Name: reconstitution of cell-cycle oscillations in microemulsions of cell-free xenopus egg extracts
Uploaded: 2018-09-27T14:30:00
Description: Watch this Scientific Journal Video about Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts at JoVE.com

We thank Madeleine Lu for constructing securin-mCherry plasmid, Lap Man Lee,&#160;Kenneth Ho and Allen P Liu&#160;for discussions about droplet generation, Jeremy B. Chang and James E. Ferrell Jr for providing GFP-NLS construct. This work was supported by the National Science Foundation (Early CAREER Grant #1553031), the National Institutes of Health (MIRA #GM119688), and a Sloan Research Fellowship.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of University of Michigan.
1. Preparation of Materials for Cell Cycle Reconstitution and Detection
<ol>
	<li>Gibson Assembly cloning for the plasmid DNA construction and mRNA purification of securin-mCherry
	<ol>
		<li>Prepare three DNA fragments including a pMTB2 vector backbone, securin, and mCherry through polymerase chain reaction (PCR) and gel purification<sup class=...

<ol>
	<li>Murray, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+cycle+extracts.">Cell cycle extracts.</a> Methods in Cell Biology. 36, 581-605 (1991).</li><li>Hannak, E., Heald, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigating+mitotic+spindle+assembly+and+function+in+vitro+using+Xenopus+laevis+egg+extracts.">Investigating mitotic spindle assembly and function in vitro using Xenopus laevis egg extracts.</a> Nature Protocols. 1, 2305-2314 (2006).</li><li>Murray, A. W., Solomon, M. J., Kirschner, M. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+cyclin+synthesis+and+degradation+in+the+control+of+maturation+promoting+factor+activity.">The role of cyclin synthesis and degradation in the control of maturation promoting factor activity.</a> Nature. 339, 280-286 (1989).</li><li>Yang, Q., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cdk1-APC/C+cell+cycle+oscillator+circuit+functions+as+a+time-delayed,+ultrasensitive+switch.">The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch.</a> Nature Cell Biology. 15, 519-525 (2013).</li><li>Chang, J. B., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitotic+trigger+waves+and+the+spatial+coordination+of+the+Xenopus+cell+cycle.">Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle.</a> Nature. 500, 603-607 (2013).</li><li>Trunnell, N. B., Poon, A. C., Kim, S. Y., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrasensitivity+in+the+Regulation+of+Cdc25C+by+Cdk1.">Ultrasensitivity in the Regulation of Cdc25C by Cdk1.</a> Molecular Cell. 41, 263-274 (2011).</li><li>Kim, S. Y., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Substrate+competition+as+a+source+of+ultrasensitivity+in+the+inactivation+of+Wee1.">Substrate competition as a source of ultrasensitivity in the inactivation of Wee1.</a> Cell. 128, 1133-1145 (2007).</li><li>Pomerening, J. R., Kim, S. Y., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Systems-level+dissection+of+the+cell-cycle+oscillator:+bypassing+positive+feedback+produces+damped+oscillations.">Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations.</a> Cell. 122, 565-578 (2005).</li><li>Pomerening, J. R., Sontag, E. D., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Building+a+cell+cycle+oscillator:+hysteresis+and+bistability+in+the+activation+of+Cdc2.">Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2.</a> Nature Cell Biology. 5, 346-351 (2003).</li><li>Telley, I. A., Gaspar, I., Ephrussi, A., Surrey, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aster+migration+determines+the+length+scale+of+nuclear+separation+in+the+Drosophila+syncytial+embryo.">Aster migration determines the length scale of nuclear separation in the Drosophila syncytial embryo.</a> The Journal of Cell Biology. 197, 887-895 (2012).</li><li>Telley, I. A., Gaspar, I., Ephrussi, A., Surrey, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+single+Drosophila+embryo+extract+for+the+study+of+mitosis+ex+vivo.">A single Drosophila embryo extract for the study of mitosis ex vivo.</a> Nature Protocols. 8, 310-324 (2013).</li><li>Tsai, T. Y. C., Theriot, J. A., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+Oscillatory+Dynamics+in+the+Cell+Cycle+of+Early+Xenopus+laevis+Embryos.">Changes in Oscillatory Dynamics in the Cell Cycle of Early Xenopus laevis Embryos.</a> PLoS Biology. 12, e1001788 (2014).</li><li>Chang, J. B., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitotic+trigger+waves+and+the+spatial+coordination+of+the+Xenopus+cell+cycle.">Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle.</a> Nature. 500, 603-607 (2013).</li><li>Yang, Q., Ferrell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cdk1-APC/C+cell+cycle+oscillator+circuit+functions+as+a+time-delayed,+ultrasensitive+switch.">The Cdk1-APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch.</a> Nature Cell Biology. 15, 519-525 (2013).</li><li>Kumagai, A., Dunphy, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Claspin,+a+novel+protein+required+for+the+activation+of+Chk1+during+a+DNA+replication+checkpoint+response+in+Xenopus+egg+extracts.">Claspin, a novel protein required for the activation of Chk1 during a DNA replication checkpoint response in Xenopus egg extracts.</a> Molecular Cell. 6, 839-849 (2000).</li><li>Chen, R. H., Murray, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+spindle+assembly+checkpoint+in+Xenopus+egg+extracts.">Characterization of spindle assembly checkpoint in Xenopus egg extracts.</a> Methods in Enzymology. 283, 572-584 (1997).</li><li>Chen, R. H., Waters, J. C., Salmon, E. D., Murray, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Association+of+spindle+assembly+checkpoint+component+XMAD2+with+unattached+kinetochores.">Association of spindle assembly checkpoint component XMAD2 with unattached kinetochores.</a> Science. 274, 242-246 (1996).</li><li>Minshull, J., Sun, H., Tonks, N. K., Murray, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+MAP+kinase-dependent+spindle+assembly+checkpoint+in+Xenopus+egg+extracts.">A MAP kinase-dependent spindle assembly checkpoint in Xenopus egg extracts.</a> Cell. 79, 475-486 (1994).</li><li>Good, M. C., Vahey, M. D., Skandarajah, A., Fletcher, D. A., Heald, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cytoplasmic+Volume+Modulates+Spindle+Size+During+Embryogenesis.">Cytoplasmic Volume Modulates Spindle Size During Embryogenesis.</a> Science. 342, 856-860 (2013).</li><li>Hazel, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+cytoplasmic+volume+are+sufficient+to+drive+spindle+scaling.">Changes in cytoplasmic volume are sufficient to drive spindle scaling.</a> Science. 342, 853-856 (2013).</li><li>Garibyan, L., Avashia, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Research+Techniques+Made+Simple:+Polymerase+Chain+Reaction+(PCR).">Research Techniques Made Simple: Polymerase Chain Reaction (PCR).</a> The Journal of Investigative Dermatology. 133, e6 (2013).</li><li>Hecker, K. H., Roux, K. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+and+low+annealing+temperatures+increase+both+specificity+and+yield+in+touchdown+and+stepdown+PCR.">High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR.</a> BioTechniques. 20, 478-485 (1996).</li><li>Gibson, D. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzymatic+assembly+of+DNA+molecules+up+to+several+hundred+kilobases.">Enzymatic assembly of DNA molecules up to several hundred kilobases.</a> Nature Methods. 6, 343-345 (2009).</li><li>Froger, A., Hall, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transformation+of+Plasmid+DNA+into+E.+coli+Using+the+Heat+Shock+Method.">Transformation of Plasmid DNA into E. coli Using the Heat Shock Method.</a> Journal of Visualized Experiments. 6, e253 (2007).</li><li>Torreilles, S. L., McClure, D. E., Green, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+and+refinement+of+euthanasia+methods+for+Xenopus+laevis.">Evaluation and refinement of euthanasia methods for Xenopus laevis.</a> Journal of the American Association for Laboratory Animal Science. 48, 512-516 (2009).</li><li>Sive, H. L., Grainger, R. M., Harland, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolating+Xenopus+laevis+Testes.">Isolating Xenopus laevis Testes.</a> Cold Spring Harbor Protocols. 2007, (2007).</li><li>Showell, C., Conlon, F. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Egg+Collection+and+In+vitro+Fertilization+of+the+Western+Clawed+Frog+Xenopus+tropicalis.">Egg Collection and In vitro Fertilization of the Western Clawed Frog Xenopus tropicalis.</a> Cold Spring Harbor Protocols. 2009, (2009).</li><li>Wilson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Methods in Enzymology. 91, 236-247 (1983).</li><li>Schutze, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+streamlined+protocol+for+emulsion+polymerase+chain+reaction+and+subsequent+purification.">A streamlined protocol for emulsion polymerase chain reaction and subsequent purification.</a> Analytical Biochemistry. 410, 155-157 (2011).</li><li>Weitz, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversity+in+the+dynamical+behaviour+of+a+compartmentalized+programmable+biochemical+oscillator.">Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator.</a> Nature Chemistry. 6, 295-302 (2014).</li><li>Ho, K. K., Lee, J. W., Durand, G., Majumder, S., Liu, A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+aggregation+with+poly(vinyl)+alcohol+surfactant+reduces+double+emulsion-encapsulated+mammalian+cell-free+expression.">Protein aggregation with poly(vinyl) alcohol surfactant reduces double emulsion-encapsulated mammalian cell-free expression.</a> PloS One. 12, e0174689 (2017).</li><li>Nakajima, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reconstitution+of+circadian+oscillation+of+cyanobacterial+KaiC+phosphorylation+in+vitro.">Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro.</a> Science. 308, 414-415 (2005).</li><li>Guan, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+robust+and+tunable+mitotic+oscillator+in+artificial+cells.">A robust and tunable mitotic oscillator in artificial cells.</a> eLife. 7, (2018).</li></ol>

We have presented a novel method for developing a high-throughput artificial cell system that enables in vitro reconstitution and long-term tracking of self-sustained cell-cycle oscillations at the single-cell level. There are several critical steps that make this method successful. First, freshly squeezed Xenopus eggs with a good quality, compared with laid eggs, tend to produce extracts with longer-lasting oscillation activity. Second, encapsulation of extracts within the surfactant-stabilized microen...

Cytoplasmic extracts prepared from Xenopus laevis eggs represent one of the most predominant models for the biochemical study of cell cycles, given the large volume of oocytes, the rapid cell cycle progression, and the capability of reconstituting mitotic events in vitro1,2. This system has allowed the initial discovery and mechanistic characterization of essential cell-cycle regulators like maturation-promoting factor (MPF) as well as downstream mitotic processes including spindle assembly and chromosome segregation1,2,3,4,5,6,7,8,9,10,11. The Xenopus egg extracts have also been used for detailed dissection of the regulatory networks of the cell cycle clock8,12,13,14 and for studies of the DNA damage/replication checkpoint15 and the mitotic spindle assembly checkpoint16,17,18.
These studies of cell cycles using the Xenopus egg extracts have mainly been based on bulk measurements. However, conventional bulk reaction assays may not mimic real cell behaviors, given a major discrepancy in their dimensions and subcellular spatial compartmentalization of reaction molecules. Moreover, bulk measurements of mitotic activities are prone to giving a limited number of cycles before quickly damping8. These disadvantages of bulk reactions have prevented the extract system to provide further understanding of complex clock dynamic properties and functions. Recent studies have encapsulated cell-free cytostatic factor-arrested (CSF) Xenopus extracts19,20 into size-defined cell-like compartments, which have helped elucidate how spindle size is modulated by the cytoplasmic volume. However, this in vitro system is arrested at metaphase of meiosis II by the action of cytostatic factor1, and a system capable of long-term sustained oscillations at the single-cell level is needed for further investigation of the cell cycle oscillator.
To study cell cycle oscillations with single-cell resolution, we have developed a cell-scale, high-throughput system for reconstitution and simultaneous measurement of multiple self-sustained mitotic oscillatory processes in individual microemulsion droplets. In this detailed video protocol, we demonstrate the creation of the artificial mitotic oscillation system by encapsulating cycling Xenopus laevis egg cytoplasm in microemulsions of sizes ranging from 10 to 300 &#181;m. In this system, mitotic oscillations including chromosome condensation and de-condensation, nuclear envelope breakdown and reformation, and the degradation and synthesis of anaphase substrates (e.g., securin-mCherry in this protocol) were successfully reconstituted.

<table border="0" cellpadding="0" cellspacing="0" width="593">
	<tbody>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">Xenopus laevis frogs</td>
			<td style="width:93px;">Xenopus-I Inc.</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:215px;">QIAprep spin miniprep kit</td>
			<td style="width:93px;">QIAGEN</td>
			<td style="width:119px;">27104</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">QIAquick PCR Purification Kit (250)</td>
			<td style="width:93px;">QIAGEN</td>
			<td style="width:119px;">28106</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">mMESSAGE mMACHINE SP6 Transcription Kit</td>
			<td style="width:93px;">Ambion</td>
			<td style="width:119px;">AM1340</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">BL21 (DE3)-T-1 competent cell</td>
			<td style="width:93px;">Sigma-Aldrich</td>
			<td style="width:119px;">B2935</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">Calcium ionophore</td>
			<td style="width:93px;">Sigma-Aldrich</td>
			<td style="width:119px;">A23187</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">Hoechst 33342</td>
			<td style="width:93px;">Sigma-Aldrich</td>
			<td style="width:119px;">B2261</td>
			<td style="width:167px;">Toxic</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:215px;">Trichloro</td>
			<td rowspan="2" style="width:93px;">Sigma-Aldrich</td>
			<td rowspan="2" style="width:119px;">448931</td>
			<td rowspan="2" style="width:167px;">Toxic</td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">(1H,1H,2H,2H-perfluorooctyl) silane</td>
		</tr>
		<tr height="64">
			<td height="64" style="height:64px;width:215px;">PFPE-PEG surfactant</td>
			<td style="width:93px;">Ran Biotechnologies</td>
			<td style="width:119px;">008-FluoroSurfactant-2wtH-50G</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">GE Healthcare Glutathione Sepharose 4B beads</td>
			<td style="width:93px;">Sigma-Aldrich</td>
			<td style="width:119px;">GE17-0756-01</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">PD-10 column</td>
			<td style="width:93px;">Sigma-Aldrich</td>
			<td style="width:119px;">GE17-0851-01</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">VitroCom miniature hollow glass tubing</td>
			<td style="width:93px;">VitroCom</td>
			<td style="width:119px;">5012</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">Olympus SZ61 Stereo Microscope</td>
			<td style="width:93px;">Olympus</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:215px;">Olympus IX83 microscope</td>
			<td style="width:93px;">Olympus</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">Olympus FV1200 confocal microscope</td>
			<td style="width:93px;">Olympus</td>
			<td style="width:119px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">NanoDrop spectrophotometer</td>
			<td style="width:93px;">Thermofisher</td>
			<td style="width:119px;">ND-2000</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="43">
			<td height="43" style="height:43px;width:215px;">0.4 mL Snap-Cap Microtubes</td>
			<td style="width:93px;">E&#38;K Scientific</td>
			<td style="width:119px;">485050-B</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="34">
			<td height="54" rowspan="2" style="height:55px;width:215px;">&#160;PureLink RNA Mini Kit</td>
			<td rowspan="2" style="width:93px;">ThermoFisher&#65288;Ambion&#65289;</td>
			<td rowspan="2" style="width:119px;">12183018A</td>
			<td rowspan="2" style="width:167px;"></td>
		</tr>
		<tr height="20">
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:215px;">Fisherbrand Analog Vortex Mixer</td>
			<td style="width:93px;">Fisher Scientific</td>
			<td style="width:119px;">2215365</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:215px;">Imaris</td>
			<td style="width:93px;">Bitplane</td>
			<td style="width:119px;">Version 7.3</td>
			<td>Image analysis software</td>
		</tr>
	</tbody>
</table>

reconstitution of cell-cycle oscillations in microemulsions of cell-free xenopus egg extracts

Real-time measurement of oscillations at the single-cell level is important to uncover the mechanisms of biological clocks. Although bulk extracts prepared from Xenopus laevis eggs have been powerful in dissecting biochemical networks underlying the cell-cycle progression, their ensemble average measurement typically leads to a damped oscillation, despite each individual oscillator being sustained. This is due to the difficulty of perfect synchronization among individual oscillators in noisy biological systems. To retrieve the single-cell dynamics of the oscillator, we developed a droplet-based artificial cell system that can reconstitute mitotic cycles in cell-like compartments encapsulating cycling cytoplasmic extracts of Xenopus laevis eggs. These simple cytoplasmic-only cells exhibit sustained oscillations for over 30 cycles. To build more complicated cells with nuclei, we added demembranated sperm chromatin to trigger nuclei self-assembly in the system. We observed a periodic progression of chromosome condensation/decondensation and nuclei envelop breakdown/reformation, like in real cells. This indicates that the mitotic oscillator functions faithfully to drive multiple downstream mitotic events. We simultaneously tracked the dynamics of the mitotic oscillator and downstream processes in individual droplets using multi-channel time-lapse fluorescence microscopy. The artificial cell-cycle system provides a high-throughput framework for quantitative manipulation and analysis of mitotic oscillations with single-cell resolution, which likely provides important insights into the regulatory machinery and functions of the clock.

In Figure 2, we show that this protocol produces mitotic oscillations in both simple, nuclear-free cells as well as complicated cells with nuclei, where the oscillator drives the cyclic alternation of nuclei formation and deformation. The nuclei-free droplets generate mitotic oscillations up to 30 undamped cycles over the time span of 92 hours, as indicated by the periodic synthesis and degradation of a fluorescence reporter securin-mCherry (<strong class="xf...

Watch this Scientific Journal Video about Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts at JoVE.com

Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts

We present a method for the generation of in vitro self-sustained mitotic oscillations at the single-cell level by encapsulating egg extracts of Xenopus laevis in water-in-oil microemulsions.

Reconstitution of Cell-cycle Oscillations in Microemulsions of Cell-free Xenopus Egg Extracts

Real-time measurement of oscillations at the single-cell level is important to uncover the mechanisms of biological clocks. Although bulk extracts ...

This method can help answer key questions in the system biology field, such as the regulating mechanism behind the mitotic network and the dynamic properties and functions of the cell cycle clock. The main advantage of this technique is that it will generate a large quantity of droplets with multiple cell cycles in each, providing us with a high-throughput framework for quantitative manipulation and analysis. To begin, discard batches of eggs that have unclear boundaries between animal and vegetal poles or irregular white spots on top of animal poles.Next, select an appropriate batch of eggs from one female frog, and transfer the eggs to a 600-milliliter beaker. Pour out an excess of 0.2x MMR buffer, and gently add cysteine in 1x extract buffer to the eggs. After this, shake the beaker vigorously by hand to remove the jelly coats of the eggs.Repeat this wash three times with a total of 800 milliliters of cysteine buffer or until the eggs aggregate and settle at the bottom of the beaker. After the jelly coat is removed, wash the eggs four times in one liter of 0.2x MMR solution. Use a glass pipette to pick up and discard the eggs that turn white.Pour the MMR buffer out of the beaker, and add 200 milliliters of calcium ionophore solution into the eggs. Use a glass pipette to stir the eggs gently until they are activated, and remove the calcium ionophore solution. Leaving the eggs in calcium ionophore solution for too long will initiate apoptosis.We stir the eggs for 1.5 minutes and check the activation efficiency. If they are not activated, resume stirring, and check more frequently until 90%activation is achieved. After the eggs settle at the bottom of the beaker, check the activation efficiency.Well-activated eggs have approximately 25%of the animal pole and 75%of the vegetal pole. Next, wash the eggs twice with a total volume of 50 milliliters of extract buffer supplemented with protease inhibitors. Then, carefully transfer the eggs to a 0.4-milliliter snap-cap microtube.Centrifuge the microtube for 60 seconds at 200 g and then at 600 g for 30 seconds to pack the eggs. Then, use a glass Pasteur pipette to remove the excess buffer on top of the eggs after each step. After this, crush the eggs at 15, 000 g for 10 minutes at four degrees Celsius.Use a razor blade to cut the tubes to separate the three layers of crushed eggs and keep the crude cytoplasm in the middle layer. Then, transfer the crude cytoplasm to clean ultracentrifuge tubes. Supplement the cytoplasm with protease inhibitors and cytochalasin B at 10 micrograms per milliliter each.Centrifuge the crude cytoplasm at 15, 000 g and four degrees Celsius for five minutes. Then, use a razor blade to cut the tube and keep the cytoplasm in the middle layer. Place the freshly prepared extracts on ice.First, add securin-mCherry mRNA to the prepared extracts. Next, add 200 microliters of 2%PFPE-PEG fluorosurfactant to the extract mRNA mixture. Use a vortex mixer to generate droplets, adjusting the vortex speed and duration as needed.Then, visually inspect the droplets to ensure they are uniform in size. Using a 200-microliter pipette, transfer the droplets floating on top and an equal volume of surfactant to a PCR tube. Dip a glass tube into the droplet layer, and wait until the droplets fill approximately 75%of the tube.Then, push the tube into the surfactant layer, and fill the tube completely. Next, fill a glass-bottomed dish with mineral oil. Then, use fine tweezers to immerse the droplet-filled tube in the oil.Use a glass pipette to remove any visible debris or leaked droplets. To avoid movement and leakage of droplets, the glass tube filled with droplets should be immersed underneath mineral oil carefully. We can either push the tube on both ends with balance or add a few drops of mineral oil on the ends of the tube simultaneously first.After this, use an epifluorescence microscope equipped with a motorized xy stage to image the droplets. Record time-lapse videos in the bright field and multiple fluorescence channels every six to nine minutes until the droplets lose their activity. Using this protocol, mitotic oscillation in both simple, nuclear-free cells and complicated cells with nuclei were produced.The nuclei-free droplets generated mitotic oscillation up to 30 undamped cycles over 92 hours. The ability of the mitotic oscillator to drive downstream mitotic events was also examined. The self-sustained mitotic oscillator drove the changes of nuclear morphology observed through the autonomous alteration of distinct cell-cycle phases.While attempting this procedure, it's important to remember to mind the time when making the extract, as it is time-sensitive, and always keep the eggs and extract on ice. After its development, this technique paved the way for researchers in the field of system biology to explore fundamental principles of complex clock properties, like tunability and stochasticity in Xenopus laevis.

reconstitution-cell-cycle-oscillations-microemulsions-cell-free

Research

JoVE Journal

Biochemistry

Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones

Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones. The generated complex can be also asymmetrically modified, after including a premodified histone pool during refolding of histone subcomplexes. These asymmetric nucleosome preparations can be readily reacted with histone-modifying enzymes to study modification cross-talk mechanisms imposed by the asymmetrically pre-incorporated PTM using nuclear magnetic resonance (NMR) spectroscopy. Particularly, the modification reactions in real-time can be mapped independently on the two sister histones by performing different types of NMR correlation experiments, tailored for the respective isotope type. This methodology provides the means to study crosstalk mechanisms that contribute to the formation and propagation of asymmetric PTM patterns on nucleosomal complexes.

This protocol describes the reconstitution of nucleosomes containing differentially isotope-labeled sister histones. At the same time, asymmetrically post-translationally modified nucleosomes can be generated after using a premodified histone copy. These preparations can be readily used to study modification crosstalk mechanisms, simultaneously on both sister histones, by using high-resolution NMR spectroscopy.

Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications ...

Purification and Reconstitution of TRPV1 for Spectroscopic Analysis

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine and remain largely unknown. With recent advances in single-particle cryo-electron microscopy (cryo-EM) shedding light on the structural features of agonist binding sites and the activation mechanism of several ion channels, the stage is set for an in-depth dynamic analysis of their gating mechanisms using spectroscopic approaches. Spectroscopic techniques such as electron paramagnetic resonance (EPR) and double electron-electron resonance (DEER) have been mainly restricted to the study of prokaryotic ion channels that can be purified in large quantities. The requirement for large amounts of functional and stable membrane proteins has hampered the study of mammalian ion channels using these approaches. EPR and DEER offer many advantages, including determination of the structure and dynamic changes of mobile protein regions, albeit at low resolution, that might be difficult to obtain by X-ray crystallography or cryo-EM, and monitoring reversible gating transition (i.e., closed, open, sensitized, and desensitized). Here, we provide protocols for obtaining milligrams of functional detergent-solubilized transient receptor potential cation channel subfamily V member 1 (TRPV1) that can be labeled for EPR and DEER spectroscopy.

This article describes specific methods to obtain biochemical quantities of detergent-solubilized TRPV1 for spectroscopic analysis. The combined protocols provide biochemical and biophysical tools that can be adapted to facilitate structural and functional studies for mammalian ion channels in a membrane-controlled environment.

Polymodal ion channels transduce multiple stimuli of different natures into allosteric changes; these dynamic conformations are challenging to determine ...

Fluorescence Live-cell Imaging of the Complete Vegetative Cell Cycle of the Slow-growing Social Bacterium Myxococcus xanthus

Fluorescence live-cell imaging of bacterial cells is a key method in the analysis of the spatial and temporal dynamics of proteins and chromosomes underlying central cell cycle events. However, imaging of these molecules in slow-growing bacteria represents a challenge due to photobleaching of fluorophores and phototoxicity during image acquisition. Here, we describe a simple protocol to circumvent these limitations in the case of Myxococcus xanthus (which has a generation time of 4 - 6 h). To this end, M. xanthus cells are grown on a thick nutrient-containing agar pad in a temperature-controlled humid environment. Under these conditions, we determine the doubling time of individual cells by following the growth of single cells. Moreover, key cellular processes such as chromosome segregation and cell division can be imaged by fluorescence live-cell imaging of cells containing relevant fluorescently labeled marker proteins such as ParB-YFP, FtsZ-GFP, and mCherry-PomX over multiple cell cycles. Subsequently, the acquired images are processed to generate montages and/or movies.

Fluorescence Live-cell Imaging of the Complete Vegetative Cell Cycle of the Slow-growing Social Bacterium Myxococcus xanthus

Bacterial cells are spatially highly organized. To follow this organization over time in slow growing Myxococcus xanthus cells, a set-up for fluorescence live-cell imaging with high spatiotemporal resolution over several generations was developed. Using this method, spatiotemporal dynamics of important proteins for chromosome segregation and cell division could be determined.

Fluorescence live-cell imaging of bacterial cells is a key method in the analysis of the spatial and temporal dynamics of proteins and chromosomes ...

In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers

Many aspects of the fundamental spatiotemporal organization of cells are governed by reaction-diffusion type systems. In vitro reconstitution of such systems allows for detailed studies of their underlying mechanisms which would not be feasible in vivo. Here, we provide a protocol for the in vitro reconstitution of the MinCDE system of Escherichia coli, which positions the cell division septum in the cell middle. The assay is designed to supply only the components necessary for self-organization, namely a membrane, the two proteins MinD and MinE and energy in the form of ATP. We therefore fabricate an open reaction chamber on a coverslip, on which a supported lipid bilayer is formed. The open design of the chamber allows for optimal preparation of the lipid bilayer and controlled manipulation of the bulk content. The two proteins, MinD and MinE, as well as ATP, are then added into the bulk volume above the membrane. Imaging is possible by many optical microscopies, as the design supports confocal, wide-field and TIRF microscopy alike. In a variation of the protocol, the lipid bilayer is formed on a patterned support, on cell-shaped PDMS microstructures, instead of glass. Lowering the bulk solution to the rim of these compartments encloses the reaction in a smaller compartment and provides boundaries that allow mimicking of in vivo oscillatory behavior. Taken together, we describe protocols to reconstitute the MinCDE system both with and without spatial confinement, allowing researchers to precisely control all aspects influencing pattern formation, such as concentration ranges and addition of other factors or proteins, and to systematically increase system complexity in a relatively simple experimental setup.

In Vitro Reconstitution of Self-Organizing Protein Patterns on Supported Lipid Bilayers

We provide a protocol for in vitro self-organization assays of MinD and MinE on a supported lipid bilayer in an open chamber. Additionally, we describe how to enclose the assay in lipid-clad PDMS microcompartments to mimic in vivo conditions by reaction confinement.

Many aspects of the fundamental spatiotemporal organization of cells are governed by reaction-diffusion type systems. In vitro reconstitution of such ...

Studying RNA Interactors of Protein Kinase RNA-Activated during the Mammalian Cell Cycle

Protein kinase RNA-activated (PKR) is a member of the innate immune response proteins and recognizes the double-stranded secondary structure of viral RNAs. When bound to viral double-stranded RNAs (dsRNAs), PKR undergoes dimerization and subsequent autophosphorylation. Phosphorylated PKR (pPKR) becomes active and induces phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2&#945;) to suppress global translation. Increasing evidence suggests that PKR can be activated under physiological conditions such as during the cell cycle or under various stress conditions without infection. However, our understanding of the RNA activators of PKR is limited due to the lack of a standardized experimental method to capture and analyze PKR-interacting dsRNAs. Here, we present an experimental protocol to specifically enrich and analyze PKR bound RNAs during the cell cycle using HeLa cells. We utilize the efficient crosslinking activity of formaldehyde to fix PKR-RNA complexes and isolate them via immunoprecipitation. PKR co-immunoprecipitated RNAs can then be further processed to generate a high-throughput sequencing library. One major class of PKR-interacting cellular dsRNAs is mitochondrial RNAs (mtRNAs), which can exist as intermolecular dsRNAs through complementary interaction between the heavy-strand and the light-strand RNAs. To study the strandedness of these duplex mtRNAs, we also present a protocol for strand-specific qRT-PCR. Our protocol is optimized for the analysis of PKR-bound RNAs, but it can be easily modified to study cellular dsRNAs or RNA-interactors of other dsRNA binding proteins.

We present experimental approaches for studying RNA-interactors of double-stranded RNA binding protein kinase RNA-activated (PKR) during the mammalian cell cycle using HeLa cells. This method utilizes formaldehyde to crosslink RNA-PKR complexes and immunoprecipitation to enrich PKR-bound RNAs. These RNAs can be further analyzed through high-throughput sequencing or qRT-PCR.

Protein kinase RNA-activated (PKR) is a member of the innate immune response proteins and recognizes the double-stranded secondary structure of viral ...

Isolation of Active Caenorhabditis elegans Nuclear Extract and Reconstitution for In Vitro Transcription

Caenorhabditis elegans has been an important model system for biological research since it was introduced in 1963. However, C. elegans has not been fully utilized in the biochemical study of biological reactions using its nuclear extracts such as in vitro transcription and DNA replication. A significant hurdle for using C. elegans in biochemical studies is disrupting the nematode&#39;s thick outer cuticle without sacrificing the activity of the nuclear extract. While several methods are used to break the cuticle, such as Dounce homogenization or sonication, they often lead to protein instability. There are no established protocols for isolating active nuclear proteins from larva or adult C. elegans for in vitro reactions. Here, the protocol describes in detail the homogenization of larval stage 4 C. elegans using a Balch homogenizer. The Balch homogenizer uses pressure to slowly force the animals through a narrow gap breaking the cuticle in the process. The uniform design and precise machining of the Balch homogenizer allow for consistent grinding of animals between experiments. Fractionating the homogenate obtained from the Balch homogenizer yields functionally active nuclear extract that can be used in an in vitro method for assaying transcription activity of C. elegans.

Isolation of Active Caenorhabditis elegans Nuclear Extract and Reconstitution for In Vitro Transcription

Here, we describe a detailed protocol for isolating active nuclear extract from larval stage 4 C. elegans and visualizing transcription activity in an in vitro system.

Caenorhabditis elegans has been an important model system for biological research since it was introduced in 1963. However, C. elegans has not been fully ...

Reconstitution of Msp1 Extraction Activity with Fully Purified Components

As the center for oxidative phosphorylation and apoptotic regulation, mitochondria play a vital role in human health. Proper mitochondrial function depends on a robust quality control system to maintain protein homeostasis (proteostasis). Declines in mitochondrial proteostasis have been linked to cancer, aging, neurodegeneration, and many other diseases. Msp1 is a AAA+ ATPase anchored in the outer mitochondrial membrane that maintains proteostasis by removing mislocalized tail-anchored proteins. Using purified components reconstituted into proteoliposomes, we have shown that Msp1 is necessary and sufficient to extract a model tail-anchored protein from a lipid bilayer. Our simplified reconstituted system overcomes several of the technical barriers that have hindered detailed study of membrane protein extraction. Here, we provide detailed methods for the generation of liposomes, membrane protein reconstitution, and the Msp1 extraction assay.

Here, we present a detailed protocol for reconstitution of Msp1 extraction activity with fully purified components in defined proteoliposomes.

As the center for oxidative phosphorylation and apoptotic regulation, mitochondria play a vital role in human health. Proper mitochondrial function ...

Identification of Hemolytic and Phospholipase Activity in Crude Extracts from Sea Anemones by Straightforward Bioassays

Sea anemone venom composition includes polypeptide and non-proteins molecules. Cytolytic components have a high biotechnological and biomedical potential for designing new molecular tools. Sea anemone venom locates in glandular cells from ectoderm and sub-cellular structures called nematocysts, both of which are distributed throughout the sea anemone body. This characteristic implies challenges because the cells and nematocyst must be lysed to release the venom components with other non-toxic molecules. Therefore, first, the venom is derived from a crude extract (mixture of different and diverse molecules and tissue debris). The next step is to detect polypeptides with specific bioactivities. Here, we describe an efficient strategy to obtain the sea anemone crude extract and bioassay to identify the presence of cytolysins. The first step involves inexpensive and straightforward techniques (stirred and freeze-thaw cycle) to release cytolysins. We obtained the highest cytolytic activity and protein (~500 mg of protein from 20 g of dry weight). Next, the polypeptide complexity of the extract was analyzed by SDS-PAGE gel detecting proteins with molecular weights between 10 kDa and 250 kDa. In the hemolytic assay, we used sheep red blood cells and determined HU50 (11.1 &plusmn; 0.3 &#181;g/mL). In contrast, the presence of phospholipases in the crude extract was determined using egg yolk as a substrate in a solid medium with agarose. Overall, this study uses an efficient and inexpensive protocol to prepare the crude extract and applies replicable bioassays to identify cytolysins, molecules with biotechnological and biomedical interests.

Here, we describe a protocol to obtain crude venom extract from sea anemone and detect its hemolytic and phospholipase activity.

Sea anemone venom composition includes polypeptide and non-proteins molecules. Cytolytic components have a high biotechnological and biomedical potential ...

Purification and Quality Control of Recombinant Septin Complexes for Cell-Free Reconstitution

Septins are a family of conserved eukaryotic GTP-binding proteins that can form cytoskeletal filaments and higher-order structures from hetero-oligomeric complexes. They interact with other cytoskeletal components and the cell membrane to participate in important cellular functions such as migration and cell division. Due to the complexity of septins' many interactions, the large number of septin genes (13 in humans), and the ability of septins to form hetero-oligomeric complexes with different subunit compositions, cell-free reconstitution is a vital strategy to understand the basics of septin biology. The present paper first describes a method to purify recombinant septins in their hetero-oligomeric form using a two-step affinity chromatography approach. Then, the process of quality control used to check for the purity and integrity of the septin complexes is detailed. This process combines native and denaturing gel electrophoresis, negative stain electron microscopy, and interferometric scattering microscopy. Finally, a description of the process to check for the polymerization ability of septin complexes using negative stain electron microscopy and fluorescent microscopy is given. This demonstrates that it is possible to produce high-quality human septin hexamers and octamers containing different isoforms of septin_9, as well as Drosophila septin hexamers.

In vitro reconstitution of cytoskeletal proteins is a vital tool to understand the basic functional properties of these proteins. The present paper describes a protocol to purify and assess the quality of recombinant septin complexes, which play a central role in cell division and migration.

Septins are a family of conserved eukaryotic GTP-binding proteins that can form cytoskeletal filaments and higher-order structures from hetero-oligomeric ...

Reconstitution of Septin Assembly at Membranes to Study Biophysical Properties and Functions

Most cells can sense and change their shape to carry out fundamental cell processes. In many eukaryotes, the septin cytoskeleton is an integral component in coordinating shape changes like cytokinesis, polarized growth, and migration. Septins are filament-forming proteins that assemble to form diverse higher-order structures and, in many cases, are found in different areas of the plasma membrane, most notably in regions of micron-scale positive curvature. Monitoring the process of septin assembly in vivo is hindered by the limitations of light microscopy in cells, as well as the complexity of interactions with both membranes and cytoskeletal elements, making it difficult to quantify septin dynamics in living systems. Fortunately, there has been substantial progress in the past decade in reconstituting the septin cytoskeleton in a cell-free system to dissect the mechanisms controlling septin assembly at high spatial and temporal resolutions. The core steps of septin assembly include septin heterooligomer association and dissociation with the membrane, polymerization into filaments, and the formation of higher-order structures through interactions between filaments. Here, we present three methods to observe septin assembly in different contexts: planar bilayers, spherical supports, and rod supports. These methods can be used to determine the biophysical parameters of septins at different stages of assembly: as single octamers binding the membrane, as filaments, and as assemblies of filaments. We use these parameters paired with measurements of curvature sampling and preferential adsorption to understand how curvature sensing operates at a variety of length and time scales.

Cell-free reconstitution has been a key tool to understand the cytoskeleton assembly, and work in the last decade has established approaches to study septin dynamics in minimal systems. Presented here are three complementary methods to observe septin assembly in different membrane contexts: planar bilayers, spherical supports, and rod supports.

Most cells can sense and change their shape to carry out fundamental cell processes. In many eukaryotes, the septin cytoskeleton is an integral component ...