Research reported in this publication was supported by the National Heart, Lung, And Blood Institute of the National Institutes of Health under Award Number R01HL167877. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

All methods mentioned below are in accordance with institutional review board (IRB) protocols and the institutional human research ethics committee. All healthy volunteers provided written and informed consent prior to blood donation. Of note, all materials referenced within the protocol can be found in the Table of Materials. While human WB and plasma are discussed throughout this protocol, the use of research animal blood and factor-depleted blood products can be purchased and substituted.
1. Whole blood collection
<ol>
	<li>Collect venous whole blood (WB) from consenting healthy volunteers using standard phlebotomy techniques. 
	CAUTION: Ensure that universal precautions are followed to reduce the risk of contact with blood or other potentially infectious materials throughout this protocol. The use of gloves, a laboratory coat, and a face shield are necessary.</li>
	<li>Collect ~50 mL of WB directly into 3.2% sodium citrate tubes and immediately pool into 50&#160;mL tubes for subsequent use. 
	NOTE: A discard tube prior to blood collection into the citrate tube is necessary in addition to ensuring that tubes are filled to their manufacturer-recommended volume. Freshly collected WB will best recapitulate the clotting dynamics of the host. Short-term storage of WB at room temperature (&#8804;4 h prior to use) is allowable. WB is not stored overnight as this has been shown to impact clotting dynamics when examined via thromboelastography15.</li>
</ol>
2. Clot formation
<ol>
	<li>Into 3 mL of citrated whole blood, add fluorescently (fluorescein isothiocyanate [FITC]) tagged fibrinogen (FITC-Fg) to a final concentration of 60 &#181;g/mL (ratio of 1:50 fluorescently tagged fibrinogen to unmodified fibrinogen assuming an endogenous plasma fibrinogen concentration of 3 mg/mL). 
	NOTE: This ratio can be increased to as high as 1:10 with minimal impact on clot morphology.13, 14 Fluorescently tagged fibrinogen can be purchased or generated by reacting fibrinogen with fluorescein isothiocyanate (FITC). Fibrinogen mixing should be done &#8804;5 min before the run begins.
	<ol>
		<li>If fibrinogen had been previously aliquoted and frozen, inspect the thawed FITC-Fg to ensure polymerization has not begun prematurely thus rendering it unusable (ensure the absence of particulates or fibers in the solution).</li>
	</ol>
	</li>
	<li>Prepare the Chandler loop setup with a 120&#160;mm diameter drum in a 37 &#176;C water bath (Figure 1). Ensure that the Chandler loop device is capable of rotating at a fixed rotational rate of 0-90 rpm during the entire clot formation process. 
	NOTE: Additional Chandler loop setup and modifications can be found in Zeng et al.16.</li>
	<li>Cut tubing (internal diameter 5/32&#34;, outer diameter 7/32&#34;) and form loops that fit firmly but not tightly around the drum. For the recommended tubing size discussed here, cut a standard 200 &#181;L PCR tube for use as a fitting to connect the ends of the tubing to form the closed loop. 
	NOTE: Different tubing sizes can be utilized to produce different-sized clots16.</li>
	<li>Initiate clotting of blood by adding 200 mM Calcium Chloride solution in a ratio of 1:17 calcium solution to whole blood. Load the blood into the tubing (fill ~50% of the tube volume) using a 3 mL syringe. Immediately place the loop onto the Chandler loop drum connecting the ends and begin rotation.
	<ol>
		<li>Ensure proper mixing with gentle inversion before loading to avoid any issues stemming from the settling of WB components.</li>
		<li>Ensure that an equal amount of blood is added to each tube every run as this can impact the clot size if not held consistent.</li>
		<li>As bubbles within the column of blood can also impact blood clotting, remove them by gently moving the tube in a &#34;see-saw&#34; like manner to facilitate the escape of bubbles before loading them onto the drum.</li>
	</ol>
	</li>
	<li>Rotate the drum partially submerged in the water bath at a rotational rate of 40 RPM to achieve a calculated shear rate of ~450 s-1. 
	NOTE: Refer to Zeng et al. for information on calculated shears based on tubing size and rotation speed (20 to 60 RPM)16. Typical venous and arterial shear rates are 20-200 s-1 and 300-1,000 s-1, respectively, with ~400-500 s-1 being representative of the pulmonary artery.</li>
	<li>Allow clots to form for 40-60 min under low light conditions to minimize photobleaching of the fluorescently tagged fibrinogen.</li>
	<li>After the desired clotting time is reached, remove the clots from the tubing and use them immediately. To ensure gentle removal of the clots without compromising structure, gently invert the tubing to allow the clot to slowly slide out of the tube into a small container. 
	NOTE: Storing formed clots in citrated plasma or PBS overnight at 4 &#176;C may impact subsequent analysis of clot digestion in the flow loop.</li>
</ol>
3. RT-FluFF instrument setup
<ol>
	<li>Ensure the flow loop apparatus is connected as seen in Figure 2 and that all connections are secure. In short, the flow loop apparatus includes, in the order of the direction of flow: Pump &#62; Dampener &#62; Inlet Pressure Sensor &#62; Clot &#62; Outlet Pressure Sensor &#62; Fluorometer &#62; Heated Reservoir &#62; Pump. Adjust the selection of pump capacity, experimental flow rate, tubing diameter and length, temperature, reservoir volume, and clot size/geometry to suit the experimental needs unique to each study. 
	NOTE: For this example, the same diameter tubing used in the Chandler loop was used for RT-FluFF. The tubing can be used for multiple runs on the same day but needs to be monitored for degradation or leaking and changed/rinsed as needed. Rinsing is recommended with warm distilled water between runs. Depending on the experimental design, it may be necessary to replace the tubing after every run.</li>
	<li>Once all tubing is secured, turn on the pressure monitor. Check that the pressure monitor reads 0 mmHg for both the inlet and outlet sensors. If it does not, open the valves to ensure that the pressure sensors are open to atmospheric pressure and zero the sensors.</li>
	<li>Turn on the heating block or water bath being used and monitor the temperature over the course of the experiment. Keep the temperature close to 37 &#176;C to mimic physiologic human body temperature.</li>
	<li>Turn on the pump to the desired flow rate to check for leaks and verify that the pressure sensors are functioning. 
	NOTE: A flow rate of ~160 mL/min in this tubing size will represent a shear rate of ~500 s-1.</li>
	<li>Turn off the pump to facilitate clot loading.</li>
</ol>
4. Loading the clot into the flow loop
<ol>
	<li>If a previously made clot that was stored is being used be sure to bring the clot to room temperature before loading it into the flow loop system.</li>
	<li>Clot mass loss is an important endpoint measurement for thrombolysis assays. It is best practice to measure clot mass just before loading it into the flow loop instead of relying on prior measurements.
	<ol>
		<li>Clot mass measurements should always be done in the same fashion every time to ensure consistency across samples and across assay days as liquid content within and on the clots can significantly impact their mass. The best practice is to gently blot clots on laboratory wipes until they no longer release a significant amount of liquid onto the wipe being careful not to compress the clot throughout the measurement process.</li>
	</ol>
	</li>
	<li>Submerge the clot in the plasma (autologous or type-matched), or other mobile phase solution used in the flow loop (such as PBS or defined media) in a shallow container such as a weighing dish. The mobile phase solution should be taken directly from the 50 mL system reservoir to control for total system volume. No thrombolytic or pharmaceutical testing agent should be present during the clot-loading stage. The total volume of the mobile phase for running the flow loop is recommended to be &#8805;50 mL and should be consistent across all samples.</li>
	<li>Remove the central section of the flow loop tubing (between inlet and outlet sensors) and attach a 10 mL syringe to one end of the tubing.</li>
	<li>Using the free end of the tubing, place it in the plasma (or mobile phase) and take up a small volume of the solution to prime the tubing. Then place the tubing inlet near the clot carefully examining the clot to identify the head (typically the slightly thicker end of the clot) and tail (end opposite the head). The head of the clot should be positioned towards the inlet pressure sensor and away from the outlet. Place the tubing at the &#34;tail&#34; end of the clot and aspirate it into the tubing with the syringe. 
	NOTE: in cases where clot head/tail directionality cannot be visually determined, directionality can best be assigned based on knowing the direction of rotation from the Chandler loop-the clot head faces in the opposite direction of the drum rotation.</li>
	<li>Attach the tubing back to the main apparatus such that the clot is closest to the outlet pressure sensor (the head of the clot should be facing away from the outlet sensor). Secure the clot in its position by puncturing the tubing and the clot head with two 30 G needles in an &#34;X&#34; pattern. Leave these needles in for the duration of the run. 
	NOTE: Depending on the dampener and pump settings, additional needles may be necessary to ensure the clot does not fragment prematurely. If necessary, a screen can be added to the tubing downstream of the clot to prevent clot fragments from circulating in the system. Once a set number of needles has been established to hold the clot, keep this consistent across conditions.</li>
	<li>Take the remainder of the mobile phase solution and put it into a 50 mL tube as the reservoir.</li>
	<li>Place the reservoir in the water bath and put in the inlet and outlet tubing (the outlet is from the fluorometer and the inlet goes into the pump head).</li>
	<li>Check that the fluorometer being used is connected and monitored. Check that the initial value is appropriate compared to a mobile phase-only system baseline at the start of the experiment. 
	NOTE: If an in-line fluorometer is not available, serial periodic sampling of the reservoir can be carried out at defined intervals throughout the flow loop analysis period. Collected fractions can be read using a 96-well plate immediately following the completion of the experiment on any commercially available spectrophotometer.</li>
	<li>Add 500 &#181;L of 100,000 ng/mL tPA directly to the reservoir volume to achieve a final 1,000 ng/mL tPA concentration in 50 mL. The volume, concentration, and specific drug added will depend upon the desired target circulating concentration and system reservoir volume.</li>
	<li>Check the following before starting the pump:
	<ol>
		<li>All junctions are secure.</li>
		<li>The two valves above the pressure sensors are in the appropriate closed position.</li>
		<li>Any residual plasma (or fluid) has been replaced in the reservoir.</li>
		<li>The thrombolytic has been added to the reservoir and properly mixed.</li>
		<li>The inlet tubing is near the bottom of the reservoir (this ensures minimal bubbles).</li>
		<li>Outlet tubing is secure and at the appropriate height for the desired pressure (dependent upon which vessel location is being modeled).</li>
		<li>The pump rotation direction is correct (Flow order: Pump &#62; Dampener &#62; Clot &#62; Fluorometer &#62; Reservoir &#62; Pump).</li>
		<li>If pump RPMs are set very high (&#62;150 rpm), start at a slower speed and ramp up to ensure the rapid change in pressure does not fragment the clot or cause tubing leakage.</li>
		<li>Ensure the system is recording the data appropriately from the fluorometer and/or supplies are prepared for periodic sampling of the mobile phase for post experiment time point reads.</li>
	</ol>
	</li>
	<li>Turn on the pump and set it to achieve the desired volumetric flow rate of 160 mL/min or increase the flow rate until the desired pressure is achieved. The system will fill with fluid and bubbles. The bubbles will artificially raise the fluorometric readings, so watch for the bubbles to clear. Once they do, turn off the lights and begin data acquisition.</li>
	<li>Leave the pump running until the clot is significantly degraded or the desired experimental time has elapsed (&#8805;60 min). Add reagents, as needed, to the system throughout the experiment via the reservoir to create unique experimental conditions testing a variety of thrombolytic variations. 
	NOTE: The experimental time will depend on the pump flow rate (shear level) and concentration of thrombolytic.</li>
	<li>Once the assay has been completed, reduce the volumetric flow rate, and remove the inlet tubing while the pump is still running to push most of the fluid in the system into the reservoir (some mobile phase will remain in the tubing). Disconnect the clot-containing tubing section at the outlet pressure sensor side of the tubing and lower it into a weigh boat.</li>
	<li>Remove the needles that hold the clot in place to collect the remnant fluid from within the system and clot/clot fragments. Use a syringe to help clear the system as needed.</li>
	<li>Weigh and process the remaining clot for additional analysis such as the calculation of percent mass lost or for histology.</li>
</ol>
5. Cleaning the system
<ol>
	<li>Between samples, rinse the entire system with warm water at a high rpm (&#62;150 rpm). Load the water into the reservoir and run through the system for at least 2 min, empty, and run again for two complete system rinses. After these rinses, if the fluorometer reading does not return to baseline, repeat the rinse process for an additional cycle. If it still has not returned to baseline, completely change the tubing before assaying the next sample. 
	NOTE: During the experiments, tubing can be reused between samples; however, due to the perforation with needles used to hold the clot in place, the tubing section between the inlet and outlet pressure sensors should be replaced after each run. Under some experimental conditions, replacing the entire tubing set after each run or clustering assays may be necessary to eliminate any sample crosscontamination.</li>
	<li>After all samples have been run for that day&#39;s experimentation, remove all tubing and discard. Scrub the T-junctions with hot water and a bristle brush until clean and leave to dry and rinse the syringe dampeners with hot water. Use 70% EtOH to help with sterility.</li>
</ol>

Combining the Chandler Loop and RT-FluFF for Ex Vivo Clot Lysis Monitoring

<ol>
	<li>Ali, M. R., 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=Aspect+of+thrombolytic+therapy:+a+review.">Aspect of thrombolytic therapy: a review.</a> Scientific World Journal. 2014, 586510 (2014).</li><li>Bhogal, P., Andersson, T., Maus, V., Mpotsaris, A., Yeo, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanical+thrombectomy-A+brief+review+of+a+revolutionary+new+treatment+for+thromboembolic+stroke.">Mechanical thrombectomy-A brief review of a revolutionary new treatment for thromboembolic stroke.</a> Clin Neuroradiol. 28 (3), 313-326 (2018).</li><li>Fluri, F., Schuhmann, M. K., Kleinschnitz, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Animal+models+of+ischemic+stroke+and+their+application+in+clinical+research.">Animal models of ischemic stroke and their application in clinical research.</a> Drug Des Devel Ther. 9, 3445-3454 (2015).</li><li>Kaiser, E. E., West, F. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large+animal+ischemic+stroke+models:+replicating+human+stroke+pathophysiology.">Large animal ischemic stroke models: replicating human stroke pathophysiology.</a> Neural Regen Res. 15 (8), 1377-1387 (2020).</li><li>Elnager, A., 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=In+vitro+whole+blood+clot+lysis+for+fibrinolytic+activity+study+using+d-dimer+and+confocal+microscopy.">In vitro whole blood clot lysis for fibrinolytic activity study using d-dimer and confocal microscopy.</a> Adv Hematol. 2014, 814684 (2014).</li><li>Prasad, S., 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=Development+of+an+in+vitro+model+to+study+clot+lysis+activity+of+thrombolytic+drugs.">Development of an in vitro model to study clot lysis activity of thrombolytic drugs.</a> Thromb J. 4, 14 (2006).</li><li>Robbie, L. A., Young, S. P., Bennett, B., Booth, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thrombi+formed+in+a+Chandler+loop+mimic+human+arterial+thrombi+in+structure+and+RAI-1+content+and+distribution.">Thrombi formed in a Chandler loop mimic human arterial thrombi in structure and RAI-1 content and distribution.</a> Thromb Haemost. 77 (3), 510-515 (1997).</li><li>Mutch, N. 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=Model+thrombi+formed+under+flow+reveal+the+role+of+factor+XIII-mediated+cross-linking+in+resistance+to+fibrinolysis.">Model thrombi formed under flow reveal the role of factor XIII-mediated cross-linking in resistance to fibrinolysis.</a> J Thromb Haemost. 8 (9), 2017-2024 (2010).</li><li>Blinc, A., Kennedy, S. D., Bryant, R. G., Marder, V. J., Francis, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+through+clots+determines+the+rate+and+pattern+of+fibrinolysis.">Flow through clots determines the rate and pattern of fibrinolysis.</a> Thromb Haemost. 71 (2), 230-235 (1994).</li><li>Mutch, N. 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=The+use+of+the+Chandler+loop+to+examine+the+interaction+potential+of+NXY-059+on+the+thrombolytic+properties+of+rtPA+on+human+thrombi+in+vitro.">The use of the Chandler loop to examine the interaction potential of NXY-059 on the thrombolytic properties of rtPA on human thrombi in vitro.</a> Br J Pharmacol. 153 (1), 124-131 (2008).</li><li>Herbig, B. A., Yu, X., Diamond, 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=Using+microfluidic+devices+to+study+thrombosis+in+pathological+blood+flows.">Using microfluidic devices to study thrombosis in pathological blood flows.</a> Biomicrofluidics. 12 (4), 042201 (2018).</li><li>Jigar Panchal, H., Kent, N. J., Knox, A. J. S., Harris, L. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microfluidics+in+haemostasis:+A+review.">Microfluidics in haemostasis: A review.</a> Molecules. 25 (4), 833 (2020).</li><li>Zeng, Z., 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=Fluorescently+conjugated+annular+fibrin+clot+for+multiplexed+real-time+digestion+analysis.">Fluorescently conjugated annular fibrin clot for multiplexed real-time digestion analysis.</a> J Mater Chem B. 9 (45), 9295-9307 (2021).</li><li>Zeng, Z., Christodoulides, A., Alves, N. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+tracking+of+fibrinolysis+under+constant+wall+shear+and+various+pulsatile+flows+in+an+in-vitro+thrombolysis+model.">Real-time tracking of fibrinolysis under constant wall shear and various pulsatile flows in an in-vitro thrombolysis model.</a> Bioeng Transl Med. 8 (3), e10511 (2023).</li><li>Christodoulides, A., Zeng, Z., Alves, N. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In-vitro+thromboelastographic+characterization+of+reconstituted+whole+blood+utilizing+cryopreserved+platelets.">In-vitro thromboelastographic characterization of reconstituted whole blood utilizing cryopreserved platelets.</a> Blood Coagul Fibrinolysis. 32 (8), 556-563 (2021).</li><li>Zeng, Z., Nallan Chakravarthula, T., Christodoulides, A., Hall, A., Alves, N. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+Chandler+loop+shear+and+tubing+size+on+thrombus+architecture.">Effect of Chandler loop shear and tubing size on thrombus architecture.</a> J Mater Sci Mater Med. 34 (5), 24 (2023).</li><li>Touma, H., Sahin, I., Gaamangwe, T., Gorbet, M. B., Peterson, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Numerical+investigation+of+fluid+flow+in+a+chandler+loop.">Numerical investigation of fluid flow in a chandler loop.</a> J Biomech Eng. 136 (7), (2014).</li><li>Wojdyla, M., Raj, S., Petrov, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Absorption+spectroscopy+of+single+red+blood+cells+in+the+presence+of+mechanical+deformations+induced+by+optical+traps.">Absorption spectroscopy of single red blood cells in the presence of mechanical deformations induced by optical traps.</a> J Biomed Opt. 17 (9), (2012).</li><li>Wu, J. H., Diamond, 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=A+fluorescence+quench+and+dequench+assay+of+fibrinogen+polymerization,+fibrinogenolysis,+or+fibrinolysis.">A fluorescence quench and dequench assay of fibrinogen polymerization, fibrinogenolysis, or fibrinolysis.</a> Anal Biochem. 224 (1), 83-91 (1995).</li></ol>

The authors have no conflicts of interest to disclose.

Clot formation and labeling 
The Chandler loop has been demonstrated to provide an easy and effective means of reproducibly generating clots that mimic in-vivo thrombi16. Fine-tuning parameters such as tubing size, rotational speeds, drum diameter, and clotting time allow for the rapid generation of clots under differing shear conditions that can capture architectural features appreciated in a range of thrombi mimicking both arterial and venous sources. The additiona...

Diseases fundamentally stemming from thrombo-embolic etiologies present a major source of morbidity and mortality in present-day society. Manifestations of thrombo-embolic pathogenesis include, but are not limited to, myocardial infarctions, ischemic strokes, deep venous thromboses, and pulmonary emboli1. A tremendous amount of ongoing research, spanning multiple disciplines, revolves around the development of safe and effective methods for dealing with pathogenic thrombosis. Variations in arterial and venous manifestations of thrombosis and varying anatomic locations have resulted in the development of different treatment approaches. However, acute treatment generally relies on the use of pharmacologic thrombolysis via plasminogen activators with the potential for mechanical thrombectomy under certain clinical circumstances2.
The development of novel pharmacologic treatment strategies fundamentally relies on both in-vivo animal models and in-vitro digestion models for preclinical testing3,4. In-vivo models naturally benefit from their ability to capture the complex interaction of various physiologic parameters on treatment efficacy that include clearance of pharmaceutical agents as well as cellular interactions with drugs. However, this same complexity often makes such models quite costly and introduces additional issues when attempting to isolate underlying pharmaco-dynamics/kinetics in animals that significantly differ from human physiology. The development of in-vitro models has helped by facilitating a distilled testing setting in which drug development and screening can be performed but often lacks the fidelity necessary to recapitulate the disease state being studied. 
Commonly found in-vitro protocols for testing novel thrombolytics rely on the utilization of clots formed and lysed under static conditions whereby the residual clot mass serves as the primary endpoint5,6. Unfortunately, such techniques fail to account for the mechanical aspects of clot lysis such as turbulent flow and trans-thrombus pressure drops that can significantly alter the pharmacodynamics of test drugs. Additionally, clots formed under static conditions contain microarchitecture that differs from physiologic clots. The presence of shear during clot formation has reproducibly been shown to impact the resulting clot characteristics such as platelet activation and fibrin-crosslinking. Clots being produced under shear flow exhibit complex heterogeneity from tip-to-tail that is absent in statically formed clots7,8. Such departures from physiologic clot architecture may impact important drug development characterization that includes drug penetration within a thrombus and subsequent lysis efficiency9. 
To address some of these limitations associated with the use of static clotting/clot-lysis models, the adoption of the Chandler loop for both clot formation and clot lysis in the presence of shear has seen a resurgence10. Although such systems allow for a better representation of flow dynamics and generate clots with more physiologically relevant architecture compared to relatively static assays, their simplified flow conditions still represent a deviation from physiologic conditions. Lastly, microfluidic approaches have also been undertaken due to their ease of imaging and uniform flow patterns; however, they remain a significant removal from the physiologic conditions expected within the larger vessels primarily affected in most clinically relevant thrombo-embolic disorders11,12. 
With the above discussion in mind, we developed a high-fidelity, in-vitro thrombolysis model for preclinical thrombolytic drug screening. The model aims at addressing some of the current pitfalls detailed above in the realm of novel thrombolytic therapy screening and was validated for reproducibility and sensitivity at varying concentrations of tissue plasminogen activator (tPA). The system described herein offers physiological shear flows utilizing a peristaltic pump, a pressure dampener, a heated reservoir, two pressure sensors, an in-line fluorometer, and a fluorescently labeled Chandler loop shear-formed clot analog to facilitate real-time tracking of fibrinolysis13. Taken together, the overall system is called the Real-Time Fluorometric Flowing Fibrinolysis Assay (RT-FluFF Assay)14 and this manuscript will discuss the intricacies of successfully setting up and running assays in this high-fidelity in-vitro thrombolysis model.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>30 G&#160;Disposable Hypodermic Needles</td>
			<td>Exel International&#160;</td>
			<td>26439</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>6 mm HSS Lathe Bar Stock Tool 150 mm Long</td>
			<td>uxcell</td>
			<td>B07SXGSQ82</td>
			<td>Chandler loop,&#160;</td>
		</tr>
		<tr>
			<td>96-Well Clear Flat Bottom UV-Transparent Microplate</td>
			<td>Corning</td>
			<td>3635</td>
			<td>Other Consumables, Non-treated acrylic copolymer, non-sterile</td>
		</tr>
		<tr>
			<td>Air-Tite Luer-lock Unsterile 60 mL Syringes</td>
			<td>Air-Tite</td>
			<td>MLB3</td>
			<td>RT-FluFF Apparatus , dampeners</td>
		</tr>
		<tr>
			<td>Arium Mini Plus Ultrapure Water System</td>
			<td>Sartorius</td>
			<td>NA</td>
			<td>DI water source</td>
		</tr>
		<tr>
			<td>Calcium Chloride</td>
			<td>Millipore Sigma</td>
			<td>C5670</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>Disposable BP Transducers</td>
			<td>AD Instruments</td>
			<td>MLT0670</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Drager Siemans HemoMed Pod</td>
			<td>Drager</td>
			<td>5588822</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Drager Siemans Patient Monitor</td>
			<td>Drager</td>
			<td>SC 7000</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Drum (cylinder, diameter 120 mm, width 85 mm)</td>
			<td></td>
			<td></td>
			<td>Chandler loop,</td>
		</tr>
		<tr>
			<td>Face Shield</td>
			<td>Moxe</td>
			<td>SHIELDS10</td>
			<td>Chandler loop,&#160;</td>
		</tr>
		<tr>
			<td>Fibrinogen From Human Plasma, Alexa Fluor 488 Conjugate</td>
			<td>Thermo Scientific</td>
			<td>F13191</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>Fitting, Polycarbonate, Four-Way Stopcock, Male Luer Lock, Non-Sterile</td>
			<td>Masterflex</td>
			<td>30600-04</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Fluorescein (FITC)</td>
			<td>Thermo Scientific</td>
			<td>119245000</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>General-Purpose Water Bath</td>
			<td>Thermo Scientific</td>
			<td>2839</td>
			<td>Chandler loop,&#160;</td>
		</tr>
		<tr>
			<td>Hotplate 4 &#215; 4</td>
			<td>Fisher Scientific</td>
			<td>1152016H</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Human Source Plasma Fresh-Frozen</td>
			<td>Zen-Bio</td>
			<td>SER-SPL</td>
			<td>Other Consumables, CPDA-1 anticoagulant</td>
		</tr>
		<tr>
			<td>Human Whole Blood&#160;</td>
			<td>Zen-Bio</td>
			<td>SER-WB-SDS&#160;</td>
			<td>Other Consumables, CPDA-1 anticoagulant</td>
		</tr>
		<tr>
			<td>L/S Easy-Load II Pump Head for High-Performance Precision Tubing, PPS Housing, SS Rotor</td>
			<td>Masterflex</td>
			<td>77200-62</td>
			<td>RT-FluFF Apparatus, Pump Head</td>
		</tr>
		<tr>
			<td>L/S Variable-Speed Digital Drive Pump with Remote I/O, 6 to 600 rpm; 90 to 260 VAC</td>
			<td>Masterflex</td>
			<td>7528-10</td>
			<td>RT-FluFF Apparatus, Pump</td>
		</tr>
		<tr>
			<td>Motor Speed Controller</td>
			<td>CoCocina</td>
			<td>ZK-MG</td>
			<td>Chandler loop,&#160;</td>
		</tr>
		<tr>
			<td>Nalgene Tubing T-Type Connectors</td>
			<td>Thermo Scientific</td>
			<td>6151-0312</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Peristaltic pump tubing&#160;</td>
			<td>Masterflex</td>
			<td>06424-15&#160;</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>Phosphate buffered saline</td>
			<td>Millipore Sigma</td>
			<td>P3813</td>
			<td>Other Consumables, Powder, pH 7.4, for preparing 1 L solutions</td>
		</tr>
		<tr>
			<td>SpectraMax M5 multi-detection microplate reader system (or other fluorescence detection)</td>
			<td>Molecular Devices</td>
			<td>M5</td>
			<td>RT-FluFF Apparatus</td>
		</tr>
		<tr>
			<td>Switching Power Supply</td>
			<td>SoulBay</td>
			<td>UC03U</td>
			<td>Chandler loop,&#160;</td>
		</tr>
		<tr>
			<td>Thermo Scientific National Target All-Plastic Disposable Syringes 10 mL</td>
			<td>Thermo Scientific</td>
			<td>S751010</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>Tissue plasminogen activator, human</td>
			<td>Millipore Sigma</td>
			<td>T0831</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>Tubing ID 1/4&#39;&#39;, OD 3/8&#39;&#39;</td>
			<td>Fisher Scientific</td>
			<td>AGL00017</td>
			<td>Other Consumables, cut into 1.5cm sections use to connect tubing to T-type connectors</td>
		</tr>
		<tr>
			<td>Tubing ID 5/32&#34;, OD 7/32&#34;</td>
			<td>Tygon</td>
			<td>ND-100-65, ADF 00009&#160;</td>
			<td>Other Consumables</td>
		</tr>
		<tr>
			<td>V3 365 nm Mini - Black Light UV Flashlight</td>
			<td>uvBeast</td>
			<td>uvB-V3-365-MINI</td>
			<td>Chandler loop, used to check completed clots</td>
		</tr>
		<tr>
			<td>ZGA37RG ZYTD520 DC Motor, 12 V, 100 rpm</td>
			<td>Pangyoo</td>
			<td>ZGA37RG</td>
			<td>Chandler loop,&#160;</td>
		</tr>
	</tbody>
</table>

tracking fibrinolysis of chandler loop-formed whole blood clots under shear flow in an in-vitro thrombolysis model

Thromboembolism and related complications are a leading cause of morbidity and mortality worldwide and various assays have been developed to test thrombolytic drug efficiency both in vitro and in vivo. There is increasing demand for more physiologically relevant in-vitro clot models for drug development due to the complexity and cost associated with animal models in addition to their often lack of translatability to human physiology. Flow, pressure, and shear rate are important characteristics of the circulatory system, with clots that are formed under flow displaying different morphology and digestion characteristics than statically formed clots. These factors are often unrepresented in conventional in-vitro clot digestion assays, which can have pharmacological implications that impact drug translational success rates.
The Real-Time Fluorometric Flowing Fibrinolysis (RT-FluFF) assay was developed as a high-fidelity thrombolysis testing platform that uses fluorescently tagged clots formed under shear flow, which are then digested using circulating plasma in the presence or absence of fibrinolytic pharmaceutical agents. Modifying the flow rates of both clot formation and clot digestion steps allows the system to imitate arterial, pulmonary, and venous conditions across highly diverse experimental setups. Measurements can be taken continuously using an in-line fluorometer or by taking discrete time points, as well as a conventional end point clot mass measurement. The RT-FluFF assay is a flexible system that allows for the real-time tracking of clot digestion under flow conditions that more accurately represent in-vivo physiological conditions while retaining the control and reproducibility of an in-vitro testing system.

Author Spotlight: Advancing Thrombolytic Testing by Integrating Flow Dynamics in In Vitro Models

Tracking Fibrinolysis of Chandler Loop-Formed Whole Blood Clots Under Shear Flow in An In-Vitro Thrombolysis Model

Thrombosis is associated with numerous medical conditions and current treatments risk severe bleeding. Circulatory system flow significantly impacts blood clot structure. Incorporating flow into in-vitro models may improve their physiological relevance, enhancing the selection of better candidates for in-vivo testing.The assays for the study of fibrinolytics predominantly utilize static clot or microfluidic systems to assess properties such as lysis time, clot structure, or viscoelasticity. Static clot lysis assays typically rely on spectrophotometric measurements or clot mass determination as endpoints to evaluate fibrinolysis efficiency. Current thrombolytic testing uses statically-formed clots, which differ structurally from those formed under flow conditions.Microfluidic systems consider flow dynamics, but their smaller scales create unique hemodynamics and clot structures. The currently developed RT-FluFF assay provides ease in monitoring fibrinolysis in real time under physiological flow conditions. This means we now have a platform that allows control over multiple parameters to mimic conditions closer to in-vivo study models for better translation when screening new thrombolytics.

Chandler loop clot formation 
In forming clots, we generally aimed for quadruplicates to ensure that if any clot outliers (based on gross morphology and mass) existed, we still had the ability to run triplicate thrombolysis assays. Assuming optimal loading conditions, clots should all be quite uniform in length (~3.3 cm), weight (~100 mg), and appearance as is represented in Figure 3. When employing FITC-Fg, we also aimed to examine clots under UV light to ensure relati...

Read this Scientific Article Protocol about Author Spotlight: Advancing Thrombolytic Testing by Integrating Flow Dynamics in In-Vitro Models at JoVE.com

In-vitro thrombolysis assays have often struggled to replicate in-vivo conditions whether in the model thrombus being digested or in the environment in which thrombolysis is occurring. Herein, we explore how coupling the Chandler loop and Real-Time Fluorometric Flowing Fibrinolysis Assay (RT-FluFF) is used for high-fidelity, ex-vivo, clot lysis monitoring.

Thromboembolism and related complications are a leading cause of morbidity and mortality worldwide and various assays have been developed to test ...

tracking-fibrinolysis-chandler-loop-formed-whole-blood-clots-under

Research

JoVE Journal

Bioengineering

Integrating Fluorescently Tagged Fibrinogen into Human Blood Clot for Enhanced Clot Visualization

Optimizing Real-Time Fluorometric Flow Loop System for Human Blood Clot Analysis

509 Views.  Indiana University School of Medicine.  In-vitro thrombolysis assays have often struggled to replicate in-vivo conditions whether in the model thrombus being digested or in the environment in which thrombolysis is occurring. Herein, we explore how coupling the Chandler loop and Real-Time Fluorometric Flowing Fibrinolysis Assay (RT-FluFF) is used for high-fidelity, ex-vivo, clot lysis monitoring.

Combining the Chandler Loop and RT-FluFF for Ex Vivo Clot Lysis Monitoring

Summary