Week 27 (April 21) Working on final report and collecting last data measurements.
Week 26 (April 14) Our group looks to make a lot of progress this final week before the report. We met with our client, and we agreed since Kim-1 has had issues through about 12 trials, we will proceed with multiplexing our other two biomarkers, NGAL and FABP1. We are also adding a PEGylation step to our process to try to further refine the specific binding of our chip. We look to gather a large amount of data from some final NGAL and FABP1 testing on a multiplex this weekend, and will troubleshoot and write up the report in the remaining days.
Week 25 (April 7) This week we have remade several chemical stocks and rod substrates, continued biomarker testing, and moved on to multiplexing experiments. FABP1, KIM1, and NGAL have all had at least one successful trial where artificial antibodies were created, protein released, and protein was captured, and we are working on establishing consistency while simultaneously moving toward multiplexing. We still need to create concentration curves for each protein for data analysis and diagnostic purposes, but we will continue this alongside multiplexing since the deadline is coming up soon. Likewise, we worked on the designsafe template this week and briefly discussed the final paper.
Week 24 (Mar 31) This week we continued our trials for the individual biomarkers respectively. We ran into a few issues with our biochips not forming the artificial antibody template properly. We suspect it is partially due to a lot of our materials getting a little old so we made a new batch of paper substrates as well as chemicals for different steps along the fabrication process. We might have to tweak some of our protocols a bit to take into account the fresher chemicals we are using. Additionally, we started the process for multiplexing with 2 biomarkers and will work towards refining that process in the next few weeks.
Week 22 (Spring break... off) Week 23 (Mar 24) We have been honing our imprinting protocol this week up to the capture phase, where we tested if the imprinted antibodies are effectively capturing hemoglobin samples it is exposed to. We are performing this step more than once for reproducibility, and are wrapping up the second time today. We also spent a couple days this last week stockpiling large amounts of stock nanorod solution and other solutions necessary for the imprinting protocol in order to streamline procedures in the coming weeks.
Week 21 (Mar 10) Tony presented the validation and verification report on Monday, and the rest of the week we have been working on finalizing LSPR and polymerization protocol for each of the biomarkers. We have each taken a protein to work on and we will be combining results at the end and working together to multiplex. A summary of this week's progress is below: Ben: Has performed 2 trials for FABP1 to find the correct polymerization concentration, with the second trial at 1uL successfully releasing protein and getting a statistically significant shift upon protein capture. Savannah: Has performed 2 trials for KIM1, with the second trial at 1uL polymer showing a statistically significant release, but not statistically significant shift after capture. Tony: In process of 1st trial for NGAL.
Week 20 (Mar 3) This week we made a lot of progress. We created a MATLAB script to help us speed up and reduce error in reading our data. We ended up making multiple biochips imprinted with Hb as a test protein and got some promising preliminary data, while refining the protocols in the process. Particularly we had some issues with the CRAIC imaging protocol, but are getting more and more consistent data now. Additionally, we started the imprinting process for FABP1, one of the AKI biomarkers. We will be testing that this weekend as well as beginning another round of imprinting with the other AKI biomarkers. Also, we worked on the V&V report and presentation and will be submitting that soon.
Week 19 (Feb 24) We have been honing our imprinting protocol this week up to the capture phase, where we tested if the imprinted antibodies are effectively capturing hemoglobin samples it is exposed to. We are performing this step more than once for reproducibility, and are wrapping up the second time today. We also spent a couple days this last week stockpiling large amounts of stock nanorod solution and other solutions necessary for the imprinting protocol in order to streamline procedures in the coming weeks.
Week 18 (Feb 17) This week we finally fixed our nanorod protocol and made a good solution. Ben experimented with different multiplex shapes and 3D printed templates, and we began optimizing the imprinting procedure. We are beginning to start the validation and verification report and will continue with imprinting next week.
Week 17 (Feb 10) This week we went into the lab 3 separate occasions and continued making nanorods. We were having issues and were trying to diagnose if it was a problem with the seed solution or the growth solution, and found that we were not creating rods well. We realized that our seed solution was not turning the correct color, and had to reduce the amount of NaBH4. With the growth solution, we are still experimenting with the adequate amount of AgNO3 to add. In the meantime, Jingyi gave us a sample of her nanorods so we can continue the imprinting procedure to test our proof of concept for a minimal prototype.
Week 16 (Feb 3) Our group spent this week beginning to print 3D templates to help cut our paper substrates. We used the exacto knives and crayons to experiment with different ways to physically isolate the testing sites on each paper substrate. Additionally, we continued to try to refine our nanorod fabrication procedure. Our rods tended to fall in the 500-600 nm range this week, and we consulted a graduate student in our client's lab, who gave us a suggestion on how to troubleshoot this. We will continue to refine the process this coming week.
Week 15 (Jan 27) This week we started prototyping by creating a new batch of gold nanorods, ordering and receiving X-acto knives, and testing a paper design for diffusion distance.
Week 14 (Jan 20) This week our group met up earlier to go over some of the progress report comments as well as figure out scheduling for this semester. We set tentative time blocks where at least 2 of each member will be present as well as division of labor. We will begin implementing our plan next week. Additionally, we ordered our materials and submitted the reimbursement request.
First Semester
Week 13 (Dec 8) Wrote progress report and presented. --End of first semester
Week 12 (Dec 1) Our group spent this week doing research and making careful decisions on how to move forward with our design project. We have decided against colorimetric detection of biomarker levels, as that was against our client's preference. We are exploring different well layouts, as certain layouts have hold the potential to shorten fabrication time and/or testing time, as well as improve sensitivity and selectivity of the biomarker binding during the test itself. Moving forward, we will spend the next week finalizing our decision on what well layout we will pursue in earnest, and continue to refine our fabrication process.
Week 11 (Nov 18) This past week in lab we focused on improving our gold nanorod quality. We created a few different growth solutions and had more symmetrical nano rods that were closer to our target wavelength. Additionally we begin the imprinting procedure on paper. We updated a lot of our protocols in the process as we begin to refine the procedure. Outside of lab, we met as a group to discuss how to split up work for the specifications. We divided up research areas to address project concerns and clarified some aspects of the project scope with our client.
Week 10 (Nov 11) This week we met with Dr. Yin to discuss improvements and refocusing our project scope and metrics for the progress report. After this discussion we realized we need to do more research on similar technologies to explain the choices of metrics. Likewise, we learned imprinting procedures in the lab and worked on creating better quality gold nanorods. Our nanorod quality has been poor, so we are meeting with Jingyi to discuss over the weekend how to improve our procedure.
Week 9 (Nov 4) Our group spent this week reviewing our graded preliminary report to look for areas of improvement and continuing our training on protocols for creating the base nanorods for the chip. We met with Ali on November 3rd to discuss where we could improve between now and the progress report. It was emphasized to us that each choice moving forward in our project is defensible and justifiable. We are going to work on doing more literature review when making decisions on the direction of our project. We were also trained further by our client today. A grad student instructed us on how to use the CRAIC spectrometer to image our paper samples. Additionally, we began the process of remaking some gold nanorods to refine our skills.
Week 8 (Oct 28) This week, our group focused on learning how to image and deposit our synthesized nanorods onto a paper substrate. Some scheduling conflicts prevented us from moving on to the next training steps, which require a large continuous time block. This following week we will focus on learning the macromolecular imprinting procedure.
Week 7 (Oct 21) This past week we worked on training protocols for fabricating gold nanorods. Additionally, we completed both EHS training and lab specific safety training. Next week we will be continuing training on chip fabrication and image analysis.
Week 6 (Oct 14) The first half of this last week consisted of preparing slides for the preliminary report presentation and talking as a group about the presentation to ensure we are all familiar with all details about our project. Since our presentation on Wednesday, we met with our client, with whom we discussed the first steps of training for us to undertake to begin working in earnest on developing our biochip. We met with Jingyi on Thursday afternoon for the first training, where she showed us how to make the gold nanorods. We will go to our client's lab again next week to continue protocol training, as well as renew our EHS training certificates.
Week 5 (Oct 7) Our primary focus for the week was working on the paper due on Friday, as well as setting a bi-weekly meeting time with Professor Singamaneni. We honed in on our disease of choice for the first paper, and met with Jingyi, our graduate advisor, to understand the next steps as well as some specifications for our project. In addition, we met multiple times as a team to discuss our project scope as well as work on the paper. Lastly, we decided that Savannah will be the one to present next week on Wednesday.
Week 4 (Sept 30) We officially decided to work with Dr. Singamaneni as our client, and we will be delivering a plasmonic biochip that will be able to detect amounts of either protein or virus as biomarkers for infectious disease in blood or urine. You should have either already received a confirmation email from him, or he will be sending it soon. We performed an extensive literature search this week including background on biomarkers for infectious disease as well as manufacturing techniques developed by the Singamaneni lab. We met with Dr. Sinamaneni and our graduate student advisor, Jingyi this week, in addition to meeting multiple times as a team.
Week 3 (Sept 23) It took us a little longer than we had hoped to narrow our choices down to one client. We are currently honing in on Dr. Singamaneni, who has expressed interest in working with us. He has posed two options to us as far as directions to take our project. The first is to develop a biochip that has diagnostic capability in detecting protein biomarkers in blood or urine samples for AKI or pathogenic diseases. This project interests our group, but we are unsure if it can fit into the scope of a year long senior design project. We are meeting with Dr. Singa this weekend to try to clarify our boundaries if we pursue this direction. The second direction we could go is to develop a smartphone app that acts as a spectrophotometer to read the biochip. While this project would be more within the scope of a design project, two of the three members of our group are just a little reluctant to undertake this option. It would be very centered around algorithm development, and that is not our strong suit nor our initial idea of what we wished to do for our senior design project. We plan to make a definite decision this weekend on which direction to take our project.
Week 2 (Sept 16) This week we contacted a total of 5 potential clients and met with 2. We will hear back by Saturday from Dr. Sigamaneni, hopefully, and then make a decision. After speaking as a group, we decided if Dr. Sigamaneni is willing to work with us, we would prefer him over Dr. Miller. We feel that Dr. Sigamaneni has a lot of expertise and we can get significant mentorship from any of his postdocs in the lab. Likewise, his technology seems more developed, and we think we still have a niche where we can work inside of that. Dr. Miller’s project seems very cool, and we would have a lot of independence. However, we don’t know if Dr. Miller has the expertise to advise us when re run into problems. We never heard back from Dr. Hemming, Dr. Wall, or Dr. Tan, so we sent follow up emails.
Week 1 (Sept 9) This afternoon Scinote seems to be down for my group. We were also a bit confused with Professor Silva's email, so we did not submit before the deadline at noon. We will keep checking whether or not scinote is working for us periodically, and will submit the report for this past week as soon as we can get on. Our team was only able to all finally get registered last night, so we were not able to submit much either.This week we narrowed down the list of clients to 2 and contacted both of them. We will be meeting with Bernard Miller tomorrow (Saturday) morning to discuss our ideas with him.