A LUCIFERASE REPORTER MINIGENOME SYSTEM FOR QUANTIFYING RESPIRATORY SYNCYTIAL VIRUS REPLICATION Melanie J. Aston1, Michael H.Chi1, Monica K. Deterding1, Matthew M. Huckabee1, Martin L. Moore2, and R. Stokes Peebles, Jr.2 1Department of Biomedical Engineering, Vanderbilt University and 2Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN Respiratory Syncytial Virus is the leading cause of respiratory tract infection in infants in the United States and worldwide. There is currently no vaccine available to treat RSV. The current method to determine RSV titer in the laboratory is the viral plaque assay, a labor, materials, and time intensive procedure. There is a need for a high throughput, inexpensive, and highly sensitive method to quantify infectious RSV. We engineered an RSV minigenome containing a luciferase reporter for high-throughput quantification of RSV replication. The minigenome is under control of the CMV promoter for constitutive expression. HEp-2 cells were transfected, and stably-transfected cell lines were selected. Luciferase bioluminescence was measured 48 hours after RSV infection in a 96-well plate. Luciferase activity was RSV-specific and dose-dependent. Introduction Respiratory Syncytial Virus is a paramyxovirus that consists of ten genes in a 15kbp negative sense genome. Figure 1 shows a schematic of the RSV genome and its life cycle within a cell. The genes in pink (N, P, M2, and L) are necessary for the transcription and replication of the virus. The viral life cycle within the cell proceeds in several steps. First the virus binds to the target cell via an unknown receptor. The genome unfolds and host cell machinery transcribes the viral Figure 1: RSV genome and intracellular life cycle genes. These genes are transcribed individually along a gradient. The mRNA’s are then translated by the host cell machinery into protein. At some point, when the proteins build up in the cell the negative sense genome is replicated into a positive sense antigenome, which serves as a template for replication of many copies of the viral genome. These new viral genomes are then packaged into new virus particles. RSV is the leading cause of bronchiolitis and pneumonia in infants under one year of age (1). Current estimates place the annual infection and mortality figures for RSV at 64 million and 800,000 respectfully. It is the leading cause of hospitalization, respiratory failure, mechanical ventilation, and viral death in infants in the United States and 1 worldwide (1). There are currently no vaccines or drugs available to treat RSV. The biggest challenge with creating a viable RSV vaccine is the bottleneck in laboratory research. This bottleneck arises from the inefficiencies in determining viral titer. The current method to determine RSV titer in the laboratory is the viral plaque assay. The plaque assay is a labor, materials, and time intensive procedure. Plaque assays can take up to 7 days to complete. Figure 2 shows a flow chart for the plaque assay. In addition, the plaque assay is not highly sensitive. To count a plaque the researcher must “eyeball” the plate and manually count the plaques or “holes” formed by dead cells. This procedure introduces subjectivity to the measurement and as a result is more prone to human error. Clearly there is a need for a high throughput, inexpensive, and highly sensitive method to Figure 2: Flow Chart for the Viral Plaque Assay (major delays are in red) quantify infectious RSV. We propose a novel luciferase based minigenome reporter system. A team at the National Institute of Health led by Dr. Peter Collins successfully created a minigenome system that expresses a reporter gene in response to RSV infection (6). This system involved an RSV minigenome under the control of the T7 promoter. The Collins group found that the N, P, M2-1 and L proteins were sufficient and necessary for expression of the minigenome and reporter gene. We chose to adopt this system because reporter gene activity was RSV specific and dependent. 2 Methods This plasmid reporter was constructed from four separate sequences. They are: a pcDNA3.1 vector, a leader sequence, a copy of the luciferase gene and a trailer sequence. They were fabricated or isolated individually and finally ligated together. In silco design was conducted using VectorNTI cloning software. We named our plasmid pRSVlucM5. The vector backbone selected was pcDNA3.1(+), a 5428 base pair plasmid purchased from Invitrogen. This plasmid was chosen for the presence of unique restriction sites, the CMV promoter, and the geneticin and ampicillin resistance genes to allow for selection. Second, pGEM-luc was selected as the luciferase gene source. The leader and trailer regions of Figure 3. (A) Diagram of the Trailer sequence, (B) Diagram of the Leader sequence the plasmid were designed based on the construct created by the Collins group (6). Within the leader is a 44 nucleotide (nt) RSV leader region, a 9 nt gene start signal of RSV nonstructural protein 1 (NS1), and a 32 nt nontranslated region of the NS1 gene (Figure 3B). The trailer sequence includes 12 nt of the nontranslated region of the RSV large polymerase (L) gene, the 12 nt L gene end signal, and the 155 nt RSV trailer region (Figure 3A). The sequences were designed with the proper restriction sites necessary for future ligation. After individual design in silco the sequences were compiled to create the final plasmid construct (Figure 4). The leader and trailer sequences were fabricated by Integrated DNA Technologies. The trailer sequence was ordered as a 191 base pair element in a minigene plasmid. Fabrication of the leader sequence Figure 4: Diagram of pRSVlucM5 proved to be more difficult. The 3 length of the leader sequence and the presence of a hairpin in the ribozyme made it impossible to fabricate as a minigene plasmid. To get around this problem we constructed the leader from four separate oligonucleotide fragments. This required additional work before the leader could be ligated. The four oligonucleotides had to be annealed together (matching one end of the double helix to the other) creating two leader portions referred to as Leader A (made up of oligos 1 & 2) and Leader B (made up of oligos 3 & 4) (See Figure 5). Initial ligations of Leader A Figure 5: Diagram of the fabrication process and Leader B proved unsuccessful. This was due to the lack of 5' phosphorylation of the sequences. T4 polynucleotide kinase purchased from NEB was used to phosphorylate Leader A and Leader B and the ligation was attempted again. The results of the ligation of Leader A and Leader B following phosphorylation proved inconclusive. The trailer sequence had to be isolated from the purchased minigene plasmid. It was designed with the HindIII and XhoI restriction sites. Using the respective restriction enzymes, the trailer was cut out of the minigene plasmid. The trailer digest was run through a 2% agarose gel using an electrophoresis machine set at 100V for 2 hours and 45 minutes to separate the trailer from the remainder of the plasmid. The trailer sequence was then extracted from the gel and saved for future use. The luciferase gene was isolated from the pGEMluc vector in a similar fashion. pGEM-luc was first cut with restriction enzyme XhoI followed by BamHI, resulting in two separate pieces of the vector, the luciferase gene (1716 base pairs), and the remainder of the plasmid (3215 base pairs). Gel purification was conducted in order to isolate the luciferase gene. A 0.7% agarose gel was prepared and the luciferase digest was run at 4 80V for 1 hour, and then 100V for an additional hour. The luciferase gene was then extracted from the gel and stored for later use. pcDNA3.1 was also cut in order to allow for future ligation with the other sequences. The vector was cut with HindIII, and then later with NotI. The enzyme cuts created two fragments of the vector, one 5360 base pairs long (functional), the other 68 base pairs long (non functional). Another 0.7% agarose gel was prepared, loaded with the digest, and run at 100V for an hour and a half. The functional 5360bp sequence was extracted from the gel and stored for later ligation. Due to inconclusive results from the Leader A and Leader B ligation we decided to conduct one large ligation of Leader A, Leader B, luciferase, Trailer, and pcDNA3.1. The four basic parts of RSVlucM5 (pcDNA3.1, luciferase, leader, and trailer) were designed with ends such that when they were cut with the appropriate restriction enzymes, they could only assemble in a particular way. However, it was possible that a series of self-dimerizations could occur that would result in other viable alternatives to pRSVlucM5. VectorNTI provided four viable alternate configurations. They were 10720 bp, 11090 bp, 11188 bp, and 21440 bp in length. From the design we know that our plasmid is only 7495 base pairs in length. In order to screen for the correct plasmid an additional digest with restriction enzyme SphI was conducted. Bacteria were first transformed with the plasmid. This bacteria was grown on ampicillin plates – this was done to weed out any bacteria that did not incorporate our plasmid. We were then able to screen for the correct plasmid from all colonies that grew. An initial 24 colonies were selected for the first round of screening. The SphI digest cut the DNA from the 24 selected colonies. A 0.7% agarose gel was again prepared and all 24 cut samples were loaded. Based on the in silco design a digest of our Figure 6: Gel image of the total plasmid digest with bands indicated 5 plasmid with SphI, would result in five segments of the following lengths 4908bp, 1146bp, 795bp, 574bp, and 72bp. We then analyzed the digest gel for this band pattern. Figure 6 shows this digest gel with the correct pattern highlighted. Over half of the colonies showed the correct digest pattern. Colonies 2 and 3 were chosen for future use. To determine if the plasmid would in fact produce luciferase in response to RSV infection, initial tests on the system were conducted. Human epithelial cells (HEp-2 cells) were plated into 30 wells of a clear 96 well plate. The plasmid was then applied via transient transfection in a gradient concentration. Four different trials were conducted using Green Fluorescent Protein (GFP) as a control for positive transfection. After a growth period of 24 hours, the cells were infected with RSV at a multiplicity of infection (MOI) of 1, following a 24 hour infection period a luciferase assay was conducted. A luciferase assay kit, from Promega Corporation, was used. The cells were transferred to a luminometer tube, reagent was added, and then each sample was read using a luminometer, courtesy of the Blackwell Laboratory. Our main goal was to generate a stably transfected cell line for future use during vaccine research. This work was done concurrently with the transient transfection. In a 6-well plate, additional HEp-2 A B C D E F G H pfu/mL mock 10 101 102 103 104 105 106 1 2 RSV INFECTION 3 4 5 6 7 8 9 REOVIRUS 10 11 12 mock 5*10-1 5*10 5*101 5*102 5*103 5*104 5*105 24 hour analysis 48 hour analysis 72 hour analysis Figure 7: Plate diagram for the stable transfection assay cells were grown and then transfected with 4μg or 8μg of plasmid. Twenty four hours following transfection, neomycin was added to the wells to kill any cells that did not take up the plasmid. Cloning discs were used to select 17 colonies to screen for specific bioluminescence activity. These colonies were grown up and plated on a 96 well plate and then a luciferase assay was conducted using a plate reader. 6 Further study of the stable transfection was conducted by studying the system over 72 hours post infection. The specificity of the system was studied by concurrently using a different virus for infection in addition to RSV. A strain of Reovirus, obtained from Terry Dermody was used in 24 of the wells (Figure 7). Cells were plated in 96 wells, and infected with RSV or Reovirus. The first luciferase assay was conducted at 24, 48 and 72 hours post infection. Both the cells and the supernatant were measured for luminescence. After transferring each sample to an opaque plate, luciferase assay reagent was added and the samples were read using the plate reader. Results and Discussion Confirmation of pRSVlucM5 Function by Transient Transfection A transient transfection of pRSVlucM5 into human epithelial (HEp-2) cells was performed to confirm that the engineered plasmid worked as designed in HEp-2 cells. Different amounts of pRSVlucM5 were transiently transfected into HEp-2 cells. The cells were subsequently infected with 106 PFU/mL of RSV and a luciferase assay was performed 24 hours later. The luciferase assay works bioluminescence, which correlates to the amount of luciferase produced by the cells. As shown in Figure 8, the amount of bioluminescence measured increased as the amount of Bioluminescence (RLU) by measuring 3000 2500 2000 1500 1000 500 0 0 0.2 0.4 0.6 0.8 1 Amount of DNA Transfected (ug) pRSVlucM5 transfected into the cells increased. These data show that the Figure 8. Three replicate transient transfections (dashed lines) show an increase in luciferase as the amount of DNA transfected increases, as measured by bioluminescence. The average of the three replicate experiments is shown as the solid line. pRSVlucM5 plasmid does work correctly in HEp-2 cells. That is, it was confirmed that HEp-2 cells transfected with the plasmid pRSVlucM5 express luciferase when infected with RSV. Furthermore, it can be gathered from the data that an increase in the amount of DNA transfected 7 results in an increase in the number of plasmids taken up by the HEp-2 cells. The increase in copy number per cell results in the increasing bioluminescence seen in the data. This relationship between copy number and bioluminescence could play a key role in the optimization of the system when screening stably transfected cell lines. Generation of HEp-2RSVM5 Cell Line by Stable Transfection HEp-2 cells were transfected with pRSVlucM5, and neomycin was applied in order to select stably transfected cells. Cells were cultured as separate cell lines and tested for luciferase activity when infected with different concentrations of RSV. A preliminary screening 6000 was performed with the resulting data from the luciferase assay shown in Figure 9. The HEp2RSVM5.4 cell line showed significant amounts of luciferase, while the remaining cell lines Bioluminescence (RLU) test of 17 cell lines 5000 4000 3000 2000 1000 0 1000 10000 100000 1000000 RSV Concentration (PFU/mL) Figure 9. HEp-2RSVM5.4 (black) shows increased bioluminescent activity, while the remaining cell lines (blue, pink, light blue, maroon) show insignificant amounts of luciferase. did not show bioluminescent activity significantly greater than the blank used from the luciferase assay. The bioluminescence of HEp-2RSVM5.4 was expected to increase with increasing RSV concentration increased, but the data does not match with the expected results. As the only cell line tested that exhibited luciferase after RSV infection, HEp2RSVM5.4 was chosen for further testing in order to determine if the relationship between bioluminescence and RSV concentration is optimal. HEp-2RSVM5.4 cells were again cultured and infected with different concentrations of RSV. A luciferase assay was performed and the resulting data is shown in Figure 10. An increase in bioluminescence was shown as the RSV concentration increased. These data suggest that HEp-2RSVM5.4 has the potential to 8 be the optimized final product. Further testing, however, was needed to determine the bioluminescence time dependence as well as to verify RSV specificity. HEp-2RSVM5.4 infected with different concentrations of RSV and Reovirus. Luciferase assays were performed 24, 48, and 72 hours after infection. 230 Bioluminescence (RLU) cells were cultured and 225 220 215 210 205 200 195 190 Figure 10 shows the 1 100 measured 24 hours 1000000 RSV Concentration (PFU/mL) results. When the bioluminescent activity is 10000 Figure 10. HEp-2RSVM5.4 shows an increase in bioluminescent activity as the RSV concentration increases. post-infection, no trend can be found. A spike in bioluminescence is found 48 hours post-infection for an RSV concentration of 1x105 PFU/mL, with bioluminescence dying out at higher RSV 800 hours post-infection, no increase in bioluminescence is detected with increasing RSV concentration. Similar to the 48 hours post-infection data, Bioluminescence (RLU) concentrations. At 72 700 600 500 400 300 200 100 0 1 100 10000 1000000 bioluminescence dies out RSV Concentration (PFU/mL) at high RSV concentrations. A luciferase assay was also Figure 11. HEp-2RSVM5.4 exhibits different bioluminescence-RSV concentration relationships depending on the amount of time between infection and luciferase assay. The times shown are 24 (black), 48 (red), and 72 (blue) hours. performed on HEp2RSVM5.4 cells infected with Reovirus. The results are shown in Figure 11, and 9 compared to the data from the RSV infected cells. It was found that the HEp2RSVM5.4 cell line is specific to RSV infection, as there is no increase in bioluminescence with Reovirus infection. Further testing is required to determine the reasons why no trend is found at lower RSV concentrations. The significant decrease in bioluminescence at high RSV concentrations is most likely due to the large amount of cell death due to infection. luciferase produced within them, resulting in decreased bioluminescence measured by the luciferase assay. It can be seen in Figure 12 that there is background luciferase in the Bioluminescence (RLU) Cells dying release the 800 700 600 500 400 300 200 100 0 1 100 10000 1000000 HEp-2RSVM5.4 cells, as there is significant bioluminescence measured at extremely low RSV Amount of Virus (PFU/mL) Figure 12. Bioluminescence is shown to be specific to RSV infection (blue), as shown by no increase in bioluminescence with Reovirus infection (pink). concentrations. This is most likely due to the incorporation of the pRSVlucM5 plasmid into the HEp-2 DNA downstream of a native promoter. This native promoter would then drive the transcription of a positive sense luciferase mRNA, which would in turn be translated into luciferase without the presence of RSV. The data collected thus far for the HEp-2RSVM5.4 cell line shows that stably transfected cells can exhibit some relationship between bioluminescence and RSV concentration. The cell line, however, does not show a significant relationship between the two. It also, exhibits background luciferase that decreases the sensitivity of the system. In order to optimize the system, more stably transfected cell lines must be cultured and screened in order to find a line with better sensitivity and no background luciferase. More testing will need to be done with the candidate cell lines in order to characterize them for use. 10 Economics The current market for our luciferase reporter system would mainly consist of research and development companies and academic researchers. Companies specifically interested in RSV research would be able to use our plasmid instead of the more costly and less time efficient plaque assay. Companies currently working on vaccines and antiviral drugs for RSV include Wyeth, MedImmune, Virion Systems, Novartis, Alnylam, Sanofi Pasteur, and Tibotec and could all be seen as a potential market for our luciferase reporter system. The development costs of our reporter system were based on the prices of the segments, reagents, and lab equipment used. The cost of the pcDNA3.1 vector was $361. The cost of the pGEM-luc necessary for luminescence of the plasmid was $83. The minigenome plasmid containing our trailer cost $274. The four leader oligonucleotides cost $78 (2x) and $98 (2x). The cloning discs were purchased for $29. Finally, miscellaneous chemicals and disposable lab equipment cost approximately $750, yielding a development cost of $1878. The future maintenance cost of this system is extremely low. The cells needed for transfection can be frozen in liquid nitrogen and used whenever needed. The plasmid would be stored in the -80oC freezer. This storage would allow for the maintenance of our system with little additional cost. We are responsible for most of the marketing distribution costs. We estimate that the cost of marketing will again be relatively low. Marketing of our system will most likely occur by attending scientific meetings and conferences. The RSV research community is relatively small so marketing could be done on an individual basis. By expanding our network of contacts through scientific conferences, marketing of our system can be cheap and feasible. The benefits of this system are shown in the comparison between our system and the plaque assay method. Our system increases the objectivity of experiments. It reduces the time from 10 hours over the course of a week to 2.5 hours over the course of 2 days. We estimate that for every eight dollars spent on the plaque assay, one dollar will be spent on the luciferase system. Our system also increases throughput from 30 samples per experiment to 240 samples per experiment. The benefit for using the cell line to screen for anti-RSV drugs would be enormous. However, further research and 11 development of the cell line is necessary before the full benefits can be understood. Based on assumptions over the course of a year the benefit to cost ratio was found to be 4.24 (See Appendix B). This demonstrates how greatly the benefits of our system outweigh its cost. This analysis was carried out assuming that our system would have a lifetime of 1 yr, however, because our system has the possibility to last many years the benefit cost ratio could increase. The life cycle for this system is dependent on the resources available to those individuals or those labs that use the system. If the labs are capable of passing the cells purchased and then freezing them, the cells are capable of lasting as long as necessary. The purchaser needs only to buy our system once in order to carry out tasks for a lifetime. As with all new technology, safety concerns must also be taken into account. The minigenome that we have created is not replicative on its own and is not infectious. So safety concerns for the actual system are nonexistent. However, it is a RSV reporter and so any lab using it must implement the proper biohazard containment precautions. This reporter cell line is more of a tool for vaccine and drug delivery research and will not be used in humans at any point, thus there are no FDA regulations for our system. Future Directions We recommend that this project be continued. As the results indicate there is significant room for the improvement of this assay system. Possible future improvements might be to optimize the transient transfection while controlling for transfection efficiency. Other avenues to consider might be to determine the sensitivity and specificity of the transient and stably transfected reporter. We also feel that significant work should be invested in selecting other stably transfected cell lines in the hopes of lowering background luciferase activity. Despite these drawbacks the authors feel that this reporter system will eventually serve as a surrogate for the plaque assay. It is also possible that this system might be employed to screen small molecule inhibitors of RSV replication. Acknowledgements We would like to thank the following people from Vanderbilt for their contributions to the project: Kasia Goleniewska (laboratory support), Kirk Lane (project advice), Jim Crowe 12 (plate reader), and Terry Dermody (reovirus). The authors further wish to thank Peter Collins from the NIAID for his guidance on this project. References 1. Respiratory Syncytial Virus. CDC, Respiratory and Enteric Viruses Branch. http://www.cdc.gov/ncidod/dvrd/revb/respiratory/rsvfeat.htm, Retrieved on 2007-10-01. 2. Kuo L, et al. Analysis of the gene start and gene end signals of human RSV - quasi-templated initiation at position 1 of the encoded mRNA. Journal of Viriology: 71, 7. July 1997, page 49444953 3. Dirks W, et al. Dicistronic transcription units for gene expression in mammalian cells. Gene:128. 1993, page 247-249 4. Fearns R, et al. Mapping the transcription and replication promoters of RSV. Journal of Virology: 76, 4. Feb. 2002, page 1663-1672 5. Peeples M, et al. Mutations in the 5' trailer region of a RSV minigenome which limit RNA replication to one step. Journal of Virology: 74, 1. Jan. 2000, page 146-155 6. Grosfeld H, et al. RNA replication by RSV is directed by the N, P, and L proteins. Journal of Virology: 69, 9. Sept. 1995, page 5677-5686 7. Schurer H, et al. A universal method to produce in vitro transcripts with homogeneous 3' ends. Nucleic Acid Research: 30, 12 (56). 2002 8. Perrotta A, et al. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature:350. Apr. 1991, page 434-436 9. Kuo L, et al. Effect of Mutations in the Gene-Start and Gene-End Squence Motifs on Transcription of Monocistronic and Dicistronic Minigenomes of Respiratory Synctial Virus. Journal of Virology: 70, 10. Oct. 1996, page 6892-6901 10. Fearns R, et al. Functional Analysis of the Genomic and Antigenomic Promoters of Human Respiratory Syncytial Virus. Journal of Virology: 74, 13. July 2000, page 6006-6014 11. Zhang Z, et al. Inhibition of Viral Replication by Ribozyme: Mutational Analysis of the Site and Mechanism of Antiviral Activity. Journal of Virology: 79, 6. Mar. 2005, page 3728-3736 12. Seyhan A, et al. Ribozyme Inhibition of Alphavirus Replication. Journal of Biological Chemistry: 277, 29. July 2002, page 25957-25962 13. Collins P, et al. Rescue of a 7502-Nucleotide (49.3% of Full-Length) Synthetic Analog of Repiratory Syncytial Virus Genomic RNA. Virology: 195. Apr. 1993, page 252-256 14. McGivern A, et al. Identification of Internal Sequences in the 3' Leader Region of Human Respiratory Syncytial Virus That Enhance Transcription and Confer Replication Processivity. Journal of Virology: 79, 4. Feb. 2005, page 2449-2460 15. Moudy R, et al. Variations in intergenic region sequences of Human respiratory syncytial virus clinical isolates: analysis of effects on transcriptional regulation. Virology: 327. June 2004, page 121-133 16. Collins P, et al. Support Plasmids and Support Proteins Required for Recovery of Recombinant Respiratory Syncytial Virus. Virology: 259. Apr. 1999, page 251-255 17. Krempl C, et al. Recombinant Respiratory Syncytial Virus with the G and F Genes Shifted to the Promoter-Proximal Positions. Journal of Virology: 76, 23. Dec. 2002, page 11931-11942 18. Fearns R, et al. Role of the M2-1 Transcription Antitermincation Protein of Respiratory Syncytial Virus in Sequential Transcription. Journal of Virology: 73, 7. July 1999, page 5852-5864 19. Lutz A, et al. Virus-inducible reporter genes as a tool for detecting and quantifying influenza A virus replication. J Virol Methods: 126, 1-2. June 2005, page 12-20 20. Ray P, et al. Construction and Validation of Improved Triple Fusion Reporter Gene Vectors for Molecular Imaging of Living Subjects. Cancer Res: 67, 7. April 2007, page 3085-3093 21. Cowton V, et al. Unraveling the complexities of respiratory syncytial virus RNA synthesis. Journal of General Virology: 87. Mar. 2006, page 1805-1821 22. Bramlage B, et al. Inhibition of luciferase expression by synthetic hammerhead ribozymes and their cellular uptake. Nucleic Acid Research: 27, 15. June 1999, page 3159-3167 13 23. Cowton V, et al. Evidence that the Respiratory Syncytial Virus Polymerase Is Recruited to Nucleotides 1 to 11 at the 3' End of the Nucleocapsid and Can Scan To Access Internal Signals. Journal of Virology: 79, 17. Sept. 2005, page 11311-11322 24. Hutchens M, et al. Applications of bioluminescence imaging to the study of infectious disease. Cellular Microbiology 2007 14 Appendix A (Innovation Workbench) Ideation Process I. II. Project Initiation a. Project name: Luciferase Luciferase Based Plasmid Reporter System for the Detection and Quantification of hRSV b. Project timeline: i. October 29th - November 2nd: Select plasmid and place order ii. October 29th - November 16th: Design and Test insertion sequence iii. November 19th-23rd: Order insertion sequence iv. November 26th - December 7th: Insert insertion sequence into plasmids and replicate v. December 10th - January 18th: Select for cells that take up plasmid and test cells for efficacy (make new insertion sequence and plasmids if necessary) vi. January 21st - February 8th: Test cells and establish best cell line vii. February 11th -29th: Establish luminescence-titer correlation c. Project team: Melanie Aston, Michael Chi, Monica Deterding, Matt Huckabee Innovation Situation Questionnaire a. Brief description of the situation The current method for determining the amount of RSV in a sample is complex and time consuming. This serves as a major bottleneck to RSV vaccine development. b. Detailed description of the situation The current method for determining the amount of RSV in a sample is complex and time consuming. It involves a lengthy plaque assay that requires 10 man hours over seven days. It is only partially objective and is thus prone to error. i. Supersystem - System - Subsystems 1. System name: Luciferase Based Plasmid Reporter System for the Detection and Quantification of hRSV 2. System structure: The system involves: Cells stably tranfected with plasmid Plate Reader Luciferin 3. Supersystems and environment N/A 4. Systems with similar problems The problem has been solved another way but it is inefficient because it measures the number of virus particles not infectivity. 15 ii. Input - Process - Output 1. Functioning of the system Our plasmid reporter system will be composed of a mammalian promoter, a luciferase gene, an RSV promoter, and a gene for neomycin resistance. The mammalian promoter will induce the production of mRNA when the plasmid is introduced to the host nucleus (mRNA will be produced even when the cell is not infected with RSV). This mRNA will travel to the cytoplasm where it will wait. Once the cell is infected, the virus will activate the viral promoter on the mRNA and cause it to make another mRNA strand that codes for the luciferase protein. The standard cellular machinery (i.e. ribosomes) will translate the mRNA into protein. This mechanism is novel because luciferase will only be expressed when the cell is infected with RSV. We will then detect the bioluminescence from this protein with a luminescence detector and establish a correlation with viral titer. 2. System inputs RSV 3. System outputs Luminescence data iii. Cause - Problem - Effect 1. Problem to be resolved Inefficiency of plaque assay 2. Mechanism causing the problem The nature of the plaque assay 3. Undesirable consequences if the problem is not resolved Wasted time and money 4. Other problems to be solved N/A iv. Past - Present - Future 1. History of the problem The use of plaque assays in the quantification of RSV has been well reported. It's problems and issues have always been apparent. 2. Pre-process time Work has already begun on our system so there is no pre-process time. 3. Post-process time The post-process time will begin once the plasmid reporter system has been developed and tested. We estimate this to be around the end of February. 16 III. c. Resources, constraints and limitations i. Available resources All laboratory equipment and materials necessary in the design and creation of the luciferase reporter system will be provided by Dr. Peebles' Lab ii. Allowable changes to the system None iii. Constraints and limitations Biological functions of cells iv. Criteria for selecting solution concepts None Problem Formulation and Brainstorming a. Directions for Innovation Find an alternative way to obtain a Plaque Assay that provides or enhances RSV Quantification. We chose to synthesize a new system Find a way to reduce Time. Find a way to reduce Money. Find a way to eliminate, reduce, or prevent Subjectivity. 17 Appendix B (Calculations) Benefit Cost Calculation (B/C) Given Our system saves $7 per experiment and 5 days per experiment. Initial investment = $1878 Assumptions each lab carries out 2 plaque assays per month and about 15 experiments with our system per month maintenance costs per year are $500 average salary for lab technician per hour is $15 Calculations B/C per year = [(benefitsmaterials + benefitstime) – maintenance costs]/(initial investment) Benefitsmaterials = $7/experiment x 15 experiments/month x 12months/yr = $1260/yr Benefitstime = $15/hr x 40hrs/month x 12months/yr = $7200/yr Therefore, B/C = ($1260+$7200-$500)/($1878) = 4.24 18