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| | Biopharmaceutical Sciences BSc | | Biopharmaceutical Sciences BSc |
| | </div> | | </div> |
| − | <div class="ModalDescription">Charlotte involves herself with all team members to assist us in our tasks and help ensure things run smoothly. During meetings she maintains structure by being just and fair, while in the lab she can be found | + | <div class="ModalDescription"> |
| − | working on isolating stress promoters
| + | <h1>Form</h1> |
| − | from Bacillus bacteria. When problems arise, Charlotte will quickly be working on a solution, making her our reliable team manager.
| + | Dr. Feng-Yih Yu is the professor of the department of biomedical at Chung Shan Medical University who specializes in screening tests, protein chemistry, food microbiology and toxicology, and immunochemical techniques and so on. We had an interview with him on 2nd, April. |
| | + | <h1>Purpose</h1> |
| | + | After decided our project topic as rapid screening of influenza, we have been looking for a better way to enhance the correctness and accuracy of rapid screening and promoting the convenience of its usage. |
| | + | Later, we found several papers which concern aptamers acting the function as antibodies, hence came up with the idea that whether it is possible to develop our influenza rapid screening with aptamers. Therefore, we visited Dr. Yu to ask if our concept is feasible. We drafted the questions below: |
| | + | <ul> |
| | + | <li>Are aptamers able to act as antibodies in screening tests?</li> |
| | + | <li>How to select aptamers and to apply them to our rapid test paper?</li> |
| | + | |
| | + | </ul> |
| | + | <h1>Process</h1> |
| | + | <ul> |
| | + | <li>Dr. Yu was developing screening tests with aptamers </li> |
| | + | <li>Yes, aptamers can perform the function of protein antibodies. In fact, they perform even better than antibodies since they are smaller in size.</li> |
| | + | <li>We apply SELEX(Systematic Evolution of Ligands by EXponential enrichment) to select the aptamers that have high affinity with our target proteins. </li> |
| | + | <li>Since Dr. Yu specialized in the screening tests of toxicant molecules, which are smaller than our target, influenza proteins, he wasn’t 100% sure whether aptamers would fit protein or not. However, Dr, Yu indicated that since the principle is the same it is supposed to work, and encouraged us to take a try. </li> |
| | + | <li>Aptamers are easier to process. If we want to have the color changed we can add nanogold or other substrates to the tails of aptamers. </li> |
| | + | </ul> |
| | + | <h1>Feedback</h1> |
| | + | After the interview, Dr. Yu confirmed that applying aptamers to screening is highly possible. Therefore, we decided to develop our influenza rapid screening test with aptamers. |
| | + | |
| | </div> | | </div> |
| | <div class="ModalFunFact"> | | <div class="ModalFunFact"> |
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| | Biopharmaceutical Sciences BSc | | Biopharmaceutical Sciences BSc |
| | </div> | | </div> |
| − | <div class="ModalDescription">Charlotte involves herself with all team members to assist us in our tasks and help ensure things run smoothly. During meetings she maintains structure by being just and fair, while in the lab she can be found | + | <div class="ModalDescription"> |
| − | working on isolating stress promoters
| + | <h1>Form</h1> |
| − | from Bacillus bacteria. When problems arise, Charlotte will quickly be working on a solution, making her our reliable team manager.
| + | We had an interview with Doctor Rung-Tzung, Tsai on April 4th at Chung-Shan Medical University. Dr. Tsai is a professor of biochemistry. His specialty is molecular biology, biochemistry, biotechnology, and structures of proteins. |
| | + | <h1>Purpose</h1> |
| | + | As a professor of biochemistry, Dr. Tsai has been studying the structure of proteins for his whole career. He has a thorough understanding of viruses, bacteria, and even animal proteins. The purpose of this interview is to understand how to decide our protein biomarker of influenza. We drafted the questions below: |
| | + | <ul> |
| | + | <li>We want to take the proteins of influenza as our target for SELEX. Could you give some advice to us?</li> |
| | + | <li>We find people often use HA and NP as influenza’s target proteins. If we want to produce them by ourselves, what recommendations or advice would you give us? </li> |
| | + | <li>How to produce proteins of high purification? </li> |
| | + | </ul> |
| | + | <h1>Process</h1> |
| | + | <ul> |
| | + | <li>There are many complex chemical reactions in the human body fluid and it’s hard to predict. Aptamers have to bind to target protein when doing SELEX. Dr. Tsai recommended us using purified protein to do SELEX. </li> |
| | + | |
| | + | <li>Generally speaking, the water-soluble ability of HA is worse than NP. Dr. Tsai thought that to easily purify, using proteins that are better water-soluble and add His tag to the tail is a better choice. We can use Nickle columns to purify proteins. </li> |
| | + | </ul> |
| | + | <h1>Feedback</h1> |
| | + | Through this interview, we have a better concept for our experimental direction. After discussed with teammates, we chose NP as our target protein. On one hand, we can use NP to distinguish between influenza type A and B; on the other hand, with the feature of better water-soluble, it’s easier to purify proteins. Last but not least, we invited Doctor Rung-Tzung, Tsai to be our instructor. |
| | + | |
| | + | |
| | </div> | | </div> |
| | <div class="ModalFunFact"> | | <div class="ModalFunFact"> |
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| | Biopharmaceutical Sciences BSc | | Biopharmaceutical Sciences BSc |
| | </div> | | </div> |
| − | <div class="ModalDescription">Charlotte involves herself with all team members to assist us in our tasks and help ensure things run smoothly. During meetings she maintains structure by being just and fair, while in the lab she can be found | + | <div class="ModalDescription"><h1>Form</h1> |
| − | working on isolating stress promoters
| + | Our team had an interview with Professor Yu-Ling Chen at Cheng Kung University Hospital on August 6th. Prof. Chen is the director of Cheng Kung University Graduate Institute of Medicine. She had written many papers about aptamer and SELEX, who is one of the authoritarian people in this field. |
| − | from Bacillus bacteria. When problems arise, Charlotte will quickly be working on a solution, making her our reliable team manager.
| + | <h1>Purpose</h1> |
| | + | We want to ask questions about our experiment. On one hand, we would like to explain to the professor about the difficulties that we had encountered during the experimental process, and asked the professor for possible reasons and solutions. On the other hand, we wanted to learn and improve our experimental process from the experience of the professor about SELEX experiments. We showed the data of our result (figure1 to figure5) to the professor and drafted the questions below: |
| | + | <ul> |
| | + | <li>We have found through experiments that there was an unknown molecule with high molecular weight that appeared after SELEX. It seemed to be related to the template concentration, primer concentration, and the number of cycles. Why? How can we solve it? </li> |
| | + | <li>From our data, it is found that as the Template concentration or the number of PCR cycles increases, a by-product of about 100 bp would appear first and resulted in the ladder-like band. Then it evolved into a by-product with high molecular weight and resulted in the band gathering near the well that had a strong signal. How can we explain this situation? </li> |
| | + | (照片) |
| | + | Figure 1. Test of template conc. Condition |
| | + | (照片) |
| | + | Figure 2. Test of template and dNTP conc. condition (Wash compared with Probe) |
| | + | (照片) |
| | + | Figure 3. Experiment to find out the best template conc. condition of PCR. |
| | + | (照片) |
| | + | Figure 4 & 5. Test of PCR cycle number. |
| | + | </ul> |
| | + | <h1>Process</h1> |
| | + | <ul> |
| | + | <li>Template concentration or a high number of Cycles may has confused the Template and the Primer, resulting in incorrect copying or an unexpected secondary structure. </li> |
| | + | <li>The number of PCR cycles was too high. The general PCR condition after SELEX is 15 cycles. After conducting SELEX for many times, the product was relatively pure, and the number of cycles of PCR could be increased. It is recommended that the PCR part be tested first to find the most suitable conditions. </li> |
| | + | <li>The band of the product that appeared at about 100 bp may be the result of the double-stranded PCR product which hadn’t denatured, so the position of the band was higher than 87 bp which we expected. If there was no band, it represented that there was no product for PCR. </li> |
| | + | <li>Although the ladder-like by-products had occurred in the past, it hadn’t occurred that all by-products gathered at the top. However, a strong signal should be caused by its high molecular weight, not its volume. |
| | + | <li>The professor recommended that we conducted SELEX experiment as follows: |
| | + | <ul> |
| | + | <li>Step: SELEX – PCR with Elution – Check by DNA page – Denature – Renature – Purify – Cryopreservation – Denature – Renature – SELEX</li> |
| | + | <li>Control the number of PCR cycles, template concentration, and primer concentration during PCR to avoid the appearance of by-products. </li> |
| | + | <li>Prior to each round of SELEX, using a Primer with beads to separate and remove the complementary sequence generated during the PCR process. </li> |
| | + | <li>Quantify the PCR product before running SELEX to determine how much DNA is added to SELEX. </li> |
| | + | <li>Increase the volume of PCR for subsequent testing and experimentation. </li> |
| | + | <li>While denaturing, the recommended temperature is 95 degrees Centigrade and the recommended time is 10 minutes. While Renaturing (folding), it is recommended to slowly return the sample to room temperature from 95 degrees Centigrade instead of putting it on ice. </li> |
| | + | </ul> |
| | + | </li> |
| | + | |
| | + | <li>The professor would start the specificity test after 5th round of SELEX. Under normal circumstances, the specificity will be enhanced successively. Usually, we can get the ideal result at the 7th to 8th round, and then we can conduct DNA sequencing. If conducting SELEX above 9-10 round, there may appear some impurities. </li> |
| | + | <li>Specificity test: Choose an unrelated protein (albumin) as a negative control, run the ELISA test with the proteins of the influenza A and B viruses, and confirm the result of DNA page after PCR. </li> |
| | + | <li>Affinity test: Conduct sequence dilution with Aptamer or Target. After getting a result of a binding curve, plot with Prism and get the KD value. </li> |
| | + | <li>The aptamer with good affinity should have a KD value below 10 nm, and an acceptable range for the value falls within 10-100 nm. </li> |
| | + | </ul> |
| | + | <h1>Feedback</h1> |
| | + | Through this interview with Prof. Chen, we learned about better condition settings during the experimental process of SELEX, which coincided with the conclusions that we had gotten from the experiment. We were more confident to revise our experimental process. From the experimental process described by the professor, we obtained some experience and skills about the experimental process of SELEX, which could reduce the time of finding the solution just by ourselves. |
| | + | |
| | + | |
| | </div> | | </div> |
| | <div class="ModalFunFact"> | | <div class="ModalFunFact"> |
Human Practice structure
Participatory Design (PD)
Participatory Design is an emerging design practice which involves different non-designers in various co-design activities throughout the process, to help ensure that the designed product/service meets their needs.
In participatory design members of the wider community are also recognized as stakeholders which are able to impact the project. The extent of their involvement can range from being passively informed of a project’s development, to actively sharing their opinions in decision making.
What
Design for humans is often looked up as a standard by many designers, but how is it for people? Market research, focus group, usability testing, and other research methods are useful but sometimes they don't let us know the really important feedback. Sometimes users don't honestly say their ideas because of courtesy. More often users don't really know what they want or what they need, or the emotional level of them is often not quantifiable.
Design with Human is a part of participatory design, bringing users into the design process, in order to understand the psychological or social aspects of the user's ideas or use in the early stages of product development. Use Cases to work together to design a solution.
Why
Designers are not users, neither are product managers nor engineers. In the process of current software development, software often involves or affects various user cultural, political or psychological factors. The knowledge that a product development team needs is not just the product development team itself, but the idea of different aspects and different fields to inspire the best solution.
Imagine that in the process of traditional product design, a product team which lacks a real understanding of the user's needs is given a goal to solve a problem, the design made at this time may not really solve the user's problem, or become a mediocre product. Usually, it becomes Product Manager Driven instead of User-Driven .
Participatory design< gives users an opportunity to participate in the design. However, it is important to know that the users involved in the design do not influence the final product development decisions. Also, they do not have the professional knowledge as the product development team to understand the operation and execution of the entire product.
How
Participatory design is used in various design fields, include industrial design, architectural design, software design, and etc. In fact, there is not a specific way to make a participatory research session, that is, the simpler the better.
Back to our team, in order to expand our influences and to make sure all our human practice activities reach their maximum efficiencies and values, we 1) evaluate who our potential stakeholders are and make sure they participated in our project design, inspiring product modifies to made final product better-fit user’s needs.2) took the research of Sanders, E. B.-N., Brandt, E., & Binder, T. (2010). “A framework for organizing the tools and techniques of participatory design.” as a reference and developed a systematic structure to help us designing activities for human practice and public engagement, it includes three key points:
- Applying with an appropriate Form
- Adhering to core principle or Purpose
- Designing a suitable Process
- Learing from Feedbacks
Furthermore, it involved stakeholders from different aspects of our product. Through this systematic structure, we can not only programmatically arrange our activities but also examine the effectiveness of them. We introduced it to our
human practice even
public engagement. We hope that aside from us, future iGEM teams can also set up their own concept on this foundation.
Form
It describes the conducted time, the kind of the activity that is taking place and how it is been held. For different purpose, there will have different places and ways which is most suitable for the activities. Participatory design sessions can be conducted with either individuals or with people in groups. We classified the forms of our activities into individual, one-to-one interviews, and groups.
Purpose
According to the designation of PD, we came up with three main principle that may be introduced to different activities:
- to stimulate participants interest,
- to let the participants gain information
- to discuss with the participants and let them generate ideas.
Moreover, we will set up a goal for each activity that might either benefit our study or can affect the public.
Process
It includes the detail of the designation of the activities or the document of what the participants do or said without judgment.
Feedbacks
It is an important part for us to realize what the participants think about. We collected the opinions, suggestions, and even encouragements from the participants which is precious to our study and even other sides of our personal abilities. We think that each activity can affect both conductors and participants. We also recorded our thoughts and what we gain from the activities.
References
- Sanders, E. B.-N., Brandt, E., & Binder, T. (2010). A framework for organizing the tools and techniques of participatory design. PDC '10 Proceedings of the 11th Biennial Participatory Design Conference, Pages 195-198
https://dl.acm.org/citation.cfm?id=1900476
https://sci-hub.tw/10.1145/1900441.1900476
- Participate in Design (P!D) http://participateindesign.org/about/organisation
- Liz Sanders, An Evolving Map of Design Practice and Design Research, 2008
- Ines Anić, Participatory Design: What is it, and what makes it so great?, 2015
