antibody titrations / controls The missing sentence was: 'In addition a lot of antibodies also bind on other cells and the amount of active antibody in the bottle might vary. Therefore you should have approximately 10^3 fold excess.... Antigen concentration is indeed only of relevance with respect to depletion. Regarding the variations in the binding kinetics we have some applications where we want to stay below 5% variation. The higher the excess of antibody,the better. We use goat anti mouse*PE Fab2 at 12ug/ml and have to run at least for 30 minutes to saturate and to keep the day to day variations between the samples low. This might be due to a lower affinity or the polyclonal nature of the antibody. As most of our samples have a normal distribution of antigen load, we estimate the degree of saturation by the shape of the distribution in the fluorescence histogram. Gerhard Nebe-v.Caron, Unilever Research, Colworth, I just want to add my annual reminder that the concentration of antibody to use in a staining mixture is essentially independent of the number of cells being stained, but is completely dependent on the stain volume! 1 ug of antibody is more than enough for (in general) well over 10^8 cells expressing a typical antigen--thus, it doesn't matter if you have 10^5, 10^6, or 10^7 cells in your tube! Indeed, many antibodies will stain equally well at 10^8 cells (in, for instance, 100 ul volume). On the other hand, a reagent titred to be used in a 50ul stain volume may not stain very well in 500 ul. Specifically: 1 ug of antibody (IgG) is about 3.6 x 10^12 molecules--which (in divalent fashion) binds 7.2x10^12 molecules of antigen. A typical antigen may be present in concentrations of 10^4 to 10^5 per cell, meaning that 1 ug of antibody would be enough to stain 7.2 x 10^7 to 7.2 x 10^8 cells. And, if only 10% of the cells express an antigen, you can multiply this by another factor of 10! mario roederer, stanford Actually, isotype controls are not a particularly good control. They are rarely matched: the F/P ratio is not the same, and how do you know if you are using them at exactly the same concentration as the reagent of choice? If you don't know that the F/P ratio is exactly the same, and if you don't know if you are using it at exactly the same concentration as your antibody reagent, then it isn't the right control. Indeed, since each one of your commercial reagents is titrated by the manufacturer to give optimal signal to background, each one is sold at a different concentration of antibody. Have you contacted the manufacturers to determine the bottled concentration of each reagent you use, so that you can use the appropriate concentration of your isotype control? And then use a different isotype concentration as the control for each reagent in your various panels? If the answer to either of these questions is "no", then how can you assert that your isotype control actually gives you the correct amount of background binding in your experiment? i.e., your "isotype control" does no more than let you that there may actually be some background binding, but doesn't give you the ability to estimate how much. In fact, I've known people to "titrate" their isotype controls to get background binding that is less than what they think their positive should be. Hmm. In another way, isotype controls are rarely used properly: most people do a single sample that has all isotype controls in all channels. This doesn't help! One must use a control for which cells are stained with all reagents EXCEPT the one of interest (and if you insist on using an isotype control for that channel, so be it). We term these controls "FMO" or "Fluorescence Minus One" controls. (For more discussion of the need of FMO controls, see my paper on Compensation in the upcoming issue of Cytometry). Staining controls are very difficult to generate. In general, the best control for antibody binding is a cell that is exactly the same as your cell of interest, but lacking the antigen of interest. Of course, this is rarely achievable. However, one will often find very similar cells that meet the bill. In immunophenotyping of peripheral blood, you can use "nonexpressing" cell types as internal controls (i.e., naive T cells can serve as a control for measuring activation markers on memory T cells). Of course, you need to be careful, because some "nonexpressing" cells actually express the marker. Isotype controls have their place. However, most people don't use them properly. In general, I counsel people NOT to use isotype controls, but rather to use their brains to come up with a set of appropriate negative controls (which MUST be included in all experiments, as others have noted). Blind reliance on isotype controls is one of the most common mistakes in publications--and leads to the erroneous placement of gates. In any case, you are correct that investigators need to be educated more. This is one of the discussions that pops up every few years on the mailing list; perhaps it's time to have a FAQ's page (no pun intended!) on the Purdue site which includes the various discussion points, and rather than coming up with a conclusion, this page can simply serve to put forth various peoples' views so that researchers can judge for themselves whether or not isotype controls are useful. mr (PS, there is no such thing as "bad data", only "bad interpretation of data."). mario roederer, stanford Yes... much of what you say would be true... if the use of isotype controls were scientific. But, as has been endlessly discussed on this list, they are NOT. (See also: O'Gorman MRG, Thomas JA: Isotype Controls-Time to Let Go?; Cytometry 38:7880, 1999.) Proper science is to use a control (compared to a test sample) in which only a single variable has been changed. not), there are several more variables in your experiment. (1) The concentration of the isotype. If you have not matched the concentration of the isotype control to each of your antibodies (and each antibody, incidentally, is used at a different concentration, so you better be using isotypes at different concentrations for each antibody you are controlling), then the isotype control is no longer a control, but another test sample. (2) The Fluor:Protein ratio (F/P) of the isotype. If the F/P ratio is different than the test antibody (and how are you ever going to know this, unless you make both antibody and isotype control yourself?) then again, you have different In the case o variables. An isotype with a higher F/P than your test antibody, even if used at the same concentration, will give you higher "background" fluorescence. (3) Sequence-specific "nonspecific" binding. Of course the isotype has a different peptide sequence than the test antibody... are you really sure that none of these amino acid differences don't contribute to some selective binding? Until you prove that your isotype control has the same F/P ratio, and that you are using it at exactly the same concentrations as each of your test antibodies (that's a lot of isotype control stains!), then your "control" is no more than another test sample. That's the kind of scientific evidence you need to provide before you can use an isotype to determine positivity in your sample. Isotype staining certainly has its place. It can indicate IF there is an issue with background binding. It can let you know that perhaps you should be careful about interpreting your staining. And this is particularly true for myeloid cells that have high levels of FcR. But the problem is that most people go beyond this "canary in the cave" use for isotypes, and use the isotypes to set boundaries for gating and identification of positive vs. negative. And that is where the isotype ceases to be science. You are correct that we are not in the business of making things easy. And this is the insidious nature of isotype controls. They let people think that they are doing something "easily", when in fact they represent only a crutch that is being improperly used. They lull researchers into thinking that they can now identify positive vs. negative. It's so comforting to think that you have an appropriate control for your staining... whereas in fact it is much more difficult to properly control background staining. Finally, I want to address your statement: "...no scientific evidence..." When I hear of people who titrate their isotype control to give lower levels of background (to the same level as their positive antibody).... well, I don't need "scientific" evidence. Legally, this could be referred to as "prima facie" evidence of bad science. You don't need scientific evidence to prove an artefact you need scientific evidence to prove positive results. The statement that there's no evidence that the use of isotype controls has hampered any results is very much like the current "arguments" made by the religious conservatives in the US in favor of "intelligent design" (vs. evolution). There we go: experiments using isotype controls to define gating boundaries... are the "intelligent design" of experimental analyses mario roederer, stanford blocking I have not had any problems (background staining) with mouse MEFs so far. For routine Fc blocking when using mouse tissue samples, I incubate the cells with 2.4G2 (anti-Fc) for 20-30 minutes on ice. Usually, I do not even wash the cells after blocking (a quick spin for removing 2.4G2 supernatant). It works really well for me. Occasionally, in my liver MNC preparations, I do get background B cell staining in spite of 2.4G2 block. I have not got around this problem yet (other than using a negative B220 gate). I have not used the Fc block after the first blocking step. I block the cells first with the anti-Fc antibody, surface stain and directly fix and permeabilize my cells for intracellular staining. Hope this helps. Sriram Venkataraman Sriram, PhD The Walther Cancer Institute Indiana University School of Medicine Indianapolis, IN 46202 2. In our hands we use a routine staining buffer (PBS) that includes Fc block in all staining and washing steps. I use 2.5% total protein in the block, 1% BSA,1% FBS and .5% nmIg. It can be pricey if you use at the recommended concentrations we are used to so we grow it up with a hybridoma Ig spitting cell line from ATCC ; MOPC-31C for staining mouse lymphocytes at 500ug/ml. The Bible for my generation was and is Harlow and Lane, Antibodies-A Laboratory Manual, Cold Spring Harbor Press for all this kind of stuff.. cell cycle/subg1 etc -apoptosis Geert Martens wrote: >we have done a series of experiments with mitochondrial poisons (such as >rotenone) in rat pancreatic beta cells, and tried to determine mitochondrial membrane potential on a semi-quantitative basis with the dye JC-1 we believe our system works fine : CCCP 10 µM for 20 minutes decreases red >fluorescence en shifts all cells to green fluorescence, and we are able to produce classical JC-1 dot plots (FL2 vs FL1 ) were uncoupling shifts the cells from upper left quadrant (high red, low green) to lower right quadrant >(low red, high green fluorescence) however, we would like to know how to convert these dot plots in CORRECT >numerical data. in If a ratio of parameters is useful, the thing to do is get a value of the ratio for each cell and then plot the distribution of values of the ratio. It is often necessary to scale the ratio values so they fit on the same measurement scale as the original parameters. When taking a fluorescence ratio, you need to use linear values of the data points, not log values; to scale the values of the ratio, you must multiply the raw values by a constant. If your data are on a log scale, you can obtain the log of the ratio a/b by subtracting log b from log a; to scale this value, you add a constant rather than multiplying, because the log of a product is the sum of the logs of the multiplier and multiplicand. However, the arithmetic is only worth the effort if the two parameters used in the ratio are very well correlated with one another, i.e., if they form a "long, skinny cluster" which comes up in different regions of a 2-D measurement space (e.g., a dot plot) under different experimental circumstances. If the two parameters aren't well correlated, the distributions of the ratios won't discriminate much better between cells in different states than will the original parameter values. If the parameters are well correlated, you need to construct a calibration curve relating the scaled ratio values to what you are trying to quantify, in this case, mitochondrial membrane potential, meaning that you have to have some way of setting that to known values. A good illustration of this methodology, dealing with bacterial membrane potential measurement using DiOC2(3), appears in Novo D, Perlmutter NG, Hunt RH, Shapiro HM: Accurate flow cytometric membrane potential measurement in bacteria using diethyloxacarbocyanine and a ratiometric technique. Cytometry 35:55-63, 1999; the material is also presented on pp. 256 and 400-402 and on the back cover of the 4th Edition of Practical Flow Cytometry. Typical clusters representing JC-1 red vs. green fluorescence (presumably mitochondrial) under different experimental conditions are not nearly as well correlated as clusters representing green vs. red DiOC2(3) fluorescence in bacteria (in the 4th Edition, compare Figure 7-31, p. 399, and Figure 7-32, p.400). It thus seems doubtful to me that there is much reward to be gained from going to the trouble of calculating, scaling, and plotting fluorescence ratios. - Howard M Shapiro Histone H3 is phosphorylated at Ser-10 during mitosis and there is an antibody that specifically detects the phosphorylated epitope of histone H3 (e.g. provided by Sigma Chemical Co). In our hands this Ab was the most reliable marker of mitotic cells (identified from prophase to telophase) applicable to cytometry (Juan et al., Cytometry 32:71-77;1998). Phosphorylated histone H3 and other markers of mitotic cells are reviewed by Juan et al. (Methods to identify mitotic cells by flow cytometry. Meth Cell Biol, 63: 343-354, 2001) Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Jake Jacobberger is correct. Most likely the phenomenon reflects rapid diffusion of the dye and/or ions from the core sample stream to the sheath stream when they meet upstream in the flow channel. The diffusion leads to a decrease of dye concentration in the sample (core) stream which breaks the equilibrium between the dye and its binding sites in the cell. The changeable staining pattern is observed until new equilibrium establishes which takes some time of flow run. We observed this phenomenon using acridine orange, the dye that is extremely sensitive with respect to even minute change in its concentration or concentration of counterions such as sodium or divalent ions in the sample stream. The phenomenon is additionally exacerbated in instruments that have long sample lines such as old Ortho instruments and can be diminished by faster flow rate. We underscored this in our old papers describing the use of acridine orange (e.g. Darzynkiewicz, Z.: Simultaneous Analysis of Cellular RNA and DNA Content. In: Methods in Cell Biology, Flow Cytometry (2nd edition). Z. Darzynkiewicz, J.P. Robinson and H.A. Crissman (eds.), Academic Press, New York, N.Y. 1994, pp. 401-420, see pages 411-412.) I wish Merry Christmas, Happy Holidays, and the very best in the New Year to all FLOWERS, Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Hello Janet, Late apoptotic cells have many features similar to these of necrotic cells, the most apparent one is loss of plasma membrane integrity. Because they do not exclude 7-AAD, PI or DAPI the dye exclusion marker is not much help to distinguish them from necrotic cells. Microscopic examination is obviously the gold standard to distinguish apoptosis from necrosis so if you cytospin the cells from parallel sample that was measured and see only apoptotic cells then you may define that the cells in the far-left peak are indeed late apoptotic. If not, I would suggest that you use another marker, such as PARP cleavage or caspase-3 activation (each of them can be detected immunocytochemically) as a marker identifying apoptotic cells. Different strategies to distinguish apoptosis from necrosis are presented in our chapter: Darzynkiewicz Z, Bedner E, Traganos F. Difficulties and pitfalls in analysis of apoptosis. In: Methods in Cell Biology. Vol. 63, CYTOMETRY, 3rd Edition. Z.Darzynkiewicz, J.P.Robinson, and H.A.Crissman, Eds. Academic Press, San Diego, CA, 2001; 527-559 Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer The Chromatin Structure Assay is in reality analysis of susceptibility of DNA in situ to denaturation, induced by acid or heat. Extensive studies have been carried out using this assay to analyze chromatin of different cells in relation to the cycle phase, three decades ago. For example, when applied to lymphocytes this assay allows one to discriminate Go from G1 cells and G2 from mitotic cells, as well as distinguish other phases of the cell cycle. More recently this assay was mentioned, with other "historical" methods applicable to cell cycle, in the review article in Cytometry (Cytometry of the cell cycle. Cycling through history. Cytometry, 58A; 21-32, 2004). The original, earlier papers on this topic are: (1) Darzynkiewicz, Z., Traganos, F., Andreeff, M., Sharpless, T., Melamed, M.R.: Different sensitivity of chromatin to acid denaturation in quiescent and cycling cells as revealed by flow cytometry. J. Histochem. Cytochem., 27:478-485, 1979;. (2) Darzynkiewicz Z., Traganos, F., Sharpless, T., Melamed, M.R.: Cell cycle related changes in nuclear chromatin of stimulated lymphocytes as measured by flow cytometry. Cancer Res.. 37:46354640, 1977. The confocal analysis of DNA denaturation by this assay is described in: Dobrucki J.,Darzynkiewicz, Z. Chromatin condensation and sensitivity of DNA in situ to denaturation during cell cycle and apoptosis. A confocal microscopy study. Micron, 32: 645-652, 2001 . Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Dr. Salinas inquires about caspase-8 assay by flow cytometry. The most specific approach would be to use Ab that reacts with the activated form of caspase-8 but not with pro-caspase-8. Although large number of caspase-8 Ab are commercially available, I have not seen yet the published data showing the use of Ab to detect activation of caspase-8 by flow cytometry. Abs against activated caspase-3 and -9 are listed in some catalogues Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Fluorescent tagging of DNA can be accomplished by the photolabeling technique, utilizing photoactivated ethidium monoazide (e.g. Riedy et al., Cytometry, 12: 133, 1991). Zbigniew Darzynkiewicz The method to differentially identify DNA replicating and apoptotic cells is described by Li et al., in Experimental Cell Res. 222, 228-237,1996. In the first step the existing DNA strand breaks in apoptotic cells are labeled with fluorochrome of a particular color using exogenous terminal transferase (TUNEL). Subsequently, the cells are illuminated with UV light to pholytically induce DNA strand breaks at the sites of BrdU incorporation. These, in turn, are labeled with another color fluorochrome using the same principle of labeling (TUNEL). DNA can be then counterstained with still another color dye to obtain simultaneous differential staining of apoptotic- vs. BrdU incoroporating- cells, and discriminate G1 vs. S vs. G2+M cells in both, apoptotic and nonapoptotic populations Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer To the ongoing discussion about obtaining cells synchronized in the cycle I would like to add the following warning: The synchronization by transient cell arrest in the cycle induces growth imbalance and dramatically alters expression of cyclins and other cell cycle regulatory proteins. For example after double thymidine block we have observed "unscheduled" expression of cyclins B1 and A in cells at the G1/S boundary, over fivefold increase in expression of cyclin E, and 40% increased total protein content [Gong et al., Cell Growth & Differentiation, 6: (November issue) 1485-93, 1995]. Kinetic and metabolic properties of so synchronized cells are much different compared to the cells from asynchronous, exponentially growing cultures. Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer The problems and difficulties in analysis of apoptosis, particularly of adherent cells, we reviewed in Meth Cell Biol 63: 527-548,2001. Extensive trypsinization and repeated centrifugations may indeed affect Annexin V assay. In our hands the immunocytochemical detection of cleaved PARP (p89) (Exp. Cell Res., 257: 290-297, 200) or of activated caspase-3 (Cytometry, 55A, 50-60, 2003) appear to be both highly sensitive and specific markers for adherent cells. Also sensitive is detection of caspase activation by FLICA. One has to be concerned, however, that during apoptosis the cells detach themselves and float in the medium. Assessing apoptotic index in cultures of adherent cells, thus, to account for the floating apoptotic cells, one has to collect the medium, centrifuge it and pool the floating cells with the trypsinized cells. Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Cyclin D1 can easily be detected - one can follow the protocols in Current Protocols in Cytometry, section 7.9, (see also Cytometry, 25: 1-13, 1996). However, the "scheduled" expression of cyclin D1 is rarely observed, as most tumor cell lines are very variable and may also express it in all phases of the cell cycle.Likewise, tumor and leukemic cells from patients. We have seen, however, that when normal cells, (e.g. fibroblasts) are at perfectly exponential growth phase (low cell density, 2 - 3 days after re-seeding) they invariably express cyclin D1 only in early portion of G1, and perhaps very late in G2 (few cells in G2/M peak); The cells in S and most G2 cells were totally cyclin D1 negative. Medium change, prior trypsinization (<12 h) or sub-confluency dramatically altered expression of cyclin D1 even in normal cells, which showed then "unscheduled" pattern of its expression vis-a-vis the cell cycle phase. We have also noticed that cold methanol cell fixation and Ab then from Immunotech (Now Coulter-Immunotech) were superior than ethanol fixation and other Abs Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Let me add a comment regarding cell killing by pyronin Y. Unlike in fixed cells, where pyronin Y binds to RNA, in live cells (at low concentration) it accumulates quite selectively in mitochondria. This makes the cells photosensitive. A short exposure to light disrupts mitochondria and rapidly kills the cells (e.g. "Cytostatic and cytotoxic properties of pyronin Y: relation to mitochondrial localization of the dye and its interaction with RNA", Cancer Res., 46: 5760-5766, 1986). In the dark, however, at 1.7 - 3.3 uM concentration, it is cytostatic (G1 arrest) when continuously present in the culture. At higher concentration (>6 uM) it seems to bind also to nucleolar and cytoplasmic RNA and arrests cells in S and G2/M. Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer The cells that are advanced in process of apoptosis lose DNA by shedding apoptotic bodies that contain granules of chromatin. Furthermore, when DNA fragmentation by CAD (caspase activated DNase) is extensive, DNA fragments become small (size of mononucleosomal DNA), and such fragments may not be properly fixed (crosslinked to protein) with formaldehyde -they may leak out of the cell during the fixation and staining procedure. Thus, the late apoptotic cells, even after fixation with formaldehyde (as it is in the case of ApoBrdU assay), may have a deficit in (fractional) DNA content. With a gross loss of DNA, fewer DNA breaks (3' OH termini) remain in the cells to be labeled with BrdU. Hence, these late apoptotic cells may also show a decreased BrdU-associated fluorescence. I would suggest to classify the events with DNA content lesser than 10% of the mean DNA content of the G1 cells as apoptotic bodies, while the events with DNA content (DNA-associated fluorescence) between 10 % to up to G1-cell cluster peak, as apoptoptic cells. Although some of the events with less than 10 % DNA than G1 cells may in fact very advanced in apoptosis cells, most such events are expected to be apoptotic bodies or cell fragments. It seems, therefore, that it is a lesser error to classify them as apoptotic bodies or fragments of apoptotic cells, than as apoptotic cells. Unfortunately intensity of light scatter signals (FS vs SS) is not much of help, because the very late apoptotic cells and large apoptotic bodies or cell fragments may have similar light scattering properties. The "veteran" Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Repeated centrifugations in general can make non-apoptotic cells annexin V-positive. Furthermore, monocytes phagocytize apoptotic bodies that are shed from the neighboring apoptotic cell, and in the process become "false-positive" apoptotic cells, by the annexin V assay (e.g. Marguet et al., Nature Cell Biol., 1999;1:454-56). This is likely to be due to the fusion of plasma membrane of apoptotic bodies with membrane of monocytes. It has to be stressed that density gradient separation of cells to estimate apoptotic index may introduce additional bias because nucleus and cytoplasm undergo condensation during apoptosis. Hence, density of apoptotic cells is markedly increased, and they may be lost from the gradient, where one expects to find them if they would be non-apoptotic (e.g. mononuclear cells band on Ficoll-Hypaque gradient). These and other potential traps and difficulties in estimation of apoptotic index are discussed at length in Vol. 63 Methods Cell Biology/Cytometry, (2001;63: 527- 546). Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer The most common cause of the "sub-G1" spreading to very low DNA values is inapppropriate cell preparation. The cells have to be fixed in the preciptating fixatives (e.g. 70 % ethanol) then hydrated, stained with PI or DAPI and measured. The fragmented, low MW DNA undergoes extraction from apoptotic cells upon their hydration and apoptotic cells usually end up with about 20 - 50 % DNA of that of G1 cells, forming a distinct sub-G1 peak. If necessary, one can enhance the extraction using high molarity phosphate buffer. It is a common practice, however, to lyse the cells in hypotonic buffers or buffers that contain detergents. When a single apoptotic cell is lysed it can release many chromatin fragments. Because these fragments have minimal DNA content logarithmic scale is then used, and the fragments are erronously identified as individual apoptotic cells. Obviously, under these conditions a single apoptotic cell may generate up to a dozen, occasionally more object counted as "apoptotic cells" . Needless to say, individual chromosomes from mitotic cells, micronuclei, etc, are also misclassified as apoptotic cells.The light scatter signal from lysed cells is not much informative. It should be noted that on rare occasions apoptosis may proceed very rapidly and DNA degraded extensively that even after fixation and apoptotic cells may end up with less than 20% DNA of that of nonapoptotic cells. In such an instance one may fix cells briefly in formaldehyde (1%, 10 min), to prevent leakage of the low MW DNA, and follow by fixation in 70% ethanol. These problems and potential pitfalls are discussed in Meth Cell Biol Vol 63, pp 257-546, 2001 Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer The "best" positive control: HL-60 cells treated with >0.15 uM camptothecin (CPT) provide a reliable model of apoptosis. Most apoptotic changes (mitochondrial, plasma membrane, DNA fragmentation, nuclear fragmentation) occur during the initial 4 h of the treatment. The advantage of this model is that only S phase cells undergo apoptosis (Del Bino et al., Cancer Res., 51: 1165, 1991). Thus, G1 and G2/M cells, within the same sample may serve as a negative control. The critical point is the cells have to rapidly progress through S phase to be sensitive to CPT. It is a collision between the progressing DNA replication fork and the lesion iduced by CPT that provides the signal inducing apoptosis. Any slowdown in S phase progression, therefore, such as due to higher density of cells in the culture (subconfluency; > 800.000 cells per ml) makes them less sensitive to CPT. 2. The issue as to whether the second "p" is silent is a subject of long and ongoing dispute. Interestingly, it become apparent quite recently that the term was already used by the father of medicine Hippocrates, to describe the falling of the bone fragments during healing , i.e. in the context related to its common use (see Esposti: Cell Death & Differ.; 5: 719, 1998). As a Greek word, it should be pronouced with two "p" (see Funder, Nature, vol . 371, 1994 (Sept. 8 issue)"Apoptosis: two p or not two p". English authors, however, often transform its prononciation to English language suppressing the second "p Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer It is difficult to answer to that question because the distinction between "Go" or "completely out of the cycle" or even "slow mode G1" is, to some extent, in semantics. The concept of Go cells was introduced by Lajtha four decades ago [Lajtha LG, Haemopoietic stem cells: concept and definitions, Blood Cells, 1979; 5: 447-55] as an operational term, to define the cells which do not enter S phase (incorporate 3H-thymidine) for the duration of at least two cell cycles. While the hematopoietic stem cells or peripheral blood lymphocytes are considered to be an example of Go cells, this term has been used by many authors indiscriminately to describe noncycling cells in general, in a variety of cell systems, including cancer cells. The first (metabolic) marker shown to distinguish Go from G1 cells was cellular RNA content reflecting the number of ribosomes per cell. Go cells, contain on average 10 times fewer ribosomes compared to cycling G1 cells (e.g. Stanners et al., J. Cell Physiol, 11: 127, 1979) and can be distinguished from G1 cells by flow cytometry based on their minimal RNA content (PNAS 73: 2881-6, 1976). Another metabolic attribute (the one that can be used supravitally) that distingushes Go from G1 cells, is the very low uptake of mitochondrial probe rhodamine 123 by the former (PNAS; 2383-2387, 1981). We reviewed all the differences in metabolic parameters between cycling and noncycling, "genuine Go" and "slow G1", or "quiescent" cells, and this allowed us to subdivide the cell cycle on several subcompartments, that can be identified by cytometry (Cytometry, 1:98-108, 1980). Since then the Ki67, cyclin D, cyclin E and status of phosphorylation of pRB were proposed as new markers distinguishing Go from G1 cells. Based on differences in expression of these proteins and of pRB phosphorylation we proposed subdivision of the Go-G1 phase on additional subcompartments (Cytometry, 25: 1-13, 1996). It should be noted, however, that cells of most tumors and transformed cell lines are unable to enter the state that would be characterized by RNA content or by cyclin expression as Go. They often express cyclins in "unscheduled" way, e.g. presenting the G2 cyclins A and B1 in G1 phase. In conclusion, in the unclear situation, instead of classifying cells as "Go" or "noncycling G1" etc, I would characterize them based on the measured molecular or cytometric attribute(s) such as "cyclin D-negative" or "cyclin D-positive a and cyclin E negative", etc Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer There are numerous methods that allow one to define in which cell cycle phase cells are dying by apoptosis. The most widely used is TUNEL assay. We reviewed these methods many times, - e.g. in Methods in Cell Biology, Vol 75 (2004) Chapter 12: "Cytometric Methods to Detect Apoptosis". It is even possible to define whether G0 or G1 lymphocytes undergo apoptosis by measurement of cellular DNA and RNA content after staining cells with acridine orange (e.g. see Huang et. al. Cytometric assessment of DNA damage in relation to cell cycle phase and apoptosis. Cell Proliferation, 38: 223-243, 2005 Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer While fixation in formaldehyde is required to detect apoptotic cells in the TUNEL assay, formaldehyde should not be used in the assay based on analysis of cellular DNA content ("sub-G1" cell population); ethanol at 50 - 80% concentration is preferred. Unlike formaldehyde, fixation in ethanol does not crosslink DNA and thus allows the low molecular weight fragmented DNA to be extracted from the cells when they are transferred from ethanol to buffer or PBS, incubated with RNase and stained with PI or DAPI, so apoptotic cells may end-up with fractional DNA content. In fact, when cells are fixed in formaldehyde, apoptotic cells often cannot be identified as the sub-G1 population. It is only when the apoptotic process is very advanced and some DNA is being lost by shedding apoptotic bodies that contain parts of fragmented nuclei, apoptotic cells may have fractional DNA content and be distinguished as "sub-G1" cells after formaldehyde fixation. It is also worth to notice that if G2M cells undergo apoptosis they may end-up with a "sub-G2M" DNA content which may locate them at the site of S-phase cells on the DNA content histograms Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Apoptotic cells are strongly labeled in TUNEL assay only when they have a large number of DNA strand breaks. This is the case when DNA fragmentation is very extensive, which occurs when internucleosomal DNA sections are cleaved. However, in some cell types (often of epithelial or fibroblast lineage) or instances DNA fragmentation stops at the initial step i.e. generating 300 - 50 kb DNA sections, and does not progress into intenucleosomal (~180 bp) sections. In the TUNEL assay such cells are only weakly labeled. It should be noted that with most TUNEL kits (including APO-BRDU) a positive control cells are provided. They are camptothecin-treated leukemic cells which are expected to have internucleosomal DNA cleavage in about 30-40 % of the cell population (S phase). This control, if found to be TUNEL positive, provides an assurance that the kit is OK. Furthermore, in the case when the control is positive but the investigated apoptotic cells are negative, it provides evidence that DNA fragmentation in the studied cells did not progress into internucleosomal DNA sections. Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer Excellent method to stain DNA in yeasts for cell cycle analysis is described by Steven Reed in CELL CYCLE. Below I am providing the link to CELL CYCLE (which still is available online). His atricle in in issue # 2. Dr. Reed also prepared a protocol on this method which is being now included in Current Protocols in Cytometry. Zbigniew Darzynkiewicz, M.D., Ph.D. Research Institute Brander Cancer clumping * There are several tips for preventing clumping. Using EDTA at up to 5mM concentrations may help prevent cation dependent cellcell adhesion. Do not keep the cells at too high a concentration either (no more than 5-6 million/ml). Likewise using Ca/Mg++ free buffers will also help. Remember adding serum to your buffers will replace the Ca/Mg++ so if you need a protein support try using BSA instead. If your cells are clumping due to dying cells, the addition of DNAse II (10u/ml) may help. Of course you could filter your sample through a nylon mesh but the important thing is to prevent clumping so you do not lose too many cells. * I use 2-5% BSA to coat the cells. I think it also helps protect the cells, when sorting, from the degassing effects at the nozzle exit. If they are really clumpy I add some DNAse [assuming the cells are alive]. data presentation There's been extensive rigorous analysis of %Positive quantitation with dim populations--look it up in the literature, there are a number of papers (see bottom of email). Many third party software programs support these types of analyses; for example, FlowJo can compare the negative and stained controls using the five somewhat-related algorithms devised by Roy Overton, Bruce Bagewell ("SED"), Cox (Cox chisquare), Kolmogorov and Smirnoff ("K-S"), as well as by our own group ("PB" or probability binning). In general, these algorithms agree quite well--although the Cox, KS and PB methods aren't strictly %Positive quantifiers (but can be adapted to be such). In my opinion, for %Positive, the best is the SED algorithm. This has significant support both from basic mathematical principles as well as from empirical analyses. The PB method has the unique facet that it can be used to "gate" on cells that are different (e.g., positive) in one or more dimensions. Now let's dispense with a few myths that you brought up! >... When the whole peak shifts, the whole population is brighter >than the Negative control population. That means it's 100% positive >- including those dim cells in the 'positive' peak that aren't as >bright as the bright cells in the negative peak. That's not really true, for a number of reasons. First, you haven't defined what you mean by "peak". If you mean the "mode" (which is what most people mean when they think of peaks), then it's not at all true; the mode can be significantly influenced by changes in underlying representations of positive and negative; an increase in the mode does not mean that the cells are 100% positive. Even if the "whole peak" (by which I assume you mean the bottom percentile as well as the top percentile) moves, this does not indicate that all the cells are positive! Consider the simple example of an unstained population that is actually comprised of two sets of cells: A & B, where "B" cells have slightly more autofluorescence than "A", but the mixture doesn't resolve and appears to be a single peak. After staining, all of the "A" cells become slightly positive, and are slightly brighter than the B cells, which are still negative. Again, the distribution doesn't resolve into 2 peaks. That's a simple case where half of the population is staining, yet "the whole peak shifts"! Is this a trivial example? Certainly not: Within lymphocytes, B cells and T cells have different autofluorescence levels--so if you were to stain one population only with a dim reagent, you might mistakenly conclude that all of the lymphocytes express that antigen! >Back to the 'small differences' case: If your negative control is >in one location, and the negative cells in the test sample are in >the same location but there are a few bright cells, then you can use >frequency analysis to get the percentage of those positive cells >(use a 2-parameter plot and a polygon region - NEVER a histogram). Well, that's a blanket statement that I must also disagree with! Why "NEVER" use a histogram? Admittedly, I use bivariate plots often to gate essentially one a one dimensional expression. But I do so with guilty pleasure. The claim appears to be that you can better separate the dim positives from the negatives on a bivariate display. And this is visually supported in many cases. However, this is purely a visual artifact! It's magic! It's not mathematically true! In fact it's.... myth! EXCEPT when there is a relationship between the expression of the dim marker and the measurement on the other axis (and there often is--particularly with something like SS or FS, when there is a size-dependence). If that's the case, then you can't use just any bivariate display, you must use the bivariate display of your interesting marker against the parameter which provides additional information. If the other parameter in the bivariate display is not mathematically related to the measurement marker, then there is no scientific basis for stating that the resolution of the dim cells (ability to gate) is better in a bivariate display. And yes, I'd be happy to follow this up with real math if necessary. One thing to consider is that dot plots are heavily influenced by the number of events you collect. Pretend that you had collected a trillion events instead of 10,000 -- all of a sudden, the distinction on that bivariate plot has disappeared! (And yet, the histogram looks no different). Furthermore, the assertion that gating on bivariate plots is better than on histograms belies the underlying assumption that the gating is completely subjective! Don't be misled by the typical elliptical (or circular) distribution of events in a bivariate display of uncorrelated parameters -- this does not help you identify boundaries any better than from a histogram, except in a subjective manner. Of course, there's nothing wrong with subjectively placing gates, as long as you are aware that this is the case. But if your are concerned about accurately estimating %Positive, then certainly any subjectivity in gate placement must be removed. Incidentally, the algorithms referenced above do an excellent job of estimating %Positive, whether the expression is bright OR dim. Manual gating fails miserably if there's no defined separation. > If you have brighter events AND your negative peak moves up, you >either have 100% positivity in your sample (with 'dims' and >'brights') OR your negative control isn't working properly and you >only have a few bright positive events. OR... your negative control works just fine, it's just that the stain has some nonspecific binding on the nonexpressing cells! Oh wait -this means your negative control isn't an adequate control... but then, that's almost always true. It's nearly impossible to have the perfect negative control. (And please, don't even get me started on isotype "controls" -- something I want to rename as "isotype uncontrols"). Nonetheless, the point is that there are lots more possibilities than the two you mention. >PS-The training videos will be available in October. Well, great! ... but I hope they carry a bit more rigorous explanations than your original response... Perhaps the self-assignment of the moniker "FlowJock" is a bit premature. (PS, I sincerely hope you don't try to claim a trademark on a term that has been in general use by the community for many years--that would be a waste of effort and community good will). mr (you may consider me as an untrademarked FlowJock) 1) Overton WR. Modified histogram subtraction technique for analysis of flow cytometry data. Cytometry. 1988 Nov;9(6):619-26. 3) Roederer M, Treister A, Moore W, Herzenberg LA. Probability binning comparison: A metric for quantitating univariate distribution differences. Cytometry. 2001 Sep 1;45(1):37-46. 4) Roederer M, Moore W, Treister A, Hardy RR, Herzenberg LA. Probability binning comparison: a metric for quantitating multivariate distribution differences. Cytometry. 2001 Sep 1;45(1):47-55. 5) Roederer M, Hardy RR. Frequency difference gating: A multivariate method for identifying subsets that differ between samples. Cytometry. 2001 Sep 1;45(1):56-64. 6) Cox C, Reeder JE, Robinson RD, Suppes SB, Wheeless LL. Comparison of frequency distributions in flow cytometry. Cytometry. 1988 Jul;9(4):291-8. Received on Wed Sep 15 15:06:28 2004 mario roederer, stanford I liked Ray's and Mario's approach to show a few examples. It shows the artistic freedom one can get on how to display the data. And they only used one data set and two software packages and far from every possible iteration of scaling smoothing and colour. And they happily accepted Fluor:CD8 as an axis label. I would have thought it to be fluorescent if that is what Fluor means. I tend to write for example CD8*FITC 525nm log which still doesn't give you bandwidth etc but tells you at least it is green fluorescence. I actually love density plots (please don't call them colour dot plots as this tends to be used for colour gated dot plots) over contours and actually most of all a 3-D display where I can see mountains or clouds. Unfortunately we can not yet print the moving pictures described in Harry Potter but that is when the fun really starts. However, it can be done in on-line publications. The confusion created by our beloved contour or dot plots can be enormous. Not for no reason one of Marc Abraham's AIR-logo's shows a dot plot under the stinker (http://www.improbable.com/bookstore/bookstoretop.html). Actually nicely shown in Mario's example of smoothed contour plots is how you can make cells vanish. Are these small populations between the single and double positive cells important? or perhaps a compensation error?... If one wants to show those cells to make a point, one would not use the smoothed contour plot. If one was to sort them, the contours would lead nowhere. From that point the old Ortho 50H software with it's grey level dot plots was far advanced at it's time. With 16 grey levels it allowed a huge dynamic range for density plots (e.g. 1=2^0 to 32768=2^15 per channel) w/o compromising the resolution at the bottom - unless you do not like the log-2 z- scale. Let's step back a bit Why do we publish? Normally to convince someone else about the importance and values of our work. Why would we add those funny little pictures? To convince the reader with a visual aid about our data, the population we have seen doing something, e.g. once you seen a cluster - you shall believe. They are descriptive sketches and nothing else as they don't give is any statistics themselves. In particular with low event numbers it becomes very important to reflect on confidence intervals of your data as nicely presented by Terry Hoy on the Royal Microscopical Society Flow Course is Sheffield a couple of weeks ago. However, the plots have something in common with statistic: Statistics are like a bikini - what they reveal is suggestive, but what they conceal is vital. (Aaron Levenstein) Now if we argue the use of plots for illustration only but the use of "solid numbers" to substantiate our work with "sound statistics" we have to keep in our mind that all this number crunching only characterises / validate the position of the dots on the screen, nothing else. We can only test the numerics of our measurements and not the measurement itself. Apart from the requirement for correct instrument set-up this is subject to scientific reasoning; about how the measurement was performed and what controls were done, if saturation was reached etc. in order to interpret the indirect measures we have undertaken. This includes detailed description of clones and concentrations and control data and "unmassaged" pictures of raw data and gated data. The question remaining is how to validate the quality of the data and who is to do it. For validation in house for example we display / print all fluorescence channels versus log side scatter ungated. For whole blood this helps as it gives you already a differentiation of lymph's, mono's and neutrophils (and eosinophils if for example using FACSlyse). Thus if you suddenly spot CD8 positive neutrophils you know that there is trouble. For cultured cell lines log forward scatter vs. fluorescence seems to be better as in a lot of cases the cells with lower forward scatter are the ones on their way out. This type of display also indicates the presence of fluorescent aggregates that can lead to problems by sticking to or coinciding with cells (how do we want to report coincidence factors?) and shows if the antigen expression is scatter / volume related or not. But this is all a matter of personal taste. I do not believe we can eradicate poor publications. On one side there is always human error. On the other side there is an incredible inflation of science and in particular the numbers of publications and journals, inevitably leading to a decay in quality. We can only try to educate people in their ability to set up experiments and analyse data. Attempts like Mike's CD-ROM approach or Paul's virtual laboratory where you can even do the virtual pipetting of antibody are leading in the right direction. The latter could even be spiked with pitfalls like changing the buffer batch in an experiment, picking one made up with water contaminated with red fluorescent algae. Now in a proper clinical setting, as I know from my brother, all the results have to be signed off and interpreted by him or a colleague as a specialist before they leave the lab for the physicians out in the University. Unless you run your samples in a core facility with an experienced cytometrist, such gate keepers may not exist. For political financial and logistic reasons a lot of people have bought their own instruments independent from an already existing expertise. The time and effort put into the proper planning and analysis of experiments by someone who knows his cytometry would cost (not money necessarily). If the gate keeper is to be the reviewer of an article then he should not only be skilled enough to understand the flow data but he also would require some validation information even if not published as it is not possible to judge complex work from one or two pictures. In that context I think that the suggested discussion board for post publishing review offered via the publisher to their subscribers speaks in favour of the publisher, as this type of feedback does allow him to improve the journal quality. I am sure we can come up with a suggested list of information that should be included on cytometry experiments if applicable and make it easier not to forget the necessary controls and I would ask James Watson (http://www.cyto.purdue.edu/flowcyt/books/bookl.htm) to join the advisory party that might be set up for that. But there will always be a lot of poor data published, for numerous reasons, and the only one to blame is the reader that believes information to be true because it was printed in a newspaper or a publication to be correct just because it was published in a scientific journal (see www.improbable.com for further enjoyment on that). gerhard nebe-von caron, unipath fixation Paraformaldehyde is a polymerized form formaldehyde. It is hardly soluble and it cannot be used as a fixative. Only formaldehyde is used as a fixative. Howeve, formaldehyde in aqueous solutions spontaneously polymerizes. Therefore, methanol is often added to slowdown the polymerization reaction. Solutions of formaldehyde (usually ~ 37%) in water, containig 10-15 % methanol as a preservative are generally called "formaldehyde"; such solutions are being sold by most reagent companies. Solutions further diluted (4-10 %) received name "formalin". Methanol-free formaldehyde, which sometimes is preferred (e.g. for fixing cells for some some histochemical reactions or in immunocytochemistry), can be obtained by hydrolysis of paraformaldehyde. This is usually done by extensive heating of paraformaldehyde solutions. Because of this procedure the methanol-free formaldehyde received (incorrrectly) the name "paraformaldehyde". In the past, this was the most common way to obtain methanol-free formaldehyde. Unfortunately, this incorrect name is still often used in the literature, generating the confusion. The methanol-free formaldehyde solutions can now be purchased. Some are called "ultrapure". We purchase such solutions (10%) from Polysciences, Inc. (800-5232575); they can be stored at room temperature. I would not recommend, however, to store them longer than one year, since formaldehyde in these solutions still has tendency to polymerize. It should be noted that all formaldehyde solutions are highly toxic and carcinogenic. Zbigniew Darzynkiewicz Catherine, Autofluorescence is usually higher with older aldehyde solutions. I would recommend using freshly prepared formaldehyde (less than one month old). Also, the addition of 0.3% Triton X100 to the antibody incubation solutions will decrease autofluorescence. --Randy Hi Catherine: Formaldehydes and glutaraldehydes are bad actors when it comes to fluorescence-based cytologic analysis. Either get away from fixation with aldehydes or the answer to the problem is aldehyde blocking. This is done by reducing the -CHO groups to -OH with sodium borohydride or by usingbland amino groups (glycine, bovine albumin, skimmed milk). The other option is to freeze cells. Make cytospins when you need them. The third option is to live with the autofluorescence. Just dedicate FITC channel to autofluorescence. Autofluorescence Eliminator Reagent http://www.chemicon.com/featured/autofluorescence.asp http://www.uhnresearch.ca/facilities/wcif/PDF/Autofluorescence.p df Good luck Padma ----------------------------------------------------------------------------------------Hi Catherine, One method is to use the violet laser for autofluorescence correction. The blue laser excites both autofluorescence and FITC/Alexa 488. The violet laser excites only the autofluorescence. Subtracting the violet excited green scan images from the FITC/Alexa 488 scan images leaves a close approximation to the specific fluorescence. Best wishes, Ed ------------------------------------------------------------------------------Dear Catherine, This is a common problem in immuno-histology. Attached is a paper that may help. I have not tried sodium borohydride in a flow setting yet, but one of the researchers who use my flow lab is going to give it a go. Regards Rob W Paraformaldehyde is a white solid polymer (HCHO)n of formaldehyde where n is at least 6. It is used as a disinfectant, fumigant, and fungicide. It is formaldehyde (HCHO), that is used as cells/tissues fixative, not "paraformaldehyde". Because formaldehyde in solution undergoes oxidation and polymerization, it is common to make fresh solutions by depolymerizing paraformaldehyde, most frequently by heating in water solution. Hence, such product is often (incorrectly) called "paraformaldehyde". The hydrolysis is a hazardous procedure, because paraformaldehyde/formaldehyde vapours are strongly irritating and carcinogenic. To make solutions of formaldehyde more stable methanol is often added, and this is called "formalin". Formalin 100% is a soluition of 37% by wt of formaldehyde gas in water, with 10-15% methanol to prevent polymerization. It is also often called "formalin 40", as it contains about 40g of formadehyde in 100 g of water. For most applications that call for "paraformaldehyde" we use the methanol-free formaldehyde, that is available from Polysciences, Inc (Warrington, PA). I do not know how they stabilize their product, but we store it up to a year, as prescribed by the vendor, and do not see any deterioration of the results. Zbigniew Darzynkiewicz, M.D., Ph.D. Brander Cancer Research Institute intracellular staining The most simple and in most cases perfect fixation procedure for intracellular proteins is using cold 70% Ethanol. It works for most proteins, you can store your samples in the fridge for a year or longer without any changes in antigen distribution, you can do a simultaneous DNA analysis for cell cycle etc. Due to the possibility of long time storage you can analyse all the samples from an experiment at the same time which improves comparability. If your protein is very small there may be a problem with loosing it, although most, even small proteins are precipitated. There have been some cases described in the literature that the conformation of some antigens may change so that the antibodies will not recognize them anymore, but these cases are very rare. The only thing you have to take care of is the possible formation of aggregates during the fixation procedure. Here is the protocol I use for intracellular immunofluorescence: Centrifuge your cells in a tube with a conical bottom, discard the supernatant, resuspend the cells completely in the remaining drop. Now comes the tricky part: Put the tube on a vortex machine, keep it shaking while adding the ethanol dropwise and slowly. This is to avoid aggregate formation. Use ~1ml ethanol for 5x10e6 cells. Keep in the fridge until use. Before staining centrifuge again, discard supernatant, resuspend cells in remaining droplet. Add 1ml Buffer (0.1%Tris.HCl, 0.1% Triton X100, 2mM MgCl2 pH7.4) the same way as when you added the ethanol (dropwise and slowly while vortexing). Wash again with the same buffer, again taking care to avoid aggregates. Wash again with trisbuffer including 20% FCS or 2% BSA and incubate for 30 min to block unspecific binding sites. Wash again blocking buffer and include your antibodies. After the last staining step was with buffer w/o FCS or BSA and analyse. Hope this helps. With kind regards, Nicole I can recommend CALTAG Fix and Perm for intracellular staining and I have used this product in both diagnostic and research laboratories. The reagents are easy to use and also allow concurrent surface staining. The FSC/SSC presentation does not alter significantly compared to other permeabilising reagents. I have no commercial interest in CALTAG products and I offer this information as my opinion only. Good luck! Cathy ----------------------------------------------------------------------------------------------- Elaine, In my experience you may need to look at different fixatives as well as permeabilization agents. We are looking at human white blood cells and we need both good intracellular perm as well as good light scatter properties (for differentiating the WBC subsets). This may not be a concern for you since you're using a cell line. If you're looking at something novel intracellularly, use something known first to validate your fix/perm . For example, with our WBC work we look for good myeloperoxidase labeling in granulocytes to validate the fix/perm. I hope this helps. Peter Peter Lopez ---------------------------------------------------------------------------------------------------------------------Hi Elaine, Ethanol is a penetrating fixative and conditions of use including cell type will govern the distance of effect into a cell, for most cells it is a total fixation. For DNA staining with dyes this is fine but for Ab you have to know they are against the fixed epitope. For most Ab used in Flow Cytometry it is preferable to Fix the cell membrane with paraformaldehyde then use a detergent to permiabilise said memebrane. FIX Paraformaldehyde fixative solution PFM 4 % (w/v) paraformaldehyde 3 % (w/v) sucrose ( I never used sucrose in my fixation mix only in the Hypertonic solution desined for membrane shedding to recover nucli. You could try it for comparison) in PBS pH 7.4. Store at 4°C in the dark for a few days. PERM Triton permeating solution 1 % (v/v) Triton-X100 in PBS pH 7.4. Store at room temperature for a few weeks. Saponine permeating solution 0.1 % w/v in PBS pH 7.4. Store at 4°C for a few days. Nonident permeating solution 0.5 % (v/v) Nonidet P-40 in PBS pH 7.4. Store at 4°C for few days. N-OctylGlucosamine (NOG) permeating solution 0.74 mg/l (w/v) NOG (This is the Critical Micelle Concentration for this detergent) in PBS pH 7.4. Store at 4°C for few days. The problems with " home brew" are reproduction, QC and shelf life so I went to a commercial product. We sell the IntraPrep kit for this which has a PFM fixation and Saponin Perm. 50 test IM2388 and 150 test IM2389 As a positive control to demonstrate perm and staining we have anti-Tubulin conjugated with FITC part 6607113 Regards Martin ---------------------------------------------------------------------------------------------Hi Elane, I did some intracellular staining in thymocytes some time ago. I fix my cells with formaldehyde solution. My experience was that is was critical, how fresh the formaldehyd solution was. I took 2% formaldehyde and end up with 1% end concentration for fixation. I attach a protocol in pdf format and hope this helps a bit Good luck Steffen ==================== Dr. Steffen Schmitt --------------------------------------------------------------------------------------------------------Elaine, We've actually pondered this same question at Cell Signaling since our customers use a variety of different fix&perm methods. We have settled on a protocol that involves fixation in 1% formaldehyde for 10 min at 37C, then permeabilization in 90% methanol. This protocol works very well for every antibody we tried. Some of our collaborators recently compared this protocol to a saponinbased fix&perm kit from Invitrogen and screened with a number of antibodies. All of the antibodies worked well with the aldehyde/methanol, but over half of them did not work at all with the saponin-based kit. The only down-side to methanol permeabilization is that the scatter characteristics of the cells are not as clear, so it may be difficult to pick out different cell types in a heterogeneous suspension on a scatter plot. This isn't an issue for researchers like you that are working with cell lines. For a detailed copy of our protocol, please visit our website (http://www.cellsignal.com), click on Support, then Research Protocols, and finally on Flow. Please feel free to contact me if you have any questions. Best of luck, --Randy Wetzel CLB protocol for membrane and intracellular FACS staining : (By Paul Baars, CLB-KVI) Reagents: PBS PBS 0.5% BSA PBS 0.1% saponin 0.5% BSA Human Pooled Serum (HPS) 4% Paraformaldehyde (PFA) in PBS Procedure (the whole procedure is performed on ice) 1. Wash the cells in a 15 ml tube in PBS 0.5% BSA 2. Suspend the cells in PBS 0.5% BSA (4x106/ml) and add direct conjugated Mab's for the membrane staining 3. Incubate for 30 min 4. Wash 1X with PBS 0.5% BSA 5. Wash 1X with PBS 6. Add 1.5 ml 4% PFA in PBS and incubate for 5 min (stopwatch!!) 7. Wash 1X with PBS 8. Wash 1X with PBS 0.1% saponin 0.5% BSA 9. Suspend the cells in PBS 0.1% saponin 0.5% BSA + 10% HPS 10. Incubate for 20 min 11. Wash 1X with PBS 0.1% saponin 0.5% BSA 12. (From now on this buffer is used until the end of the procedure) 13. Suspend the cells in a x 50ml (a= number of different intracellular staining) and pipette the cells in a 96-well dish 14. Add Mab's to the intracellular antigen and control Mab's (diluted in saponin buffer) 15. Incubate for 30 min 16. Wash 3X 17. Measure the cells on the FACS We know that other permeabilization procedures are also successful for Granzyme staining e.g. the BFA fixation, john voorn For B27 as a PE or APC conjugate, we typically use 1 mcg/ml final concentration. We titer every lot. I don't know what the stock concentration of your B27 mAb is, so if you want the exact calculation you will have to do the calculation or send me the concentration offline. A guess is that the stock concentration is 200 mcg/ml (100 mcg in 500 uL) and you are using it at a 1:285 dilution, which gives a final concentration of 0.7 mcg/ml. Looks pretty reasonable to me. A common mistake that is further propagated by many of the Ab companies is to use antibodies by mass as for example, requiring "0.5 mcg per test". The variable that makes the difference is mAb concentration, not total amount. We typically stain in 50 ul and thus "per test" only requite 1/4 the total mass of mAb to maintain the same concentration as you would when staining in 200 ul. Calman Prussin Allergic Diseases Section NIAID/ NIH Although I agree monensin is not the perfect blocker of intracellular transport, I think your response is a bit exaggerated. What toxicity data are you citing? The Jung paper demonstrated monensin toxicity only after 16 hours. Both monensin and BFA need only be in the culture for 2-4 hours for maximal effect (my data and others). Also consider that the strong stimuli (PMA/ionomycin) that are often used to effect sufficient cytokine expression are also causing cell death. A couple of hours of monensin may not be the largest perturbation in the system. I have not compared a large number of cytokines, but for huIL-2 and IFN I do not see a significant difference in the mean fluorescence intensity or % positives between BFA and monensin. The main reason for using monensin in the past was that it was dramatically cheaper. Sigma now sells BFA at a reasonable price. It is worth having a through discussion of the relative merits of each, as I am eager to switch to a better reagent. I look forward to hearing from you to substantiate your statement. Intracellularly Backed Up in Bethesda, Calman Prussin Allergic Diseases Section NIAID/ NIH The protocol that I find most useful for permeabilisation for the detection of internal antigens is to use saponin. It is relatively gentle (ie it doesn't put enormous holes in the cytoplasm or the cell membrane) and can be used in conjunction with surface staining or DNA staining. You may have to play about with conditions but a good starting point is to treat cells with 0.3% saponin for about 15mins at room temperature before doing the antigen detection and then to use 0.1% saponin in all subsequent steps. Be careful with the washing steps as it is easy to lose all your cells! We have found that the permeabilisation is best at room temperature and that the saoponin needs to be present all the time as the permeabilisation effect can be reversed. As with all intracellular staining washing is important, but if you are using directly conjugated antibody, this reduces the steps and reduces cell loss. Hope that this is of some use. Derek Davies Imperial Cancer Research Fund London Hi Dr. Roy and fellow flowers: I do this all the time. I have abandoned Western blot in favor of intracellular flow cytometry, and I have compared indirect to direct staining, with similar results. I use either a biotinylated first step or an unlabeled first step. If I use an unlabeled, I use a ligand-affinitypurified polyclonal, and a labeled F(ab2') for the second step. I block with Ig of the same species as the F(ab2'). I have successfully seen p38, STAT3, JAK2, and a lot of cytokines. The first step does not have to be one specifically for flow to work--if it works in westerns and immunohistochemistry chances are excellent that the Ab will work here too. A major pitfall is not blocking sufficiently and not washing sufficiently. I block with several mg/ml Ig for about 1 hr on ice after permeabilization. Also, the first wash after adding Ig, Ab, or second step must be with buffer added and left there for the same length of time as the incubation step. For example, if you left Ab on for 45 min, you must spin out the Ab and then leave the wash buffer on for 45 min, then proceed with the subsequent washes as usual. Another thing I found was that Caltag fix & permeabilization reagents gave me superior signal to noise ratios for phospho-Ab labeling, while Pharmingen or home-made reagents gave me very good results for intracellular cytokines. See these references for more details: Fleisher et al., Clin Immunol 90:425-430, 1999 Barton & Murphy Cytokine 12:18-27, 2000 Feel free to contact me for more info. Best, Beverly Barton Assistant Professor Dept. of Surgery polarisation Maris Handley wrote- >Someone recently brought me an article entitled: Fluorescence polarization >assay by flow >cytometry. The authors are J.M. Rolland, K. Dimitropoulos, G.R. Hocking, >and R.C. Naim. >The article is from 1985. My first question is whether anyone is >routinely looking at >fluorescence polarization in 2001? If not, is this because there is a >newer method, >or better technology for looking at subtle cellular changes? >I would be interested in talking to anyone who has experience with these >kinds of >measurements. See pages 327-9 of the 3rd Edition of Practical Flow Cytometry for additional background information. The fluorescence polarization assay in question was based on observations made by Boris and Lea Cercek, working in Manchester, England in the mid-1970's, that the polarization of fluorescein fluorescence in lymphocytes (produced by intracellular enzymatic hydrolysis of fluorescein diacetate, also known as FDA) changed within a relatively short time after mitogenic stimulation by phytohemagglutinin (PHA). The measurements, described as showing changes in the "structuredness of cytoplasmic matrix", or SCM, were originally done on lymphocyte suspensions in a spectrofluorometer. The Cerceks also reported that lymphocytes from patients with cancer exhibited a diminished polarization response to PHA, but, unlike patients without cancer, showed a polarization response to proteins derived from cancer cells, and proposed this as a test for cancer. While Rolland et al and others attempted to implement the assay using flow cytometry, with varying degrees of success, the most precise single cell fluorescence polarization measurement system is the Cellscan, developed by Prof. Mordechai (Motti) Deutsch and his colleagues at Bar Ilan University in Israel. They have published numerous papers in recent years (see bibliography below), and now believe that the polarization changes reflect changes in the cytoskeleton and/or intracellular hydration state. Motti Deutsch has criticized the notion of measuring polarization in flow, because the constant observation time means fewer photons are counted for cells with weaker fluorescence, making measurements less precise. Computation of the polarization value requires taking a ratio, and the change in this ratio is relatively small, meaning that any source of imprecision decreases the likelihood of obtaining significant results. The Cellscan illuminates the cell with very low intensity light (minimizing bleaching) for as long as is necessary to count 10,000 photons in each of two polarizations for each of two fluorescence wavelengths, providing a very precise polarization measurement. I don't know of recent data bearing on whether commercial flow cytometers are up to the job. An overall problem with the polarization assay is that the Cellscan apparatus, while precise for polarization measurements, has not been equipped with sufficient multiparameter measurement capability to allow determination of other cellular characteristics, such as phenotype, activation antigen expression, RNA or DNA content, cytoplasmic calcium concentration, or membrane potential, which also reflect lymphocyte activation. The differences in lymphocyte activation patterns between patients with and without cancer that are reported to be detected by the polarization assay should presumably be detectable using more widely accepted indicators of lymphocyte activation, but the necessary comparison experiments remain to be done. I personally think this would be worthwhile, because some of the results I have seen from both the Cellscan and flow cytometric studies suggest that pursuing this line of inquiry could yield some interesting new information relevant to tumor immunology. Older references cited in the book; the newer papers are: Deutsch M, Weinreb A: An apparatus for high-precision repetitive sequential optical measurement of living cells. Cytometry 1994; 16:214-26 Ron IG, Deutsch M, Tirosh R, Weinreb A, Eisenthal A, Chaitchik S: Fluorescence polarisation changes in lymphocyte cytoplasm as a diagnostic test for breast carcinoma. Eur J Cancer 1995; 31A:917-20 Eisenthal A, Marder O, Dotan D, Baron S, LifschitzMercer B, Chaitchik S, Tirosh R, Weinreb A, Deutsch M Decrease of intracellular fluorescein fluorescence polarization (IFFP) in human peripheral blood lymphocytes undergoing stimulation with phytohaemagglutinin (PHA), concanavalin A (ConA), pokeweed mitogen (PWM) and anti-CD3 antibody. Biol Cell 1996; 86:145-50 Marder O, Shoval S, Eisenthal A, Fireman E, Skornick Y, Lifschitz-Mercer B, Tirosh R, Weinreb A, Deutsch M: Effect of interleukin-1 alpha, interleukin-1 beta and tumor necrosis factor-alpha on the intracellular fluorescein fluorescence polarization of human lung fibroblasts. Pathobiology 1996; 64:123-30 Deutsch M, Ron I, Weinreb A, Tirosh R, Chaitchik S: Lymphocyte fluorescence polarization measurements with the cellscan system: application to the SCM cancer test. Cytometry 1996; 23:159-65 Eisenthal A, Marder O, Lifschitz-Mercer B, Skornick Y, Tirosh R, Weinreb A, Deutsch M Inhibition of mitogen-induced changes in intracellular fluorescein fluorescence polarization of human peripheral blood lymphocytes by colchicine, vinblastine and cytochalasin B. Cell Struct Funct 1996; 21:159-66 Zurgil N, Deutsch M, Tirosh R, Brodie C: Indication that intracellular fluorescence polarization of T lymphocytes is cell cycle dependent. Cell Struct Funct 1996; 21:271-6 Rahmani H, Deutsch M, Ron I, Gerbat S, Tirosh R, Weinreb A, Chaitchik S, Lalchuk S: Adaptation of the cellscan technique for the SCM test in breast cancer. Eur J Cancer 1996;32A:1758-65; Comment in: Eur J Cancer. 1997; 33:1333-5 Merimsky O, Kaplan B, Deutsch M, Tirosh R, Weinreb A, Chaitchik S: Detection of melanoma by monitoring the intracellular fluorescein fluorescence polarization changes in lymphocytes. Cancer Detect Prev 1997; 21:167-77 Eisenthal A, Marder O, Lifschitz-Mercer B, Skornick Y, Fixler D, Avtalyon R, Tirosh R, Deutsch M: Influenza A virus affects the response of human peripheral blood mononuclear cells to phytohaemagglutinin A by altering the cytoskeleton. Pathobiology 1997;65:69-74 Sunray M, Deutsch M, Kaufman M, Tirosh R, Weinreb A, Rachmani H: Cell activation influences cell staining kinetics Spectrochim Acta A Mol Biomol Spectrosc 1997;53A:1645-53 Cohen-Kashi M, Deutsch M, Tirosh R, Rachmani H, Weinreb A: Carboxyfluorescein as a fluorescent probe for cytoplasmic effects of lymphocyte stimulation.Spectrochim Acta A Mol Biomol Spectrosc 1997; 53A:1655-61 Eisenthal A, Marder O, Lifschitz-Mercer B, Skornick Y, Tirosh R, Irlin Y, Avtalion R, Deutsch M: Infection of K562 cells with influenza A virus increases their susceptibility to natural killer lysis. Pathobiology 1997; 65:331-40 Fixler D, Tirosh R, Eisenthal A, Marder O, Irlin Y, Lalchuk S, Deutsch M: Monitoring of effector and target cell stimulation during conjugation by fluorescence polarization. Biol Cell 1997; 89:443-52 Gelman-Zhornitsky E, Deutsch M, Tirosh R, Yishay Y, Weinreb A, Shapiro HM: 2, 7'- bis-(carboxyethyl)-5-(6)carboxyfluorescein (BCECF) as a probe for intracellular fluorescence polarization measurements. J Biomed Optics. 1997; 2:186-194 Avtalion N, Avtalion R, Tirosh R, Sheinberg A, Weinreb A, Avinoach I, Deutsch M: Preparation of a diagnostic antigen of human melanoma based on lymphocyte activation as measured by intracellular fluorescein fluorescence polarization. Cancer Detect Prev 1999; 23:64-71 Sunray M, Kaufman M, Zurgil N, Deutsch M: The trace and subgrouping of lymphocyte activation by dynamic fluorescence intensity and polarization measurements. Biochem Biophys Res Commun 1999; 261:712-9 Zurgil N, Levy Y, Deutsch M, Gilburd B, George J, Harats D, Kaufman M, Shoenfeld Y: Reactivity of peripheral blood lymphocytes to oxidized lowdensity lipoprotein: a novel system to estimate atherosclerosis employing the Cellscan. Clin Cardiol 1999; 22:526-32 Zurgil N, Kaufman M, Solodiev I, Deutsch M: Determination of cellular thiol levels in individual viable lymphocytes by means of fluorescence intensity and polarization. J Immunol Methods 1999; 229:23-34 Zurgil N, Schiffer Z, Shafran Y, Kaufman M, Deutsch M: Fluorescein fluorescence hyperpolarization as an early kinetic measure of the apoptotic process. Biochem Biophys Res Commun 2000; 268:155-63 Deutsch M, Zurgil N, Kaufman M, Berke G: Fluorescence polarization as an early measure of Tlymphocyte stimulation.Methods Mol Biol 2000; 134:221-42 eutsch M, Kaufman M, Shapiro H, Zurgil N: Analysis of enzyme kinetics in individual living cells utilizing fluorescence intensity and polarization measurements. Cytometry 2000;39:36-44 -Howard software crashes Things that will make your Calibur Mac Crash: 1. Directly saving data to a peripheral (zip, memory stick, external hard drive). Save it to the HD and transfer after acquisition is complete. Remove peripheral memory device while acquiring. That USB connection isn't as fast as the computer is and so things lock up. 2. Connecting to network during acquisition. Turn off file sharing in control panels or disconnect the mac from the network completely. Try setting tcp/ip setting in control panels to "only when needed." 3. Computer is set to sleep. Change sleep setting to "never" in energy saver control panel. 4. A mouse with a damaged cord. Replace the mouse. 5. If you use FileGuard, making new folder from inside CQ (folder button in Parameter Description window). Make new folder in desired location before opening CQ, then navigate to & choose your folder in CQ. 6. Multi-tasking while acquiring. Specifically, avoid RAM intensive applications. Things to prevent a Calibur Mac Crash: 1. Rebuild the HardDrive. Hold down "Option" and "Apple" keys while restarting computer. 2. De-frag the HardDrive. I use Norton Disk Dr at least twice a month and run the diagnostic and de-fragment the HD. 3. Don't use PC formatted zip (problematic for those users from PC based labs). 4. Don't analyze data on acquisition machines. 5. Keep your HD less than 50% full. 6. Stay away from USB hubs if possible. 7. Zap the P-RAM. This will re-set your preferences. Hold down "Option," "Apple," "P," and "R" keys on restart. The appearance of the sub-G0/G1 is highly variable between cell types, and even the same cell type at differing levels of activation. Cycling cells in particular (with less compacted chromatin) are particularly likely to give confusing results, especially with the accumulation of subcellular objects (cell fragments, fragmented chromatin, other trash) at the low threshold of instrument sensitivity. The contribution of S + G2/M cell apoptosis to the "pot" further complicates the issue of data interpretation. And if we can't clearly separate intact apoptotic cells from apoptosis-associated debris, we are not really measuring cell-by-cell apoptosis anymore. We strongly encourage our investigators to use sub-G0/G1 ONLY as a preliminary, qualitative indicator of cell death, not as a quantitative assay - unless the apoptotic peak is really clear, which does not happen most of the time. It should always be backed up with additional assays, especially biochemical ones like caspase activation. And most journal reviewers, grant review panels, etc. won't be impressed anymore if DNA loss is the only criterion for measuring cell death - there are lots of other nice flow apoptosis assays available now, some of them fairly economical. Enjoy, Bill Telford I have not had any problems (background staining) with mouse MEFs so far. For routine Fc blocking when using mouse tissue samples, I incubate the cells with 2.4G2 (anti-Fc) for 20-30 minutes on ice. Usually, I do not even wash the cells after blocking (a quick spin for removing 2.4G2 supernatant). It works really well for me. Ocassionally, in my liver MNC preparations, I do get background B cell staining inspite of 2.4G2 block. I have not got around this problem yet (other than using a negative B220 gate). I have not used the Fc block after the first blocking step. I block the cells first with the anti-Fc antibody, surface stain and directly fix and permeabilize my cells for intracellular staining. Hope this helps. Sriram Venkataraman Sriram, PhD Postdoctoral Fellow The Walther Cancer Institute Indiana University School of Medicine Indianapolis, IN 46202 viability Thanks. You are right ! I was using different definition of viability - > the pragmatic rather than the logical one. I defined cell viability in > terms of survival of tumor cells treated with antitumor drugs - are they > later able to proliferate/ form colonies ?. Since I am working on > antitumor drugs/strategies, I must developed such "tunel vision" in > interpreting live vs dead cells (identifying reproductive cell death with > cell death) > Regards > Zbigniew Robert, Mitotracker Red CMXRos remains in mitochondria after cell fixation/permeabilization. We do not have experience with Mitotracker Green but Haugland makes note in his Handbook that it does not remain in the cell after fixation/permeabilization. Using non-fixed, live, cells we were able to measure Mitotracker Red, as well as tetramethylrhodamine methyl ester (TMRM, Sigma) fluorescence, each in combination with FLICA (Fig 3 in our recent Cytometry paper), using just 488 nm excitation, in FacsScan. Vermuellen et al., (Exp. Hematol 30, 1107-1114, 2002) also had nice results with TMRM e.g in combination with Annexin V using FaacsScan. We did not check whether TMRM can be fixed. Best wishes and regards Zbigniew Dear All, Neither MTT nor PI is a reliable assay of cell viability. The PI assay is based on the detection of the loss of plasma membrane capability to exclude this dye. Early apoptotic cells exclude PI. Only necrotic and late apoptotic cells stain with PI. Thus, early apoptotic cells, although for all practical reasons they are dead (certainly reproductively dead), are recognized as live cells by this assay. On the other hand MTT assay measures the "cell redox activity", that is to a large extent mitochondrial but may also be non-mitochondrial (e.g. see Bernas and Dobrucki, Cytometry, 2002;47:236-242). The agents that arrest the cell cycle progression (e.g activating cell cycle checkpoints, inhibitors of DNA polymerase etc) induce unbalanced cell growth. In the absence of DNA replication the cells grow in size, including the increase in mitochondrial mass and activity. Such cells are are moribound - at certain degree of growth unbalance they are irreversibly commited to die. By the MTT assay, however, not only such cells are detectable as live, but with time one sees their increased capacity to reduce MTT. It may appear, therefore that cells in cultures proliferate (this can be seen for up to three days), whereas in fact they are reproductively dead. One has to note that some vendors advertise the MTT kits as "Cell Proliferation Assays", which is quite misleading. The gold standard in viability assays is clonogenicity test. Unfortunately it is cumbersome and time consuming. With each new drug/cell system measured by MTT or other rapid/automatic assays, it is advised to run at least once the clonogenicity test, for comparison. Zbigniew Darzynkiewicz, M.D., Ph.D. This is a fabulous way to do viability testing! Once you do this method, you will never do a trypan blue (yech) again. I learned to do this in the Herzenberg laboratory at Stanford, brought it to the VRC--and we've now incorporated it in our clinical trials. Every time we thaw PBMC for doing immune function assays, we assess the viability by fluorescence first (and, in fact, if viability is below a treshhold, I think 60%, we discard the sample). We've even developed an SOP for it. We use a combination of acridine orange and ethidium bromide (not PI)--under a fluorescence scope, "green" is live and "red" is dead--no ifs, ands, or buts--and easily scored by even the most green students with risking a red face. In any case, our procedure is to prepare 3 mg/ml ethidium bromide in absolute ethanol and 5 mg/ml acridine orange in ethanol. Store this stock in a dark vial, refrigerated. To make a working solution, take 1 microliter of each added to 1 milliliter of PBS. This we store at room temp by the fluorescence microscope, and make fresh every few weeks. Please note that AO and EB are considered highly carcinogenic: use gloves and a face mask when preparing the concentrated stock solution, and use gloves when handling the working solution. Dilute cells with an equal volume of the working solution and immediately look on the fluorescence microscope (you can also dilute 1:10 if the cell count is too high). Remember to take this dilution into account when you calculate original numbers. EB, you could mr (PS, if you don't have I hesitate to disagree with Maryalice, especially given her powerful admonition that whoever says otherwise knows absolutely nothing about PI exclusion... but... "he who hesitates is last". Actually, we found that we can stain with PI, then fix with 0.5% paraformaldehyde, and have the ability to discriminate live/dead for about 2 hours afterward (perhaps as long as 4-6 hours). Waiting overnight, however, is right out--the PI leaks out of dead cells (and, if present in the medium, leaks into live cells). As Mark points out, you should add the PI before the PF, and if you need to wait more than several hours, use EMA (which is considerably less practical for various reasons). We tested this extensively, because of the importance of doing live/dead discrimination, as well as the practicality of fixing cells (for example, from infectious samples). Note that we did not test higher concentrations of paraformaldehyde or other fixatives. mr (PS, with regard to removal of adherent endothelial or tumor cells becoming PI+ : note that a variety of protocols, as asserted already on this list, can transiently permeabilize cells. I would try removing the cells, washing them well in regular medium, waiting 30 minutes, and then adding PI).