The authors thank all members of the Green, Pardee and Pena labs as well as all co-authors of previous manuscripts pertaining to the work disclosed in this manuscript. S.J.R.d.S. was supported by a PhD fellowship sponsored by the Foundation for Science and Technology of Pernambuco (FACEPE), Brazil, reference number IBPG-1321-2.12/18, and currently is supported by a Postdoctoral Fellowship sponsored by the University of Toronto, Canada. P.B. is supported by the William Knapp Buckley Award from the Faculty of Pharmacy, University of Toronto. M.K. was supported by the Precision Medicine Initiative (PRiME) at the University of Toronto internal fellowship number PRMF2019-002. This work was supported by funds to K.P from the Canada Research Chairs Program (Files 950-231075 and 950-233107), the University of Toronto&#39;s Major Research Project Management Fund, the CIHR Foundation Grant Program (201610FDN-375469), and to L.P, A.A.G., and K.P through the CIHR/IDRC Team Grant: Canada-Latin/America-Caribbean Zika Virus Program (FRN: 149783), as well as by funds to K.P. from the Canada&#39;s International Development Research Centre (grant 109434-001) through the Canadian 2019 Novel Coronavirus (COVID-19) Rapid Research Funding Opportunity. This work was also supported by funds to A.A.G. from an Arizona Biomedical Research Commission New Investigator Award (ADHS16-162400), the Gates Foundation (OPP1160667), an NIH Director&#39;s New Innovator Award (1DP2GM126892), an NIH R21 award (1R21AI136571-01A1) to K.P./A.A.G, and an Alfred P. Sloan Fellowship (FG-2017-9108). Figure 1 was created with Biorender.com under academic license to K.P.

<ol>
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K.P. and A.A.G. are co-inventors of paper-based toehold sensor related technologies. Y.G., S.C., and K.P. are co-founders of LSK Technologies, Inc. and are co-inventors of the PLUM-related technologies. M.K., K.P. and A.A.G. are co-founders of En Carta Diagnostics Ltd. Other authors have no conflicts of interest. Patents: PLUM device: Y.G., S.C., and K.P. patent application was filed by University of Toronto and assigned to LSK Technologies Inc. U. S. Provisional Patent Application No. 62/982,323 filed February 27, 2020; Toehold switch patent: A.A.G., P.Y., and J.J. C. "Riboregulator compositions and methods of use", Patent. WO2014074648A3 filed November 6, 2012; Paper-based diagnostic patent: K.P. and J.J.C. "Paper-based synthetic gene networks" U.S. patent pending No. US15/963,831 filed December 6, 2013; Zika patent 1: K.P., A.A.G., M.K.T., D.B., G.L., T.F., and J.J.C., "Portable, Low-Cost Virus Detection and Strain Identification Platform," U. S. Provisional Patent Application No. 62/403,778 filed October 4, 2016; Zika patent 2: K.P., A. A.G., M.K.T., D.B., G.L., T.F., and J.J.C., "Portable, Low-Cost Virus Detection and Strain Identification Platform," U. S. Provisional Patent Application No. 62/341,221 filed May 25, 2016.

The combined paper-based system described here can bring clinically relevant molecular diagnostics, with performance that is functionally comparable to RT-qPCR, to the point-of-need6. Importantly, for remote settings, the availability of diagnostics on-site can decrease the time to results from days to hours. Highlighting the programmability of this approach, the pipeline that has been described can be used to detect virtually any pathogen target. We have paired the molecular tools with a purpose-built portable plate reader, which is compact and compatible with battery operation (8&#8211;9 h) and provides onboard data analysis to enable distributed applications. In other work, we have validated the combined hardware and Zika virus diagnostic platform with 268 patient samples, in parallel with RT-qPCR, and found a diagnostic accuracy of 98.5%24. Taken together, our goal is to enable the technology transfer of this platform to researchers so that it can be repurposed and improved by the community to address unmet diagnostic needs.
The in silico toehold switch design process has been integrated and automated into a pipeline that can be divided into three stages. The first stage generates a pool of toehold switch designs that hybridize to the target sequence in one nucleotide increments. The second stage examines the secondary structure and toehold switch availability and eliminates sensors with in-frame premature stop codons. A scoring function that considers multiple factors (e.g., defect level of the toehold switch, toehold switch availability, and target site accessibility) is then implemented to select top toehold switch designs based on overall scores. In the final stage, a list of sequences is generated for the top toehold switch designs and their corresponding target triggers. The top sensor sequences should be screened for specificity against the human transcriptome and closely related viral genomes using NCBI/Primer-BLAST25. It is also best practice to screen the sensor target sites for sequence conservation in the Zika viral genome to ensure that the sensors will provide broad and robust detection. Several versions of toehold switch design software have been developed and the design algorithm allows users to generate two versions, either series A6&#160;or series B toehold switches6. In this article, the focus has been on the series B toehold switch design.
Following commercial DNA synthesis, the toehold switches can be rapidly assembled, and then tested by performing an initial screen against a synthetic target trigger sequence that corresponds to short regions (200-300 nt) of the target genome. For screening the performance of toehold switch-based sensors, it is ideal to add the target sequence in the form of RNA. In this article, the steps required to add in vitro transcribed trigger RNA have been outlined. However, if available, full-length genome templates such as quantified viral RNA extracts or commercial synthetic RNA genomes or standards can be used. Using full-length RNA genomes for initial toehold switch screening is beneficial as it can inform whether additional factors, such as RNA secondary structure, will affect sensor performance. To optimize the ON/OFF ratio of candidate switches, the toehold switch DNA can be titrated into the cell-free reaction. This step can also serve to identify high-performing toehold switches (fold amplification, or high ON/OFF ratio) and omit leaky toehold switches (high signal in the absence of the target RNA) from downstream characterization steps.
To improve the limit of detection of the top-performing toehold switch candidates, NASBA is used to increase clinically-relevant concentrations of target Zika viral RNA to a level that can be detected by toehold switches6. Different combinations of forward and reverse primer sets are screened to determine the best NASBA primer and toehold switch combinations to enable detection at clinically relevant concentrations. Once an ideal primer set and toehold switch combination has been identified, the assay is taken forward to clinical validation. It is important to note that the toehold switch and NASBA screening stages can be labor and resource-intensive and therefore test development is best suited to well-resourced research sites. Although we have not applied process automation, it is likely that this could accelerate the iterative design, build, and test cycle32. Fortunately, the turnaround time from sensor design and testing to deployment can be remarkably short (less than a week), making this strategy ideal for time-critical situations, such as epidemic outbreaks6.
Even after a biosensor with clinically relevant sensitivity has been developed, there are technical challenges that need to be addressed. Since this protocol involves manual operation and is a multi-step procedure, there is a risk of cross contamination between samples. We do our best to abate this risk through careful laboratory practice. In a recent clinical trial of 268 patient samples, we did not encounter any contamination issues; however, it is an important consideration24. With this in mind, the protocol remains a laboratory assay and requires a skilled user with command of proper molecular biology techniques. An additional consideration for deployment&#160;is the RNA isolation from patient samples. Here we describe RNA isolation using column-based nucleic acid extraction kits. However, in other work, we have demonstrated an effective and simple boiling lysis method (95 &#176;C for 2 min) for low-burden patient sample processing6. This strategy nearly eliminates the cost&#160;associated with RNA extraction and avoids the use of column-based nucleic acid extraction kits, which can pose a logistics challenge in low-resource settings or supply chain issues during crises, such as the COVID-19 pandemic33.
As we have seen during the COVID-19 pandemic, the instruments used to perform RT-qPCR can themselves serve as a bottleneck and limit patient access to testing. This factor, which is also largely financial, leads to a centralized testing mode that&#160;can limit diagnostic access. For example, during the 2015/2016 Zika outbreak, only five national reference labs were available in Brazil, which caused delays in patient testing. Without considering the potential benefit of economies of scale, the current cost of goods for the portable plate reader is ~$500 USD, which even if increased five-fold to account for labor and commercial margin, still provides an affordable instrument. This compares well to RT-qPCR instruments that range in cost from $15,000-$90,000 USD34. Furthermore, the estimated cost per test for the cell-free assay in Latin America is around $5.48 USD, while the cost per test of RT-qPCR in Brazil was ~$10-11 USD at the time of the Zika outbreak36. Beyond the cost of equipment, the portable plate reader has a small footprint (20 cm3), automatic analysis, data upload to the cloud via internet, and can be run on battery power. These features dramatically expand the potential settings where testing can be deployed and concomitantly expands the patient population that can be served.
To date the most common commercial E. coli CFPS platforms are the S30 and PURE systems37; however, a key consideration in improving access to diagnostics in low- and middle-income countries is the limited domestic availability of these reagents. An important step toward resolving this challenge is the development of local CFPS production. The Federici lab has recently made significant progress toward developing a non-commercial platform to implement toehold switch-based sensors in lysate-based cell-free systems, reaching a 2.7 fM LOD with Zika virus RNA14. Not only does this achievement allow the reagents to be made in the country of use, avoiding import tariffs and delays, but labor costs also scale to local rates and thus the overall cost can be significantly lowered. In the work outlined by the Federici group, the cost of producing the CFPS expression reaction (5 &#181;L) in Chile was 6.9 cents (USD)35,38, providing a dual incentive (improved logistics and cost) for implementing lysate-based systems35,38.
The placement of RT-qPCR-comparable testing into distributed diagnostic networks could bring significant advantages over current practices that are dependent on the transportation of samples to centralized RT-qPCR facilities. In peri-urban settings, where Zika cases were concentrated, the physical distance between a patient and the diagnostic facility slows diagnosis and increases the risk that results will not reach the patient at a clinically relevant time. It is our hope that the work presented here can contribute to enabling the research community, through the transfer of knowledge, to create decentralized biotechnologies and portable hardware for human health, agriculture and environmental monitoring.

RT-qPCR has remained the gold standard technology for clinical diagnostics due to its excellent sensitivity and specificity. Although highly robust, the method depends on expensive, specialized equipment and reagents that require temperature-controlled distribution and storage. This presents significant barriers to the accessibility of quality diagnostics globally, particularly in times of disease outbreaks and in regions where access to well-equipped labs is limited1,2. This was observed during the 2015/2016 Zika virus outbreak in Brazil. With only five centralized laboratories available to provide RT-qPCR testing, significant bottlenecks resulted, limiting access to diagnostics. This was especially challenging for individuals in peri-urban settings, who were more severely impacted by the outbreak3,4. In an effort to improve access to diagnostics, the protocol shows a platform that has been developed with the potential to provide decentralized, low-cost, and high-capacity diagnostics in low-resource settings. As a part of this, a diagnostic discovery pipeline was established, coupling isothermal amplification and synthetic RNA switch-based sensors with paper-based cell-free expression systems5,6.
Cell-free protein synthesis (CFPS) systems, in particular E. coli based cell-free systems, are an attractive platform for a wide range of biosensing applications from environmental monitoring7,8 to pathogen diagnostics5,6,9,10,11,12. Comprising the components necessary for transcription and translation, CFPS systems have significant advantages over whole-cell biosensors. Specifically, sensing is not limited by a cell wall and, in general, they are modular in design, biosafe, inexpensive, and can be freeze-dried for portable use. The ability to freeze-dry gene circuit-based reactions onto substrates such as paper or textiles, enables transport, long-term storage at room temperature5, and even incorporation into wearable technology13.
Previous work has demonstrated that E. coli cell-free systems can be used to detect numerous analytes, for example, toxic metals such as mercury, antibiotics such as tetracycline7,14, endocrine-disrupting chemicals15,16, biomarkers such as hippuric acid17, pathogen-associated quorum sensing molecules9,18 and illicit substances such as cocaine17, and gamma hydroxybutyrate (GHB)19. For the sequence-specific detection of nucleic acids, strategies have for the most part relied on the use of switch-based biosensors coupled to isothermal amplification techniques. Toehold switches are synthetic riboregulators (also referred to as simply &#39;switches&#39; in the rest of the text) that contain a hairpin structure that blocks downstream translation by sequestering the ribosomal binding site (RBS) and the start codon. Upon interaction with their target trigger RNA, the hairpin structure is relieved and subsequent translation of a reporter open reading frame is enabled20.
Isothermal amplification can also be used as molecular diagnostics21; however, these methods are prone to nonspecific amplification, which can reduce the specificity and thereby the accuracy of the test to below that of RT-qPCR 22. In the work reported here, isothermal amplification upstream of the switch-based sensors was used to provide combined signal amplification that enables clinically relevant detection of nucleic acids (femtomolar to attomolar). This pairing of the two methods also provides two sequence-specific checkpoints that, in combination, provide a high level of specificity. Using this approach, previous work has demonstrated the detection of viruses such as Zika6, Ebola5, Norovirus10, as well as pathogenic bacteria such as C. difficile23 and antibiotic resistant Typhoid12. Most recently, cell-free toehold switches have been demonstrated for SARS-CoV-2 detection in efforts to provide accessible diagnostics for the COVID-19 pandemic11,12,13.
The following protocol outlines the development and validation of cell-free, paper-based synthetic toehold switch assay for Zika virus detection, from in silico biosensor design, through the assembly and optimization steps, to field validation with patient samples. The protocol begins with the in silico design of RNA toehold switch-based sensors and isothermal amplification primers specific for the Zika viral RNA. Although numerous isothermal amplification methods exist, here the use of nucleic acid sequence-based amplification (NASBA) to increase the concentration of viral RNA target present in the reaction, enabling clinically significant sensitivity was demonstrated. Practically, isothermal amplification methods have the advantage of operating at a constant temperature, eliminating the need for specialized equipment, such as thermal cyclers, which are generally limited to centralized locations.
Next, the process of assembling the synthetic toehold switch sensors with reporter coding sequences through overlap extension PCR, and screening the synthetic toehold switch sensors for optimal performance in cell-free systems using synthetic RNA is described. For this set of Zika virus sensors, we have selected the lacZ gene encoding the &#946;-galactosidase enzyme, which is able to cleave a colorimetric substrate, chlorophenol red-&#946;-D-galactopyranoside (CPRG), to produce a yellow to purple color change that can be detected by eye or with a plate reader. Once top-performing synthetic switches are identified, the process for screening primers for nucleic acid sequence-based isothermal amplification of the corresponding target sequence using synthetic RNA to find sets that provide the best sensitivity is described.
Finally, the performance of the diagnostic platform is validated on-site in Latin America (Figure 1). To determine the clinical diagnostic accuracy, the paper-based cell-free assay is performed using Zika virus samples from patients; in parallel a gold standard RT-qPCR assay is performed for comparison. To monitor colorimetric cell-free assays, we enable on-site quantification of results in regions where thermal cyclers are not available. The hand-assembled plate reader called Portable, Low-Cost, User-friendly, Multimodal (PLUM; hereafter referred to as portable plate reader) is also introduced here24. Initially developed as a companion device for cell-free synthetic toehold switch diagnostics, the portable plate reader offers an accessible way to incubate and read results in a high-throughput manner, providing integrated, computer vision-based software analysis for users.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/63223/63223fig1v9.jpg" /> 
Figure 1: Workflow for testing patient samples using paper-based cell-free toehold switch reactions.&#160;<a href="https://www.jove.com/files/ftp_upload/63223/63223fig1v8large.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>384 well plate covers - aluminum</td>
			<td>Sarstedt</td>
			<td>95.1995</td>
			<td>Used to cover the 384-well plates before they are inserted into the PLUM reader</td>
		</tr>
		<tr>
			<td>384 well plate covers - transparent</td>
			<td>Sarstedt</td>
			<td>95.1994</td>
			<td>Used to cover the 384-well plates before they are inserted into the BioTek plate reader</td>
		</tr>
		<tr>
			<td>384 well plates</td>
			<td>VWR</td>
			<td>CA11006-180</td>
			<td>2 mm paper-based diagnostics are placed into the wells of these plates for quantification</td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>BioShop Canada</td>
			<td>AGA001.500</td>
			<td>Gel electrophoresis</td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>BioShop Canada</td>
			<td>ALB001.500</td>
			<td>Blocking agent for the Whatman filter paper</td>
		</tr>
		<tr>
			<td>Cell free reactions</td>
			<td>New England Biolabs</td>
			<td>E6800L</td>
			<td>PURExpress</td>
		</tr>
		<tr>
			<td>CPRG</td>
			<td>Roche</td>
			<td>10884308001</td>
			<td>Chlorophenol red-b-D-galactopyranoside</td>
		</tr>
		<tr>
			<td>Disposable Sterile Biopsy Punches</td>
			<td>Integra Miltex</td>
			<td>23233-31</td>
			<td>Used to create 2 mm paper discs that fit into a 384-well plate</td>
		</tr>
		<tr>
			<td>DNAse I</td>
			<td>Thermo Scientific</td>
			<td>K2981</td>
			<td>Digests template DNA following incubation of the in vitro transcription reaction</td>
		</tr>
		<tr>
			<td>DNAse I Kit</td>
			<td>Thermo Scientific</td>
			<td>74104</td>
			<td>DNase I Kit For removing template DNA from IVT RNA</td>
		</tr>
		<tr>
			<td>dNTPs</td>
			<td>New England Biolabs</td>
			<td>N0446S</td>
			<td>Used for PCRs</td>
		</tr>
		<tr>
			<td>electrophoresis system</td>
			<td>Bio-Rad</td>
			<td>1704487</td>
			<td>Used to run the agarose gels</td>
		</tr>
		<tr>
			<td>Gel imaging station</td>
			<td>Bio-Rad</td>
			<td>1708265</td>
			<td>ChemiDoc XRS+ Imaging System</td>
		</tr>
		<tr>
			<td>IVT kit</td>
			<td>New England Biolabs</td>
			<td>E2040S</td>
			<td>Used for in vitro transcribing template (trigger) RNA for switch screening</td>
		</tr>
		<tr>
			<td>Nanodrop One</td>
			<td>Thermo Scientific</td>
			<td>ND-ONE-W</td>
			<td>Used for determining nucleic acid concentrations</td>
		</tr>
		<tr>
			<td>NASBA kit</td>
			<td>Life Sciences Advanced Technologies</td>
			<td>NWK-1</td>
			<td>Isothermal amplification reaction components</td>
		</tr>
		<tr>
			<td>Nuclease free H20</td>
			<td>invitrogen</td>
			<td>10977015</td>
			<td>Added to reaction mixes</td>
		</tr>
		<tr>
			<td>PAGE electrophoresis system</td>
			<td>Biorad</td>
			<td>1658001FC</td>
			<td>Used to cast and run polyacrylamide gels</td>
		</tr>
		<tr>
			<td>pCOLADuet-LacZ DNA</td>
			<td>Addgene</td>
			<td>75006</td>
			<td>https://www.addgene.org/75006/</td>
		</tr>
		<tr>
			<td>Phusion polymerase/reactioin buffer</td>
			<td>New England Biolabs</td>
			<td>M0530L</td>
			<td>Used for PCRs</td>
		</tr>
		<tr>
			<td>Plate reader</td>
			<td>BioTek</td>
			<td>BioTek NEO2</td>
			<td>Multi Mode Plate Reader, Synergy Neo2</td>
		</tr>
		<tr>
			<td>Primers</td>
			<td>Integrated DNA Technologies</td>
			<td></td>
			<td>Custom oligo synthesis</td>
		</tr>
		<tr>
			<td>Q5 polymerase/reaction buffer</td>
			<td>New England Biolabs</td>
			<td>M0491L</td>
			<td>Used for PCRs</td>
		</tr>
		<tr>
			<td>Qiagen PCR Puriifcation Kit</td>
			<td>QIAGEN</td>
			<td>27106</td>
			<td>QIAprep Spin Miniprep Kit</td>
		</tr>
		<tr>
			<td>RNA loading dye</td>
			<td>New England Biolabs</td>
			<td>B0363S</td>
			<td>2X RNA loading dye</td>
		</tr>
		<tr>
			<td>RNA Purification Kit</td>
			<td>QIAGEN</td>
			<td>EN0521</td>
			<td>QIAamp Viral RNA extraction kit</td>
		</tr>
		<tr>
			<td>RNase inhibitor</td>
			<td>New England Biolabs</td>
			<td>M0314S</td>
			<td>Used to prevent contamination of RNases A, B, and C</td>
		</tr>
		<tr>
			<td>RT-qPCR kit</td>
			<td>QIAGEN</td>
			<td>208352</td>
			<td>QuantiNova Probe RT-PCR Kit</td>
		</tr>
		<tr>
			<td>SYBR Gold</td>
			<td>Invitrogen S11494</td>
			<td>S11494</td>
			<td>PAGE gel stain for nucleic acids</td>
		</tr>
		<tr>
			<td>TAE Buffer</td>
			<td>BioShop Canada</td>
			<td>TAE222.4</td>
			<td>Gel electrophoresis buffer</td>
		</tr>
		<tr>
			<td>Thermal Cycler</td>
			<td>Applied Biosystems</td>
			<td>4484073</td>
			<td>Used for temperature cycling and incubating reactions</td>
		</tr>
		<tr>
			<td>Whatman 42 filter paper</td>
			<td>GE Healthcare</td>
			<td>1442-042</td>
			<td>Used to imbed molecular components for paper-based diagnostics</td>
		</tr>
	</tbody>
</table>

design to implementation study for development and patient validation of paper-based toehold switch diagnostics

Access to low-burden molecular diagnostics that can be deployed into the community for testing is increasingly important and has meaningful wider implications for the well-being of societies and economic stability. Recent years have seen several new isothermal diagnostic modalities emerge to meet the need for rapid, low-cost molecular diagnostics. We have contributed to this effort through the development and patient validation of toehold switch-based diagnostics, including diagnostics for the mosquito-borne Zika and chikungunya viruses, which provided performance comparable to gold-standard reverse transcription-quantitative polymerase chain reaction (RT-qPCR) based assays. These diagnostics are inexpensive to develop and manufacture, and they have the potential to provide diagnostic capacity to low-resource environments. Here the protocol provides all the steps necessary for the development of a switch-based assay for Zika virus detection. The article takes readers through the stepwise diagnostic development process. First, genomic sequences of Zika virus serve as inputs for the computational design of candidate switches using open-source software. Next, the assembly of the sensors for empirical screening with synthetic RNA sequences and optimization of diagnostic sensitivity is shown. Once complete, validation is performed with patient samples in parallel with RT-qPCR, and a purpose-built optical reader, PLUM. This work provides a technical roadmap to researchers for the development of low-cost toehold switch-based sensors for applications in human health, agriculture, and environmental monitoring.

Following the computational design pipeline, the construction of three toehold switches was performed by PCR. The PCR products were analyzed using agarose gel electrophoresis (Figure 2). The presence of a clear band around 3,000 bp, roughly the size of the lacZ gene coupled to a toehold switch, typically indicates a successful reaction. Alternatively, a lane without a band, multiple bands, or a band of the incorrect size, indicates a failed PCR. In the case of a failed PCR, the reaction conditions and/or primer sequences should be optimized.
The assembled toehold switches were screened to assess each sensor against its respective in vitro transcribed trigger RNA (Figure 3). While all three sensors displayed an increased OD570 absorbance, switch&#160;27B (Figure 3A) had the most rapid on-rate. Switches 33B and, to a lesser extent, 47B showed an increased OD570 absorbance in the absence of target trigger RNA, indicating that these switches possess some background activity or leakiness (Figure 3B,C)-a trait not wanted in a candidate sensor as it can reduce specificity. To more clearly identify the sensor with the highest ON/OFF signal ratio, the fold change of OD570 absorbance was calculated (see supplemental information section 5) and plotted (Figure 4). From this analysis, it is clear that switch 27B is the sensor that has the best performance with an ON/OFF&#160;ratio of around 60.
The sensitivity of the top-performing toehold switch (27B) was then evaluated by determining the lowest RNA concentration required to activate the toehold switch&#160;when coupled with a NASBA reaction. The graph illustrates that the top-performing Zika sensors can detect RNA at concentrations as low as 1.24 molecules per &#181;L (equivalent to ~2 aM; Figure 5).
After switch 27B was identified and validated, the sensor materials were distributed to the team members in Recife in the Pernambuco state of Brazil. In Brazil, the clinical diagnostic accuracy of the Zika virus diagnostic platform was assessed using Zika virus patient samples, in parallel with RT-qPCR for comparison. To validate the paper-based Zika diagnostic platform, the portable plate reader was used, which is capable of incubating and reading the colorimetric output of paper-based sensors. The color change from yellow to purple is used to identify a positive sample, while a negative sample remains yellow (Figure 6). An additional option for visualizing the results generated by the portable plate reader (Figure 8) is to plot the colorimetric response for each paper-based reaction over time. Samples were tested in triplicate and those that exceeded the threshold (red line set to 1) were considered positive, while samples below the threshold were considered negative (Figure 6 and Figure 7).
Finally, to evaluate and compare the clinical performance of the Zika toehold switch sensor with the current gold standard method for diagnosing Zika virus infection, all patient samples were tested in parallel with RT-qPCR. The amplification plot of two representative patient samples was tested in triplicate for the detection of Zika virus by RT-qPCR (Figure 9). The samples are considered positive when the cycle threshold (Ct) value is &#8804;38; the red line indicates a positive sample and the blue line indicates a negative sample for Zika virus.
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/63223/63223fig2v6.jpg" /> 
Figure 2: Agarose gel electrophoresis to assess the quality of PCR products. PCR products are analyzed on a 1% agarose gel in 1X TAE, run at 80 V for 90 min. A single clear band typically indicates a successful reaction. Lane 1: 1 kb DNA ladder; Lanes 2-4: 27B switch DNA, 33B trigger DNA, and 47B trigger DNA, respectively.The numbers on the left-hand side represent band size in bp. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/63223/63223fig03v6.jpg" /> 
Figure 3: Prototyping three toehold switches for paper-based Zika sensors. The performance of three paper-based RNA toehold switch sensors was measured at 37 &#176;C for over 130 min. Each graph contains two traces, one represents the switch only control, while the other represents the switch and trigger. The three graphs represent data acquired using toehold switch sensors 27B (A), 33B (B), and 47B (C). Error bars represent the standard error of the mean (SEM) from three replicates. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig03v6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/63223/63223fig04v7.jpg" /> 
Figure 4: Top-performing sensors are identified by calculating the fold change in absorbance at 570 nm. Fold change (or maximum ON/OFF ratio) is calculated by measuring the ratio of absorbance (OD570) at 130 min between the switch only control, and the switch plus trigger CFPS assay. Error bars represent SEM from three replicates. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig4v8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/63223/63223fig05v7.jpg" /> 
Figure 5: Sensitivity assessment of top-performing switch. In vitro transcribed Zika RNA is titrated into NASBA reactions. After a 1 h incubation, the reactions were added to cell-free PURExpress reactions on paper discs at a ratio of 1:7. The fold change after 130 min at 37 &#176;C is plotted. This figure has been reproduced&#160;from24. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig05v4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/63223/63223fig6v9.jpg" /> 
Figure 6: Portable plate reader capture page loaded with captured image data. This figure shows a sample picture of the final image captured by the portable plate reader during a data collection run. The original date/time stamp is visible at the top of the image. Yellow color indicates control or negative reactions, and the purple color indicates a positive reaction. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig6v8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/63223/63223fig7v9.jpg" /> 
Figure 7: Data analysis mode. On the left, users select the data sets they would like to plot; the graphs are then displayed on the right with unique colors for each sample or control set. The dashed red line serves as a threshold for determining positive and negative samples. Samples tested in triplicate that exceed the threshold are considered positive, while samples below the threshold are deemed negative. Error bars represent standard deviation (SD) from three replicates. Ctrl 1 to Ctrl 5 indicates controls. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig7v8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 8" class="xfigimg" src="/files/ftp_upload/63223/63223fig8v8.jpg" /> 
Figure 8. PLUM, a portable plate reader. This&#160;portable plate reader acts as a lab-in-a-box and serves as a temperature-controlled plate reader to incubate and monitor colorimetric reactions. This portable device can provide quantitative and high-throughput measurements of the paper-based Zika sensors on-site. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig8v8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 9" class="xfigimg" src="/files/ftp_upload/63223/63223fig9v9.jpg" /> 
Figure 9: RT-qPCR plot of the amplification of two patient samples tested in triplicate for the detection of the Zika virus. Samples are considered positive when the cycle threshold (Ct) value is &#8804;38. The dotted red line serves as a threshold for determining positive and negative samples. The red trace indicates a positive sample, and the blue trace indicates a negative sample. &#916;Rn (delta Rn) value represents the normalized magnitude of the fluorescence signal detected by the RT-qPCR instrument for all the samples tested. <a href="https://www.jove.com/files/ftp_upload/63223/63223fig9v8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Supplementary Protocol File. <a href="https://www.jove.com/files/ftp_upload/63223/Supplementary_protocol_R2_RE_KJ.docx" target="_blank">Please click here to download this File.</a>
Supplemental Figures.&#160;<a href="https://www.jove.com/files/ftp_upload/63223/Supplemental_Figures.zip" target="_blank">Please click here to download these&#160;figures.</a>

Watch this Scientific Journal Video about Design to Implementation Study for Development and Patient Validation of Paper-Based Toehold Switch Diagnostics at JoVE.com

Design to Implementation Study for Development and Patient Validation of Paper-Based Toehold Switch Diagnostics

Access to decentralized, low-cost, and high-capacity diagnostics that can be deployed into the community for decentralized testing is critical for combating global health crises. This manuscript describes how to build paper-based diagnostics for viral RNA sequences that can be detected with a portable optical reader.

Access to low-burden molecular diagnostics that can be deployed into the community for testing is increasingly important and has meaningful wider ...

design-to-implementation-study-for-development-patient-validation

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JoVE Journal

Bioengineering

2.7K Views.  University of Toronto. Access to decentralized, low-cost, and high-capacity diagnostics that can be deployed into the community for decentralized testing is critical for combating global health crises. This manuscript describes how to build paper-based diagnostics for viral RNA sequences that can be detected with a portable optical reader.

Video: Design to Implementation Study for Development and Patient Validation of Paper-Based Toehold Switch Diagnostics

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic valve leaflets are composed of interstitial cells suspended within an extracellular matrix (ECM) and are lined with an endothelial cell monolayer. The valve withstands a harsh, dynamic environment and is constantly exposed to shear, flexion, tension, and compression. Research has shown calcific lesions in diseased valves occur in areas of high mechanical stress as a result of endothelial disruption or interstitial matrix damage1-3. Hence, it is not surprising that epidemiological studies have shown high blood pressure to be a leading risk factor in the onset of aortic valve disease4. 
The only treatment option currently available for valve disease is surgical replacement of the diseased valve with a bioprosthetic or mechanical valve5. Improved understanding of valve biology in response to physical stresses would help elucidate the mechanisms of valve pathogenesis. In turn, this could help in the development of non-invasive therapies such as pharmaceutical intervention or prevention. Several bioreactors have been previously developed to study the mechanobiology of native or engineered heart valves6-9. Pulsatile bioreactors have also been developed to study a range of tissues including cartilage10, bone11 and bladder12. The aim of this work was to develop a cyclic pressure system that could be used to elucidate the biological response of aortic valve leaflets to increased pressure loads. 
The system consisted of an acrylic chamber in which to place samples and produce cyclic pressure, viton diaphragm solenoid valves to control the timing of the pressure cycle, and a computer to control electrical devices. The pressure was monitored using a pressure transducer, and the signal was conditioned using a load cell conditioner. A LabVIEW program regulated the pressure using an analog device to pump compressed air into the system at the appropriate rate. The system mimicked the dynamic transvalvular pressure levels associated with the aortic valve; a saw tooth wave produced a gradual increase in pressure, typical of the transvalvular pressure gradient that is present across the valve during diastole, followed by a sharp pressure drop depicting valve opening in systole. The LabVIEW program allowed users to control the magnitude and frequency of cyclic pressure. The system was able to subject tissue samples to physiological and pathological pressure conditions. This device can be used to increase our understanding of how heart valves respond to changes in the local mechanical environment.

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

A cyclic pressure bioreactor capable of subjecting heart valve tissue to physiological and pathological pressure conditions has been designed. A LabVIEW program allows users to control pressure magnitude, amplitude and frequency. This device can be used to study the mechanobiology of heart valve tissue or isolated cells.

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic ...

Characterization of Complex Systems Using the Design of Experiments Approach: Transient Protein Expression in Tobacco as a Case Study

Plants provide multiple benefits for the production of biopharmaceuticals including low costs, scalability, and safety. Transient expression offers the additional advantage of short development and production times, but expression levels can vary significantly between batches thus giving rise to regulatory concerns in the context of good manufacturing practice. We used a design of experiments (DoE) approach to determine the impact of major factors such as regulatory elements in the expression construct, plant growth and development parameters, and the incubation conditions during expression, on the variability of expression between batches. We tested plants expressing a model anti-HIV monoclonal antibody (2G12) and a fluorescent marker protein (DsRed). We discuss the rationale for selecting certain properties of the model and identify its potential limitations. The general approach can easily be transferred to other problems because the principles of the model are broadly applicable: knowledge-based parameter selection, complexity reduction by splitting the initial problem into smaller modules, software-guided setup of optimal experiment combinations and step-wise design augmentation. Therefore, the methodology is not only useful for characterizing protein expression in plants but also for the investigation of other complex systems lacking a mechanistic description. The predictive equations describing the interconnectivity between parameters can be used to establish mechanistic models for other complex systems.

We describe a design of experiments approach that can be used to determine and model the influence of transgene regulatory elements, plant growth and development parameters, and incubation conditions on the transient expression of monoclonal antibodies and reporter proteins in plants.

Plants provide multiple benefits for the production of biopharmaceuticals including low costs, scalability, and safety. Transient expression offers the ...

Paper-based Devices for Isolation and Characterization of Extracellular Vesicles

Extracellular vesicles (EVs), membranous particles released from various types of cells, hold a great potential for clinical applications. They contain nucleic acid and protein cargo and are increasingly recognized as a means of intercellular communication utilized by both eukaryote and prokaryote cells. However, due to their small size, current protocols for isolation of EVs are often time consuming, cumbersome, and require large sample volumes and expensive equipment, such as an ultracentrifuge. To address these limitations, we developed a paper-based immunoaffinity platform for separating subgroups of EVs that is easy, efficient, and requires sample volumes as low as 10 &#956;l. Biological samples can be pipetted directly onto paper test zones that have been chemically modified with capture molecules that have high affinity to specific EV surface markers. We validate the assay by using scanning electron microscopy (SEM), paper-based enzyme-linked immunosorbent assays (P-ELISA), and transcriptome analysis. These paper-based devices will enable the study of EVs in the clinic and the research setting to help advance our understanding of EV functions in health and disease.

This protocol details a method to isolate extracellular vesicles (EVs), small membranous particles released from cells, from as little as 10 &#956;l serum samples. This approach circumvents the need for ultracentrifugation, requires only a few minutes of assay time, and enables the isolation of EVs from samples of limited volumes.

Extracellular vesicles (EVs), membranous particles released from various types of cells, hold a great potential for clinical applications. They contain ...

Construction of Defined Human Engineered Cardiac Tissues to Study Mechanisms of Cardiac Cell Therapy

Human cardiac tissue engineering can fundamentally impact therapeutic discovery through the development of new species-specific screening systems that replicate the biofidelity of three-dimensional native human myocardium, while also enabling a controlled level of biological complexity, and allowing non-destructive longitudinal monitoring of tissue contractile function. Initially, human engineered cardiac tissues (hECT) were created using the entire cell population obtained from directed differentiation of human pluripotent stem cells, which typically yielded less than 50% cardiomyocytes. However, to create reliable predictive models of human myocardium, and to elucidate mechanisms of heterocellular interaction, it is essential to accurately control the biological composition in engineered tissues. 
To address this limitation, we utilize live cell sorting for the cardiac surface marker SIRP&#945; and the fibroblast marker CD90 to create tissues containing a 3:1 ratio of these cell types, respectively, that are then mixed together and added to a collagen-based matrix solution. Resulting hECTs are, thus, completely defined in both their cellular and extracellular matrix composition.
Here we describe the construction of defined hECTs as a model system to understand mechanisms of cell-cell interactions in cell therapies, using an example of human bone marrow-derived mesenchymal stem cells (hMSC) that are currently being used in human clinical trials. The defined tissue composition is imperative to understand how the hMSCs may be interacting with the endogenous cardiac cell types to enhance tissue function. A bioreactor system is also described that simultaneously cultures six hECTs in parallel, permitting more efficient use of the cells after sorting.

This manuscript describes the creation of defined engineered cardiac tissues using surface marker expression and cell sorting. The defined tissues can then be used in a multi-tissue bioreactor to investigate mechanisms of cardiac cell therapy in order to provide a functional, yet controlled, model system of the human heart.

Human cardiac tissue engineering can fundamentally impact therapeutic discovery through the development of new species-specific screening systems that ...

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available &#34;design space&#34; represented by &#34;devices&#34; created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophistication and scale of synthetic biology research necessitates an efficient, reproducible way to accommodate large-scale, complex, and high throughput device construction.
Here, a DNA assembly protocol using the Type-IIS restriction endonuclease based Modular Cloning (MoClo) technique is automated on two liquid-handling robotic platforms. Automated liquid-handling robots require careful, often times tedious optimization of pipetting parameters for liquids of different viscosities (e.g. enzymes, DNA, water, buffers), as well as explicit programming to ensure correct aspiration and dispensing of DNA parts and reagents. This makes manual script writing for complex assemblies just as problematic as manual DNA assembly, and necessitates a software tool that can automate script generation. To this end, we have developed a web-based software tool, http://mocloassembly.com, for generating combinatorial DNA device libraries from basic DNA parts uploaded as Genbank files. We provide access to the tool, and an export file from our liquid handler software which includes optimized liquid classes, labware parameters, and deck layout. All DNA parts used are available through Addgene, and their digital maps can be accessed via the Boston University BDC ICE Registry. Together, these elements provide a foundation for other organizations to automate modular cloning experiments and similar protocols.
The automated DNA assembly workflow presented here enables the repeatable, automated, high-throughput production of DNA devices, and reduces the risk of human error arising from repetitive manual pipetting. Sequencing data show the automated DNA assembly reactions generated from this workflow are ~95% correct and require as little as 4% as much hands-on time, compared to manual reaction preparation.

Here, an automated workflow to perform modular DNA &#34;device&#34; assembly using a modular cloning DNA assembly method on liquid-handling robots is presented. The protocol uses an intuitive software tool for generating liquid handler picklists for combinatorial DNA device library generation, which we demonstrate using two liquid handling platforms.

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available &#34;design space&#34; ...

Design and Implementation of an Automated Illuminating, Culturing, and Sampling System for Microbial Optogenetic Applications

Optogenetic systems utilize genetically-encoded proteins that change conformation in response to specific wavelengths of light to alter cellular processes. There is a need for culturing and measuring systems that incorporate programmed illumination and stimulation of optogenetic systems. We present a protocol for building and using a continuous culturing apparatus to illuminate microbial cells with programmed doses of light, and automatically acquire and analyze images of cells in the effluent. The operation of this apparatus as a chemostat allows the growth rate and the cellular environment to be tightly controlled. The effluent of the continuous cell culture is regularly sampled and the cells are imaged by multi-channel microscopy. The culturing, sampling, imaging, and image analysis are fully automated so that dynamic responses in the fluorescence intensity and cellular morphology of cells sampled from the culture effluent are measured over multiple days without user input. We demonstrate the utility of this culturing apparatus by dynamically inducing protein production in a strain of Saccharomyces cerevisiae engineered with an optogenetic system that activates transcription.

We designed a continuous culturing apparatus for use with optogenetic systems to illuminate cultures of microbes and regularly image cells in the effluent with an inverted microscope. The culturing, sampling, imaging, and image analysis are fully automated so that dynamic responses to illumination can be measured over several days.

Optogenetic systems utilize genetically-encoded proteins that change conformation in response to specific wavelengths of light to alter cellular ...

Magnetic Levitation Coupled with Portable Imaging and Analysis for Disease Diagnostics

Currently, many clinical diagnostic procedures are complex, costly, inefficient, and inaccessible to a large population in the world. The requirements for specialized equipment and trained personnel require that many diagnostic tests be performed at remote, centralized clinical laboratories. Magnetic levitation is a simple yet powerful technique and can be applied to levitate cells, which are suspended in a paramagnetic solution and placed in a magnetic field, at a position determined by equilibrium between a magnetic force and a buoyancy force. Here, we present a versatile platform technology designed for point-of-care diagnostics which uses magnetic levitation coupled to microscopic imaging and automated analysis to determine the density distribution of a patient's cells as a useful diagnostic indicator. We present two platforms operating on this principle: (i) a smartphone-compatible version of the technology, where the built-in smartphone camera is used to image cells in the magnetic field and a smartphone application processes the images and to measures the density distribution of the cells and (ii) a self-contained version where a camera board is used to capture images and an embedded processing unit with attached thin-film-transistor (TFT) screen measures and displays the results. Demonstrated applications include: (i) measuring the altered distribution of a cell population with a disease phenotype compared to a healthy phenotype, which is applied to sickle cell disease diagnosis, and (ii) separation of different cell types based on their characteristic densities, which is applied to separate white blood cells from red blood cells for white blood cell cytometry. These applications, as well as future extensions of the essential density-based measurements enabled by this portable, user-friendly platform technology, will significantly enhance disease diagnostic capabilities at the point of care.

We present a magnetic levitation technique coupled with automated imaging and analysis in both a smartphone-compatible device and a device with embedded imaging and processing. This is applied to measure the density distribution of cells with two demonstrated biomedical applications: sickle cell disease diagnosis and separating white and red blood cells.

Currently, many clinical diagnostic procedures are complex, costly, inefficient, and inaccessible to a large population in the world. The requirements for ...

Fabrication of Three-dimensional Paper-based Microfluidic Devices for Immunoassays

Paper wicks fluids autonomously due to capillary action. By patterning paper with hydrophobic barriers, the transport of fluids can be controlled and directed within a layer of paper. Moreover, stacking multiple layers of patterned paper creates sophisticated three-dimensional microfluidic networks that can support the development of analytical and bioanalytical assays. Paper-based microfluidic devices are inexpensive, portable, easy to use, and require no external equipment to operate. As a result, they hold great promise as a platform for point-of-care diagnostics. In order to properly evaluate the utility and analytical performance of paper-based devices, suitable methods must be developed to ensure their manufacture is reproducible and at a scale that is appropriate for laboratory settings. In this manuscript, a method to fabricate a general device architecture that can be used for paper-based immunoassays is described. We use a form of additive manufacturing (multi-layer lamination) to prepare devices that comprise multiple layers of patterned paper and patterned adhesive. In addition to demonstrating the proper use of these three-dimensional paper-based microfluidic devices with an immunoassay for human chorionic gonadotropin (hCG), errors in the manufacturing process that may result in device failures are discussed. We expect this approach to manufacturing paper-based devices will find broad utility in the development of analytical applications designed specifically for limited-resource settings.

We detail a method to fabricate three-dimensional paper-based microfluidic devices for use in the development of immunoassays. Our approach to device assembly is a type of multilayer, additive manufacturing. We demonstrate a sandwich immunoassay to provide representative results for these types of paper-based devices.

Paper wicks fluids autonomously due to capillary action. By patterning paper with hydrophobic barriers, the transport of fluids can be controlled and ...

Fabrication and Validation of an Organ-on-chip System with Integrated Electrodes to Directly Quantify Transendothelial Electrical Resistance

Organs-on-chips, in vitro models involving the culture of (human) tissues inside microfluidic devices, are rapidly emerging and promise to provide useful research tools for studying human health and disease. To characterize the barrier function of cell layers cultured inside organ-on-chip devices, often transendothelial or transepithelial electrical resistance (TEER) is measured. To this end, electrodes are usually integrated into the chip by micromachining methods to provide more stable measurements than is achieved with manual insertion of electrodes into the inlets of the chip. However, these electrodes frequently hamper visual inspection of the studied cell layer or require expensive cleanroom processes for fabrication. To overcome these limitations, the device described here contains four easily integrated electrodes that are placed and fixed outside of the culture area, making visual inspection possible. Using these four electrodes the resistance of six measurement paths can be quantified, from which the TEER can be directly isolated, independent of the resistance of culture medium-filled microchannels. The blood-brain barrier was replicated in this device and its TEER was monitored to show the device applicability. This chip, the integrated electrodes and the TEER determination method are generally applicable in organs-on-chips, both to mimic other organs or to be incorporated into existing organ-on-chip systems.

This publication describes the fabrication of an organ-on-chip device with integrated electrodes for direct quantification of transendothelial electrical resistance (TEER). For validation, the blood-brain barrier was mimicked inside this microfluidic device and its barrier function was monitored. The presented methods for electrode integration and direct TEER quantification are generally applicable.

Organs-on-chips, in vitro models involving the culture of (human) tissues inside microfluidic devices, are rapidly emerging and promise to provide useful ...

Anatomically Realistic Neonatal Heart Model for Use in Neonatal Patient Simulators

Neonatal patient simulators (NPS) are artificial patient surrogates used in the context of medical simulation training. Neonatologists and nursing staff practice clinical interventions such as chest compressions to ensure patient survival in the case of bradycardia or cardiac arrest. The simulators used currently are of low physical fidelity and therefore cannot provide qualitative insight into the procedure of chest compressions. The embedding of an anatomically realistic heart model in future simulators enables the detection of cardiac output generated during chest compressions; this can provide clinicians with an output parameter, which can deepen the understanding of the effect of the compressions in relation to the amount of blood flow generated. Before this monitoring can be achieved, an anatomically realistic heart model must be created containing: two atria, two ventricles, four heart valves, pulmonary veins and arteries, and systemic veins and arteries. This protocol describes the procedure for creating such a functional artificial neonatal heart model by utilizing a combination of magnetic resonance imaging (MRI), 3D printing, and casting in the form of cold injection molding. Using this method with flexible 3D printed inner molds in the injection molding process, an anatomically realistic heart model can be obtained.

This protocol describes a procedure for creating functional artificial neonatal heart models by utilizing a combination of magnetic resonance imaging, 3D printing, and injection molding. The purpose of these models is for integration into the next generation of neonatal patient simulators and as a tool for physiological and anatomical studies.

Neonatal patient simulators (NPS) are artificial patient surrogates used in the context of medical simulation training. Neonatologists and nursing staff ...