National Institutes of Health, NHLBI (RD, PY, PS).
American Heart Association (JL).
Stanford University, VPUE Grant (JL).

Adapted from prior study1.
1. Conjugation of Annexin V to SPIO
<ol>
	<li>Oxidize SPIO particles (Ocean Nanotech Inc., 5 mg/mL) for 1 hr at 20 &deg;C in the dark in solution with 0.15 M sodium periodate (NaIO4) (4:1 weight:weight ratio)2.</li>
	<li>Incubate the oxidized SPIO for 12 hr with purified ANX protein (1:1 ratio, weight:weight) in 0.15 M sodium borate (Na2B4O7 10H2O) at 20 &deg;C.</li>
	<li>Reduce the mixture further for 1 hr with sodium borohydride (NaBH4)under the fume hood and then quench with 0.15 M Tris-HCl.</li>
	<li>Separate the free ANX from ANX-SPIO by centrifugation at 14,000 x g (75 &mu;m pore Microcon filter, Millipore, Billerica, MA).</li>
	<li>Further refine the compound by removing unbound impurities using a Magnetic Separator device (Ocean Nanotech, Inc.).</li>
	<li>Quantify the filter retentate (ANX-SPIO) protein levels by Bradford protein assay and store at -80 &deg;C at 2 mg/mL in 0.1 M Tris-HCl with 1% serum albumin and protease inhibitors (Halt Protease Inhibitor, Thermo Scientific, 1-50 mg/mg ANX).</li>
</ol>
2. Dynamic Light Scattering
<ol>
	<li>Separately dilute the SPIO and ANX-SPIO in PBS to an optical density of 0.1 and analyze by dynamic light scattering in a Zetasizer Nano DLS machine (Malvern Inc., Worcestershire, UK)3.</li>
	<li>Obtain monomodal peaks (ideally) for the compound, with a Z-average particle size and polydispersity index (PDI). Compare this size to the DLS-measured size of the iron oxide nanoparticle alone. ANX-SPIO DLS results showed a conjugate particle hydrodynamic diameter of 78 nm with a PDI of 0.131, reflecting a homogenous ANX-SPIO species3.</li>
</ol>
3. Cell Culture, Induction of Apoptosis in Culture, and MRI of Cultured Cells
<ol>
	<li>Culture adult mouse bone marrow mesenchymal stem cells (mMSCs) in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (Invitrogen, Inc.), preferably at passage 20-304.</li>
	<li>Induce apoptosis in the culture cells by treating for varying times at 37 &deg;C with DOX (Sigma, 1 mM in 0.9% saline, 1 &mu;M concentration in media)12.</li>
	<li>Quantify the amount of apoptosis in culture using either MRI with ANX-SPIO (described in 3.4 below) or using microscopy after TUNEL stain (APO-BrdUTM TUNEL Assay Kit, Molecular Probes/Invitrogen, Eugene, OR) or after stain with ANX-FITC (Roche, Switzerland).</li>
	<li>Label the cells with ANX-SPIO (10 mg protein/mL medium except as noted), or with an equivalent weight of free SPIO (5 mg), for 15 min at 37 &deg;C. Wash 4 times with PBS, and overlay with 1 mL of 1% agarose to prevent diffusion of the SPIO nanoparticles. Perform MRI of the dishes (described below). Alternatively, wash the cells and trypsinize after DOX and ANX-SPIO labeling, then allow the cells to form pellets in Eppendorf tubes.</li>
</ol>
4. In Vitro MRI
<ol>
	<li>Use a 1.5 or 3 Tesla GE Signa EXCITE scanner with standard knee receiver coil for in vitro MRI analysis.</li>
	<li>Place the culture dishes or tubes into an agar phantom, and image using a gradient-echo spoiled gradient sequence: Repetition Time (TR) 550 ms, Echo Time (TE) 10 ms, flip angle 15&deg;, matrix 256 x 256, field-of-view 3 cm x 3 cm, slice thickness 1.3 mm, number of averages (NEX) 2, spacing 0 mm5. Image axially through the cell layer on the plate for T2* signal loss, using regions-of-interest (ROIs) of a fixed area (for instance, 0.8 mm2). Adjust for background using control ROI signal from the agar phantom. Measure the background noise from the signal of the air surrounding the phantom.</li>
	<li>Calculate the MRI Contrast-to-Noise Ratio (CNR: [SI sample ROI-SI control ROI]/[SD of SI of background noise], where SI is signal intensity, and SD is standard deviation) was calculated for each culture dish.</li>
</ol>
5. Representative Results
Measurement of T2* signal loss in vitro requires a homogeneous agar phantom and the lack of air bubbles, which will create signal void artifact. This artifact is difficult to distinguish from genuine T2* signal loss of SPIO, and is critical to interpretable results. Please see Figure 1 for an example of an air artifact as well as genuine iron oxide T2* signal loss.
For in vitro culture dish imaging, apply an appropriate volume of agar gel to each culture dish, so that sufficient axial MRI slices, which are approximately 1 mm thick, can be made to adequately image the entire dish. Figure 2 illustrates the expected MRI signal from individual culture plates in agar. There is typically some signal variation at the edges of the plate, so analysis of regions of interest should avoid these uneven areas.
<img alt="Figure 1" src="/files/ftp_upload/3775/3775fig1.jpg" /> 
Figure 1. ANX-SPIO detects apoptosis in cultured neonatal rat cardiomyocytes. Figure 1A shows a photo of pelleted neonatal cardiomyocytes treated with control solution (left tube), ANX-SPIO (middle tube), and DOX+ANX-SPIO (right tube). Note the brownish color of the DOX+ANX-SPIO treated cells, reflecting increased retention of the ANX-SPIO compound in apoptotic cells. Figure 1B In vitro MRI images show the intense T2* signal loss of the DOX+ANX-SPIO cells. Also, an air bubble is seen between the 4th and 5th Eppendorf tubes (small black signal void), which is similar to the signal void of ANX-SPIO, and which can affect analysis of CNR.
<img alt="Figure 2" src="/files/ftp_upload/3775/3775fig2.jpg" /> 
Figure 2. ANX-SPIO binding is specific for apoptotic cells in culture. Figure 2A demonstrates apoptotic rat neonatal cardiomyocytes on culture dishes, subjected to either ANX-FLUOS staining or ANX-SPIO staining, with low and high concentrations (left and right, respectively) of ANX-SPIO. Note the different T2* signal loss (black signal) of apoptotic cells that were treated with fluorescent ANX (ANX-FLUOS) and low levels versus high levels of ANX-SPIO. The increased T2* signal loss on the right is associated with a markedly reduced ANX-FLUOS signal, which has been competed off by higher ASX-SPIO concentrations. Figure 2B illustrates the competitive binding of ANX-SPIO versus ANX-FLUOS signal and the dissociation constant, Ki. The X-axis denotes the Annexin protein concentration in log scale.
Movie 1. <a href="https://www.jove.com/files/ftp_upload/3775/3775movie1.mov" target="_blank"> Click here to view supplemental movie</a>.

<ol>
	<li>Dash, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+molecular+MRI+probe+to+detect+treatment+of+cardiac+apoptosis+in+vivo.">A molecular MRI probe to detect treatment of cardiac apoptosis in vivo.</a> Magn. Reson. Med. , (2011).</li><li>Khym, J. X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+reaction+of+methylamine+with+periodate-oxidized+adenosine+5'-phosphate.">The reaction of methylamine with periodate-oxidized adenosine 5'-phosphate.</a> Biochemistry. 2, 344-350 (1963).</li><li>Liu, Y. Y., Yu, Y., Zhang, G. B., Tang, M. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation,+characterization,+and+controlled+release+of+novel+nanoparticles+based+on+MMA/beta-CD+copolymers.">Preparation, characterization, and controlled release of novel nanoparticles based on MMA/beta-CD copolymers.</a> Macromol. Biosci. 7, 1250-1257 (2007).</li><li>Seo, W. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FeCo/graphitic-shell+nanocrystals+as+advanced+magnetic-resonance-imaging+and+near-infrared+agents.">FeCo/graphitic-shell nanocrystals as advanced magnetic-resonance-imaging and near-infrared agents.</a> Nat. Mater. 5, 971-976 (2006).</li><li>Hsiao, J. 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No conflicts of interest declared.

The described conjugation method for linking SPIO to Annexin V exploits the side chain amine groups of Annexin and the carboxyl moieties of the SPIO nanoparticle. Through specific oxidation-reduction steps, covalent linkage of these compounds can be achieved, and the resulting functionalized nanoparticle can be isolated. This method may be generalized to other proteins and nanoparticles of interest.
The most critical steps are the oxidation and reduction conditions, carried out in the approp...

<table border="1">
	<tbody>
 	<tr>
 	<td>Name of Reagent</td>
 <td>Company</td>
 <td>Catalogue #</td>
 </tr>
 <tr>
 	<td>Superparamagnetic iron oxide</td>
 <td>Ocean Nanotech, Inc.</td>
 <td>ICK-40-005</td>
 </tr>
 <tr>
 	<td>Doxorubicin</td>
 <td>Sigma</td>
 <td>D1515-10MG</td>
 </tr>
 <tr>
 	<td>SuperMag Separator</td>
 <td>Ocean Nanotech, Inc.</td>
 <td>N/A</td>
 </tr>
 <tr>
 	<td>Zetasizer Nano DLS machine</td>
 <td>Malvern, Inc</td>
 <td>N/A</td>
 </tr>
 </tbody>
 </table>

synthesis of an in vivo mri-detectable apoptosis probe

Cellular apoptosis is a prominent feature of many diseases, and this programmed cell death typically occurs before clinical manifestations of disease are evident. A means to detect apoptosis in its earliest, reversible stages would afford a pre-clinical 'window' during which preventive or therapeutic measures could be taken to protect the heart from permanent damage. We present herein a simple and robust method to conjugate human Annexin V (ANX), which avidly binds to cells in the earliest, reversible stages of apoptosis, to superparamagnetic iron oxide (SPIO) nanoparticles, which serve as an MRI-detectable contrast agent. The conjugation method begins with an oxidation of the SPIO nanoparticles, which oxidizes carboxyl groups on the polysaccharide shell of SPIO. Purified ANX protein is then added in the setting of a sodium borate solution to facilitate covalent interaction of ANX with SPIO in a reducing buffer. A final reduction step with sodium borohydride is performed to complete the reduction, and then the reaction is quenched. Unconjugated ANX is removed from the mix by microcentrifuge filtration. The size and purity of the ANX-SPIO product is verified by dynamic light scattering (DLS). This method does not require addition to, or modification of, the polysaccharide SPIO shell, as opposed to cross-linked iron oxide particle conjugation methods or biotin-labeled nanoparticles. As a result, this method represents a simple, robust approach that may be extended to conjugation of other proteins of interest.

Watch this Scientific Journal Video about Synthesis of an In vivo MRI-detectable Apoptosis Probe at JoVE.com

Synthesis of an In vivo MRI-detectable Apoptosis Probe

Early detection of apoptosis may identify at-risk cell populations in a variety of diseases. Here we demonstrate a method to link an early apoptosis-detection protein (Annexin V) to a MRI-detectable iron oxide nanoparticle (SPIO). This method may be extended to other proteins of interest to generate MRI-detectable molecular imaging probes.

Synthesis of an In vivo MRI-detectable Apoptosis Probe

Cellular apoptosis is a prominent feature of many diseases, and this programmed cell death typically occurs before clinical manifestations of disease are ...

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9.1K Views.  Stanford University Medical Center. Early detection of apoptosis may identify at-risk cell populations in a variety of diseases. Here we demonstrate a method to link an early apoptosis-detection protein (Annexin V) to a MRI-detectable iron oxide nanoparticle (SPIO). This method may be extended to other proteins of interest to generate MRI-detectable molecular imaging probes.

Video: Synthesis of an In vivo MRI-detectable Apoptosis Probe

Homemade Site Directed Mutagenesis of Whole Plasmids

Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. With this method the cloned target gene can be altered by substitution, deletion or insertion of a few bases directly into a plasmid. It works by simply amplifying the whole plasmid, in a non PCR-based thermocycling reaction. During the reaction mutagenic primers, carrying the desired mutation, are integrated into the newly synthesized plasmid. In this video tutorial we demonstrate an easy and cost effective way to introduce base substitutions into a plasmid. The protocol works with standard reagents and is independent from commercial kits, which often are very expensive. Applying this protocol can reduce the total cost of a reaction to an eighth of what it costs using some of the commercial kits. In this video we also comment on critical steps during the process and give detailed instructions on how to design the mutagenic primers.

Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. Here we demonstrate an easy and cost effective way to introduce base substitutions into a plasmid using standard reagents.

Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. With this method the cloned ...

Photoconversion of Purified Fluorescent Proteins and Dual-probe Optical Highlighting in Live Cells

Photoconvertible fluorescent proteins (pc-FPs) are a class of fluorescent proteins with "optical highlighter" capability, meaning that the color of fluorescence can be changed by exposure to light of a specific wavelength. Optical highlighting allows noninvasive marking of a subpopulation of fluorescent molecules, and is therefore ideal for tracking single cells or organelles.
Critical parameters for efficient photoconversion are the intensity and the exposure time of the photoconversion light. If the intensity is too low, photoconversion will be slow or not occur at all. On the other hand, too much intensity or too long exposure can photobleach the protein and thereby reduce the efficiency of photoconversion.
This protocol describes a general approach how to set up a confocal laser scanning microscope for pc-FP photoconversion applications. First, we describe a procedure for preparing purified protein droplet samples. This sample format is very convenient for studying the photophysical behavior of fluorescent proteins under the microscope. Second, we will use the protein droplet sample to show how to configure the microscope for photoconversion. And finally, we will show how to perform optical highlighting in live cells, including dual-probe optical highlighting with mOrange2 and Dronpa.

This protocol describes a general approach to perform photoconversion of fluorescent proteins on a confocal laser scanning microscope. We describe procedures for the photoconversion of puried protein samples, as well as for dual-probe optical highlighting in live cells with mOrange2 and Dronpa.

Photoconvertible fluorescent proteins (pc-FPs) are a class of fluorescent proteins with "optical highlighter" capability, meaning that the color of ...

In vivo Imaging and Therapeutic Treatments in an Orthotopic Mouse Model of Ovarian Cancer

Human cancer and response to therapy is better represented in orthotopic animal models. This paper describes the development of an orthotopic mouse model of ovarian cancer, treatment of cancer via oral delivery of drugs, and monitoring of tumor cell behavior in response to drug treatment in real time using in vivo imaging system. In this orthotopic model, ovarian tumor cells expressing luciferase are applied topically by injecting them directly into the mouse bursa where each ovary is enclosed. Upon injection of D-luciferin, a substrate of firefly luciferase, luciferase-expressing cells generate bioluminescence signals. This signal is detected by the in vivo imaging system and allows for a non-invasive means of monitoring tumor growth, distribution, and regression in individual animals. Drug administration via oral gavage allows for a maximum dosing volume of 10 mL/kg body weight to be delivered directly to the stomach and closely resembles delivery of drugs in clinical treatments. Therefore, techniques described here, development of an orthotopic mouse model of ovarian cancer, oral delivery of drugs, and in vivo imaging, are useful for better understanding of human ovarian cancer and treatment and will improve targeting this disease.

In vivo Imaging and Therapeutic Treatments in an Orthotopic Mouse Model of Ovarian Cancer

Orthotopic animal models of ovarian cancer replicate better human disease and therefore enhance our understanding of cancer progression and tumor response to therapy. A mouse model receives an intrabursal injection of luciferase-expressing ovarian tumor cells. Treatment is administered via oral gavage. Tumor growth is monitored by in vivo imaging system.

Human cancer and response to therapy is better represented in orthotopic animal models.  This paper describes the development of an orthotopic mouse model ...

Activation of Apoptosis by Cytoplasmic Microinjection of Cytochrome c

Apoptosis, or programmed cell death, is a conserved and highly regulated pathway by which cells die1. Apoptosis can be triggered when cells encounter a wide range of cytotoxic stresses. These insults initiate signaling cascades that ultimately cause the release of cytochrome c from the mitochondrial intermembrane space to the cytoplasm2. The release of cytochrome c from mitochondria is a key event that triggers the rapid activation of caspases, the key cellular proteases which ultimately execute cell death3-4.
The pathway of apoptosis is regulated at points upstream and downstream of cytochrome c release from mitochondria5. In order to study the post-mitochondrial regulation of caspase activation, many investigators have turned to direct cytoplasmic microinjection of holocytochrome c (heme-attached) protein into cells6-9. Cytochrome c is normally localized to the mitochondria where attachment of a heme group is necessary to enable it to activate apoptosis10-11. Therefore, to directly activate caspases, it is necessary to inject the holocytochrome c protein instead of its cDNA, because while the expression of cytochrome c from cDNA constructs will result in mitochondrial targeting and heme attachment, it will be sequestered from cytosolic caspases. Thus, the direct cytosolic microinjection of purified heme-attached cytochrome c protein is a useful tool to mimic mitochondrial cytochrome c release and apoptosis without the use of toxic insults which cause cellular and mitochondrial damage.
In this article, we describe a method for the microinjection of cytochrome c protein into cells, using mouse embryonic fibroblasts (MEFs) and primary sympathetic neurons as examples. While this protocol focuses on the injection of cytochrome c for investigations of apoptosis, the techniques shown here can also be easily adapted for microinjection of other proteins of interest.

Activation of Apoptosis by Cytoplasmic Microinjection of Cytochrome c

In this protocol, we describe the direct cytoplasmic microinjection of cytochrome c protein into fibroblasts and primary sympathetic neurons. This technique allows for the introduction of cytochrome c protein into the cytoplasm of cells and mimics the release of cytochrome c from mitochondria, which occurs during apoptosis.

Apoptosis, or programmed cell death, is a conserved and highly regulated pathway by which cells die1.  Apoptosis can be triggered when cells encounter a ...

The Tomato/GFP-FLP/FRT Method for Live Imaging of Mosaic Adult Drosophila Photoreceptor Cells

The Drosophila eye is widely used as a model for studies of development and neuronal degeneration. With the powerful mitotic recombination technique, elegant genetic screens based on clonal analysis have led to the identification of signaling pathways involved in eye development and photoreceptor (PR) differentiation at larval stages. We describe here the Tomato/GFP-FLP/FRT method, which can be used for rapid clonal analysis in the eye of living adult Drosophila. Fluorescent photoreceptor cells are imaged with the cornea neutralization technique, on retinas with mosaic clones generated by flipase-mediated recombination. This method has several major advantages over classical histological sectioning of the retina: it can be used for high-throughput screening and has proved an effective method for identifying the factors regulating PR survival and function. It can be used for kinetic analyses of PR degeneration in the same living animal over several weeks, to demonstrate the requirement for specific genes for PR survival or function in the adult fly. This method is also useful for addressing cell autonomy issues in developmental mutants, such as those in which the establishment of planar cell polarity is affected.

The Tomato/GFP-FLP/FRT Method for Live Imaging of Mosaic Adult Drosophila Photoreceptor Cells

The Tomato/GFP-FLP/FRT method involves visualizing mosaic photoreceptor cells in living Drosophila. It can be used to follow individual photoreceptor cell fates in the retina for days or weeks. This method is ideal for studies of retinal degeneration and neurodegenerative diseases or photoreceptor cell development.

The Drosophila eye is widely used as a model  for studies of development and neuronal degeneration. With the powerful mitotic  recombination technique, ...

Analysis of Apoptosis in Zebrafish Embryos by Whole-mount Immunofluorescence to Detect Activated Caspase 3

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis in zebrafish embryos. The whole-mount analysis provides spatial information in regard to tissue specificity of apoptosing cells, although sectioning and/or colabeling is ultimately required to pinpoint the exact cell types undergoing apoptosis. The whole-mount Casp3 assay is optimized for analysis of fixed embryos between the 4-cell stage and 32 hr-post-fertilization and is useful for a number of applications, including analysis of zebrafish mutants and morphants, overexpression of mutant and wild-type mRNAs, and exposure to chemicals. Compared to acridine orange staining, which can identify apoptotic cells in live embryos in a matter of hours, Casp3 and TUNEL assays take considerably longer to complete (2-4 days). However, because of the dynamic nature of apoptotic cell formation and clearance, analysis of fixed embryos ensures accurate comparison of apoptotic cells across multiple samples at specific time points. We have also found the Casp3 assay to be superior to analysis of apoptotic cells by the whole-mount TUNEL assay in regard to cost and reliability. Overall, the Casp3 assay represents a robust, highly reproducible assay in which to analyze apoptotic cells in early zebrafish embryos.

Certain genetic perturbations or exposure to toxins can disrupt normal developmental processes leading to death of specific cell types. The analysis of activated Caspase 3 by whole-mount immunofluorescence in zebrafish embryos reveals stage- and tissue-specific localization of cells specifically undergoing apoptosis.

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis ...

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos

Many cellular processes are controlled by multisubunit protein complexes. Frequently these complexes form transiently and require native environment to assemble. Therefore, to identify these functional protein complexes, it is important to stabilize them in vivo before cell lysis and subsequent purification. Here we describe a method used to isolate large bona fide protein complexes from Drosophila embryos. This method is based on embryo permeabilization and stabilization of the complexes inside the embryos by in vivo crosslinking using a low concentration of formaldehyde, which can easily cross the cell membrane. Subsequently, the protein complex of interest is immunopurified followed by gel purification and analyzed by mass spectrometry. We illustrate this method using purification of a Tudor protein complex, which is essential for germline development. Tudor is a large protein, which contains multiple Tudor domains - small modules that interact with methylated arginines or lysines of target proteins. This method can be adapted for isolation of native protein complexes from different organisms and tissues.

An in vivo Crosslinking Approach to Isolate Protein Complexes From Drosophila Embryos

Multi-component protein complexes play crucial roles during cellular function and development. Here we describe a method used to isolate native protein complexes from Drosophila embryos after in vivo crosslinking followed by purification of the crosslinked complexes for subsequent structure-function analysis.

Many cellular processes are controlled by multisubunit protein complexes. Frequently these complexes form transiently and require native environment to ...

Measurement of Heme Synthesis Levels in Mammalian Cells

Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in various molecular and cellular processes such as gene transcription, translation, cell differentiation and cell proliferation. The biosynthesis levels of heme vary across different tissues and cell types and is altered in diseased conditions such as anemia, neuropathy and cancer. This technique uses [4-14C] 5-aminolevulinic acid ([14C] 5-ALA), one of the early precursors in the heme biosynthesis pathway to measure the levels of heme synthesis in mammalian cells. This assay involves incubation of cells with [14C] 5-ALA followed by extraction of heme and measurement of the radioactivity incorporated into heme. This procedure is accurate and quick. This method measures the relative levels of heme biosynthesis rather than the total heme content. To demonstrate the use of this technique the levels of heme biosynthesis were measured in several mammalian cell lines.

Altered intracellular heme levels are associated with common diseases such as cancer. Thus, there is a need to measure heme biosynthesis levels in diverse cells. The goal of this protocol is to provide a fast and sensitive method to measure and compare the levels of heme synthesis in different cells.

Heme serves as the prosthetic group for a wide variety of proteins known as hemoproteins, such as hemoglobin, myoglobin and cytochromes. It is involved in ...

Strategies for Tracking Anastasis, A Cell Survival Phenomenon that Reverses Apoptosis

Anastasis (Greek for &#8220;rising to life&#8221;) refers to the recovery of dying cells. Before these cells recover, they have passed through important checkpoints of apoptosis, including mitochondrial fragmentation, release of mitochondrial cytochrome c into the cytosol, activation of caspases, chromatin condensation, DNA damage, nuclear fragmentation, plasma membrane blebbing, cell shrinkage, cell surface exposure of phosphatidylserine, and formation of apoptotic bodies. Anastasis can occur when apoptotic stimuli are removed prior to death, thereby allowing dying cells to reverse apoptosis and potentially other death mechanisms. Therefore, anastasis appears to involve physiological healing processes that could also sustain damaged cells inappropriately. The functions and mechanisms of anastasis are still unclear, hampered in part by the limited tools for detecting past events after the recovery of apparently healthy cells. Strategies to detect anastasis will enable studies of the physiological mechanisms, the hazards of undead cells in disease pathology, and potential therapeutics to modulate anastasis. Here, we describe effective strategies using live cell microscopy and a mammalian caspase biosensor&#160;for identifying and tracking anastasis in mammalian cells.

The term anastasis refers to the phenomenon in which dying cells reverse a cell suicide process at a late stage, repair themselves, and ultimately survive. Here we demonstrate protocols for detecting and tracking cells that undergo anastasis.

Anastasis (Greek for &#8220;rising to life&#8221;) refers to the recovery of dying cells. Before these cells recover, they have passed through important ...

Assessment of Selective mRNA Translation in Mammalian Cells by Polysome Profiling

Regulation of protein synthesis represents a key control point in cellular response to stress. In particular, discreet RNA regulatory elements were shown to allow to selective translation of specific mRNAs, which typically encode for proteins required for a particular stress response. Identification of these mRNAs, as well as the characterization of regulatory mechanisms responsible for selective translation has been at the forefront of molecular biology for some time. Polysome profiling is a cornerstone method in these studies. The goal of polysome profiling is to capture mRNA translation by immobilizing actively translating ribosomes on different transcripts and separate the resulting polyribosomes by ultracentrifugation on a sucrose gradient, thus allowing for a distinction between highly translated transcripts and poorly translated ones. These can then be further characterized by traditional biochemical and molecular biology methods. Importantly, combining polysome profiling with high throughput genomic approaches allows for a large scale analysis of translational regulation.

The ability of cells to adapt to stress is crucial for their survival. Regulation of mRNA translation is one such adaptation strategy, providing for rapid regulation of the proteome. Here, we provide a standardized polysome profiling protocol to identify specific mRNAs that are selectively translated under stress conditions.

Regulation of protein synthesis represents a key control point in cellular response to stress. In particular, discreet RNA regulatory elements were shown ...