Name: spatiotemporal analysis of cytokinetic events in fission yeast
Uploaded: 2017-02-20T14:00:00
Description: Watch this Scientific Journal Video about Spatiotemporal Analysis of Cytokinetic Events in Fission Yeast at JoVE.com

This work was supported by startup funds from The University of Tennessee and TN-SCORE, a multi-disciplinary research program sponsored by NSF-EPSCoR (EPS-1004083).

1. Preparation of Sample
<ol>
	<li>Grow fission yeast cells expressing the spindle pole body marker Sad1-mCherry23 and type II myosin regulatory light chain Rlc1-Tomato24 in YE liquid media at 32 &#176;C for 8 generations. 
	NOTE: For temperature sensitive mutants, grow cells at 25 &#176;C. Grow cells to mid-log phase to an O.D.600 of 0.5 in YE. For more on fission yeast growth conditions refer to the Fission yeast lab manual25.</li...

<ol>
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C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+(1,3)beta-D-glucan+synthase+subunit+Bgs1p+is+responsible+for+the+fission+yeast+primary+septum+formation.">The (1,3)beta-D-glucan synthase subunit Bgs1p is responsible for the fission yeast primary septum formation.</a> Mol Microbiol. 65 (1), 201-217 (2007).</li><li>Cortes, J. C., 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=Cooperation+between+Paxillin-like+Protein+Pxl1+and+Glucan+Synthase+Bgs1+Is+Essential+for+Actomyosin+Ring+Stability+and+Septum+Formation+in+Fission+Yeast.">Cooperation between Paxillin-like Protein Pxl1 and Glucan Synthase Bgs1 Is Essential for Actomyosin Ring Stability and Septum Formation in Fission Yeast.</a> PLoS Genet. 11 (7), e1005358 (2015).</li><li>Cortes, J. C., Ishiguro, J., Duran, A., Ribas, 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=Localization+of+the+(1,3)beta-D-glucan+synthase+catalytic+subunit+homologue+Bgs1p/Cps1p+from+fission+yeast+suggests+that+it+is+involved+in+septation,+polarized+growth,+mating,+spore+wall+formation+and+spore+germination.">Localization of the (1,3)beta-D-glucan synthase catalytic subunit homologue Bgs1p/Cps1p from fission yeast suggests that it is involved in septation, polarized growth, mating, spore wall formation and spore germination.</a> J Cell Sci. 115 (Pt 21), 4081-4096 (2002).</li><li>Liu, J., Tang, X., Wang, H., Oliferenko, S., Balasubramanian, M. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+localization+of+the+integral+membrane+protein+Cps1p+to+the+cell+division+site+is+dependent+on+the+actomyosin+ring+and+the+septation-inducing+network+in+Schizosaccharomyces+pombe.">The localization of the integral membrane protein Cps1p to the cell division site is dependent on the actomyosin ring and the septation-inducing network in Schizosaccharomyces pombe.</a> Mol Biol Cell. 13 (3), 989-1000 (2002).</li><li>Royou, A., Field, C., Sisson, J. C., Sullivan, W., Karess, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reassessing+the+role+and+dynamics+of+nonmuscle+myosin+II+during+furrow+formation+in+early+Drosophila+embryos.">Reassessing the role and dynamics of nonmuscle myosin II during furrow formation in early Drosophila embryos.</a> Mol Biol Cell. 15 (2), 838-850 (2004).</li><li>Figard, L., Xu, H., Garcia, H. G., Golding, I., Sokac, A. 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L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dma1+ubiquitinates+the+SIN+scaffold,+Sid4,+to+impede+the+mitotic+localization+of+Plo1+kinase.">Dma1 ubiquitinates the SIN scaffold, Sid4, to impede the mitotic localization of Plo1 kinase.</a> EMBO J. 30 (2), 341-354 (2011).</li><li>Yonetani, A., Chang, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+cytokinesis+by+the+formin+cdc12p.">Regulation of cytokinesis by the formin cdc12p.</a> Curr Biol. 20 (6), 561-566 (2010).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Fission Yeast: A laboratory Manual. , (2016).</li><li>Hachet, O., Simanis, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mid1p/anillin+and+the+septation+initiation+network+orchestrate+contractile+ring+assembly+for+cytokinesis.">Mid1p/anillin and the septation initiation network orchestrate contractile ring assembly for cytokinesis.</a> Genes Dev. 22 (22), 3205-3216 (2008).</li><li>Zhou, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+contractile+ring+coordinates+curvature-dependent+septum+assembly+during+fission+yeast+cytokinesis.">The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis.</a> Mol Biol Cell. 26 (1), 78-90 (2015).</li><li>Chen, B. 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Here we have described a protocol to study cytokinetic events in fission yeast in a temporal manner. The protocol described here provides temporal resolution of different cytokinetic events with reference to each other; timing of protein recruitment or loss with reference to cytokinetic phase; structure of the ring throughout the different phases of cytokinesis; and the progression of cytokinesis with reference to mitosis. With this protocol it is possible to precisely define the cytokinetic phase that may be altered in ...

Cytokinesis, the final step in cell division, is a complex process essential for proper differentiation, development, and survival of an organism. Cytokinesis involves multiple events that are organized to ensure successful cell separation while maintaining genomic integrity1. Cytokinesis involves events where an actomyosin ring once assembled undergoes constriction, which is concurrent with membrane expansion and furrowing, and extracellular cellular matrix remodeling, finally followed by cell abscission1,2,3. Improper organization of cytokinetic events can lead to cell separation and ploidy defects, and may cause diseases like cancer4,5,6,7,8. The fundamental principles that enable organization of cytokinetic events are not well understood, thus leading to roadblocks in our understanding of the etiology of these diseases.
The fission yeast Schizosaccharomyces pombe (S.&#160;pombe)&#160;is an excellent model system to study cytokinesis due to the conserved nature of the proteins involved1. In fission yeast, after actomyosin ring assembly, the ring enters a maturation/dwell phase where it does not constrict9. Maturation ends with initiation of actomyosin ring constriction, concurrent with membrane furrowing and septum ingression. Seminal work over the years have given us a fairly good understanding of actomyosin ring assembly in fission yeast1,9,10. In some eukaryotes, including fission yeast, successful assembly of the actomyosin ring is not sufficient for membrane furrowing. In fission yeast, ring constriction alone does not provide sufficient force to overcome internal turgor pressure for furrow formation11. A recent model indicates that this force is instead provided by septum ingression11. In another model, the role of plasma membrane extension has been suggested to contribute to furrow formation12,13. Ring constriction and membrane furrowing do not occur in Bgs1/Cps1 temperature sensitive mutant cps1-191, the major enzyme for primary septum formation14,15. Cells lacking Bgs1 show defective primary septum and prolonged ring constriction15,16. Bgs1 is recruited to the cell division site for septum ingression during maturation after actomyosin ring assembly17,18. Similarly, during cellularization in Drosophila embryos, ring constriction is biphasic with a significantly slow initial constriction rate19, resembling the maturation phase observed in fission yeast. Biphasic ring constriction may slow down membrane furrowing to allow for sufficient membrane expansion20 and modification of extracellular matrix. This suggests that after actomyosin ring assembly, ring constriction occurs efficiently only when the cell has satisfied the requirements for furrow formation. It is not well understood what conditions are required for actomyosin ring constriction after ring assembly, nor the molecular events that regulate this process. We have recently shown that following actomyosin ring assembly the small GTPase Cdc42 undergoes a unique spatiotemporal activation pattern21. This pattern is established by the unique localization pattern of the Cdc42 guanidine nucleotide exchange factors (GEFs) that activate Cdc42. The GEF Gef1 localizes to the assembled actomyosin ring and promotes onset of ring constriction and septum ingression, while Scd1 localizes to the furrowing membrane and promotes normal septum formation. We find that the Cdc42 activation pattern established by its GEFs lead to the regulation of distinct cytokinetic events.
To understand the molecular mechanism of events that eventually lead to cell separation following actomyosin ring assembly, one needs to follow the distinct cytokinetic events in time and space. In fission yeast, cytokinesis first involves the assembly of precursor nodes around the nucleus, which eventually recruit the type II myosin, the formin Cdc12, and other proteins required for actomyosin ring assembly. To time the distinct cytokinetic events and provide a frame of reference, the separation of spindle pole body markers (spindle formation) is considered as time 022. The assembly of the actomyosin ring can be followed by monitoring over time the intensity of a fluorescently tagged actomyosin ring protein such as the type II myosin regulatory light chain Rlc1. Here we describe a microscopic approach to analyze different stages of cytokinesis over time.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Yeast extract media</td>
			<td>Sunrise Science Products</td>
			<td>YES 225</td>
			<td>0.5% w/v yeast extract, 3% w/v glucose, 225mg/L adenine, histidine, leucine, uracil, and lysine</td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>SeaKem LE agarose, Lonza</td>
			<td>50001</td>
			<td></td>
		</tr>
		<tr>
			<td>Ascorbic acid</td>
			<td>Sigma-Aldrich</td>
			<td>A4544</td>
			<td></td>
		</tr>
		<tr>
			<td>Glass Bottomed culture dish</td>
			<td>MatTek Corporation</td>
			<td>P35G-1.5-14-C</td>
			<td>Coverslip No. 1.5 was used. This will vary as per the microscope specifications used.&#160;</td>
		</tr>
		<tr>
			<td>VT-Hawk 2D array laser scanning confocal microscopy system</td>
			<td>Visitech International, UK</td>
			<td></td>
			<td>with an Olympus IX-83 inverted microscope with a 100X / numerical aperture 1.49 UAPO lens (Olympus) and EM-CCD digital camera (Hamamatsu).&#160;</td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>NIH</td>
			<td></td>
			<td>Image analysis software</td>
		</tr>
	</tbody>
</table>

spatiotemporal analysis of cytokinetic events in fission yeast

Cytokinesis, the final step in cell division is critical for maintaining genome integrity. Proper cytokinesis is important for cell differentiation and development. Cytokinesis involves a series of events that are well coordinated in time and space. Cytokinesis involves the formation of an actomyosin ring at the division site, followed by ring constriction, membrane furrow formation and extra cellular matrix remodeling. The fission yeast, Schizosaccharomyces pombe (S.&#160;pombe)&#160;is a well-studied model system that has revealed with substantial clarity the initial events in cytokinesis. However, we do not understand clearly how different cytokinetic events are coordinated spatiotemporally. To determine this, one needs to analyze the different cytokinetic events in great details in both time and in space. Here we describe a microscopy approach to examine different cytokinetic events in live cells. With this approach it is possible to time different cytokinetic events and determine the time of recruitment of different proteins during cytokinesis. In addition, we describe protocols to compare protein localization, and distribution at the site of cell division. This is a basic protocol to study cytokinesis in fission yeast and can also be used for other yeasts and fungal systems.

Fission yeast cells expressing the ring marker, Rlc1-GFP (green, Figure 2) and spindle pole body marker Sad1-mCherry (red, Figure 2) were imaged during cytokinesis. Onset of spindle pole body marker (white arrow, Figures 2A, B) is considered as time 0. Rlc1-GFP signal appears at time -4 min with reference to spindle pole body separation (red arrow, Figures 2A, 2B). Rlc1-GFP signal forms a continuous ring 10 min post spindle pole body sepa...

Watch this Scientific Journal Video about Spatiotemporal Analysis of Cytokinetic Events in Fission Yeast at JoVE.com

Spatiotemporal Analysis of Cytokinetic Events in Fission Yeast

The fission yeast, Schizosaccharomyces pombe&#160;is an excellent model system to study cytokinesis, the final stage in cell division. Here we describe a microscopy approach to analyze different cytokinetic events in live fission yeast cells.

Cytokinesis, the final step in cell division is critical for maintaining genome integrity. Proper cytokinesis is important for cell differentiation and ...

The overall goal of this live cell microscopy technique is to study to the spatiotemporal events that occur during cytokinesis in the fission yeast model system. This method can help answer key questions in the cytokinetic field such as the molecular details of the different stages of cytokinesis over time. The main advantage of this technique is that different spatial components of the cytokinetic machinery can be analyzed over long periods of time with minimal toxicity to the cells.Though this method can provide insight into cytokinesis and fission yeast, it can also be applied to budding yeast and other fungi. To begin this procedure, pour three to four milliliters of melted media laced with Vitamin C onto a glass-bottomed culture dish. Once the media has solidified, use a sharp scalpel to gently raise the media slab from the culture dish, and place a pipette tip between the media slab and the culture dish to prevent the slab from falling back into the dish.Next load two to five microliters of re-suspended cell culture between the media slab and the glass bottom of the culture dish. Then very gently remove the pipette tip and place the media slab back in its original position on the culture dish. Incubate the cells in the culture dish for 30 minutes to an hour in the dark at the temperature the microscopy will be performed.When the cells are ready for imaging, place a drop of wild on the outer side of the glass on the culture dish. Place the culture dish on an inverted microscope. Focus on the medial plane of the cells, and ensure that they are well-spaced and not too crowded.Make sure to start image acquisition of the cells in a suitable stage of the cell cycle. In this experiment, it is late G2.Next, program the image acquisition software. Set the exposure time for DIC to 100 milliseconds.For GFP and RFP filters, use exposure times of 75 milliseconds. Set the laser power to 50%but note that this will vary depending upon the individual experiment. To capture images in three dimensions, program the software to acquire Z series.Use of a maximum step size of 4 micrometers and a distance of 3.0 micrometers around the central focus point of the cells for the capture of 16 Z frames per time point for the total Z distance of 6 micrometers. These parameters can be altered in accordance with the thickness of the cell. Set the program to take images every two minutes.Select the exposure time based on the requirements of the experiment. In this example, 75 milliseconds is used. Program the software to stop acquisition after 90 minutes.And then start the image acquisition. ImageJ software is used to analyze the image. To begin, open the image series for each of the wavelengths.Select a cell to be studied. Double click on the line option of the toolbar to open another window to adjust the line width. Adjust the line width to correspond to the cell width which is about 40 to 50 pixels for a wild type cell.Draw a line along the long axis of the cell of interest. Click on analyze then tools then ROI manager and then click on add. This will add the selected line to the ROI window for later use.Do not close this window. Click on the image of interest then select edit, then selection, then straighten. Check process entire stack to straighten the cell horizontally.Click on image then transform then rotate 90 degrees right to straighten the image vertically. Click on image then stacks then make montage. This will open a window for assigning the number of rows and columns for the stack, the scale factor for the image size, the first and last slice or frame for the montage, and the frame increment for the montage.Check label slices and hit enter. As a window with a montage of the cell of interest is shown, open the image series for the other wavelength. In the ROI manager, click on the line identifier to select the same cell on the second image file.Repeat the previous steps to open a montage of the second image. On the image with the spindle pole body marker, Sad1-mCherry, look for the separation of the spindle pole body marker, and mark that time point as time zero. Follow the signal of the ring protein Rlc1-tomato on the image over time, and look for the signal that appears as a distinct line as opposed to the patches of Rlc1-tomato.This time point marks completion of actomyosin ring assembly or the start of the maturation phase. Next scroll through the movie over time to determine when the Rlc1-tomato ring starts to decrease in size. This is marked as the end of maturation phase or onset of ring constriction.Follow the Rlc1-tomato signal over time throughout constriction until it appears as a dot in the middle of the cell axis. This is marked as the end of ring constriction or end of septum ingression. Following the montage of DIC images, determine when abscission is completed.Record the time point when the cells physically separate. Begin this analysis by selecting a cell with a visible actomyosin ring. Double click on the line option of the ImageJ toolbar.Adjust the line width to correspond to the ring thickness about 15 to 20 pixels. Draw a line along the ring, taking care to ensure the entire thickness of the ring is included. Click on analyze, then tools, then ROI Manager, and click on add.This will add the select line to the ROI window for later use. Do not close this window. Click on the image of interest and select edit, then selection, then straighten.Check process entire stack to straighten the ring horizontally. Reset the intensity of the brightest plane in the straighten Z stack using image, then adjust, then brightness and contrast, then reset. Click on the tab SGK then 3D project to open a dialogue box.Change the projection method to brightest point and slice spacing to two to three pixels. Finally, change the axis of rotation to X or Y-axis depending upon the desired viewing angle. Click interpolate and click OK to generate a 3D projection of the image.Use the scroll bar beneath the image to rotate the image. Next, open the image series for the other wavelength. Click on the line identifier in the ROI manager to select the same ring on the second image file.Repeat the previous steps to open a 3D ring in the image with the other wavelength. With both 3D image rings open, click on image, then color, then merge channels. Select each image from the dropdown menu for the corresponding color desired and click OK.Compare the localization of different markers with regards to the localization at the cytokinetic ring or ingressing membrane.Fission yeast cells expressed in the spindle pole body marker, Sad1-mCherry and ring marker Rlc1-GFP were imaged during cytokinesis. Spindle pole body separation occurred at 17 minutes, designated as time zero. Rlc1-GFP appears at the division site four minutes before spindle pole body separation.After spindle pole body separation, ring maturation starts at ten minutes. Ring constriction begins at 31 minutes, and ends at 53 minutes. Finally, cell abscission occurs at 80 minutes after spindle pole body separation.The timeline of cytokinetic events determined in the previous images can be plotted in a graph with reference to mitosis as determined by the distance between the spindle pole body markers. Analysis of the ring marker Rlc1-tomato and the septum membrane marker Bgs1-GFP at the division site throughout cytokinesis reveal that the ring assembled before Bgs1-GFP recruitment. As the ring constricts, Bgs1-GFP also localizes to the ingressing membrane adjacent to the constricting ring.Finally, Rlc1-tomato signal dissipates after ring constriction while Bgs1-GFP appears as a disk, remaining within the membrane barrier. The efficiency of cytokinetic events can be determined by the distribution of proteins along the ring. Here Cdc15-GFP distribution along the ring is even on the left image but uneven on the right image.Once mastered, this technique can be done in two to three hours if performed properly. While attempting this procedure, it's important to remember to choose cells with an appropriate field, ideally containing six to eight well-spaced cells in late G2 or early M phase, with no visible impurities in the agar. After watching this video, you should have a good understanding of how to spatiotemporally analyze protein localization during cytokinesis.

spatiotemporal-analysis-of-cytokinetic-events-in-fission-yeast

Research

JoVE Journal

Biology

Measuring Replicative Life Span in the Budding Yeast

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The budding yeast Saccharomyces cerevisiae has been used extensively to study the biology of aging, and several determinants of yeast longevity have been shown to be conserved in multicellular eukaryotes, including worms, flies, and mice 1. Due to the lack of easily quantified age-associated phenotypes, aging in yeast has been assayed almost exclusively by measuring the life span of cells in different contexts, with two different life span paradigms in common usage 2. Chronological life span refers to the length of time that a mother cell can survive in a non-dividing, quiescence-like state, and is proposed to serve as a model for aging of post-mitotic cells in multicellular eukaryotes. Replicative life span, in contrast, refers the number of daughter cells produced by a mother cell prior to senescence, and is thought to provide a model of aging in mitotically active cells. Here we present a generalized protocol for measuring the replicative life span of budding yeast mother cells. The goal of the replicative life span assay is to determine how many times each mother cell buds. The mother and daughter cells can be easily differentiated by an experienced researcher using a standard light microscope (total magnification 160X), such as the Zeiss Axioscope 40 or another comparable model. Physical separation of daughter cells from mother cells is achieved using a manual micromanipulator equipped with a fiber-optic needle. Typical laboratory yeast strains produce 20-30 daughter cells per mother and one life span experiment requires 2-3 weeks.

In this article we present a general protocol for measuring the replicative life span of yeast mother cells.

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The budding ...

Analysis of the Development of a Morphological Phenotype as a Function of Protein Concentration in Budding Yeast

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of phenotype development as a function of protein concentration at population and single-cell levels in Saccharomyces cerevisiae. Although this protocol is based on the overexpression of a protein, it can easily be adapted for morphological phenotypes dependent on suppression of protein expression. Our lab is interested in studying the signaling properties of the endocytic adaptor protein epsin. To that purpose we used a dominant negative approach in which we over-expressed the conserved Epsin N-Terminal Homology (ENTH) domain in order to interfere with the functions of endogenous epsin-2 (Ent2 or YLR206W). We observed that overexpression of the ENTH domain of Ent2 (ENTH2) in wild type cells led to a cell division defect that is dependent on the mislocalization of a family of scaffolding proteins, septins.

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of phenotype development as a function of protein concentration at population and single-cell levels in Saccharomyces cerevisiae.

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of ...

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 ...

Live Cell Imaging of Early Autophagy Events: Omegasomes and Beyond

Autophagy is a cellular response triggered by the lack of nutrients, especially the absence of amino acids. Autophagy is defined by the formation of double membrane structures, called autophagosomes, that sequester cytoplasm, long-lived proteins and protein aggregates, defective organelles, and even viruses or bacteria. Autophagosomes eventually fuse with lysosomes leading to bulk degradation of their content, with the produced nutrients being recycled back to the cytoplasm. Therefore, autophagy is crucial for cell homeostasis, and dysregulation of autophagy can lead to disease, most notably neurodegeneration, ageing and cancer.	
	Autophagosome formation is a very elaborate process, for which cells have allocated a specific group of proteins, called the core autophagy machinery. The core autophagy machinery is functionally complemented by additional proteins involved in diverse cellular processes, e.g. in membrane trafficking, in mitochondrial and lysosomal biology. Coordination of these proteins for the formation and degradation of autophagosomes constitutes the highly dynamic and sophisticated response of autophagy. Live cell imaging allows one to follow the molecular contribution of each autophagy-related protein down to the level of a single autophagosome formation event and in real time, therefore this technique offers a high temporal and spatial resolution.	
	Here we use a cell line stably expressing GFP-DFCP1, to establish a spatial and temporal context for our analysis. DFCP1 marks omegasomes, which are precursor structures leading to autophagosomes formation. A protein of interest (POI) can be marked with either a red or cyan fluorescent tag. Different organelles, like the ER, mitochondria and lysosomes, are all involved in different steps of autophagosome formation, and can be marked using a specific tracker dye. Time-lapse microscopy of autophagy in this experimental set up, allows information to be extracted about the fourth dimension, i.e. time. Hence we can follow the contribution of the POI to autophagy in space and time.

Time-lapse microscopy of fluorescently labeled autophagy markers allows monitoring of the dynamic autophagy response with high temporal resolution. Using specific autophagy and organelle markers in a combination of 3 different colors, we can follow the contribution of a protein to autophagosome formation in a robust spatial and temporal context.

Autophagy is a  cellular response triggered by the lack of nutrients, especially the absence of  amino acids. Autophagy is defined by the formation of ...

Spatiotemporal Mapping of Motility in Ex Vivo Preparations of the Intestines

Multiple approaches have been used to record and evaluate gastrointestinal motility including: recording changes in muscle tension, intraluminal pressure, and membrane potential. All of these approaches depend on measurement of activity at one or multiple locations along the gut simultaneously which are then interpreted to provide a sense of overall motility patterns. Recently, the development of video recording and spatiotemporal mapping (STmap) techniques have made it possible to observe and analyze complex patterns in ex vivo whole segments of colon and intestine. Once recorded and digitized, video records can be converted to STmaps in which the luminal diameter is converted to grayscale or color [called diameter maps (Dmaps)]. STmaps can provide data on motility direction (i.e., stationary, peristaltic, antiperistaltic), velocity, duration, frequency and strength of contractile motility patterns. Advantages of this approach include: analysis of interaction or simultaneous development of different motility patterns in different regions of the same segment, visualization of motility pattern changes over time, and analysis of how activity in one region influences activity in another region. Video recordings can be replayed with different timescales and analysis parameters so that separate STmaps and motility patterns can be analyzed in more detail. This protocol specifically details the effects of intraluminal fluid distension and intraluminal stimuli that affect motility generation. The use of luminal receptor agonists and antagonists provides mechanistic information on how specific patterns are initiated and how one pattern can be converted into another pattern. The technique is limited by the ability to only measure motility that causes changes in luminal diameter, without providing data on intraluminal pressure changes or muscle tension, and by the generation of artifacts based upon experimental setup; although, analysis methods can account for these issues. When compared to previous techniques the video recording and STmap approach provides a more comprehensive understanding of gastrointestinal motility.

Spatiotemporal Mapping of Motility in Ex Vivo Preparations of the Intestines

Recently available video recording and spatiotemporal mapping (STmap) techniques make it possible to visualize and quantify both propagating and mixing patterns of intestinal motility. The goal of this protocol is to explain the generation and analysis of STmaps using the GastroIntestinal Motility Monitoring (GIMM) system.

Multiple approaches have been used to record and evaluate gastrointestinal motility including: recording changes in muscle tension, intraluminal pressure, ...

Microscopy of Fission Yeast Sexual Lifecycle

The fission yeast Schizosaccharomyces pombe has been an invaluable model system in studying the regulation of the mitotic cell cycle progression, the mechanics of cell division and cell polarity. Furthermore, classical experiments on its sexual reproduction have yielded results pivotal to current understanding of DNA recombination and meiosis. More recent analysis of fission yeast mating has raised interesting questions on extrinsic stimuli response mechanisms, polarized cell growth and cell-cell fusion. To study these topics in detail we have developed a simple protocol for microscopy of the entire sexual lifecycle. The method described here is easily adjusted to study specific mating stages. Briefly, after being grown to exponential phase in a nitrogen-rich medium, cell cultures are shifted to a nitrogen-deprived medium for periods of time suited to the stage of the sexual lifecycle that will be explored. Cells are then mounted on custom, easily built agarose pad chambers for imaging. This approach allows cells to be monitored from the onset of mating to the final formation of spores.

We provide a reproducible basic method for the long-term microscopy of the fission yeast sexual lifecycle. With minor adjustments described, the presented protocol allows research focus on different steps of the reproductive process.

The fission yeast Schizosaccharomyces pombe has been an invaluable model system in studying the regulation of the mitotic cell cycle progression, the ...

Applications of pHluorin for Quantitative, Kinetic and High-throughput Analysis of Endocytosis in Budding Yeast

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal remodeling and vesicular trafficking in living cells. Quantitative methodologies using chimeric GFP fusions have been developed for many applications; however, GFP is somewhat resistant to proteolysis, thus its fluorescence persists in the lysosome/vacuole, which can impede quantification of cargo trafficking in the endocytic pathway. An alternative method for quantifying endocytosis and post-endocytic trafficking events makes use of superecliptic pHluorin, a pH-sensitive variant of GFP that is quenched in acidic environments. Chimeric fusion of pHluorin to the cytoplasmic tail of transmembrane cargo proteins results in a dampening of fluorescence upon incorporation of the cargo into multivesicular bodies (MVBs) and delivery to the lysosome/vacuole lumen. Thus, quenching of vacuolar fluorescence facilitates quantification of endocytosis and early events in the endocytic pathway. This paper describes methods using pHluorin-tagged cargos for quantification of endocytosis via fluorescence microscopy, as well as population-based assays using flow cytometry.

Accurate quantification of vesicular trafficking events often provides key insights into roles for specific proteins and the effects of mutations. This paper presents methods for using superecliptic pHluorin, a pH-sensitive GFP variant, as a tool for quantification of endocytic events in living cells using quantitative fluorescence microscopy and flow cytometry.

Green fluorescent protein (GFP) and its variants are widely used tools for studying protein localization and dynamics of events such as cytoskeletal ...

High-resolution Imaging and Analysis of Individual Astral Microtubule Dynamics in Budding Yeast

Dynamic microtubules are fundamental to many cellular processes, and accurate measurements of microtubule dynamics can provide insight into how cells regulate these processes and how genetic mutations impact regulation. The quantification of microtubule dynamics in metazoan models has a number of associated challenges, including a high microtubule density and limitations on genetic manipulations. In contrast, the budding yeast model offers advantages that overcome these challenges. This protocol describes a method to measure the dynamics of single microtubules in living yeast cells. Cells expressing fluorescently tagged tubulin are adhered to assembled slide chambers, allowing for stable time-lapse image acquisition. A detailed guide for high-speed, four-dimensional image acquisition is also provided, as well as a protocol for quantifying the properties of dynamic microtubules in confocal image stacks. This method, combined with conventional yeast genetics, provides an approach that is uniquely suited for quantitatively assessing the effects of microtubule regulators or mutations that alter the activity of tubulin subunits.

Budding yeast is an advantageous model for studying microtubule dynamics in vivo due to its powerful genetics and the simplicity of its microtubule cytoskeleton. The following protocol describes how to transform and culture yeast cells, acquire confocal microscopy images, and quantitatively analyze microtubule dynamics in living yeast cells.

Dynamic microtubules are fundamental to many cellular processes, and accurate measurements of microtubule dynamics can provide insight into how cells ...

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

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 not interfere with cell physiology, and requires minimal experimental handling. The low levels of technical interference enable researchers to study cells across multiple cycles of mitosis and to observe meiosis from beginning to end. Using fluorescent tags such as Green Fluorescent Protein (GFP) and Red Fluorescent Protein (RFP), researchers can analyze different factors whose functions are important for processes like transcription, DNA replication, cohesion, and segregation. Coupled with data analysis using Fiji (a free, optimized ImageJ version), live-cell imaging offers various ways of assessing protein movement, localization, stability, and timing, as well as nuclear dynamics and chromosome segregation. However, as is the case with other microscopy methods, live-cell imaging is limited by the intrinsic properties of light, which put a limit to the resolution power at high magnifications, and is also sensitive to photobleaching or phototoxicity at high wavelength frequencies. However, with some care, investigators can bypass these physical limitations by carefully choosing the right conditions, strains, and fluorescent markers to allow for the appropriate visualization of mitotic and meiotic events.

Here, we present live-cell imaging which is a non-toxic microscopy method that allows researchers to study protein behavior and nuclear dynamics in living fission yeast cells during mitosis and meiosis.

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 ...

Quantifying Spatiotemporal Parameters of Cellular Exocytosis in Micropatterned Cells

Live imaging of the pHluorin tagged Soluble N-ethylmaleimide-sensitive-factor Attachment protein REceptor (v-SNARE) Vesicle-associated membrane protein 7 (VAMP7) by total internal reflection fluorescence microscopy (TIRFM) is a straightforward way to explore secretion from the lysosomal compartment. Taking advantage of cell culture on micropatterned surfaces to normalize cell shape, a variety of statistical tools were employed to perform a spatial analysis of secretory patterns. Using Ripley&#8217;s K function and a statistical test based on the nearest neighbor distance (NND), we confirmed that secretion from lysosomes is not a random process but shows significant clustering. Of note, our analysis revealed that exocytosis events are also clustered in nonadhesion areas, indicating that adhesion molecules are not the only structures that can induce secretory hot spots at the plasma membrane. Still, we found that cell adhesion enhances clustering. In addition to precisely defined adhesive and nonadhesive areas, the circular geometry of these micropatterns allows the use of polar coordinates, simplifying analyses. We used Kernel Density Estimation (KDE) and the cumulative distribution function on polar coordinates of exocytosis events to identify enriched areas of exocytosis. In ring-shaped micropattern cells, clustering occurred at the border between the adhesive and nonadhesive areas. Our analysis illustrates how statistical tools can be employed to investigate spatial distributions of diverse biological processes.

Live imaging of lysosomal exocytosis on micropatterned cells allows a spatial quantification of this process. Morphology normalization using micropatterns is an outstanding tool to uncover general rules about the spatial distribution of cellular processes.

Live imaging of the pHluorin tagged Soluble N-ethylmaleimide-sensitive-factor Attachment protein REceptor (v-SNARE) Vesicle-associated membrane protein 7 ...