This research was conducted with support under Grant Nos. R01EB012521, R01EB028782, and T32 GM008339 from the National Institutes of Health.

1. Prepare parts for well plate perfusion
<ol>
	<li>Prepare tubing
	<ol>
		<li>Cut two lengths of silicone tubing (1.6 mm inner diameter) for each cell culture to be perfused. Ensure that the piece used as the upstream tubing is long enough to reach from the syringe pump to the cell culture inside the incubator, and that the downstream piece can reach from the cell culture to the furthest extended position of the fraction collector.</li>
		<li>Give each piece of tubing a unique label on both of its end...

<ol>
	<li>Welsh, D. K., Yoo, S. H., Liu, A. C., Takahashi, J. S., Kay, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bioluminescence+imaging+of+individual+fibroblasts+reveals+persistent,+independently+phased+circadian+rhythms+of+clock+gene+expression.">Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression.</a> Current Biology. 14 (24), 2289-2295 (2004).</li><li>Talaei, K., 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+mathematical+model+of+the+dynamics+of+cytokine+expression+and+human+immune+cell+activation+in+response+to+the+pathogen+Staphylococcus+aureus.">A mathematical model of the dynamics of cytokine expression and human immune cell activation in response to the pathogen Staphylococcus aureus.</a> Frontiers in Cellular and Infection Microbiology. 11, 711153 (2021).</li><li>Kemas, A. M., Youhanna, S., Zandi Shafagh, R., Lauschke, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Insulin-dependent+glucose+consumption+dynamics+in+3D+primary+human+liver+cultures+measured+by+a+sensitive+and+specific+glucose+sensor+with+nanoliter+input+volume.">Insulin-dependent glucose consumption dynamics in 3D primary human liver cultures measured by a sensitive and specific glucose sensor with nanoliter input volume.</a> FASEB Journal. 35 (3), 21305 (2021).</li><li>Muzzey, D., van Oudenaarden, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+time-lapse+fluorescence+microscopy+in+single+cells.">Quantitative time-lapse fluorescence microscopy in single cells.</a> Annual Review of Cell and Developmental Biology. 25, 301-327 (2009).</li><li>Calligaro, H., Kinane, C., Bennis, M., Coutanson, C., Dkhissi-Benyahya, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+standardized+method+to+assess+the+endogenous+activity+and+the+light-response+of+the+retinal+clock+in+mammals.">A standardized method to assess the endogenous activity and the light-response of the retinal clock in mammals.</a> Molecular Vision. 26, 106-116 (2020).</li><li>Battat, S., Weitz, D. A., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+outlook+on+microfluidics:+the+promise+and+the+challenge.">An outlook on microfluidics: the promise and the challenge.</a> Lab on a Chip. 22 (3), 530-536 (2022).</li><li>Petrenko, V., Saini, C., Perrin, L., Dibner, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Parallel+measurement+of+circadian+clock+gene+expression+and+hormone+secretion+in+human+primary+cell+cultures.">Parallel measurement of circadian clock gene expression and hormone secretion in human primary cell cultures.</a> Journal of Visualized Experiments. (117), e54673 (2016).</li><li>Yamagishi, K., Enomoto, T., Ohmiya, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Perfusion-culture-based+secreted+bioluminescence+reporter+assay+in+living+cells.">Perfusion-culture-based secreted bioluminescence reporter assay in living cells.</a> Analytical Biochemistry. 354 (1), 15-21 (2006).</li><li>Watanabe, 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=Multichannel+perfusion+culture+bioluminescence+reporter+system+for+long-term+detection+in+living+cells.">Multichannel perfusion culture bioluminescence reporter system for long-term detection in living cells.</a> Analytical Biochemistry. 402 (1), 107-109 (2010).</li><li>Murakami, N., Nakamura, H., Nishi, R., Marumoto, N., Nasu, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+circadian+oscillation+of+melatonin+release+in+pineal+cells+of+house+sparrow,+pigeon+and+Japanese+quail,+using+cell+perfusion+systems.">Comparison of circadian oscillation of melatonin release in pineal cells of house sparrow, pigeon and Japanese quail, using cell perfusion systems.</a> Brain Research. 651 (1-2), 209-214 (1994).</li><li>Erickson, P., Houwayek, T., Burr, A., Teryek, M., Parekkadan, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+continuous+flow+cell+culture+system+for+precision+cell+stimulation+and+time-resolved+profiling+of+cell+secretion.">A continuous flow cell culture system for precision cell stimulation and time-resolved profiling of cell secretion.</a> Analytical Biochemistry. 625, 114213 (2021).</li><li>Saltzman, W. 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> Drug Delivery: Engineering Principles for Drug Therapy. , (2001).</li><li>Fogler, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Elements of Chemical Reaction Engineering. 4th edn. , (2006).</li><li>Conesa, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Chemical Reactor Design: Mathematical Modeling and Applications. , (2019).</li><li>Toson, P., Doshi, P., Jajcevic, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Explicit+residence+time+distribution+of+a+generalised+cascade+of+continuous+stirred+tank+reactors+for+a+description+of+short+recirculation+time+(bypassing).">Explicit residence time distribution of a generalised cascade of continuous stirred tank reactors for a description of short recirculation time (bypassing).</a> Processes. 7 (9), 615 (2019).</li><li>Tamayo, A. G., Shukor, S., Burr, A., Erickson, P., Parekkadan, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tracking+leukemic+T-cell+transcriptional+dynamics+in+vivo+with+a+blood-based+reporter+assay.">Tracking leukemic T-cell transcriptional dynamics in vivo with a blood-based reporter assay.</a> FEBS Open Biology. 10 (9), 1868-1879 (2020).</li><li>Newell, B., Bailey, J., Islam, A., Hopkins, L., Lant, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterising+bioreactor+mixing+with+residence+time+distribution+(RTD)+tests.">Characterising bioreactor mixing with residence time distribution (RTD) tests.</a> Water Science and Technology. 37 (12), 43-47 (1998).</li><li>Dubois, J., Tremblay, L., Lepage, M., Vermette, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+dynamics+within+a+bioreactor+for+tissue+engineering+by+residence+time+distribution+analysis+combined+with+fluorescence+and+magnetic+resonance+imaging+to+investigate+forced+permeability+and+apparent+diffusion+coefficient+in+a+perfusion+cell+culture+chamber.">Flow dynamics within a bioreactor for tissue engineering by residence time distribution analysis combined with fluorescence and magnetic resonance imaging to investigate forced permeability and apparent diffusion coefficient in a perfusion cell culture chamber.</a> Biotechnology and Bioengineering. 108 (10), 2488-2498 (2011).</li><li>Gaida, L. B., 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=Liquid+and+gas+residence+time+distribution+in+a+two-stage+bioreactor+with+cell+recycle.">Liquid and gas residence time distribution in a two-stage bioreactor with cell recycle.</a> HAL Open Science. , (2008).</li><li>Rodrigues, M. E., Costa, A. R., Henriques, M., Azeredo, J., Oliveira, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wave+characterization+for+mammalian+cell+culture:+residence+time+distribution.">Wave characterization for mammalian cell culture: residence time distribution.</a> New Biotechnology. 29 (3), 402-408 (2012).</li><li>Olivet, D., Valls, J., Gordillo, M. A., Freix&#243;, A., S&#225;nchez, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Application+of+residence+time+distribution+technique+to+the+study+of+the+hydrodynamic+behaviour+of+a+full-scale+wastewater+treatment+plant+plug-flow+bioreactor.">Application of residence time distribution technique to the study of the hydrodynamic behaviour of a full-scale wastewater treatment plant plug-flow bioreactor.</a> Journal of Chemical Technology and Biotechnology. 80 (4), 425-432 (2005).</li></ol>

This work describes the assembly and operation of a perfusion cell culture system with multiple medium sources demonstrated with a specific example in which the dynamics of NF-&#954;B-driven gene expression in response to a transient pulse of TNF-&#945; were measured. The RTDs of the perfusion system components were measured and modeled, and signal convolution was used to predict both the exposure of the cells to the TNF-&#945; pulse and the TNF-&#945; distribution in the collected effluent medium fractions. The cells we...

Many important biological processes occur in cell and tissue cultures on the timescale of minutes to hours1,2,3. While some of these phenomena may be observed and recorded in an automated fashion using time-lapse microscopy4, bioluminescence1, or other methods, experiments involving the collection of culture supernatant samples for chemical analysis are often performed manually in static cell cultures. Manual sampling limits the feasibility of certain studies due to the inconvenience of frequent or after-hours sampling timepoints. Further shortcomings of static culture methods include experiments involving controlled, transient exposures to chemical stimuli. In static cultures, stimuli must be added and removed manually, and stimulus profiles are limited to step changes over time, while medium changes also add and remove other medium components, which can affect cells in an uncontrolled manner5. Fluidic systems can overcome these challenges, but existing devices pose other challenges. Microfluidic devices come with the prohibitive costs of specialized equipment and training to produce and use, require microanalytical methods to process samples, and cells are difficult to recover from the devices after perfusion6. Few macrofluidic systems have been created for the types of experiments described here7,8,9,10, and they are built of multiple custom parts made in-house and require multiple pumps or fraction collectors. Furthermore, the authors are not aware of any commercially available macrofluidic perfusion cell culture systems other than stirred tank bioreactors for suspension culture, which are useful for biomanufacturing, though are not designed for modeling and studying physiology.
The authors previously reported on the design of a low-cost perfusion bioreactor system composed almost entirely of commercially available parts11. The base version of the system enables multiple cultures in a well plate to be kept in a CO2 incubator and continuously perfused with medium from a syringe pump, while the effluent medium streams from the cultures are automatically fractionated into samples over time using a fraction collector with a custom modification. Thus, this system enables automated sampling of culture medium supernatant and continuous solute input to the cultures over time. The system is macrofluidic and modular and can be easily modified to meet the needs of novel experiment designs.
The overall goal of the method presented here is to construct, characterize, and use a perfusion cell culture system that enables experiments in which the secretion or absorption rates of substances by cells over time is measured, and/or cells are exposed to precise, transient solute signals. This video article explains how to assemble the base setup, which is capable of perfusing up to six cell cultures simultaneously using a single syringe pump and modified fraction collector. Two useful variants on the base system that make use of additional pumps and parts to allow for experiments that expose cells to transient solute concentration signals, including brief pulses and pharmacokinetic-like profiles12, are also presented, shown in Figure 1.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63935/63935fig01.jpg" /> 
Figure 1: Three variations on the perfusion system design. (Top) The basic perfusion system. (Middle) The perfusion system with a stopcock for multiple medium sources. (Bottom) The perfusion system with a stirred tank to mimic a well-mixed volume of distribution. <a href="https://www.jove.com/files/ftp_upload/63935/63935fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Due to dispersion and diffusion within the flow, the solute signals become distorted or &#34;smeared&#34; as they travel through the flow system. This distortion can be quantified through the use of residence time distributions (RTDs)13. This article explains how to perform tracer experiments on components of the perfusion system (Figure 2), and provides MATLAB scripts to generate RTDs from measured data. A detailed explanation of this analysis can be found in the authors&#39; previous paper11. Additional MATLAB scripts fit appropriate functions to the RTDs and extract physical parameters, and perform signal convolution using RTDs to predict how solute signal input by the user will propagate and distort through the perfusion system14.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63935/63935fig02.jpg" /> 
Figure 2: Residence time distributions. The RTDs of flow system components, such as this length of tubing, are measured by inputting a pulse of tracer to the system and measuring how it &#34;smears&#34; by the time it exits into the collected fractions. This figure has been modified from Erickson et al.11. <a href="https://www.jove.com/files/ftp_upload/63935/63935fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>18 Gauge 1 1/2- in Disposable Probe Needle For Use With Syringes and Dispensing Machines</td>
			<td>Grainger</td>
			<td>5FVK2</td>
			<td></td>
		</tr>
		<tr>
			<td>293T Cells</td>
			<td>ATCC</td>
			<td>CRL-3216</td>
			<td>HEK 293T cells used in the Representative Results experiment.</td>
		</tr>
		<tr>
			<td>96-Well Clear Bottom Plates, Corning</td>
			<td>VWR</td>
			<td>89091-010</td>
			<td>Plates for measuring dye concentrations in RTD experiments and GLuc in representative results experiment.</td>
		</tr>
		<tr>
			<td>BD&#160;Disposable Syringes with Luer-Lok Tips, 5 mL</td>
			<td>Fisher Scientific</td>
			<td>14-829-45</td>
			<td></td>
		</tr>
		<tr>
			<td>BioFrac Fraction Collector&#160;</td>
			<td>Bio-Rad</td>
			<td>7410002</td>
			<td>Fraction collector that can be used for a single stream, or modified using our method to enable collection from multiple streams.</td>
		</tr>
		<tr>
			<td>Clear High-Strength UV-Resistant Acrylic 12&#34; x 12&#34; x 1/8&#34;</td>
			<td>McMaster-Carr</td>
			<td>4615T93</td>
			<td>This sheet is cut using a laser cutter according to the DXF file in the supplemental materials to produce the multi-head dispenser that can be attached to the BioFrac fraction collector.</td>
		</tr>
		<tr>
			<td>Coelenterazine native</td>
			<td>NanoLight Technology</td>
			<td>303</td>
			<td>Substrate used in Gaussia luciferase bioluminescence assay in representative results.</td>
		</tr>
		<tr>
			<td>Corning Costar TC-Treated Multiple Well Plates, size 48&#160;wells, polystyrene plate, flat bottom wells</td>
			<td>Millipore Sigma</td>
			<td>CLS3548</td>
			<td>Used to grow and perfuse 293T cells in representative results.</td>
		</tr>
		<tr>
			<td>Corning&#160;Costar Flat Bottom Cell Culture Plates, size 12 wells</td>
			<td>Fisher Scientific</td>
			<td>720081</td>
			<td>Can be plugged and used as a stirred tank to produce pharmacokinetic profiles in perfusion. Can also contain cells for perfusion.</td>
		</tr>
		<tr>
			<td>DMEM, high glucose</td>
			<td>ThermoFisher Scientific</td>
			<td>11965126</td>
			<td></td>
		</tr>
		<tr>
			<td>Epilog Zing 24 Laser</td>
			<td>Cutting Edge Systems</td>
			<td>Epilog Zing 24</td>
			<td>Laser cutter used to produce multi-head dispenser from acrylic sheet. Other laser cutters may be used.</td>
		</tr>
		<tr>
			<td>Fisherbrand Sterile Syringes for Single Use, Luer-Lock, 20 mL</td>
			<td>Fisher Scientific</td>
			<td>14-955-460</td>
			<td></td>
		</tr>
		<tr>
			<td>Fisherbrand Sterile Syringes for Single Use, Luer-Lock, 60 mL</td>
			<td>Fisher Scientific</td>
			<td>14-955-461</td>
			<td></td>
		</tr>
		<tr>
			<td>Fisherbrand Premium Microcentrifuge Tubes: 1.5mL</td>
			<td>Fisher Scientific</td>
			<td>05-408-129</td>
			<td>Microcentrifuge tubes for collecting fractions.</td>
		</tr>
		<tr>
			<td>Fisherbrand&#160;Round Bottom Disposable Borosilicate Glass Tubes with Plain End</td>
			<td>Fisher Scientific</td>
			<td>14-961-26</td>
			<td>Glass tubes for collecting fractions.</td>
		</tr>
		<tr>
			<td>Fisherbrand&#160;SureOne Micropoint Pipette Tips, Universal Fit, Non-Filtered</td>
			<td>Fisher Scientific</td>
			<td>2707410</td>
			<td>300 ul pipette tips that best fit the multi-head dispenser and tubing to act as dispensing tips.</td>
		</tr>
		<tr>
			<td>Gibco&#160;DPBS, powder, no calcium, no magnesium</td>
			<td>Fisher Scientific</td>
			<td>21600010</td>
			<td>Phosphate buffered saline.</td>
		</tr>
		<tr>
			<td>Labline 4625 Titer Shaker</td>
			<td>Marshall Scientific</td>
			<td>Labline 4625 Titer Shaker</td>
			<td>Orbital shaker used to keep stirred tanks mixed.</td>
		</tr>
		<tr>
			<td>Masterflex Fitting, Polycarbonate, Four-Way Stopcock, Male Luer Lock, Non-Sterile; 10/PK</td>
			<td>Cole-Parmer</td>
			<td>EW-30600-04</td>
			<td>Used to join multiple inlet streams for RTD experiments and cell culture experiments.</td>
		</tr>
		<tr>
			<td>Masterflex Fitting, Polycarbonate, Straight, Female Luer x Cap; 25/PK</td>
			<td>Masterflex</td>
			<td>UX-45501-28</td>
			<td></td>
		</tr>
		<tr>
			<td>Masterflex Fitting, Polypropylene, Straight, Female Luer to Hosebarb Adapters, 1/16&#34;</td>
			<td>Cole-Parmer</td>
			<td>EW-45508-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Masterflex Fitting, Polypropylene, Straight, Male Luer Lock to Hosebarb Adapter, 1/16&#34; ID</td>
			<td>Cole-Parmer</td>
			<td>EW-45518-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Masterflex Fitting, Polypropylene, Straight, Male Luer Lock to Plug Adapter; 25/PK</td>
			<td>Masterflex</td>
			<td>EW-30800-30</td>
			<td></td>
		</tr>
		<tr>
			<td>Masterflex L/S Precision Pump Tubing, Platinum-Cured Silicone, L/S 14; 25 ft</td>
			<td>Masterflex</td>
			<td>EW-96410-14</td>
			<td></td>
		</tr>
		<tr>
			<td>MATLAB</td>
			<td>MathWorks</td>
			<td>R2019b</td>
			<td>Version R2019b. Newer versions may also be used. Some older versions may work.</td>
		</tr>
		<tr>
			<td>NE-1600 Six Channel Programmable Syringe Pump</td>
			<td>New Era Pump Systems</td>
			<td>NE-1600</td>
			<td></td>
		</tr>
		<tr>
			<td>Rack Set F1</td>
			<td>Bio-Rad</td>
			<td>7410010</td>
			<td>Racks to hold collecting tubes in the fraction collector.</td>
		</tr>
		<tr>
			<td>Recombinant Human TNF-alpha (HEK293-expressed) Protein, CF</td>
			<td>Bio-Techne</td>
			<td>10291-TA-020</td>
			<td>Cytokine used to stimulate 293T cells in representative results.</td>
		</tr>
		<tr>
			<td>Saint Gobain Solid Stoppers, Versilic Silicone, Size: 00, Bottom 10.5mm</td>
			<td>Saint Gobain</td>
			<td>DX263015-50</td>
			<td>Fits 48-well plates.</td>
		</tr>
		<tr>
			<td>Saint Gobain Solid Stoppers, Versilic Silicone, Size: 4 Bottom 21mm</td>
			<td>Saint Gobain</td>
			<td>DX263027-10</td>
			<td>Fits 12-well plates.</td>
		</tr>
		<tr>
			<td>Sodium Hydroxide, 10.0 N Aqueous Solution APHA; 1 L</td>
			<td>Spectrum Chemicals</td>
			<td>S-395-1LT</td>
			<td></td>
		</tr>
		<tr>
			<td>SolidWorks</td>
			<td>Dassault Systems</td>
			<td>SolidWorks</td>
			<td>CAD software used to create the multi-head dispenser DXF file.</td>
		</tr>
		<tr>
			<td>Varioskan LUX multimode microplate reader</td>
			<td>ThermoFisher Scientific</td>
			<td>VL0000D0</td>
			<td>Plate reader.</td>
		</tr>
		<tr>
			<td>Wilton Color Right Performance Color System Base Refill, Blue</td>
			<td>Michaels</td>
			<td>10404779</td>
			<td>Blue food dye containing Brilliant Blue FCF, used as a tracer in RTD experiments. Absorbance spectrum peaks at 628 nm.</td>
		</tr>
	</tbody>
</table>

multi-stream perfusion bioreactor integrated with outlet fractionation for dynamic cell culture

Certain cell and tissue functions operate within the dynamic time scale of minutes to hours that are poorly resolved by conventional culture systems. This work has developed a low-cost perfusion bioreactor system that allows culture medium to be continuously perfused into a cell culture module and fractionated in a downstream module to measure dynamics on this scale. The system is constructed almost entirely from commercially available parts and can be parallelized to conduct independent experiments in conventional multi-well cell culture plates simultaneously. This video article demonstrates how to assemble the base setup, which requires only a single multichannel syringe pump and a modified fraction collector to perfuse up to six cultures in parallel. Useful variants on the modular design are also presented that allow for controlled stimulation dynamics, such as solute pulses or pharmacokinetic-like profiles. Importantly, as solute signals travel through the system, they are distorted due to solute dispersion. Furthermore, a method for measuring the residence time distributions (RTDs) of the components of the perfusion setup with a tracer using MATLAB is described. RTDs are useful to calculate how solute signals are distorted by the flow in the multi-compartment system. This system is highly robust and reproducible, so basic researchers can easily adopt it without the need for specialized fabrication facilities.

The perfusion system with multiple medium sources from section 5 of the protocol was used to measure the expression dynamics of a reporter gene driven by the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-&#954;B) transcription factor in human embryonic kidney 293 (HEK293) cells in response to a 1.5 h pulse of tumor necrosis factor alpha (TNF-&#945;). HEK293 cells were stably transduced using lentiviral vectors with a gene construct containing Gaussia luciferase (GLuc), driven by a promoter called NFK...

Watch this Scientific Journal Video about Multi-Stream Perfusion Bioreactor Integrated with Outlet Fractionation for Dynamic Cell Culture at JoVE.com

Multi-Stream Perfusion Bioreactor Integrated with Outlet Fractionation for Dynamic Cell Culture

This paper presents a method to construct and operate a low-cost, multichannel perfusion cell culture system for measuring the dynamics of secretion and absorption rates of solutes in cellular processes. The system can also expose cells to dynamic stimulus profiles.

Certain cell and tissue functions operate within the dynamic time scale of minutes to hours that are poorly resolved by conventional culture systems. This ...

This method helps understand how secretion rates change with time and how cells respond to time varying solid signals. The main advantages of this technique are that its low cost, requires little training and the profusion system setup can be adapted for novel experiments. Begin by filling one syringe with a background solution and load it into the first syringe pump.Fill another syringe with tracer solution and load it into the second syringe pump. Connect both syringes to two of the three ports of a four-way stopcock using luer connectors. Close the stopcock to the background solution and pump the tracer solution into the stopcock until it drips out the open port.Stop the pump and do not adjust the syringe further. Ensure that the syringe pumps moving bar is pushed up against the syringe plungers so that the flow begins immediately when the pump is started. Close the stopcock to the tracer solution and pump the background solution into the stopcock until all residual tracer solution has been flushed out of the open port.Stop the pump and do not adjust the syringe further. Set up the flow system component desired for RTD analysis. Insert the end into a pipette tip dispenser and pump background solution through the component until it is entirely filled.Set the pump for the tracer solution to the desired flow rate. Close the stopcock to the background solution and start the flow of the tracer solution. At the same time, start the fraction collector.Continue the flow of tracer solution for a short period of time to approximate an impulse input of the tracer. A pulse duration of 10 minutes is recommended for RTDs at a flow rate of one milliliter per hour. Stop the tracer solution pump at the end of the tracer solution pulse period.Quickly close the stopcock to the tracer solution and start the flow of the background solution at the same flow rate. Allow the background solution to flow and collect fractions until all of the tracer has passed through the system and into the collected fractions. Under sterile conditions, insert the stoppers with needles into the well plate cultures with the needles pulled up.After the stopper is in place, lower the needles to the desired height for perfusion as the height of the outlet needle determines the stable liquid level. Cap the needles with male luer caps and keep the whole wellplate in an incubator set at 37 degrees Celsius until use. Prepare the two media to be used for perfusion, labeling the medium that will be dispensed first as one and the other medium two.For each culture to be perfused, fill one syringe with medium one to last the whole duration of its dispension plus enough volume to initially fill the perfusion system. Fill a second syringe with medium two to last the whole duration of its dispension. Connect both syringes to two of the three ports of a four way stopcock.A length of tubing to connect the syringes to the stopcocks may be required. Prepare the stopcocks by closing the stopcock for medium one and dispensing medium two into the stopcock until it just begins to drip out the open port. Then close the stopcock for medium two and dispense medium one into the stopcock until all residual medium two has been flushed out of the open port.Attach the upstream tubing to the open stopcock port using a female to barb luer connector. Insert a male to barb luer connector on the other end of the tube. Dispense medium one from the syringe until the upstream tube is filled with medium and proceed with the preparation of downstream tubing as demonstrated earlier.Insert a male to barb luer connector into one end of the downstream tubing and cap it with a female luer cap. Carefully bring all prepared tubing, syringes and the well plate to the incubator that will be used for perfusion. Place the syringe pump and fraction collector in the desired locations near the incubator.Place the syringe pump on top of or near the incubator and place the fraction collector next to the incubator near the port. Load the syringes into the pump. Bundle together the capped ends of all the upstream and downstream tubes and push them from the outside of the incubator to the inside through the port.Insert the open ends of the downstream tubes into the dispensing pipette tips of the fraction collector's multi-head dispenser. Inside the incubator, pull as much slack of the upstream tubes as possible into the incubator to maximize the length of tubing through which the flowing medium can receive heat and carbon dioxide. For each plugged well, quickly uncap the needles and the upstream and downstream tubes for that well, then attach them together with their luer connectors.Once all parts are connected, briefly run the syringe pump at a relatively high speed to ensure that all streams are flowing properly. At this point, if it is desired to begin the experiment with the downstream tubes full of the medium, continue running the pump until all are filled, otherwise, stop the pump. Set the syringe pump flow rate for medium one and the frequency of fraction collection and start both machines simultaneously to begin the experiment.When the medium source needs to be changed, quickly stop the syringe pump for medium one. Turn the stopcock closed to medium one and start the syringe pump for medium two. If desired later, switch the source back to medium one similarly.Collect fractions for the desired experiment duration. The tracer concentrations in the fractions from two RTD experiments were measured and input into the RTD from data MATLAB script to produce the two RTDs. Single tubes and multiple pieces of tubing in series fit well by a single axial dispersion model and adding a perfused 48 well plate in line caused negligible deviation allowing both the one meter tube RTD and the entire system's RTD to fit by axial dispersion functions.An example of a poor model fit was demonstrated using the axial dispersion model fitted to the one meter tube RTD data and was plotted alongside the data. The initial parameter guesses were changed to produce a good model fit where tau was approximately equal to the perfusion system volume divided by its volumetric flow rate. A 90 minute pulse of TNF-alpha was defined as the input signal to the system and was convolved with the one meter tubing RTD to determine the TNF-alpha signal at the well plate inlet.The input signal was also convolved with the RTD of the entire system to determine the TNF-alpha signal at the outlet of the system in the collected fractions. HEK 293 cells were engineered to secrete GLuc driven by a promoter containing the NF-kappaB response element. The experiment revealed a significant expression increase and slow decrease in GLuc expression driven by NF-kappaB following TNF-alpha exposure.Variations of the system are described in accompanying paper, including a simpler setup for experiments that don't require inputting signals and exposing cells to pharma-hu connective solute profiles.

multi-stream-perfusion-bioreactor-integrated-with-outlet

Research

JoVE Journal

Bioengineering

2.0K visualizações.  Rutgers University. Este método ajuda a entender como as taxas de secreção mudam com o tempo e como as células respondem ao tempo variando sinais sólidos. As principais vantagens dessa técnica são que seu baixo custo, requer pouco treinamento e a configuração do sistema de profusão pode ser adaptada para novos experimentos. Comece preenchendo uma seringa com uma solução de fundo e carregue-a na primeira bomba de seringa.Encha outra seringa com solução de rastreador e carregue-a na segunda bo...