This work was supported by NIH grant R01 GM104010. Thanks for assistance with fluorescence microscopy to Vytas Bindokas and Christine Labno at the Integrated Microscopy Core Facility, which is supported by the NIH-funded Cancer Center Support Grant P30 CA014599.

1. Preparation
<ol>
	<li>Make nonfluorescent minimal NSD medium2. The absence of riboflavin is expected to reduce background intracellular green fluorescence and associated phototoxicity.</li>
	<li>Grow the yeast strain overnight at ~23 &#176;C to logarithmic phase in 5 mL NSD in a 50 mL baffled flask with good aeration. About 3-4 h prior to analysis, dilute the yeast culture in fresh NSD&#160;so that the final OD600 will be 0.5-0.8 at the time of imaging.</li>
	<li>Prepare a 2 mg/mL solution of concanavalin A (ConA). If desired, freeze aliquots of this solution in liquid nitrogen and store at -80 &#176;C.</li>
	<li>Spin the ConA solution for 5 min at full speed in a microcentrifuge to remove particulate matter that may interfere with imaging. Then add 250 &#181;L of the supernatant to a clean 35 mm coverglass bottom microscopy dish. After 15 min, wash 2-3 times with 2 mL of dH2O and let dry.</li>
	<li>Add 250 &#181;L of the yeast culture to the ConA-coated dish, wait 10 min to allow the cells to adhere, and gently wash 2-3 times with 2 mL NSD. Cover the cells with 2 mL fresh NSD.</li>
</ol>
2. Imaging
<ol>
	<li>Use a 63x or 100x oil immersion lens. A numerical aperture (NA) of 1.40 is sufficient, but a higher NA lens can also be used.</li>
	<li>Format the frame size to 256 x 128 (width x height). If a larger frame size is needed, increasing the width will not reduce the scan speed as long as the confocal microscope is equipped with a resonant scanner.</li>
	<li>Adjust the zoom factor to make the pixel size ~80 nm.</li>
	<li>Use the maximum scan speed, which is typically on the order of 8 kHz. Turn on bidirectional X scanning if it is available, and if control experiments confirm that the scans from the two directions are in register.</li>
	<li>Set the line accumulation to 4 or 6. Be sure to use accumulation (summing) instead of averaging.</li>
	<li>Set the pinhole to 1.2 Airy units. Empirically, when imaging live yeast cells, this setting captures more photons than the standard choice of 1.0 Airy unit while causing no appreciable loss of resolution.</li>
	<li>For each fluorescence channel, set the excitation wavelength, assign a high sensitivity detector, set the emission wavelength range, and turn on photon counting mode if available. The wavelength choices will depend on the fluorophores. As an example, excite GFP fluorescence at 485&#160;nm and collect from 495-550 nm, and excite mScarlet&#160;fluorescence at 555&#160;nm and collect from 562-625&#160;nm.</li>
	<li>Set the intensity of each laser to be as low as possible. This setting must be determined empirically. An appropriate intensity will result in capture of a noisy but interpretable image sequence, with the fluorescence signal bleaching no more than 50% by the end of a 5 min movie. On the confocal microscope used here (see Table of Materials), this intensity corresponds to a laser power setting on the order of 5%.</li>
	<li>Use notch filters or time gating to avoid capturing reflected light from the coverslip. If time gating is available, set the gating window to 0.6-10.0 ns.</li>
	<li>Turn on brightfield imaging and use a low sensitivity detector for data collection. Set the gain to a level that makes the cells clearly visible. Do not use differential interference contrast (DIC) because the prism will interfere with the capture of reliable fluorescence data.</li>
	<li>Set the Z-step interval to 0.25-0.35 &#181;m. Image the entire volume of the yeast cells by collecting about 20-25 optical sections per Z-stack. Specify the directionality of imaging such that &#34;down&#34; moves toward the coverslip.</li>
	<li>For a typical movie, set the time interval between Z-stacks to 2 s and set the movie duration to 5 to 10 min. Depending on the compartment under study, reduce the interval to make shorter movies of relatively fast dynamics, or increase the interval to make longer movies of relatively slow dynamics.</li>
	<li>Save the movie as a LIF&#160;file with the brightfield images in the last channel. Higher bit depths are unnecessary at this stage, and the processing pipeline is configured to accept 8-bit TIFF data.</li>
</ol>
3. Deconvolution
<ol>
	<li>Launch the deconvolution software (see Table of Materials), using the Classic Maximum Likelihood Estimation algorithm.</li>
	<li>Open the data set generated in step 2.13. Select &#34;Deconvolution wizard&#34;. Inspect the values displayed in the &#34;Parameter wizard&#34;. The imaging parameters should be detected and correctly displayed. Under &#34;Refractive indexes&#34;, change the &#34;Embedding med.&#34; value to 1.40 to approximate the yeast cytoplasm.&#160;Under &#8220;coverslip&#8221;, select &#8220;Launch editor&#8221; and &#8220;Estimate position&#8221; and &#8220;OK&#8221; to set the coverslip position. Select &#34;Set all verified&#34; and &#34;Accept&#34;.</li>
	<li>Proceed through the &#34;Deconvolution wizard&#34; for each fluorescence channel. Select &#34;Manual&#34; as the mode for background estimation. Inspect the raw data fluorescence intensity profile to determine an estimated background value, which is typically about 0.1.</li>
	<li>In the deconvolution setup menu, enter a &#34;Maximum iterations&#34; value of 40 and turn off bleach correction. Enter an estimated SNR value, which is typically about 5.0. Click &#34;Deconvolve&#34;.</li>
	<li>If necessary, return to the original data file, adjust the background and SNR values, and repeat the deconvolution, until noise is sufficiently removed without eliminating genuine fluorescence from dim structures.</li>
	<li>Merge the brightfield and deconvolved fluorescence channels. For subsequent movie editing steps in ImageJ, arrange the channels such that red is first, green (if present) is next, blue (if present) is next, and brightfield is last. Save the image sequence as an 8-bit TIFF file.</li>
</ol>
4. Bleach Correction and Movie Generation
<ol>
	<li>Import the deconvolved image sequence into ImageJ and convert it into a hyperstack by choosing Image &#62; Hyperstacks &#62; Stack to Hyperstack. Select &#34;xyzct&#34; from the drop-down menu, and fill in the number of channels, Z-stack slices, and time frames (http://wiki.cmci.info/downloads/bleach_corrector).</li>
	<li>Choose Image &#62; Color &#62; Split Channels.</li>
	<li>Correct the fluorescence channels for photobleaching using the ImageJ plugin available from http://wiki.cmci.info/downloads/bleach_corrector. Once that plugin has been downloaded and installed, choose Plugins &#62; EMBLtools &#62; Bleach Correction. Select &#34;Exponential Fit.&#34;</li>
	<li>To merge the brightfield and bleach-corrected fluorescence channels into a hyperstack, choose Image &#62; Color &#62; Merge Channels. Save the resulting hyperstack as an 8-bit TIFF file.</li>
	<li><a href="https://www.jove.com/files/ftp_upload/58618/ImageJ.zip" target="_blank">Install the custom ImageJ plugins provided with this protocol.</a> Follow the instructions in the accompanying document to view, edit, and quantify the image sequence, and to produce a final movie of the projected Z-stacks.</li>
</ol>

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The authors declare that they have no competing financial interests.

4D confocal imaging of yeast organelles requires careful tuning of multiple parameters. The major concern is photobleaching and phototoxicity. A typical 4D movie involves collecting thousands of optical sections, so the laser illumination must be kept as low as possible. Tandem fluorescent protein tags can be used to boost the signal without increasing expression of the tagged protein16,17. Maximizing the scan speed helps to limit photodamage, and also allows Z-s...

Compartments of the endomembrane system are in constant flux, and their full characterization requires live cell imaging. Described here is a protocol that employs 4D (time-lapse 3D) confocal microscopy to visualize fluorescently labeled compartments in budding yeasts. The method was developed to track the dynamics of secretory compartments in Pichia pastoris and Saccharomyces cerevisiae1,2,3. This protocol focuses on S. cerevisiae, which has a nonstacked Golgi in which the individual cisternae are optically resolvable4. The unusual Golgi organization in S. cerevisiae enabled the demonstration by 4D microscopy that a Golgi cisterna initially labels with resident early Golgi proteins, and then loses those proteins while acquiring resident late Golgi proteins3,5. This transition can be visualized by creating a strain in which the early Golgi protein Vrg4 is labeled with GFP while the late Golgi protein Sec7 is labeled with a monomeric red fluorescent protein. When individual cisternae are tracked, maturation is observed as a green-to-red conversion3. This type of analysis can provide valuable information about protein localization and compartment identity. For example, two proteins with slightly offset arrival and departure times might sometimes appear to label different compartments in static images, but can be seen in 4D movies to label the same compartment at different time points6,7. Thus, 4D microscopy reveals phenomena that would not otherwise be evident.
Informative 4D microscopy of yeast compartments can be achieved with appropriate procedures and equipment2. Whenever possible, fluorescent protein tagging is performed by gene replacement8 to avoid overexpression artifacts. Because intracellular structures are often very dynamic, 4D imaging is needed to ensure that a structure is tracked reliably over time. The protocol described here employs a laser scanning confocal microscope equipped with high sensitivity detectors. With this device, the entire cell volume of S. cerevisiae can be imaged by confocal microscopy approximately every 1-3 s, with 2 s intervals being typical. Data can be collected for up to 5-15 min depending on the labeling densities of the fluorophores and their photophysical properties. The main hurdle is to minimize photobleaching. For this purpose, the laser intensities are kept as low as possible, the confocal scan speed is maximized, and the optical parameters are configured to image at the Nyquist limit in order to capture the relevant information while avoiding excessive light exposure. These settings are also expected to alleviate phototoxicity, a factor that is often overlooked during live cell imaging9,10,11. The resulting noisy data are processed with bleach correction and deconvolution algorithms to facilitate quantification of fluorescence intensities.
Even with high quality 4D movies, the analysis is tricky because yeast compartments tend to be numerous, heterogeneous, and mobile. Due to the intrinsic limitations of confocal microscopy and the non-optimal settings required for prolonged 4D imaging, fluorescent structures that are near each other are hard to resolve. This problem can be circumvented by focusing on the small number of fluorescent structures that remain optically resolvable for the duration of the labeling period, with the assumption that those structures are representative of the whole population of labeled compartments. Fluorescent compartments that can be reliably tracked are identified by viewing movies of projected Z-stacks and by creating a series of montages in which the optical sections for each time point are arrayed on a computer screen. This analysis employs custom ImageJ12 plugins, which allow an individual structure to be tracked in isolation.
Recent methods papers covered the use of fluorescent proteins in yeast13 as well as the theory and practice of 4D confocal imaging of yeast cells2. This protocol focuses on the key practical aspects of a 4D imaging experiment. It includes some enhancements to previously described procedures, as well as updated versions of the ImageJ plugin code and documentation. The example shown focuses on Golgi dynamics, but this protocol is equally suitable for imaging other yeast compartments.

<table border="0" cellpadding="0" cellspacing="0" style="width:587px;" width="587">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">35 mm glass bottom dishes No. 1.5</td>
			<td style="width:85px;">MatTek</td>
			<td style="width:119px;">P35G-0.170-14-C</td>
			<td style="width:167px;">Imaging dishes</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:216px;">Concanavalin A powder</td>
			<td style="width:85px;">Sigma-Aldrich</td>
			<td style="width:119px;">C2010</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Trolox</td>
			<td style="width:85px;">Vector Laboratories</td>
			<td style="width:119px;">CB-1000</td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Leica SP8 confocal microscope</td>
			<td style="width:85px;">Leica Microsystems</td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Leica Application Suite X&#160;</td>
			<td style="width:85px;">Leica Microsystems</td>
			<td style="width:119px;"></td>
			<td>Microscope software</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:216px;">Huygens Essential software, version 17.04</td>
			<td style="width:85px;">Scientific Volume Imaging</td>
			<td style="width:119px;"></td>
			<td>Deconvolution software</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">ImageJ</td>
			<td style="width:85px;">NIH</td>
			<td style="width:119px;"></td>
			<td>Image processing and analysis software</td>
		</tr>
	</tbody>
</table>

4d microscopy of yeast

The goal of this protocol is to characterize how membrane compartments form and transform in live cells of budding yeast. Many intracellular compartments in yeast are dynamic, and a full understanding of their properties requires time-lapse imaging. Multi-color 4D confocal fluorescence microscopy is a powerful method for tracking the behavior and composition of an intracellular compartment on a time scale of 5-15 min. Rigorous analysis of compartment dynamics requires the capture of thousands of optical sections. To achieve this aim, photobleaching and phototoxicity are minimized by scanning rapidly at very low laser power, and the pixel dimensions and Z-step intervals are set to the largest values that are compatible with sampling the image at full resolution. The resulting 4D data sets are noisy but can be smoothed by deconvolution. Even with high quality data, the analysis phase is challenging because intracellular structures are often numerous, heterogeneous, and mobile. To meet this need, custom ImageJ plugins were written to array 4D data on a computer screen, identify structures of interest, edit the data to isolate individual structures, quantify the fluorescence time courses, and make movies of the projected Z-stacks. 4D movies are particularly useful for distinguishing stable compartments from transient compartments that turn over by maturation. Such movies can also be used to characterize events such as compartment fusion, and to test the effects of specific mutations or other perturbations.

The example given here documents and quantifies the maturation of two yeast Golgi cisternae as visualized by dual-color 4D confocal microscopy3. A yeast cell contains on the order of 10-15 Golgi cisternae, each of which matures over a time course of approximately 2-4 min. Maturation can be visualized by tagging the early Golgi marker Vrg4 with GFP and by tagging the late Golgi marker Sec7 with a red fluorescent protein such as mCherry or mScarlet. An individual cis...

Watch this Scientific Journal Video about 4D Microscopy of Yeast at JoVE.com

4D Microscopy of Yeast

This protocol describes the analysis of fluorescently labeled intracellular compartments in budding yeast using multi-color 4D (time-lapse 3D) confocal microscopy. The imaging parameters are chosen to capture adequate signals while limiting photodamage. Custom ImageJ plugins allow labeled structures to be tracked and quantitatively analyzed.

The goal of this protocol is to characterize how membrane compartments form and transform in live cells of budding yeast. Many intracellular compartments ...

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8.4K Views.  University of Chicago. This protocol describes the analysis of fluorescently labeled intracellular compartments in budding yeast using multi-color 4D (time-lapse 3D) confocal microscopy. The imaging parameters are chosen to capture adequate signals while limiting photodamage. Custom ImageJ plugins allow labeled structures to be tracked and quantitatively analyzed.

Video: 4D Microscopy of Yeast

Purification of Mitochondria from Yeast Cells

Mitochondria are the main site of ATP production during aerobic metabolism in eukaryotic non-photosynthetic cells1. These complex organelles also play essential roles in apoptotic cell death2, cell survival3, mammalian development4, neuronal development and function4, intracellular signalling5, and longevity regulation6. Our understanding of these complex biological processes controlled by mitochondria relies on robust methods for assessing their morphology, their protein and lipid composition, the integrity of their DNA, and their numerous vital functions. The budding yeast Saccharomyces cerevisiae, a genetically and biochemically manipulable unicellular eukaryote with annotated genome and well-defined proteome, is a valuable model for studying the molecular and cellular mechanisms underlying essential biological functions of mitochondria. For these types of studies, it is crucial to have highly pure mitochondria. Here we present a detailed description of a rapid and effective method for purification of yeast mitochondria. This method enables the isolation of highly pure mitochondria that are essentially free of contamination by other organelles and retain their structural and functional integrity after their purification. Mitochondria purified by this method are suitable for cell-free reconstitution of essential mitochondrial processes and can be used for the analysis of mitochondrial structure and functions, mitochondrial proteome and lipidome, and mitochondrial DNA.

We describe a rapid and effective method for purification of mitochondria from the yeast Saccharomyces cerevisiae. This method enables the high-yield isolation of pure mitochondria that are essentially free of contamination by other organelles and retain their structural and functional integrity after their purification.

Mitochondria are the main site of ATP production during aerobic metabolism in eukaryotic non-photosynthetic cells1. These complex organelles also play ...

Yeast Colony Embedding Method

Patterning of different cell types in embryos is a key mechanism in metazoan development. Communities of microorganisms, such as colonies and biofilms also display patterns of cell types. For example, in the yeast S. cerevisiae, sporulated cells and pseudohyphal cells are not uniformly distributed in colonies. The functional importance of patterning and the molecular mechanisms that underlie these patterns are still poorly understood.
One challenge with respect to investigating patterns of cell types in fungal colonies is that unlike metazoan tissue, cells in colonies are relatively weakly attached to one another. In particular, fungal colonies do not contain the same extensive level of extracellular matrix found in most tissues . Here we report on a method for embedding and sectioning yeast colonies that reveals the interior patterns of cell types in these colonies. The method can be used to prepare thick sections (0.5 &mu;) useful for light microscopy and thin sections (0.1 &mu;) suitable for transmission electron microscopy. Asci and pseudohyphal cells can easily be distinguished from ovoid yeast cells by light microscopy , while the interior structure of these cells can be visualized by EM.
The method is based on surrounding colonies with agar, infiltrating them with Spurr's medium, and then sectioning. Colonies with a diameter in the range of 1-2 mm are suitable for this protocol. In addition to visualizing the interior of colonies, the method allows visualization of the region of the colony that invades the underlying agar.

A method for embedding yeast colonies allowing sectioning for light and electron microscopy. This protocol allows determination of the distribution of sporulated cells and pseudohyphal cells within colonies providing a new tool toward understanding the organization of cell types within a fungal community.

Patterning of  different cell types in embryos is a key mechanism in metazoan development. Communities of microorganisms, such as colonies and biofilms ...

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

Autophagy is important for turnover of cellular components under a range of different conditions. It serves an essential homeostatic function as well as a quality control mechanism that can target and selectively degrade cellular material including organelles1-4. For example, damaged or redundant mitochondria (Fig. 1), not disposed of by autophagy, can represent a threat to cellular homeostasis and cell survival. In the yeast, Saccharomyces cerevisiae, nutrient deprivation (e.g., nitrogen starvation) or damage can promote selective turnover of mitochondria by autophagy in a process termed mitophagy 5-9.
We describe a simple fluorescence microscopy approach to assess autophagy. For clarity we restrict our description here to show how the approach can be used to monitor mitophagy in yeast cells. The assay makes use of a fluorescent reporter, Rosella, which is a dual-emission biosensor comprising a relatively pH-stable red fluorescent protein linked to a pH-sensitive green fluorescent protein. The operation of this reporter relies on differences in pH between the vacuole (pH ~ 5.0-5.5) and mitochondria (pH ~ 8.2) in living cells. Under growing conditions, wild type cells exhibit both red and green fluorescence distributed in a manner characteristic of the mitochondria. Fluorescence emission is not associated with the vacuole. When subjected to nitrogen starvation, a condition which induces mitophagy, in addition to red and green fluorescence labeling the mitochondria, cells exhibit the accumulation of red, but not green fluorescence, in the acidic vacuolar lumen representing the delivery of mitochondria to the vacuole. Scoring cells with red, but not green fluorescent vacuoles can be used as a measure of mitophagic activity in cells5,10-12.

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

A robust approach to monitor the delivery of organelles to the acidic lumen of the yeast vacuole for degradation and recycling is described. The method relies on the specific labeling of target organelles with a genetically encoded dual-emission fluorescence pH-biosensor, and visualization of individual cells using fluorescence microscopy.

Autophagy is important for turnover of cellular components under a range of different conditions. It serves an essential homeostatic function as well as a ...

High-throughput Yeast Plasmid Overexpression Screen

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, including those with direct relevance to human disease. Because of its short generation time and well-characterized genome, a major experimental advantage of the yeast model system is the ability to perform genetic screens to identify genes and pathways that are involved in a given process. Over the last thirty years such genetic screens have been used to elucidate the cell cycle, secretory pathway, and many more highly conserved aspects of eukaryotic cell biology 1-5. In the last few years, several genomewide libraries of yeast strains and plasmids have been generated 6-10. These collections now allow for the systematic interrogation of gene function using gain- and loss-of-function approaches 11-16. Here we provide a detailed protocol for the use of a high-throughput yeast transformation protocol with a liquid handling robot to perform a plasmid overexpression screen, using an arrayed library of 5,500 yeast plasmids. We have been using these screens to identify genetic modifiers of toxicity associated with the accumulation of aggregation-prone human neurodegenerative disease proteins. The methods presented here are readily adaptable to the study of other cellular phenotypes of interest.

Here we describe a plasmid overexpression screen in Saccharomyces cerevisiae, using an arrayed plasmid library and a high-throughput yeast transformation protocol with a liquid handling robot.

The budding yeast, Saccharomyces cerevisiae, is a powerful model system for defining fundamental mechanisms of many important cellular processes, ...

Competitive Genomic Screens of Barcoded Yeast Libraries

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily. The tempo of these advances is accelerating, promising greater depth and breadth. In light of these extraordinary advances, the need for fast, parallel methods to define gene function becomes ever more important. Collections of genome-wide deletion mutants in yeasts and E. coli have served as workhorses for functional characterization of gene function, but this approach is not scalable, current gene-deletion approaches require each of the thousands of genes that comprise a genome to be deleted and verified. Only after this work is complete can we pursue high-throughput phenotyping. Over the past decade, our laboratory has refined a portfolio of competitive, miniaturized, high-throughput genome-wide assays that can be performed in parallel. This parallelization is possible because of the inclusion of DNA 'tags', or 'barcodes,' into each mutant, with the barcode serving as a proxy for the mutation and one can measure the barcode abundance to assess mutant fitness. In this study, we seek to fill the gap between DNA sequence and barcoded mutant collections. To accomplish this we introduce a combined transposon disruption-barcoding approach that opens up parallel barcode assays to newly sequenced, but poorly characterized microbes. To illustrate this approach we present a new Candida albicans barcoded disruption collection and describe how both microarray-based and next generation sequencing-based platforms can be used to collect 10,000 - 1,000,000 gene-gene and drug-gene interactions in a single experiment.

We have developed comprehensive, unbiased genome-wide screens to understand gene-drug and gene-environment interactions. Methods for screening these mutant collections are presented.

By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily.  The tempo of these advances is ...

Chromatographic Purification of Highly Active Yeast Ribosomes

Eukaryotic ribosomes are much more labile as compared to their eubacterial and archael counterparts, thus posing a significant challenge to researchers. Particularly troublesome is the fact that lysis of cells releases a large number of proteases and nucleases which can degrade ribosomes. Thus, it is important to separate ribosomes from these enzymes as quickly as possible. Unfortunately, conventional differential ultracentrifugation methods leaves ribosomes exposed to these enzymes for unacceptably long periods of time, impacting their structural integrity and functionality. To address this problem, we utilize a chromatographic method using a cysteine charged Sulfolink resin. This simple and rapid application significantly reduces co-purifying proteolytic and nucleolytic activities, producing high yields of intact, highly biochemically active yeast ribosomes. We suggest that this method should also be applicable to mammalian ribosomes. The simplicity of the method, and the enhanced purity and activity of chromatographically purified ribosome represents a significant technical advancement for the study of eukaryotic ribosomes.

Contamination of preparations of eukaryotic ribosomes purified by traditional methods by co-purifying nucleases and proteases negatively impacts on downstream biochemical and structural analyses. A rapid and simple chromatographic purification method is used to solve this problem using yeast ribosomes as a model system.

Eukaryotic ribosomes are much more labile as compared to their eubacterial and archael counterparts, thus posing a significant challenge to researchers.  ...

Quantitative Live Cell Fluorescence-microscopy Analysis of Fission Yeast

Several microscopy techniques are available today that can detect a specific protein within the cell. During the last decade live cell imaging using fluorochromes like Green Fluorescent Protein (GFP) directly attached to the protein of interest has become increasingly popular 1. Using GFP and similar fluorochromes the subcellular localisations and movements of proteins can be detected in a fluorescent microscope. Moreover, also the subnuclear localisation of a certain region of a chromosome can be studied using this technique. GFP is fused to the Lac Repressor protein (LacR) and ectopically expressed in the cell where tandem repeats of the lacO sequence has been inserted into the region of interest on the chromosome2. The LacR-GFP will bind to the lacO repeats and that area of the genome will be visible as a green dot in the fluorescence microscope. Yeast is especially suited for this type of manipulation since homologous recombination is very efficient and thereby enables targeted integration of the lacO repeats and engineered fusion proteins with GFP 3. Here we describe a quantitative method for live cell analysis of fission yeast. Additional protocols for live cell analysis of fission yeast can be found, for example on how to make a movie of the meiotic chromosomal behaviour 4. In this particular experiment we focus on subnuclear organisation and how it is affected during gene induction. We have labelled a gene cluster, named Chr1, by the introduction of lacO binding sites in the vicinity of the genes. The gene cluster is enriched for genes that are induced early during nitrogen starvation of fission yeast 5. In the strain the nuclear membrane (NM) is labelled by the attachment of mCherry to the NM protein Cut11 giving rise to a red fluorescent signal. The Spindle Pole body (SPB) compound Sid4 is fused to Red Fluorescent Protein (Sid4-mRFP) 6. In vegetatively growing yeast cells the centromeres are always attached to the SPB that is embedded in the NM 7. The SPB is identified as a large round structure in the NM. By imaging before and 20 minutes after depletion of the nitrogen source we can determine the distance between the gene cluster (GFP) and the NM/SPB. The mean or median distances before and after nitrogen depletion are compared and we can thus quantify whether or not there is a shift in subcellular localisation of the gene cluster after nitrogen depletion.

The fission yeast, Schizosaccharomyces pombe, is a good model system to study basic cellular processes. Here we describe a method to perform quantitative live cell analysis of fission yeast. In this particular experiment we focus on organisation of the genome within the cell nucleus, but the method can also be used to study cytosolic factors.

Several microscopy techniques are available today that can detect a specific protein within the cell. During the last decade live cell imaging using ...

4D Imaging of Protein Aggregation in Live Cells

One of the key tasks of any living cell is maintaining the proper folding of newly synthesized proteins in the face of ever-changing environmental conditions and an intracellular environment that is tightly packed, sticky, and hazardous to protein stability1. The ability to dynamically balance protein production, folding and degradation demands highly-specialized quality control machinery, whose absolute necessity is observed best when it malfunctions. Diseases such as ALS, Alzheimer's, Parkinson's, and certain forms of Cystic Fibrosis have a direct link to protein folding quality control components2, and therefore future therapeutic development requires a basic understanding of underlying processes. Our experimental challenge is to understand how cells integrate damage signals and mount responses that are tailored to diverse circumstances.
The primary reason why protein misfolding represents an existential threat to the cell is the propensity of incorrectly folded proteins to aggregate, thus causing a global perturbation of the crowded and delicate intracellular folding environment1. The folding health, or "proteostasis," of the cellular proteome is maintained, even under the duress of aging, stress and oxidative damage, by the coordinated action of different mechanistic units in an elaborate quality control system3,4. A specialized machinery of molecular chaperones can bind non-native polypeptides and promote their folding into the native state1, target them for degradation by the ubiquitin-proteasome system5, or direct them to protective aggregation inclusions6-9.
In eukaryotes, the cytosolic aggregation quality control load is partitioned between two compartments8-10: the juxtanuclear quality control compartment (JUNQ) and the insoluble protein deposit (IPOD) (Figure 1 - model). Proteins that are ubiquitinated by the protein folding quality control machinery are delivered to the JUNQ, where they are processed for degradation by the proteasome. Misfolded proteins that are not ubiquitinated are diverted to the IPOD, where they are actively aggregated in a protective compartment.
Up until this point, the methodological paradigm of live-cell fluorescence microscopy has largely been to label proteins and track their locations in the cell at specific time-points and usually in two dimensions. As new technologies have begun to grant experimenters unprecedented access to the submicron scale in living cells, the dynamic architecture of the cytosol has come into view as a challenging new frontier for experimental characterization. We present a method for rapidly monitoring the 3D spatial distributions of multiple fluorescently labeled proteins in the yeast cytosol over time. 3D timelapse (4D imaging) is not merely a technical challenge; rather, it also facilitates a dramatic shift in the conceptual framework used to analyze cellular structure.
We utilize a cytosolic folding sensor protein in live yeast to visualize distinct fates for misfolded proteins in cellular aggregation quality control, using rapid 4D fluorescent imaging. The temperature sensitive mutant of the Ubc9 protein10-12 (Ubc9ts) is extremely effective both as a sensor of cellular proteostasis, and a physiological model for tracking aggregation quality control. As with most ts proteins, Ubc9ts is fully folded and functional at permissive temperatures due to active cellular chaperones. Above 30 &deg;C, or when the cell faces misfolding stress, Ubc9ts misfolds and follows the fate of a native globular protein that has been misfolded due to mutation, heat denaturation, or oxidative damage. By fusing it to GFP or other fluorophores, it can be tracked in 3D as it forms Stress Foci, or is directed to JUNQ or IPOD.

Cellular viability depends on timely and efficient management of protein misfolding. Here we describe a method for visualizing the different potential fates of a misfolded protein: refolding, degradation, or sequestration in inclusions. We demonstrate the use of a folding sensor, Ubc9ts, for monitoring proteostasis and aggregation quality control in live cells using 4D microscopy.

One of the key tasks of any living cell is maintaining the proper folding of newly synthesized proteins in the face of ever-changing environmental ...

Analyzing Craniofacial Morphogenesis in Zebrafish Using 4D Confocal Microscopy

Time-lapse imaging is a technique that allows for the direct observation of the process of morphogenesis, or the generation of shape. Due to their optical clarity and amenability to genetic manipulation, the zebrafish embryo has become a popular model organism with which to perform time-lapse analysis of morphogenesis in living embryos. Confocal imaging of a live zebrafish embryo requires that a tissue of interest is persistently labeled with a fluorescent marker, such as a transgene or injected dye. The process demands that the embryo is anesthetized and held in place in such a way that healthy development proceeds normally. Parameters for imaging must be set to account for three-dimensional growth and to balance the demands of resolving individual cells while getting quick snapshots of development. Our results demonstrate the ability to perform long-term in vivo imaging of fluorescence-labeled zebrafish embryos and to detect varied tissue behaviors in the cranial neural crest that cause craniofacial abnormalities. Developmental delays caused by anesthesia and mounting are minimal, and embryos are unharmed by the process. Time-lapse imaged embryos can be returned to liquid medium and subsequently imaged or fixed at later points in development. With an increasing abundance of transgenic zebrafish lines and well-characterized fate mapping and transplantation techniques, imaging any desired tissue is possible. As such, time-lapse in vivo imaging combines powerfully with zebrafish genetic methods, including analyses of mutant and microinjected embryos.

Time-lapse confocal imaging is a powerful technique useful for characterizing embryonic development. Here, we describe the methodology and characterize craniofacial morphogenesis in wild-type, as well as pdgfra, smad5, and smo mutant embryos.

Time-lapse imaging is a technique that allows for the direct observation of the process of morphogenesis, or the generation of shape. Due to their optical ...

Surface Spreading and Immunostaining of Yeast Chromosomes

The small size of nuclei of the budding yeast Saccharomyces cerevisiae limits the utility of light microscopy for analysis of the subnuclear distribution of chromatin-bound proteins. Surface spreading of yeast nuclei results in expansion of chromatin without loss of bound proteins. A method for surface spreading balances fixation of DNA bound proteins with detergent treatment. The method demonstrated is slightly modified from that described by Josef Loidl and Franz Klein1,2. The method has been used to characterize the localization of many chromatin-bound proteins at various stages of the mitotic cell cycle, but is especially useful for the study of meiotic chromosome structures such as meiotic recombinosomes and the synaptonemal complex. We also describe a modification that does not require use of Lipsol, a proprietary detergent, which was called for in the original procedure, but no longer commercially available. An immunostaining protocol that is compatible with the chromosome spreading method is also described.

A method for surface-spreading chromosomes from budding yeast is presented. This method is derived from a method previously described by Loidl and Klein. In addition, we demonstrate a procedure for immunostaining of spread chromosomes.

The small size of nuclei of the budding yeast Saccharomyces cerevisiae limits the utility of light microscopy for analysis of the subnuclear distribution ...

4D Microscopy of Yeast

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Purification of Mitochondria from Yeast Cells

Yeast Colony Embedding Method

A Fluorescence Microscopy Assay for Monitoring Mitophagy in the Yeast Saccharomyces cerevisiae

High-throughput Yeast Plasmid Overexpression Screen

Competitive Genomic Screens of Barcoded Yeast Libraries

Chromatographic Purification of Highly Active Yeast Ribosomes

Quantitative Live Cell Fluorescence-microscopy Analysis of Fission Yeast

4D Imaging of Protein Aggregation in Live Cells

Analyzing Craniofacial Morphogenesis in Zebrafish Using 4D Confocal Microscopy

Surface Spreading and Immunostaining of Yeast Chromosomes