Name: application of high-speed super-resolution speed microscopy in live primary cilium
Uploaded: 2018-01-16T12:30:00
Description: Watch this Scientific Journal Video about Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium at JoVE.com

We thank Dr. Kristen Verhey (University of Michigan, Ann Arbor) and Dr. Gregory Pazour (University of Massachusetts Medical School) for providing some plasmids. The project was supported by grants from the National Institutes of Health (NIH GM097037, GM116204 and GM122552 to W.Y.).

1. NIH-3T3 cell preparation for SPEED microscopy from stock
<ol>
	<li>1.5 weeks in advance of the experiment, recover a fresh culture of NIH-3T3 cells from a frozen stock by thawing at 37 &#176;C and transferring the cells to a 25 cm2 cell culture flask with 3 mL of Dulbecco&#39;s Modified Eagle&#39;s Medium (DMEM) supplemented with 110 mg/mL sodium pyruvate, 2 mM glutamine, 10% fetal bovine serum, and 1% penicillin/streptomycin.</li>
	<li>Incubate the cells at 37 &#176;C in a 5% CO2 incubator.</l...

<ol>
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This protocol describes the application of SPEED microscopy to the primary cilium, a cellular signaling organelle that is highly reliant on efficient protein transport. SPEED microscopy can provide high resolution (&#60; 10 nm) locations for fluorescently-labeled molecules as they pass through the single point illumination centered on the TZ. Previously it has been applied to study the protein trafficking through the NPC6,7,8. H...

Since stated by Ernst Abbe in 1873, the resolution of conventional light microscopy has been believed to be limited to approximately 200 nm due to light diffraction from the objective1,2. Currently, super-resolution light microscopy techniques break this limitation and allow the capture of dynamic images with sub-diffraction (&#60; 200 nm) resolution. The techniques generally fall into two broad categories: stimulated emission depletion (STED) microscopy based approaches, which generate sub-diffraction illumination volume due to nonlinear optical response of fluorophores in samples3; and photoactivated light microscopy (PALM) and stochastic optical reconstruction microscopy (STORM)-based super-resolution techniques, which utilize mathematical functions to localize the centroids of fluorophores and then reconstitute these centroids to form super-resolution images4,5. Currently, due to the relatively uncomplicated optical setup, PALM and STORM are extensively employed by only activating a small subset of fluorophores in each frame of a long video of a biological preparation. This allows for the more accurate localization by 2D Gaussian fitting of the fluorescent spot, termed the point spread function (PSF), of fluorescently-labeled proteins in each frame of the video. The 2D location of each fluorescently-labeled molecule can then be superimposed on a single imaging plane to produce a super-resolution image of the biological preparation1,2. While these single-molecule localization, super-resolution approaches to microscopy certainly revolutionized how imaging of biological samples was performed, there are still challenges to be overcome. For example, STORM and PALM can achieve their best spatial resolutions after fixation of biological samples and thus present a static representation of the fluorescently-labeled proteins, which is a similar limitation of electron microscopy. Additionally, to achieve high spatial resolution for each fluorescently-labeled protein in live cells, samples must be imaged at very long framerates which are unable to capture protein dynamics. Therefore, it is necessary to overcome these main technical hurdles.
To obtain a high spatiotemporal resolution that is well-suited for detecting fast-moving proteins or RNAs in live cells, we have developed super-resolution SPEED microscopy in our laboratory (Figure 1)6,7,8. Several major technical advances in SPEED microscopy have previously enabled us to successfully track nucleocytoplasmic transport of small molecules, proteins, mRNA and virus through native nuclear pore complexes (NPCs)6,7,8. Briefly, the following features of SPEED microscopy will be used to track fast-moving macromolecules through sub-micrometer rotationally symmetrical structures in live cells, such as NPCs and primary cilia: (1) An inclined or a vertical illumination PSF enables the excitation of single molecules within a small diffraction-limit volume in the focal plane (Figure 1); (2) The inclined PSF can greatly avoid out-of-focus fluorescence and thus improve the signal-to-noise ratio. (3) The optical density of 100-500 kW/ cm2 in the illumination PSF allows thousands of photons to be collected from single fluorophores with fast detection speeds (&#62; 500 Hz). (4) The fast detection speed also greatly reduces the single-molecule spatial localization error (&#60; 10 nm) in determining the spatial trajectories of moving fluorescent molecules in live cells, because molecular diffusion is one of major factors causing imperfections of single-molecule localization for moving molecules. (5) Well-established 2D to 3D transformation algorithms enable us to provide 3D spatial probability density maps of transport routes for molecules in the NPC or the primary cilium. It is noteworthy that our conversion process between the Cartesian and the cylindrical coordination system is used to generate a 3D spatial probability density map rather than 3D single-molecule tracking (Figure 2). Previously, electron microscopy data have revealed that the NPC9,10 and the primary cilium11 both have a rotationally symmetrical structure. In principle, randomly diffusing molecules moving through the NPC or primary cilium should also have rotationally symmetrical distributions. As shown in Figure 2, a high number of randomly diffusing molecules inside the cylinder would generate rotationally symmetrical distributions at the cross-section view as that in the NPC, further resulting in an approximately uniform spatial distribution within each very small sub-region between two neighboring rings (Figure 2E). This uniform distribution leads that the spatial distribution along &#952; dimension in the cylindrical system is constant. Then the 3D coordinates (R, X, &#952;) can be simplified to be the 2D coordinates (R, X, constant). Actually, our conversion process between the Cartesian and the cylindrical systems is from 2D (X, Y) to 2D (R, X, constant). The constant &#952;, refers to the spatial density p in Figure 2E, is calculated by using the equation A<img alt="Equation 1" src="/files/ftp_upload/56475/56475eq1.jpg" />.
Ultimately, single-molecule tracking has broad application in biological research, thus, it is natural that a plethora of techniques will be developed to fill specific biological niches12,13,14. Such is the case with SPEED microscopy. Previously, when coupled with a 3D transformation algorithm, this technique was developed to resolve 3D transport routes of transiting molecules through the NPCs, a sub-diffraction-sized and rotationally symmetric biological structure6. In this paper, primary cilia are shown to be excellent model organelles as well. Primary cilia are cylindrical, antenna-like organelles (~125 nm radius) that project from the surface of most mammalian cells15,16,17. They are responsible for receiving external signals and transmitting an intracellular response typically associated with growth and metabolism15,16. Therefore, flux of structural proteins, recycling of transmembrane receptors, and transmission of intracellular messengers are vital responsibilities of primary cilia. At the juncture between the primary cilia and the cell body is a critical selectivity barrier, called the transition zone or TZ, through which all this protein transport must occur11,18,19,20. In addition to the gating function of the TZ, at least two transport processes, intraflagellar transport and passive diffusion, are thought to be responsible for the movement of protein through this region16,21,22. From a human health standpoint, the loss of primary cilia and subsequent deregulation of downstream signaling is characteristic of many cancers. In addition, many genetic diseases, such as Bardet-Biedl syndrome and polycystic kidney disease, are associated with defective protein transport23. Both the sub-diffraction limit size and the complex process of selective protein transport through the TZ make the primary cilia a prime target for this technique. In this methods paper, we will demonstrate the tracking of a ciliary transmembrane protein, somatostatin receptor 3 (SSTR3)24, labeled externally with Alexa Fluor 647 and a component of IFT, IFT2025, labeled with a fused GFP molecule.

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		<tr height="47">
			<td height="47" style="height:47px;width:123px;">25 cm2 tissue culture dish</td>
			<td style="width:204px;">Corning</td>
			<td style="width:101px;">VV-01936-00</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:123px;">Penicillin/streptomycin</td>
			<td style="width:204px;">ThermoFisher</td>
			<td style="width:101px;">15140122</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:123px;">Fetal bovine serum</td>
			<td style="width:204px;">ThermoFisher</td>
			<td style="width:101px;">10438018</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:123px;">DMEM</td>
			<td style="width:204px;">ThermoFisher</td>
			<td style="width:101px;">10566-016</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:123px;">OPTIMEM</td>
			<td style="width:204px;">ThermoFisher</td>
			<td style="width:101px;">31985062</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:123px;">Trypsin</td>
			<td style="width:204px;">ThermoFisher</td>
			<td style="width:101px;">25300054</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:123px;">Phosphate buffered saline</td>
			<td style="width:204px;">Sigma-Aldrich</td>
			<td style="width:101px;">P3813-1PAK</td>
			<td style="width:191px;"></td>
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		<tr height="22">
			<td height="22" style="height:22px;width:123px;">Transit LT1</td>
			<td style="width:204px;">Mirus</td>
			<td style="width:101px;">MIR 2300</td>
			<td style="width:191px;"></td>
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		<tr height="43">
			<td height="43" style="height:43px;width:123px;">35 mm glass bottom dish</td>
			<td style="width:204px;">MatTek</td>
			<td style="width:101px;">P35GCOL-0-14-C</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:123px;">AlexaFluor 647-conjugated streptavidin</td>
			<td style="width:204px;">ThermoFisher</td>
			<td style="width:101px;">S21374</td>
			<td style="width:191px;"></td>
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		<tr height="22">
			<td height="22" style="height:22px;width:123px;">Biotin</td>
			<td style="width:204px;">Sigma-Aldrich</td>
			<td style="width:101px;">B4501-100MG</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:123px;">633 nm He-Ne laser</td>
			<td style="width:204px;">Melles Griot</td>
			<td style="width:101px;">25-LHP-928-249</td>
			<td style="width:191px;"></td>
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		<tr height="43">
			<td height="43" style="height:43px;width:123px;">561 nm solid state laser</td>
			<td style="width:204px;">Coherent</td>
			<td style="width:101px;">OBIS 561-50 LS</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:123px;">488 nm solid state laser</td>
			<td style="width:204px;">Coherent</td>
			<td style="width:101px;">1185053</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:123px;">Inverted fluorescence microscope</td>
			<td style="width:204px;">Olympus</td>
			<td style="width:101px;">IX81</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="85">
			<td height="85" style="height:85px;width:123px;">1.4-NA 100&#215; oil-immersion apochromatic objective</td>
			<td style="width:204px;">Olympus</td>
			<td style="width:101px;">UPLSAPO 100&#215;</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="106">
			<td height="106" style="height:106px;width:123px;">On-chip multiplication gain charge-coupled-device camera</td>
			<td style="width:204px;">Roper Scientific</td>
			<td style="width:101px;">Cascade 128+</td>
			<td style="width:191px;"></td>
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		<tr height="64">
			<td height="64" style="height:64px;width:123px;">Dichroic filter</td>
			<td style="width:204px;">Semrock</td>
			<td style="width:101px;">Di01- R405/488/561/635-25x36</td>
			<td style="width:191px;"></td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:123px;">Emission filter</td>
			<td style="width:204px;">Semrock</td>
			<td style="width:101px;">NF01-405/488/561/635-25X5.0</td>
			<td style="width:191px;"></td>
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		<tr height="22">
			<td height="22" style="height:22px;width:123px;">Slidebook 6.0</td>
			<td>Intelligent Imaging Innovations</td>
			<td></td>
			<td style="width:191px;">digital microscopy software</td>
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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.

This section demonstrates the data obtained from performing SPEED microscopy at the TZ of primary cilia to study the transport route of SSTR3 connected by a ~15 nm external linker to Alexa647 (Figure 3A). It serves the dual purpose of verifying the 3D transformation algorithm. Alexa647 should only label the external surface of the primary cilium and therefore, the 3D transport route should reveal a high-density transport route at that locatio...

Watch this Scientific Journal Video about Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium at JoVE.com

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

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.

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

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High Speed Droplet-based Delivery System for Passive Pumping in Microfluidic Devices

Microfluidic 장치에 수동 펌핑을위한 고속 비말 기반 전달 시스템

A novel microfluidic system has been developed that uses the phenomenon of passive pumping along with a user controlled droplet based fluid delivery ...

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생물학

Super-resolution Imaging of the Bacterial Division Machinery

세균 본부 기계의 슈퍼 해상도 이미징

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

Test Samples for Optimizing STORM Super-Resolution Microscopy

최적화 STORM 슈퍼 해상도 현미경에 대한 테스트 샘플

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

단일 비리온 원자력 현미경 검사및 초분해성 형광 이미징을 위한 샘플 준비

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)

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

고속 3D 구조 조명 현미경을 사용하여 라이브 박테리아의 Cytokinetic Z 반지의 슈퍼 해상도 이미징 (F3D-SIM)

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

Three-dimensional Super Resolution Microscopy of F-actin Filaments by Interferometric PhotoActivated Localization Microscopy (iPALM)

Three-dimensional Super Resolution Microscopy of F-actin Filaments by Interferometric PhotoActivated Localization Microscopy iPALM

입체 슈퍼의 간섭 광 활성화 현지화 현미경으로 F-액틴 필라멘트의 해상도 현미경 (iPALM)

Fluorescence microscopy enables direct visualization of specific biomolecules within cells. However, for conventional fluorescence microscopy, the spatial ...

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

VirusMapper 슈퍼 해상도 현미경을위한 오픈 소스 단일 입자 분석

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

Ground State Depletion Super-resolution Imaging in Mammalian Cells

포유류 세포에 있는 바닥 상태 고갈 슈퍼 해상도 영상

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

Examination of Mitotic and Meiotic Fission Yeast Nuclear Dynamics by Fluorescence Live-cell Microscopy

형광 라이브 세포 현미경 검사법에 의한 미토틱 및 Meiotic 핵분열 효모 핵 역학의 검사

Live-cell imaging is a microscopy technique used to examine cell and protein dynamics in living cells. This imaging method is not toxic, generally does ...

High-Accuracy Correction of 3D Chromatic Shifts in the Age of Super-Resolution Biological Imaging Using Chromagnon

High-Accuracy Correction of 3D Chromatic Shifts in the Age of Super-Resolution Biological Imaging Using Chromagnon

크로마뇽을 이용한 초분해능 생물학적 이미징 시대의 3D 색채 시프트의 고정밀 교정

Quantitative multicolor fluorescence microscopy relies on the careful spatial matching of color channels acquired at different wavelengths. Due to ...