This work was supported by a grant to M.K and B.K.K. from the Ellison Medical Foundation. M. K. is an Ellison Medical Foundation New Scholar in Aging. We would like to thank Soumya Kotireddy for assistance during filming.

Part 1: Prepare strains and plates for replicative life span analysis
This section describes the preparation of the solid YEPD plates for use in the replicative life span experiment and the preparation of yeast cells for life span analysis.
<ol>
	<li>Using appropriate sterile technique, prepare YEPD agar plates (1% yeast extract, 2% bacto-peptone, 2% agar, 2% glucose) that will be used for culturing yeast cells and for replicative life span analysis. You should prepare at least 2 plates for every 4-5 strains to be analyzed in the life span experiment. Plates should be prepared at least 2 days before the life span experiment and allowed to dry before beginning the life span assay. If the experiment will not be initiated within 4-5 days of pouring the plates, they should be placed in a refrigerated incubator and wrapped in parafilm or plastic to prevent dessication.</li>
	<li>Remove yeast strains from frozen stocks and streak for single colonies onto YEPD agar plates. Up to 6 strains can easily be streaked on the same YEPD plate by partitioning the plate into equally sized pie-shaped wedges.</li>
	<li>Incubate the cells at 30&#176;C for 2 days.</li>
	<li>Remove cells from the incubator and patch cells from a single colony onto a fresh YEPD plate. Two patches from two different colonies should be generated for each strain. At this time, the strains to be analyzed should be coded to ensure the replicative life span experiment is performed &#34;blind&#34;, where the dissectors do not know the identity of individual strains.</li>
	<li>Incubate the patched, coded cells at 30&#176;C until the following evening.</li>
	<li>Remove the cells and lightly patch cells from each coded strain to fresh YEPD plates, which will serve as the experimental plates used for the replicative life span analysis. Cells should be patched along a vertical line on the left side of the YEPD plate (Figure 1). Approximately 3-5 patches per plate is optimal, assuming replicative life span analysis on 20 cells from each patch. It is not necessary (nor desirable) to transfer a large number of cells to the fresh YEPD plate, as this will cause the cells to grow thickly during the overnight incubation, which may limit their subsequent replicative life span.</li>
	<li>Incubate the freshly patched plates overnight on the bench top.</li>
</ol>
Part 2: Position cells for replicative life span analysis.
In this section we describe how to position the yeast cells on the plate and how to obtain virgin daughter cells for replicative life span analysis. From this point on, all plates should be parafilmed, except when undergoing dissection, in order to prevent dessication.
<ol>
	<li>Using a microscope equipped with a microdissection apparatus suitable for yeast, transfer approximately 50 cells from the first patched strain to a position on the plate distal to the patched cells . If your microscope stage is graded, these gradations can be used to ensure the cells will be easy to find during subsequent iterations. On the Zeiss Axioscope 40, cells from the first patched strain can be placed at coordinates 90 x 10 and arrayed vertically from there.</li>
	<li>Clean the needle of cells by repeatedly touching the agar surface, then create a hole in the agar by forcing the needle through the agar surface. This hole will serve as a marker to orient you on the plate during subsequent iterations of dissection and daughter cell removal. Be careful not to get yeast cells in the hole, or they will grow and form a colony.</li>
	<li>Directly above the hole, vertically align individual yeast cells into 20 evenly spaced positions, with 1-3 needle diameters (~100 &#956;M) between each cell position (Figure 1). Every few cells, place two cells adjacent to each other in the same position in the line rather than one. This allows for redundancy during virgin daughter cell selection, if one of the transferred cells fails to divide.</li>
	<li>Between the 10th and 11th positions in the line, create a horizontal series of 7-8 holes in the agar. This will serve as a marker to orient you on the plate during subsequent iterations of dissection and daughter cell removal. Be careful not to get yeast cells in the holes, or they will grow and form a colony.</li>
	<li>Repeat steps 2.1-2.4 for each patch on the plate, continuing to array cells vertically along the same axis. For step 2.2, the number of holes created should correspond to the patch number (one hole for the first patch, two holes for the second, etc.).</li>
	<li>Once cells have been arrayed for each patch, parafilm the plate and incubate at 30&#176;C for approximately 2 hours.</li>
	<li>Repeat steps 2.1-2.6 for each plate in the experiment.</li>
</ol>
Part 3: Obtain virgin daughter cells for life span analysis
In this section we initiate the life span analysis by ensuring that each cell starts as a virgin daughter cell.
<ol>
	<li>Remove the plates from the incubator and verify that most of the arrayed cells have undergone a cell division. If additional time is needed to allow cell division to be completed, return the plate to the incubator.</li>
	<li>Beginning with the first arrayed cell, use the needle to detach daughter cells from the mother cell by gently placing the needle on top of the attached cells. It is sometimes helpful to tap the side of the microscope base while the needle is resting on the cells.</li>
	<li>Place the detached daughter cell in the vertical line, replacing the mother cell and any additional daughter cells and moving them temporarily aside.</li>
	<li>Repeat step 3.2 and 3.3 for each of the arrayed cells. If a cell fails to divide, take a daughter cell from one of the redundant cells positioned in step 2.3. When finished, you should have 20 daughter cells for each patch aligned vertically on the life span plate.</li>
	<li>Collect all of the mother cells and extra daughter cells into a pile and transfer them back to an area near the patches (&#34;the graveyard&#34;). It is important to keep unwanted cells far from the cells undergoing life span analysis to prevent formation of microcolonies and depletion of local nutrients.</li>
	<li>Parafilm the plate and incubate at 30&#176;C for approximately 2 hours.</li>
	<li>Repeat steps 3.2-3.6 for each plate in the experiment.</li>
</ol>
Part 4: Measuring the replicative capacity of individual cells
<ol>
	<li>Prepare the life span data sheets. A life span data sheet can be a simple grid where each row corresponds to an individual mother cell and each column corresponds to an age-point (Figure 2). Label each data sheet according to the number of strains to be analyzed.</li>
	<li>Remove the plates from the incubator and verify that most of the arrayed cells have undergone at least one cell division. If additional time is needed to allow cell division to be completed, return the plate to the incubator.</li>
	<li>Beginning with the first arrayed cell on the first plate, visually observe the mother and daughter cell(s) and determine the number of cell divisions that have occurred. It is generally easy to determine how many daughter cells a mother has produced, based on characteristic patterns of cell arrangements. Record the number of daughter cells produced by the mother cell in the appropriate box on the life span score sheet.</li>
	<li>Use the needle to detach daughter cells from the mother cell as described in step 3.2.</li>
	<li>Retain the mother cell in its position in the vertical line and move the daughter cell(s) to temporarily aside.</li>
	<li>Repeat steps 4.3-4.5 for each of the arrayed cells.</li>
	<li>Collect all of the discarded daughter cells and move them to the &#39;graveyard&#39;, located near the original patches.</li>
	<li>Parafilm the plate and incubate at 30&#176;C for 2-3 hours.</li>
	<li>Repeat steps 4.3-4.8 for each plate in the experiment.</li>
	<li>Repeat steps 4.2-4.9 until all mother cells have stopped dividing. As the mother cells age, the cell cycle progression becomes slower and it will be desirable to incubate the plate for longer periods of time between age-points. Plates can be placed at 4&#176;C overnight.</li>
</ol>
Part 5: Representative Results.
The raw data produced by a replicative life span experiment is a list numbers corresponding to daughter cells produced by each mother cell at each age-point (Figure 2). By summing each row of the score sheet, the replicative life span for each mother cell is obtained. Data for mother cells from the same experimental group can be pooled to generate a survival curve (Figure 3A) and to perform statistical calculations, such as mean life span, median life span, and standard deviation. A non-parametric test, such as the Wilcoxon Rank-Sum test, can be performed to determine whether significant differences in life span were detected between experimental groups. When the experiment works correctly, the survival curve should be roughly consistent with Gompertz-Makeham kinetics showing a sigmoidal shap with low early mortality followed a relatively rapid decline in survival and a flattening out of the curve a later ages. Most wild-type strains have replicative life span values in the 20-30 generation range, although variation outside of this range has been reported.
<img alt="figure 1" src="/files/ftp_upload/1209/1209fig1.jpg" /> 
<img alt="Figure 1.5" src="/files/ftp_upload/1209/fig1.2.jpg" /> 
Figure 1. Diagram of a typical replicative life span plate. The evening before beginning microdissection of yeast cells, 3-5 strains are lightly patched onto the surface of a YEPD plate (red boxes) in a vertical line along one side of the plate. Following growth overnight, approximately 30 individual cells from each strain are arrayed vertically into a line containing 20 positions. Life span analysis will be performed on v virgin daughter cells obtained from these initial cells. Extra cells obtained from microdissection during the experiment (e.g. unwanted daughter cells) are placed in &#34;the graveyard&#34; (gray oval), which is located far away from the experimental cells in order to avoid local depletion of nutrients as colonies are formed.
<img alt="figure 2" src="/files/ftp_upload/1209/1209fig2.jpg" /> 
Figure 2. A replicative life span tally sheet. Raw data from a replicative life span experiment is shown. Each row corresponds to a single yeast mother cell and each column corresponds to an age-point. The number entered in each box is the number of daughter cells produced by that mother cell at that age-point. Each strain is labeled with a coded number such that the individual dissecting the yeast cells has no knowledge of the identity of the strains being analyzed. Twenty cells are assayed for each strain.
<img alt="figure 3" src="/files/ftp_upload/1209/1209fig3.jpg" /> 
Figure 3. Representative survival and growth curves from a replicative life span experiment. (A) Survival curves are obtained by plotting the fraction of mother cells still alive as a function of replicative age (number of cell divisions. (B) Growth curves are obtained by plotting the average number of daughter cells produced by a given strain as a function of age-point. In this example, strain #2 is longer-lived but is slower growing, as evidenced by the reduced initial slope of the growth plot.

<ol>
	<li>Kaeberlein, M., Burtner, C. R., Kennedy, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+developments+in+yeast+aging.">Recent developments in yeast aging.</a> PLoS Genet. 3, (2007).</li><li>Kaeberlein, M., Conn, P. 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> Handbook of models for human aging. , 109-120 (2006).</li><li>Smith, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+evidence+for+conserved+longevity+pathways+between+divergent+eukaryotic+species.">Quantitative evidence for conserved longevity pathways between divergent eukaryotic species.</a> Genome Res. 18, 564-570 (2008).</li><li>Steinkraus, K. A., Kaeberlein, M., Kennedy, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replicative+aging+in+yeast:+the+means+to+the+end.">Replicative aging in yeast: the means to the end.</a> Annu Rev Cell Dev Biol. 24, 29-54 (2008).</li><li>Murakami, C. J., Burtner, C. R., Kennedy, B. K., Kaeberlein, 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+method+for+high-throughput+quantitative+analysis+of+yeast+chronological+life+span.">A method for high-throughput quantitative analysis of yeast chronological life span.</a> J Gerontol A Biol Sci Med Sci. 63, 113-121 (2008).</li><li>Jiang, J. C., Jaruga, E., Repnevskaya, M. V., Jazwinski, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+intervention+resembling+caloric+restriction+prolongs+life+span+and+retards+aging+in+yeast.">An intervention resembling caloric restriction prolongs life span and retards aging in yeast.</a> Faseb J. 14, 2135-2137 (2000).</li><li>Kaeberlein, M., Kirkland, K. T., Fields, S., Kennedy, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sir2-independent+life+span+extension+by+calorie+restriction+in+yeast.">Sir2-independent life span extension by calorie restriction in yeast.</a> PLoS Biol. 2, E296-E296 (2004).</li><li>Lin, S. J., Defossez, P. A., Guarente, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Requirement+of+NAD+and+SIR2+for+life-span+extension+by+calorie+restriction+in+Saccharomyces+cerevisiae.">Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae.</a> Science. 289, 2126-2128 (2000).</li><li>Kaeberlein, M., Kennedy, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+identification+in+yeast+of+conserved+ageing+genes.">Large-scale identification in yeast of conserved ageing genes.</a> Mech Ageing Dev. 126, 17-21 (2005).</li><li>Kaeberlein, M. <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+yeast+replicative+life+span+by+TOR+and+Sch9+in+response+to+nutrients.">Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients.</a> Science. 310, 1193-1196 (2005).</li></ol>

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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.

Watch this Scientific Journal Video about Measuring Replicative Life Span in the Budding Yeast at JoVE.com

Measuring Replicative Life Span in the Budding Yeast

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 ...

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20.5K Views.  University of Washington. In this article we present a general protocol for measuring the replicative life span of yeast mother cells.

Video: Measuring Replicative Life Span in the Budding Yeast

Measuring Caenorhabditis elegans Life Span on Solid Media

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The nematode Caenorhabditis elegans has emerged as a principal model used to study the biology of aging. Because virtually every biological subsystem undergoes functional decline with increasing age, life span is the primary endpoint of interest when considering total rate of aging. In nematodes, life span is typically defined as the number of days an animal remains responsive to external stimuli. Nematodes can be propagated either in liquid media or on solid media in plates, and techniques have been developed for measuring life span under both conditions. Here we present a generalized protocol for measuring life span of nematodes maintained on solid nematode growth media and fed a diet of UV-killed bacteria. These procedures can easily be adapted to assay life span under various common conditions, including a diet consisting of live bacteria, dietary restriction, and RNA interference.

Measuring Caenorhabditis elegans Life Span on Solid Media

In this article we present a general protocol for measuring life span of nematodes maintained on solid media with UV-killed bacterial food.

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

Quantifying Yeast Chronological Life Span by Outgrowth of Aged Cells

The budding yeast Saccharomyces cerevisiae has proven to be an important model organism in the field of aging research 1. The replicative and chronological life spans are two established paradigms used to study aging in yeast. Replicative aging is defined as the number of daughter cells a single yeast mother cell produces before senescence; chronological aging is defined by the length of time cells can survive in a non-dividing, quiescence-like state 2. We have developed a high-throughput method for quantitative measurement of chronological life span. This method involves aging the cells in a defined medium under agitation and at constant temperature. At each age-point, a sub-population of cells is removed from the aging culture and inoculated into rich growth medium. A high-resolution growth curve is then obtained for this sub-population of aged cells using a Bioscreen C MBR machine. An algorithm is then applied to determine the relative proportion of viable cells in each sub-population based on the growth kinetics at each age-point. This method requires substantially less time and resources compared to other chronological lifespan assays while maintaining reproducibility and precision. The high-throughput nature of this assay should allow for large-scale genetic and chemical screens to identify novel longevity modifiers for further testing in more complex organisms.

Chronological aging in yeast refers to the loss of cell viability associated with time in stationary phase. Here we describe a high-throughput method for quantitatively determining yeast chronological life span.

The budding yeast Saccharomyces cerevisiae has proven to be an important model organism in the field of aging research 1. The replicative and ...

Purification of the M. magneticum Strain AMB-1 Magnetosome Associated Protein MamA&Delta;41

Magnetotactic bacteria comprise a diverse group of aquatic microorganisms that are able to orientate themselves along geomagnetic fields. This behavior is believed to aid their search for suitable environments (1). This capability is conferred by the magnetosome, a subcellular organelle that consists of a linear-chain assembly of lipid vesicles each able to biomineralize and enclose a ~50-nm crystal of magnetite or greigite. A principle component of the magnetosome that was shown to be required for the formation of functional vesicles is MamA. MamA is a highly abundant magnetosome-associated protein which is one of the most characterized magnetosome-associated proteins in vivo (2-6). This article focuses on the purification of MamA, which despite being studied in vivo, no clear functional or structural details have been identified for it. Bioinformatics analysis suggested that MamA is a tetra-tricopeptide repeat (TPR) containing protein. TPR is a structural motif found as such or forming part of a bigger fold in a wide range of proteins, it serves as a template for protein-protein interactions and mediates multi-protein complexes (7). TPRs are involved in many crucial tasks in eukaryotic cell organelle processes and many bacterial pathways (8-14). In order to understand MamA, a unique TPR containing protein, highly purified protein is required as a first step. In this article, we present the purification protocol for a stable MamA deletion mutant (MamA&Delta;41) from M. magneticum AMB-1.

Purification of the &lt;em&gt;M. magneticum&lt;/em&gt; Strain AMB-1 Magnetosome Associated Protein MamA&amp;Delta;41

MamA is a unique Magnetosome associated protein which was shown to be involved in magnetosome activation. Here we present the purification protocol of MamA deletion mutant (MamA&Delta;41) from M. magneticum AMB-1.

Magnetotactic bacteria comprise a diverse group of aquatic microorganisms that are able to orientate themselves along geomagnetic fields. This behavior is ...

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 ...

Measuring Caenorhabditis elegans Life Span in 96 Well Microtiter Plates

Lifespan is a biological process regulated by several genetic pathways. One strategy to investigate the biology of aging is to study animals that harbor mutations in components of age-regulatory pathways. If these mutations perturb the function of the age-regulatory pathway and therefore alter the lifespan of the entire organism, they provide important mechanistic insights1-3.
Another strategy to investigate the regulation of lifespan is to use small molecules to perturb age-regulatory pathways. To date, a number of molecules are known to extend lifespan in various model organisms and are used as tools to study the biology of aging4-16. The number of molecules identified thus far is small compared to the genetic "toolset" that is available to study the biology of aging.
Caenorhabditis elegans is one of the principle models used to study aging because of its excellent genetics and short lifespan of three weeks. More recently, C.elegans has emerged as a model organism for phenotype based drug screens5,7,16-20 because of its small size and its ability to grow in microtiter plates.
Here we present an assay to measure C.elegans lifespan in 96 well microtiter plates. The assay was developed and successfully used to screen large libraries for molecules that extend C.elegans lifespan7. The reliability of the assay was evaluated in multiple tests: first, by measuring the lifespan of wild type animals grown at different temperatures; second, by measuring the lifespan of mutants with altered lifespans; third, by measuring changes in lifespan in response to different concentrations of the antidepressant Mirtazepine. Mirtazepine has previously been shown to extend lifespan in C.elegans7. The results of these tests show that the assay is able to replicate previous findings from other assays and is quantitative. The microtiter format also makes this lifespan assay compatible with automated liquid handling systems and allows integration into automated platforms.

Measuring Caenorhabditis elegans Life Span in 96 Well Microtiter Plates

In this protocol we present a method to measure Caenorhabditis elegans lifespan in 96 well microtiter plates.

Lifespan is a biological process regulated by several genetic pathways. One strategy to investigate the biology of aging is to study animals that harbor ...

Measuring the Kinetics of mRNA Transcription in Single Living Cells

The transcriptional activity of RNA polymerase II (Pol II) is a dynamic process and therefore measuring the kinetics of the transcriptional process in vivo is of importance. Pol II kinetics have been measured using biochemical or molecular methods.1-3 In recent years, with the development of new visualization methods, it has become possible to follow transcription as it occurs in real time in single living cells.4 Herein we describe how to perform analysis of Pol II elongation kinetics on a specific gene in living cells.5, 6 Using a cell line in which a specific gene locus (DNA), its mRNA product, and the final protein product can be fluorescently labeled and visualized in vivo, it is possible to detect the actual transcription of mRNAs on the gene of interest.7, 8 The mRNA is fluorescently tagged using the MS2 system for tagging mRNAs in vivo, where the 3'UTR of the mRNA transcripts contain 24 MS2 stem-loop repeats, which provide highly specific binding sites for the YFP-MS2 coat protein that labels the mRNA as it is transcribed.9 To monitor the kinetics of transcription we use the Fluorescence Recovery After Photobleaching (FRAP) method. By photobleaching the YFP-MS2-tagged nascent transcripts at the site of transcription and then following the recovery of this signal over time, we obtain the synthesis rate of the newly made mRNAs.5 In other words, YFP-MS2 fluorescence recovery reflects the generation of new MS2 stem-loops in the nascent transcripts and their binding by fluorescent free YFP-MS2 molecules entering from the surrounding nucleoplasm. The FRAP recovery curves are then analyzed using mathematical mechanistic models formalized by a series of differential equations, in order to retrieve the kinetic time parameters of transcription.

RNA polymerase II transcriptional kinetics are measured on specific genes in living cells. mRNAs transcribed from the gene of interest are fluorescently tagged and using Fluorescence Recovery After Photobleaching (FRAP) the in vivo kinetics of transcriptional elongation are obtained.

The transcriptional activity of RNA polymerase II (Pol II) is a dynamic process and therefore measuring the kinetics of the transcriptional process in ...

Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS

Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challenges to obtaining and analyzing fluorescence movies of single cells. We describe here a simple protocol using a commercially available microfluidic culture device to generate such data, and a MATLAB-based, graphical user interface (GUI) -based software package to quantify the fluorescence images. The software segments and tracks cells, enables the user to visually curate errors in the data, and automatically assigns lineage and division times. The GUI further analyzes the time series to produce whole cell traces as well as their first and second time derivatives. While the software was designed for S. cerevisiae, its modularity and versatility should allow it to serve as a platform for studying other cell types with few modifications.

We present a simple protocol to obtain fluorescence microscopy movies of growing yeast cells, and a GUI-based software package to extract single-cell time series data. The analysis includes automated lineage and division time assignment integrated with visual inspection and manual curation of tracked data.

Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies ...

Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously hard to disrupt. Here we describe the use of a bead mill homogenizer for the extraction of proteins into buffers optimized to maintain the functions, interactions and post-translational modifications of proteins. Logarithmically growing cells expressing the protein of interest are grown in a liquid growth media of choice. The growth media may be supplemented with reagents to induce protein expression from inducible promoters (e.g. galactose), synchronize cell cycle stage (e.g. nocodazole), or inhibit proteasome function (e.g. MG132). Cells are then pelleted and resuspended in a suitable buffer containing protease and/or phosphatase inhibitors and are either processed immediately or frozen in liquid nitrogen for later use. Homogenization is accomplished by six cycles of 20 sec&#160;bead-beating (5.5 m/sec), each followed by one minute incubation on ice. The resulting homogenate is cleared by centrifugation and small particulates can be removed by filtration. The resulting cleared whole cell extract (WCE) is precipitated using 20% TCA for direct analysis of total proteins by SDS-PAGE followed by Western blotting. Extracts are also suitable for affinity purification of specific proteins, the detection of post-translational modifications, or the analysis of co-purifying proteins. As is the case for most protein purification protocols, some enzymes and proteins may require unique conditions or buffer compositions for their purification and others may be unstable or insoluble under the conditions stated. In the latter case, the protocol presented may provide a useful starting point to empirically determine the best bead-beating strategy for protein extraction and purification. We show the extraction and purification of an epitope-tagged SUMO E3 ligase, Siz1, a cell cycle regulated protein that becomes both sumoylated and phosphorylated, as well as a SUMO-targeted ubiquitin ligase subunit, Slx5.

The preparation of high quality yeast cell extracts is a necessary first step in the analysis of individual proteins or entire proteomes. Here we describe a fast, efficient, and reliable homogenization protocol for budding yeast cells that has been optimized to preserve protein functions, interactions, and post-translational modifications.

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously ...

Measuring the Osmotic Water Permeability Coefficient (Pf) of Spherical Cells: Isolated Plant Protoplasts as an Example

Studying AQP regulation mechanisms is crucial for the understanding of water relations at both the cellular and the whole plant levels. Presented here is a simple and very efficient method for the determination of the osmotic water permeability coefficient (Pf) in plant protoplasts, applicable in principle also to other spherical cells such as frog oocytes. The first step of the assay is the isolation of protoplasts from the plant tissue of interest by enzymatic digestion into a chamber with an appropriate isotonic solution. The second step consists of an osmotic challenge assay: protoplasts immobilized on the bottom of the chamber are submitted to a constant perfusion starting with an isotonic solution and followed by a hypotonic solution. The cell swelling is video recorded. In the third step, the images are processed offline to yield volume changes, and the time course of the volume changes is correlated with the time course of the change in osmolarity of the chamber perfusion medium, using a curve fitting procedure written in Matlab (the &#8216;PfFit&#8217;), to yield Pf.

Measuring the Osmotic Water Permeability Coefficient Pf of Spherical Cells: Isolated Plant Protoplasts as an Example

Measuring the osmotic water permeability coefficient (Pf) of cells can help understand the regulatory mechanisms of aquaporins (AQPs). Pf determination in spherical plant cell protoplasts presented here involves protoplasts isolation and numerical analysis of their initial rate of volume change as a result of an osmotic challenge during constant bath perfusion.

Studying AQP regulation mechanisms is crucial for the understanding of water relations at both the cellular and the whole plant levels. Presented here is ...

Protein Purification Technique that Allows Detection of Sumoylation and Ubiquitination of Budding Yeast Kinetochore Proteins Ndc10 and Ndc80

Post-translational Modifications (PTMs), such as phosphorylation, methylation, acetylation, ubiquitination, and sumoylation, regulate the cellular function of many proteins. PTMs of kinetochore proteins that associate with centromeric DNA mediate faithful chromosome segregation to maintain genome stability. Biochemical approaches such as mass spectrometry and western blot analysis are most commonly used for identification of PTMs. Here, a protein purification method is described that allows the detection of both sumoylation and ubiquitination of the kinetochore proteins, Ndc10 and Ndc80, in Saccharomyces cerevisiae. A strain that expresses polyhistidine-Flag-tagged Smt3 (HF-Smt3) and Myc-tagged Ndc10 or Ndc80 was constructed and used for our studies. For detection of sumoylation, we devised a protocol to affinity purify His-tagged sumoylated proteins by using nickel beads and used western blot analysis with anti-Myc antibody to detect sumoylated Ndc10 and Ndc80. For detection of ubiquitination, we devised a protocol for immunoprecipitation of Myc-tagged proteins and used western blot analysis with anti-Ub antibody to show that Ndc10 and Ndc80 are ubiquitinated. Our results show that epitope tagged-protein of interest in the His-Flag tagged Smt3 strain facilitates the detection of multiple PTMs. Future studies should allow exploitation of this technique to identify and characterize protein interactions that are dependent on a specific PTM.

This manuscript describes the detection of sumoylation and ubiquitination of kinetochore proteins, Ndc10 and Ndc80, in the budding yeast Saccharomyces cerevisiae.