This work was supported by NIH grant GM50936 to DKB.

NOTE: Some steps of the protocol below require working in a clean fume hood. In addition, the method requires a yeast tetrad dissection microscope equipped with a 10X long working distance objective to monitor spheroplasting. The microscope should be set up in the hood ahead of time. Remove the micromanipulator arm and plate holder from the scope and place these items in a safe place away from the work area.
1. Preparation of Spheroplasts
<ol>
	<li>Grow yeast under desired conditions. Use about 2 x 108 cells for each sample, e.g. 4 ml of a culture at OD600 1.4 = 5 x 107 cells/ml. Although immediate processing of samples may be preferable in some cases, for most applications, cell aliquots can be stored on ice for up to 8 hours before being processed.</li>
	<li>Transfer cell suspension to a 15 ml centrifuge tube and spin in a clinical centrifuge at setting 5 (2345 rpm/857.5 x g) for 3 min to pellet the cells.</li>
	<li>Decant the medium taking care not to lose cells from the pellet. Gently resuspend the cells in 1 ml ZK buffer and then add 40 &#181;l 1 M dithiothreitol (DTT). Incubate 2 min with gentle mixing. Pellet cells as before (see step 1.2).</li>
	<li>Resuspend pellets in 1 ml ZK buffer. Add 5 &#181;l of a freshly prepared solution of zymolyase 100T that has been thoroughly mixed. Incubate for 20-30 min at 30 &#176;C to remove the cell wall and produce spheroplasts.</li>
	<li>Assay a 10 &#181;l droplet of cell suspension on a microscope slide to determine if spheroplasting is complete. Cells viewed under the dissection microscope without a coverslip. Cells should appear bloated and round rather than slightly oblong and should lyse following addition of 20 &#181;l of water. If cells fail to lyse, return the sample to 30 &#176;C and re-assay every 10 min until water induced lysis is readily observed. Pellet cells as before (see step 1.2).</li>
	<li>Gently resuspend and wash cell pellet in 2.5 ml cold MES/sorbitol buffer. Pellet cells as before (see step 1.2). Gently resuspend cell pellet in 300-400 &#181;l cold MES/sorbitol buffer. Cells can be kept on ice at this stage for several hours.</li>
</ol>
2. Chromosome Spreading &#160;
NOTE: The glass surfaces upon which chromosomes will be spread&#8212;either slides or coverslips&#8212;should be prepared ahead of time. Each slide or coverslip should be submerged in water, then EtOH, then allowed to dry, and polished with lens paper. If chromosomes will be spread on coverslips, the coverslip should be affixed to a slide with Scotch tape or rubber cement.&#160; Unless otherwise mentioned, the rest of the protocol will describe spreading on either a slide or coverslip
<ol>
	<li>Using a P20 pipettor, pipet 20 &#181;l of cell suspension onto the surface of a clean slide.</li>
	<li>Using a P200 pipettor, add 40 &#181;l of the 3% PFA/sucrose solution and gently mix the solution by &#8220;swirling&#8221; the slide with the hand until Schlieren lines disappear. Place slide under microscope and confirm that cells are in focus. The PFA solution should be freshly-prepared in the fume hood on the day of use. &#160; 
	NOTE: If the protein of interest has not been examined by the method previously, it is advisable to prepare additional slides using solutions that contain 2 and 4% PFA to determine if retention of the protein is sensitive to fixation conditions. A 4% PFA/sucrose solution is used in cases where it is desirable to visualize associated tubulin microtubules. The disadvantage of the higher fixative concentration is that the chromosomes will be &#8220;underspread,&#8221; 2%PFA also tends to yield &#8220;underspread&#8221; chromosomes.</li>
	<li>Using a P200 pipettor, add 80 &#181;l of 1% Lipsol, swirl as before to mix solutions as completely as possible, start a timer. If Lipsol is not available, 80 &#181;l 1% NP40 or 80 &#181;l dH2O may be substituted (see Representative Results, Figure 2).</li>
	<li>Watch the cells carefully and gently swirl the slide every 15 sec. When roughly 80% of cells have lysed (disappeared) stop the timer, immediately remove the slide from the microscope, add 80 &#181;l of PFA/sucrose solution, and swirl to mix. Lysis should occur from between 30 and 90 sec after starting the timer. &#160; 
	NOTE: If several slides show lysis at about the same time, one can eventually omit microscopic monitoring for the remainder of the slides and simply carefully time the period between addition of lipsol and addition of the final aliquot of fixative. However, this short cut is only reliable when preparing multiple slides from the same sample. It is best to monitor lysis of each sample microscopically when different slides are prepared from samples taken at different times or from different cultures.</li>
	<li>Place the slide on a clean flat surface and spread the liquid across the entire unfrosted surface of the slide using the side of a clean, disposable Pasture pipet held below the meniscus of the &#8220;puddle&#8221; but above the surface of the slide itself, i.e. do not &#8220;rake&#8221; the surface of the slide with the pipet. Do not reuse pipet on different slides to avoid contamination of samples.</li>
	<li>Leave the slides to dry overnight in the fume hood. Insoluble nuclear components will settle onto the slide surface and bind to it. For large experiments, planning the use of space for the drying step is important.</li>
	<li>Once dried, optimal results are obtained by progressing to the immunostaining stage on the same day. However, the dried sucrose solution embeds the spread chromosomes in a &#8220;honey&#8221; that allows freezing of samples: slides can be transferred to a plastic slide box and stored at -20 &#176;C for years.</li>
</ol>
3. Immunostaining
<ol>
	<li>Dip slides in 0.2% Photo-Flo for 30 sec. to remove honey. Lean slides on an edge, with the edge resting on a paper towel, to remove residual Photo-Flo.</li>
	<li>Dip slides in 1x TBS for 5 min to wash. Remove excess liquid by leaning slides on an edge, but do not let them dry out.</li>
	<li>Lay slides frosted side up, pipet 300 &#181;l TBS/BSA onto the slide across the unfrosted portion of the slide.</li>
	<li>Incubate in a moist chamber at RT for 15 min. (large plastic container lined with water saturated paper towels under a perforated metal plate or plastic slide box with saturated paper towels).</li>
	<li>Drain slides by resting a short edge of the slide on a paper towel and leaning the slide against an appropriate support (such as a test tube rack). Do not allow surface to dry.</li>
	<li>Immediately apply 80 &#181;l of TBS/BSA buffer containing the appropriate dilution of primary antibody. If antibody is limiting, use 40 &#181;l and a 22 x 22 mm coverslip. For crude rabbit serum, this is typically between a 1/50 and 1/500 dilution. &#160; 
	NOTE: Perform titrations for new antibody preparations. The most dilute preparation that yields high signal above background is chosen. To control for the level of background staining, nuclei should be prepared from the appropriate deletion mutant strain and/or duplicate slides should be stained with pre-immune serum.</li>
	<li>Place a polished 22 x 50 mm coverslip on the slide avoiding bubbles. Do this by holding the coverslip between the thumb and index finger along the long edge at positions near one short edge. Holding the coverslip at a 30&#176; angle relative to slide, the short edge farthest from the fingers is lowered until it rests on the slide just inside the edge of the &#8220;puddle&#8221; closest to the frosted region of the slide. Then slowly lower the coverslip in a smooth motion until the fingers holding the slide touch the bench, and then release. Do not attempt to adjust the position of the coverslip once it lands. &#160; 
	NOTE: If chromosome spreads were prepared on affixed coverslips (rather than directly on the surface of slides), this sample coverslip will remain affixed to the slide throughout the staining and washing steps. An additional coverslip will be placed on top of the sample coverslip to evenly distribute the antibody solution during staining and then discarded.</li>
	<li>Place slides in a sealed moist chamber and incubate overnight at 4 &#176;C.</li>
	<li>Holding the frosted edge transfer the slides to a glass slide staining rack and submerge in a staining jar containing TBS.</li>
	<li>Gently dip the slide up and down to remove the coverslip. Try not to use too much force to do this. Wash the slides 2x 10 min by submerging in TBS. Remove slides from rack and drain excess liquid by touching edge to paper towel. Do not let surface dry.</li>
	<li>Working under subdued light, immediately add 80 &#181;l TBS/BSA containing a 1/1,000 fold dilution of fluorochrome conjugated secondary antibody (or 40 &#181;l with a 22 x 22 mm coverslip). Add coverslip as before and incubate at 4 &#176;C for 2 hr in the moist chamber in the dark.</li>
	<li>Remove coverslips as before, drain slides, and allow surface to air dry for 1 to 2 hr in the dark. Lean slides on paper towels as before. &#160; 
	NOTE: If spreading was performed on a mounted coverslip, detach the coverslip from the slide before drying. Coverslips are then dried as described for slides in the previous step.</li>
	<li>Working under subdued light, add about 30 &#181;l of mounting medium containing DAPI (three 10 &#181;l droplets) and then carefully lower a coverslip. If the spreads are on coverslips, place the droplets of mounting medium on a clean slide and lower the coverslip, chromosome side down, onto the slide.</li>
	<li>Still under subdued light, wait 2 min for coverslip to settle and seal edges of coverslip with clear nail polish. Place slides in a flat slide box. &#160; 
	NOTE: For STED microscopy, mount with ProLong Gold. Use 30 &#181;l of ProLong Gold without DAPI and allow to cure overnight. Sealing with nail polish is unnecessary.</li>
	<li>View slides by widefield epifluorescence microscopy with a 40 or 100X objective using a filter set appropriate for DAPI to focus. Optionally store the slide in the dark at 4 &#176;C for several weeks. Do not freeze.</li>
</ol>

<ol>
	<li>Loidl, J., Nairz, K., Klein, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Meiotic+chromosome+synapsis+in+a+haploid+yeast.">Meiotic chromosome synapsis in a haploid yeast.</a> Chromosoma. 100 (4), 221-228 (1991).</li><li>Loidl, J., Klein, F., Engebrecht, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+and+morphological+approaches+for+the+analysis+of+meiotic+chromosomes+in+yeast.">Genetic and morphological approaches for the analysis of meiotic chromosomes in yeast.</a> Methods in cell biology. 53, 257-285 (1998).</li><li>Lydall, D., Nikolsky, Y., Bishop, D. K., Weinert, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+meiotic+recombination+checkpoint+controlled+by+mitotic+checkpoint+genes.">A meiotic recombination checkpoint controlled by mitotic checkpoint genes.</a> Nature. 383 (6603), 840-843 (1996).</li><li>Bishop, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RecA+homologs+Dmc1+and+Rad51+interact+to+form+multiple+nuclear+complexes+prior+to+meiotic+chromosome+synapsis.">RecA homologs Dmc1 and Rad51 interact to form multiple nuclear complexes prior to meiotic chromosome synapsis.</a> Cell. 79, 1081-1092 (1994).</li><li>Rabitsch, K. P., Galova, M., Schleiffer, A., Buonomo, S. B., Nasmyth, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+genomics+identifies+Monopolin:+a+kinetochore+protein+required+for+segregation+of+homologs+during+meiosis+I.">Functional genomics identifies Monopolin: a kinetochore protein required for segregation of homologs during meiosis I.</a> Cell. 103 (7), 1155-1168 (2000).</li><li>Gasior, S. L., Olivares, H., Ear, U., Hari, D. M., Weichselbaum, R., Bishop, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assembly+of+RecA-like+recombinases:+Distinct+roles+for+mediator+proteins+in+mitosis+and+meiosis.">Assembly of RecA-like recombinases: Distinct roles for mediator proteins in mitosis and meiosis.</a> PNAS. 98 (15), 8411-8418 (2001).</li><li>Biggins, S., Murray, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+budding+yeast+protein+kinase+Ipl1/Aurora+allows+the+absence+of+tension+to+activate+the+spindle+checkpoint.">The budding yeast protein kinase Ipl1/Aurora allows the absence of tension to activate the spindle checkpoint.</a> Genes &amp; Development. 15 (23), 3118-3129 (2001).</li><li>Dresser, M. E., Giroux, C. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Meiotic+chromosome+behavior+in+spread+preparations+of+yeast.">Meiotic chromosome behavior in spread preparations of yeast.</a> The Journal of Cell Biology. , (1988).</li><li>Lao, J. P., Cloud, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Meiotic+crossover+control+by+concerted+action+of+Rad51-Dmc1+in+homolog+template+bias+and+robust+homeostatic+regulation.">Meiotic crossover control by concerted action of Rad51-Dmc1 in homolog template bias and robust homeostatic regulation.</a> PLOS Genetics. 9 (12), e1003978-e1003978 (2013).</li><li>Vonesch, C., Unser, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+fast+thresholded+landweber+algorithm+for+wavelet-regularized+multidimensional+deconvolution.+IEEE+transactions+on+image+processing+:+a+publication+of+the.">A fast thresholded landweber algorithm for wavelet-regularized multidimensional deconvolution. IEEE transactions on image processing : a publication of the.</a> IEEE Signal Processing Society. 17 (4), 539-549 (2008).</li></ol>

The authors declare no competing financial interests.

The appearance of spread nuclei critically depends upon the balance between fixation and lysis/detergent treatment. As discussed above, the preservation of varying cellular structures requires the use of different PFA concentrations. For most proteins, 3% PFA is optimal. However, preservation of spindles requires use of 4% PFA. Even with a single set of reagents, the timing of lysis relative to fixation can also affect the quality of spread nuclei. For the most consistent results, the time of lysis should be normalize...

The budding yeast Saccharomyces cerevisiae offers many advantages for studies of molecular mechanisms of biological processes, including the study of proteins that control chromosome function. Although there are well-known advantages of budding yeast for genetic, molecular, and biochemical studies, cytological studies of the distribution of proteins in the cell&#8217;s nucleus is complicated by its small size. The typical yeast nucleus has a diameter of less than one micron, which is only about 5 times the resolution limit of visible light. Thus, the amount of information about the distribution of nuclear proteins that can be obtained from conventional immunostaining or by using fluorescent protein tags, such as green fluorescent protein (GFP), is limited. A useful approach to characterizing the subnuclear distribution of proteins is chromosome surface spreading. This approach involves removing the cell wall, disrupting cell and nuclear membranes, and allowing the insoluble contents of the nucleus to settle onto the surface of a microscope slide. These insoluble components include the nuclear matrix and the chromosomes. In addition to allowing removal of soluble nuclear contents, which enhances the ability to detect chromatin bound proteins, the chromosome spreading method results in substantial decompression of chromosomes such that the spread nuclei have diameters of around 3 to 5 &#181;m (for diploid meiotic nuclei) and 2 to 3 &#181;m for diploid mitotic nuclei. This decompression allows detection of nuclear substructure that is relatively difficult or impossible to resolve in intact nuclei.
An obvious shortcoming to chromosome spreading is the possibility that the spreading procedure may partially or completely disrupt the structure of interest. Of particular concern is that a particular chromosome bound protein might be lost as a consequence of the spreading procedure. This potential complication should be kept in mind when interpreting data. One example of a protein that is sensitive to the spreading procedure is beta-tubulin. Under some conditions, the spindle, which is comprised mainly of tubulin, is preserved during spreading3. Visualization of the spindle is often useful to stage nuclei of interest. However, visualizing tubulin requires treatment with a high concentration fixative; spindles are lost under the standard conditions described below. This example illustrates that, when analyzing the distribution of a previously uncharacterized protein, it is important to vary the concentration of fixative to determine how sensitive the protein is to such variation. In spite of the concern regarding the impact of the spreading conditions on chromosome structure, the utility and power of the spreading method has been demonstrated in many contexts and has broad utility in characterization of mitotic and, especially meiotic cells4-7.
Two spreading methods have been used extensively. The first of these methods, developed by Dresser and Giroux8, avoids the use of detergent and can yield spread preparations that appear to have relatively well-preserved chromosome morphology when stained for the DNA-specific dye DAPI. However, this method is relatively difficult to perfect and the quality of the spread nuclei varies dramatically, when one region of a slide is compared to other regions. This problem can complicate quantitative approaches that involve imaging many unselected nuclei from one slide to avoid data acquisition bias. The second chromosome spreading method, developed by Loidl and Klein1, involves balancing fixation by paraformaldehyde, with lysis and chromatin decompression promoted by a detergent solution. When properly performed, this method gives very reproducible results with less region-to-region variation compared to the Dresser and Giroux method. This presentation focuses on a modified version of the method of Loidl and Klein, because of its reliability and simplicity.
Chromosome spreading is not complicated or time-consuming; up to 100 slides can be prepared for immunostaining in a single day. Furthermore, the spread preparations may be stored in the freezer for years prior to immunostaining, and thus labs can develop a repository of frozen chromosome spreads that can be used when new biological questions arise or new staining reagents become available.
The chromosome spreading method is most commonly used in combination with immunostaining and widefield fluorescence microscopy, but it is also possible to prepare slides for super-resolution light microscopic methods such as stimulated emission depletion (STED) microscopy.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Zymolyase</td>
			<td>US Biological&#160;</td>
			<td>Z1004</td>
			<td>Prepare 20 mg/mL solution in 50 mM Tris pH 7.5 supplemented with 2% glucose. Prepare fresh each experiment and store at 4&#176;C until ready for use.</td>
		</tr>
		<tr>
			<td>Lipsol&#160;</td>
			<td>L.I.P. Ltd&#160;</td>
			<td>no longer commercially available</td>
			<td>Prepare 1% (v/v) solution in water. Store on ice.</td>
		</tr>
		<tr>
			<td>NP-40</td>
			<td>USB</td>
			<td>19628</td>
			<td>Prepare 1% (v/v) solution in water. Store on ice.</td>
		</tr>
		<tr>
			<td>Tween 20</td>
			<td>Sigma</td>
			<td>P2287</td>
			<td></td>
		</tr>
		<tr>
			<td>Slides</td>
			<td>Corning</td>
			<td>2948-75x25</td>
			<td></td>
		</tr>
		<tr>
			<td>Standard coverslip</td>
			<td>Fisher</td>
			<td>12-544-E or 12-540-B</td>
			<td></td>
		</tr>
		<tr>
			<td>High resolution coverslips</td>
			<td>Fisher</td>
			<td>12-542-B</td>
			<td></td>
		</tr>
		<tr>
			<td>Photo-Flo 200 solution</td>
			<td>Kodak</td>
			<td>P-7417</td>
			<td>Prepare 0.2% (v/v) solution in water.&#160;</td>
		</tr>
		<tr>
			<td>TBS</td>
			<td></td>
			<td></td>
			<td>137 mM NaCl, 2.7 mM KCl, 24.7 mM Tris, pH 8</td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Sigma</td>
			<td>A2153</td>
			<td>Prepare a 1% (w/v) solution in TBS. Store at 4&#176;C for up to a month.</td>
		</tr>
		<tr>
			<td>Primary antibody</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa Fluor 488 Donkey Anti-Rabbit</td>
			<td>Invitrogen</td>
			<td>A-21206</td>
			<td></td>
		</tr>
		<tr>
			<td>IgG (H+L) Antibody</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Vectashield mounting media with DAPI</td>
			<td>Vector 
			Laboratories</td>
			<td>H-1200</td>
			<td></td>
		</tr>
		<tr>
			<td>ProLong Gold</td>
			<td>Invitrogen</td>
			<td>P36930</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic slide box</td>
			<td>Fisher</td>
			<td>03-448-1</td>
			<td>Store slides containing dried spreads in slots at -20&#176;C. Also, use as a wet chamber.</td>
		</tr>
		<tr>
			<td>Cardboard slide box</td>
			<td>Fisher</td>
			<td>12-587-10</td>
			<td>Use to conveniently transport stained/sealed slides or store at 4&#176;C.</td>
		</tr>
		<tr>
			<td>Coplin jar</td>
			<td>Fisher</td>
			<td>08-816</td>
			<td>Use as a wash basin for slides.&#160;</td>
		</tr>
	</tbody>
</table>

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.

The appearance of spread nuclei critically depends upon the balance between chromosome fixation and de-compaction. Even when the reagents are properly balanced, variation in the degree of chromosome de-compaction can occur in different regions of the same slide and/or between different slides. Thus, the quality of spreads in a given region of a slide should be assessed before images are interpreted.
The effects of &#8220;overspreading&#8221; and &#8220;underspreading&#8221; can be illustrated ...

Watch this Scientific Journal Video about Surface Spreading and Immunostaining of Yeast Chromosomes at JoVE.com

Surface Spreading and Immunostaining of Yeast Chromosomes

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 ...

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9.9K Views.  University of Chicago. 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.

Video: Surface Spreading and Immunostaining of Yeast Chromosomes

PDMS Device Fabrication and Surface Modification

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 ...

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.  ...

Immunostaining of Dissected Zebrafish Embryonic Heart

Zebrafish embryo becomes a popular in vivo vertebrate model for studying cardiac development and human heart diseases due to its advantageous embryology and genetics 1,2. About 100-200 embryos are readily available every week from a single pair of adult fish. The transparent embryos that develop ex utero make them ideal for assessing cardiac defects 3. The expression of any gene can be manipulated via morpholino technology or RNA injection 4. Moreover, forward genetic screens have already generated a list of mutants that affect different perspectives of cardiogenesis 5. 
Whole mount immunostaining is an important technique in this animal model to reveal the expression pattern of the targeted protein to a particular tissue 6. However, high resolution images that can reveal cellular or subcellular structures have been difficult, mainly due to the physical location of the heart and the poor penetration of the antibodies. 
 Here, we present a method to address these bottlenecks by dissecting heart first and then conducting the staining process on the surface of a microscope slide. To prevent the loss of small heart samples and to facilitate solution handling, we restricted the heart samples within a circle on the surface of the microscope slides drawn by an immEdge pen. After the staining, the fluorescence signals can be directly observed by a compound microscope. 
Our new method significantly improves the penetration for antibodies, since a heart from an embryonic fish only consists of few cell layers. High quality images from intact hearts can be obtained within a much reduced procession time for zebrafish embryos aged from day 2 to day 6. Our method can be potentially extended to stain other organs dissected from either zebrafish or other small animals.

A rapid way to conduct immunostaining of zebrafish embryonic heart is described. Compared to the whole mount immunostaining approach, this method dramatically increases the penetration of the antibodies, which allows obtaining high resolution images that reveal cellular/subcellular structures in the heart within a much reduced processing time.

Zebrafish embryo becomes a popular in vivo vertebrate model for studying cardiac development and human heart diseases due to its advantageous embryology ...

Avidity-based Extracellular Interaction Screening (AVEXIS) for the Scalable Detection of Low-affinity Extracellular Receptor-Ligand Interactions

Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ensuring cohesion within multicellular organisms. Proteins predicted to form extracellular interactions are encoded by approximately a quarter of human genes1, but despite their importance and abundance, the majority of these proteins have no documented binding partner. Primarily, this is due to their biochemical intractability: membrane-embedded proteins are difficult to solubilise in their native conformation and contain structurally-important posttranslational modifications. Also, the interaction affinities between receptor proteins are often characterised by extremely low interaction strengths (half-lives &lt; 1 second) precluding their detection with many commonly-used high throughput methods2. 
Here, we describe an assay, AVEXIS (AVidity-based EXtracellular Interaction Screen) that overcomes these technical challenges enabling the detection of very weak protein interactions (t1/2 &le; 0.1 sec) with a low false positive rate3. The assay is usually implemented in a high throughput format to enable the systematic screening of many thousands of interactions in a convenient microtitre plate format (Fig. 1). It relies on the production of soluble recombinant protein libraries that contain the ectodomain fragments of cell surface receptors or secreted proteins within which to screen for interactions; therefore, this approach is suitable for type I, type II, GPI-linked cell surface receptors and secreted proteins but not for multipass membrane proteins such as ion channels or transporters.
The recombinant protein libraries are produced using a convenient and high-level mammalian expression system4, to ensure that important posttranslational modifications such as glycosylation and disulphide bonds are added. Expressed recombinant proteins are secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (&beta;-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA (Fig. 1). The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, we have shown that interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates3.

Avidity-based Extracellular Interaction Screening AVEXIS for the Scalable Detection of Low-affinity Extracellular Receptor-Ligand Interactions

AVEXIS is a high throughput protein interaction assay developed to systematically screen for novel extracellular receptor-ligand pairs involved in cellular recognition processes. It is specifically designed to detect transient protein interactions that are difficult to identify using other high throughput approaches.

Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ...

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform3,4. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies5. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented4,6.
Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations7,8.
Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila9, allows the user to visualize more details on chromosomes than the regular squashing technique10. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time11. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH12. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Genome assemblies based on massively parallel DNA sequencing technologies are usually highly fragmented. The development of physical chromosome maps can potentially improve genome assemblies. Here, we demonstrate innovative approaches to chromosome preparation, fluorescent in situ hybridization, and imaging that significantly increase throughput of the physical map development.

Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place ...

Dissection and Immunostaining of Imaginal Discs from Drosophila melanogaster

A significant portion of post-embryonic development in the fruit fly, Drosophila melanogaster, takes place within a set of sac-like structures called imaginal discs. These discs give rise to a high percentage of adult structures that are found within the adult fly. Here we describe a protocol that has been optimized to recover these discs and prepare them for analysis with antibodies, transcriptional reporters and protein traps. This procedure is best suited for thin tissues like imaginal discs, but can be easily modified for use with thicker tissues such as the larval brain and adult ovary. The written protocol and accompanying video will guide the reader/viewer through the dissection of third instar larvae, fixation of tissue, and treatment of imaginal discs with antibodies. The protocol can be used to dissect imaginal discs from younger first and second instar larvae as well. The advantage of this protocol is that it is relatively short and it has been optimized for the high quality preservation of the dissected tissue. Another advantage is that the fixation procedure that is employed works well with the overwhelming number of antibodies that recognize Drosophila proteins. In our experience, there is a very small number of sensitive antibodies that do not work well with this procedure. In these situations, the remedy appears to be to use an alternate fixation cocktail while continuing to follow the guidelines that we have set forth for the dissection steps and antibody incubations.

Dissection and Immunostaining of Imaginal Discs from Drosophila melanogaster

The adult structures of Drosophila are derived from sac-like structures called imaginal discs. Analysis of these discs provides insight into many developmental processes including tissue determination, compartment boundary establishment, cell proliferation, cell fate specification, and planar cell polarity. This protocol is used to prepare imaginal discs for light/fluorescent microscopy.

A significant portion of post-embryonic development in the fruit fly, Drosophila melanogaster, takes place within a set of sac-like structures called ...