 20 % SEAblock, in PBS</td>
		</tr>
		<tr>
			<td>Secondary antibody incubation solution</td>
			<td></td>
			<td></td>
			<td>1:1000 in PBS</td>
		</tr>
	</tbody>
</table>

ground state depletion super-resolution imaging in mammalian cells

Gli avanzamenti nella biologia delle cellule e microscopia fluorescente sono intimamente correlati, con l'avanzata capacità di visualizzare eventi cellulari causando spesso drammatici salti nella nostra comprensione di come le cellule funzione. Lo sviluppo e la disponibilità della microscopia di Super-risoluzione ha notevolmente ampliato i limiti di risoluzione ottica da ~ 250-20 nm. I biologi non sono più limitati a descrivere le interazioni molecolari in termini di colocalizzazione all'interno di una zona di diffrazione limitata, piuttosto è ora possibile visualizzare le interazioni dinamiche delle singole molecole. Qui, descriviamo un protocollo per la visualizzazione e la quantificazione delle proteine cellulari da microscopia di svuotamento di stato fondamentale per l'imaging cellulare fisso. Forniamo esempi da due proteine di membrana diversi, un elemento del Traslocone il reticolo endoplasmatico, sec61β e un membrana plasmatica localizzato tensione-gated L-tipo Ca2 + canale (CaV1.2). Vengono descritti il microscopio specifici parametri, metodi di fissazione, foto-commutazione formulazione di buffer e insidie e sfide di elaborazione delle immagini.

Come documentato nell'introduzione, ci sono molti microscopia di Super-risoluzione diverse modalità di formazione immagine. Questo protocollo, si concentra su formazione immagine di Super-risoluzione GSD. Immagini rappresentative e mappe di localizzazione sono mostrate in Figura 2 e Figura 3.
La figura 2 Mostra delle cellule COS-7 transfet...

Watch this Scientific Journal Video about Ground State Depletion Super-resolution Imaging in Mammalian Cells at JoVE.com

Ground State Depletion Super-resolution Imaging in Mammalian Cells

Questo articolo descrive un protocollo per l'individuazione di uno o più del plasma e/o proteine di membrana intracellulare mediante microscopia ad alta super-risoluzione stato fondamentale lo svuotamento (GSD) in cellule di mammifero. Andremo a discutere i vantaggi e le considerazioni di utilizzare tali approcci per la visualizzazione e la quantificazione delle proteine cellulari.

Stato fondamentale lo svuotamento super-resolution Imaging in cellule di mammifero

Advances in fluorescent microscopy and cell biology are intimately correlated, with the enhanced ability to visualize cellular events often leading to ...

The overall goal of this fluorescent imaging technique is to visualize and quantify cellular proteins in fixed cells at subdiffraction-limited resolution using a form of super-resolution microscopy called ground state depletion microscopy and individual molecule return. This method helps answer key questions in the field of cell biology and membrane biophysics, as it circumvents diffraction-limited resolution, which helps investigators more precisely define, visualize and quantify the distribution of cellular proteins. The main advantage of this protocol is that it enables the acquisition of images with an approximate ten-fold improvement in resolution over conventional fluorescence microscopy imaging approaches, such as confocal microscopy.Demonstrating the procedure will be Oscar Vivas, a post-doc in my laboratory, and Karen Hannigan, a post-doc in Rose Dixon's laboratory. To begin, prepare the cover slips and cells as described in the accompanying text protocol. Then fix the samples and perform immunocytochemistry in order to label the plasma membrane and/or intracellular membrane proteins of interest.Next, prepare the oxygen scavenging Glock solution by first adding 12.5 microliters of a catalase stock solution, 3.5 milligrams of glucose oxidase, and 0.5 microliters of one molar Tris to 49.5 microliters of PBS in a 1.5 milliliter microcentrifuge tube. Close the tube and briefly vortex it to dissolve the components. Then centrifuge the solution for three minutes.Now, prepare the photo switching inducing thial solution by dissolving beta-mercaptoethylamine solution into PBS to a concentration of 100 millimolar and modify the pH to 8.0. Aliquot and store the thial solution in the freezer for up to one week. Immediately before imaging, mix the thial and oxygen scavenging components together with a saline buffer and store the solution on ice.Using 100 microliters of the prepared photo switching buffer, mount cover slips containing stained cells onto the depression slides. Next, seal the edges of the cover slip with a silicone glue to prevent rapid oxidation of the imaging buffer. Wait several minutes until the silicone glue has fully cured, prior to imaging.Otherwise, the cover slip will drift. To begin, select an appropriate laser to illuminate the sample, based on the chosen fluorophore. For an Alexa 647 fluorophore, use a 642 nanometer laser.Next, chose the appropriate dichroic imaging cube and objective lens. Open the imaging software. Select the 2D acquisition mode then set the exposure time to 11 milliseconds.Also, set the EM Gain to 300 and select an appropriate detection threshold. Next, turn on Auto Event Control and set the number of Events Per Images to eight. Enter the Pixel Size as 20 nanometers.In the GSD Tools tab, go to the High Resolution Image Calculation options and ensure that Histogram Mode is selected. To image proteins at the plasma membrane, select TIRF mode and modify the incidence angle to determine the penetration depth. Then, set the laser intensity to 100%in order to send electrons to the dark state.Next, select Single Molecule Detection while pumping and set to acquire automatically when the frame correlation is 0.20. For acquisition, set laser intensity to 50%and the number of acquisition frames to 60, 000. Then begin taking images.To quantify protein cluster size, open the image file of a 10 nanometer histogram single molecule localization map in ImageJ. In the Image menu, go to Adjust and use the Auto option to optimize the brightness and contrast of the image. Then, under the Type menu, choose 8-bit.Next, open the Analyze menu, click Set Scale and enter the values shown here. Then, in the Analyze menu, select Set Measurements and check the box beside the Area option. Back in the Image menu, select Adjust, Threshold, and then select Over/Under.Move the maximum value to 255, the minimum value to one and click Apply. Finally, open the Analyze menu and select Analyze Particles. Place a check mark to select Pixel units, Display results and Summarize.Then set the size to four to infinity, select the Bare Outlines option and click OK.The cell imaged here was transfected with the endoplasmic reticulum protein, mCherry-Sec61 beta, and imaged using both defraction-limited TIRF microscopy and super-resolution GSD microscopy in TIRF mode. These curves represent the diameter of the ER tubules. The image on the right shows an improvement in the lateral resolution and represents a more accurate representation of the structure of ER tubules.The improvement in resolution offered by super-resolution GSD imaging is further demonstrated in these images, showing a labeled cardiac myocyte with an anti-CAV 1.2 antibody. Using GSD mode, the improvement in the lateral resolution is prominent and separate clusters of channels are easier to identify. Once mastered, this protocol can be completed in less than three days.The super-resolution imaging of a single cell takes 10 to 30 minutes, depending on the number of frames required. Following this procedure, other methods like electromicroscopy can be performed in order to answer addition questions like how the fluorescent protein of interest interacts with the complex cellular environment. After watching this video, you should have a good understanding of how to prepare, acquire and analyze samples to visualize one or more cellular proteins for super-resolution microscopy using ground state depletion followed by individual molecule return.

ground-state-depletion-super-resolution-imaging-in-mammalian-cells

Research

JoVE Journal

Biology

Long-term Imaging Mammalian Cells using Wide-Field Microscopy

A lungo termine Imaging cellule di mammifero utilizzando Wide-Field Microscopia

Ricerca

Biologia

MISSION esiRNA for RNAi Screening in Mammalian Cells

RNA interference (RNAi) is a basic cellular mechanism for the control of gene expression. RNAi is induced by short double-stranded RNAs also known as small interfering RNAs (siRNAs). The short double-stranded RNAs originate from longer double stranded precursors by the activity of Dicer, a protein of the RNase III family of endonucleases. The resulting fragments are components of the RNA-induced silencing complex (RISC), directing it to the cognate target mRNA. RISC cleaves the target mRNA thereby reducing the expression of the encoded protein1,2,3. RNAi has become a powerful and widely used experimental method for loss of gene function studies in mammalian cells utilizing small interfering RNAs.
Currently two main methods are available for the production of small interfering RNAs. One method involves chemical synthesis, whereas an alternative method employs endonucleolytic cleavage of target specific long double-stranded RNAs by RNase III in vitro. Thereby, a diverse pool of siRNA-like oligonucleotides is produced which is also known as endoribonuclease-prepared siRNA or esiRNA. A comparison of efficacy of chemically derived siRNAs and esiRNAs shows that both triggers are potent in target-gene silencing. Differences can, however, be seen when comparing specificity. Many single chemically synthesized siRNAs produce prominent off-target effects, whereas the complex mixture inherent in esiRNAs leads to a more specific knockdown10.
In this study, we present the design of genome-scale MISSION esiRNA libraries and its utilization for RNAi screening exemplified by a DNA-content screen for the identification of genes involved in cell cycle progression. We show how to optimize the transfection protocol and the assay for screening in high throughput. We also demonstrate how large data-sets can be evaluated statistically and present methods to validate primary hits. Finally, we give potential starting points for further functional characterizations of validated hits.

Here we use a human esiRNA library in a high-throughput screen for genes involved in cell division. We demonstrate how to set up and conduct an esiRNA screens, as well as how to analyze and validate the results.

EsiRNA MISSIONE per lo screening RNAi in cellule di mammifero

RNA interference (RNAi) is a basic cellular mechanism for the control of gene expression. RNAi is induced by short double-stranded RNAs also known as ...

Super-resolution Imaging of the Bacterial Division Machinery

Bacterial cell division requires the coordinated assembly of more than ten essential proteins at midcell1,2. Central to this process is the formation of a ring-like suprastructure (Z-ring) by the FtsZ protein at the division plan3,4. The Z-ring consists of multiple single-stranded FtsZ protofilaments, and understanding the arrangement of the protofilaments inside the Z-ring will provide insight into the mechanism of Z-ring assembly and its function as a force generator5,6. This information has remained elusive due to current limitations in conventional fluorescence microscopy and electron microscopy. Conventional fluorescence microscopy is unable to provide a high-resolution image of the Z-ring due to the diffraction limit of light (~200 nm). Electron cryotomographic imaging has detected scattered FtsZ protofilaments in small C. crescentus cells7, but is difficult to apply to larger cells such as E. coli or B. subtilis. Here we describe the application of a super-resolution fluorescence microscopy method, Photoactivated Localization Microscopy (PALM), to quantitatively characterize the structural organization of the E. coli Z-ring8.
	PALM imaging offers both high spatial resolution (~35 nm) and specific labeling to enable unambiguous identification of target proteins. We labeled FtsZ with the photoactivatable fluorescent protein mEos2, which switches from green fluorescence (excitation = 488 nm) to red fluorescence (excitation = 561 nm) upon activation at 405 nm9. During a PALM experiment, single FtsZ-mEos2 molecules are stochastically activated and the corresponding centroid positions of the single molecules are determined with &lt;20 nm precision. A super-resolution image of the Z-ring is then reconstructed by superimposing the centroid positions of all detected FtsZ-mEos2 molecules.
	Using this method, we found that the Z-ring has a fixed width of ~100 nm and is composed of a loose bundle of FtsZ protofilaments that overlap with each other in three dimensions. These data provide a springboard for further investigations of the cell cycle dependent changes of the Z-ring10 and can be applied to other proteins of interest.

We describe a super-resolution imaging method to probe the structural organization of the bacterial FtsZ-ring, an essential apparatus for cell division. This method is based on quantitative analyses of photoactivated localization microscopy (PALM) images and can be applied to other bacterial cytoskeletal proteins.

Super-risoluzione Imaging della Divisione Macchine batterica

Bacterial cell division requires the coordinated  assembly of more than ten essential proteins at midcell1,2. Central  to this process is the formation of ...

Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity and functionality of the gut community will provide insight into the effects of gut microbiota on mosquito life traits. Metagenomic RNA-Seq has become an important tool to analyze transcriptomes from various microbes present in a microbial community. Messenger RNA usually comprises only 1-3% of total RNA, while rRNA constitutes approximately 90%. It is challenging to enrich messenger RNA from a metagenomic microbial RNA sample because most prokaryotic mRNA species lack stable poly(A) tails. This prevents oligo d(T) mediated mRNA isolation. Here, we describe a protocol that employs sample derived rRNA capture probes to remove rRNA from a metagenomic total RNA sample. To begin, both mosquito and microbial small and large subunit rRNA fragments are amplified from a metagenomic community DNA sample. Then, the community specific biotinylated antisense ribosomal RNA probes are synthesized in vitro using T7 RNA polymerase. The biotinylated rRNA probes are hybridized to the total RNA. The hybrids are captured by streptavidin-coated beads and removed from the total RNA. This subtraction-based protocol efficiently removes both mosquito and microbial rRNA from the total RNA sample. The mRNA enriched sample is further processed for RNA amplification and RNA-Seq.

A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.

L&#39;esaurimento delle RNA ribosomiale per metagenomiche Gut Mosquito RNA-seq

The mosquito gut accommodates dynamic microbial communities across different stages of the insect's life cycle. Characterization of the genetic capacity ...

Test Samples for Optimizing STORM Super-Resolution Microscopy

STORM is a recently developed super-resolution microscopy technique with up to 10 times better resolution than standard fluorescence microscopy techniques. However, as the image is acquired in a very different way than normal, by building up an image molecule-by-molecule, there are some significant challenges for users in trying to optimize their image acquisition. In order to aid this process and gain more insight into how STORM works we present the preparation of 3 test samples and the methodology of acquiring and processing STORM super-resolution images with typical resolutions of between 30-50 nm. By combining the test samples with the use of the freely available rainSTORM processing software it is possible to obtain a great deal of information about image quality and resolution. Using these metrics it is then possible to optimize the imaging procedure from the optics, to sample preparation, dye choice, buffer conditions, and image acquisition settings. We also show examples of some common problems that result in poor image quality, such as lateral drift, where the sample moves during image acquisition and density related problems resulting in the 'mislocalization' phenomenon.

We describe the preparation of three test samples and how they can be used to optimize and assess the performance of STORM microscopes. Using these examples we show how to acquire raw data and then process it to acquire super-resolution images in cells of approximately 30-50 nm resolution.

I campioni di prova per ottimizzare STORM Super-Resolution Microscopia

STORM is a recently developed super-resolution microscopy technique with up to 10 times better resolution than standard fluorescence microscopy ...

Sample Preparation for Single Virion Atomic Force Microscopy and Super-resolution Fluorescence Imaging

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule imaging assays which allows adhesion of single virions to glass surfaces with specificity. This preparation is based on grafting the surface of the glass with a mixture of PLL-g-PEG and PLL-g-PEG-Biotin, adding a layer of avidin, and finally creating virion anchors through attachment of biotinylated virus specific antibodies. We have applied this technique across a range of experiments including atomic force microscopy (AFM) and super-resolution fluorescence imaging. This sample preparation method results in a control adhesion of the virions to the surface.

The attachment of virions to a surface is a requirement for single virion imaging by Super-resolution fluorescence imaging or atomic force microscopy (AFM). Here we demonstrate a sample preparation method for controlled adhesion of virions to glass surfaces suitable for use in AFM and super-resolution fluorescence imaging.

Preparazione del campione per microscopia a forza atomica Virion singola e imaging a fluorescenza a super risoluzione

Immobilization of virions to glass surfaces is a critical step in single virion imaging. Here we present a technique&#160;adopted from single molecule ...

Super-resolution Imaging of the Cytokinetic Z Ring in Live Bacteria Using Fast 3D-Structured Illumination Microscopy (f3D-SIM)

Imaging of biological samples using fluorescence microscopy has advanced substantially with new technologies to overcome the resolution barrier of the diffraction of light allowing super-resolution of live samples. There are currently three main types of super-resolution techniques &#8211; stimulated emission depletion (STED), single-molecule localization microscopy (including techniques such as PALM, STORM, and GDSIM), and structured illumination microscopy (SIM). While STED and single-molecule localization techniques show the largest increases in resolution, they have been slower to offer increased speeds of image acquisition. Three-dimensional SIM (3D-SIM) is a wide-field fluorescence microscopy technique that offers a number of advantages over both single-molecule localization and STED. Resolution is improved, with typical lateral and axial resolutions of 110 and 280 nm, respectively and depth of sampling of up to 30 &#181;m from the coverslip, allowing for imaging of whole cells. Recent advancements (fast 3D-SIM) in the technology increasing the capture rate of raw images allows for fast capture of biological processes occurring in seconds, while significantly reducing photo-toxicity and photobleaching. Here we describe the use of one such method to image bacterial cells harboring the fluorescently-labelled cytokinetic FtsZ protein to show how cells are analyzed and the type of unique information that this technique can provide.

Super-resolution Imaging of the Cytokinetic Z Ring in Live Bacteria Using Fast 3D-Structured Illumination Microscopy f3D-SIM

Spatiotemporal information about dynamic proteins inside live cells is crucial for understanding biology. A type of super-resolution microscopy called fast 3D-structured illumination microscopy (f3D-SIM) reveals unique information about the cytokinetic Z ring in bacteria: both its bead-like appearance and the rapid dynamics of FtsZ within the ring.

Super-Resolution Imaging del Cytokinetic Z Anello in batteri vivi Uso di Fast 3D Structured Illumination Microscopy (F3D-SIM)

Imaging of biological samples using fluorescence microscopy has advanced substantially with new technologies to overcome the resolution barrier of the ...

Imaging Local Ca2+ Signals in Cultured Mammalian Cells

Cytosolic Ca2+ ions regulate numerous aspects of cellular activity in almost all cell types, controlling processes as wide-ranging as gene transcription, electrical excitability and cell proliferation. The diversity and specificity of Ca2+ signaling derives from mechanisms by which Ca2+ signals are generated to act over different time and spatial scales, ranging from cell-wide oscillations and waves occurring over the periods of minutes to local transient Ca2+ microdomains (Ca2+ puffs) lasting milliseconds. Recent advances in electron multiplied CCD (EMCCD) cameras now allow for imaging of local Ca2+ signals with a 128 x 128 pixel spatial resolution at rates of &#62;500 frames sec-1 (fps). This approach is highly parallel and enables the simultaneous monitoring of hundreds of channels or puff sites in a single experiment. However, the vast amounts of data generated (ca. 1 Gb per min) render visual identification and analysis of local Ca2+ events impracticable. Here we describe and demonstrate the procedures for the acquisition, detection, and analysis of local IP3-mediated Ca2+ signals in intact mammalian cells loaded with Ca2+ indicators using both wide-field epi-fluorescence (WF) and total internal reflection fluorescence (TIRF) microscopy. Furthermore, we describe an algorithm developed within the open-source software environment Python that automates the identification and analysis of these local Ca2+ signals. The algorithm localizes sites of Ca2+ release with sub-pixel resolution; allows user review of data; and outputs time sequences of fluorescence ratio signals together with amplitude and kinetic data in an Excel-compatible table.

Imaging Local Ca2+ Signals in Cultured Mammalian Cells

Here we present techniques for imaging local IP3-mediated Ca2+ events using fluorescence microscopy in intact mammalian cells loaded with Ca2+ indicators together with an algorithm that automates identification and analysis of these events.

Imaging locale Ca<sup&gt; 2+</sup&gt; Segnali in cellule di mammifero coltivate

Cytosolic Ca2+ ions regulate numerous aspects of cellular activity in almost all cell types, controlling processes as wide-ranging as gene transcription, ...

Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper

Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm allows for the routine imaging of nanoscale biological complexes and processes. This increase in resolution also means that methods popular in electron microscopy, such as single-particle analysis, can readily be applied to super-resolution fluorescence microscopy. By combining this analytical approach with super-resolution optical imaging, it becomes possible to take advantage of the molecule-specific labeling capacity of fluorescence microscopy to generate structural maps of molecular elements within a metastable structure. To this end, we have developed a novel algorithm &#8212; VirusMapper &#8212; packaged as an easy-to-use, high-performance, and high-throughput ImageJ plugin. This article presents an in-depth guide to this software, showcasing its ability to uncover novel structural features in biological molecular complexes. Here, we present how to assemble compatible data and provide a step-by-step protocol on how to use this algorithm to apply single-particle analysis to super-resolution images.

This manuscript uses the Fiji-based open-source software package VirusMapper to apply single-particle analysis to super-resolution microscopy images in order to generate precise models of nanoscale structure.

Analisi singola particella open-source per Super-risoluzione Microscopia con VirusMapper

Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm ...

Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium

The primary cilium is a microtubule-based protrusion on the surface of many eukaryotic cells and contains a unique complement of proteins that function critically in cell motility and signaling. Since cilia are incapable of synthesizing their own protein, nearly 200 unique ciliary proteins need to be trafficked between the cytosol and primary cilia. However, it is still a technical challenge to map three-dimensional (3D) locations of transport pathways for these proteins in live primary cilia due to the limitations of currently existing techniques. To conquer the challenge, recently we have developed and employed a high-speed virtual 3D super-resolution microscopy, termed single-point edge-excitation sub-diffraction (SPEED) microscopy, to determine the 3D spatial location of transport pathways for both cytosolic and membrane proteins in primary cilia of live cells. In this article, we will demonstrate the detailed setup of SPEED microscopy, the preparation of cells expressing fluorescence-protein-labeled ciliary proteins, the real-time single-molecule tracking of individual proteins in live cilium and the achievement of 3D spatial probability density maps of transport routes for ciliary proteins.

Recently we mapped the three-dimensional (3D) spatial locations of transport routes for various proteins translocating inside primary cilia in live cells. Here this paper details the experimental setup, the process of biological samples and the data analyses for the 3D super-resolution fluorescence imaging approach newly applied in live primary cilia.

Applicazione di microscopia di velocità ad alta velocità super-risoluzione in Live cilio primario

The primary cilium is a microtubule-based protrusion on the surface of many eukaryotic cells and contains a unique complement of proteins that function ...