Difference between revisions of "Team:Austin LASA/Human Practices"

Revision as of 03:44, 18 October 2018

const p = t => h('p', null, t);
h(g.Page, {title: 'Integrated Human Practices', prev: 'https://2018.igem.org/Team:Austin_LASA/Safety', next: 'https://2018.igem.org/Team:Austin_LASA/Model', selector: [5, 0]},
  h(g.Section, {title: 'SILVER MEDAL CRITERIA'},
    p('We believe that our work is a positive impact because early detection of HIV-1 can lead to a reduction in mortality of up to 75%. Currently, the detection methods for HIV in resource deficient areas are time consuming or require a lot of resources and expertise. We have detailed this in the “Why HIV Detection in Infants” section of our Description page further. After realizing this problem, we wanted to make a quick and low resource method of detection, which led to our current project. The possibility of such a method reducing infant mortality is a possibility, which is nothing but a positive impact.'),
    p('We investigated the struggles of HIV diagnosis by talking to someone who had traveled to Malawi and had experienced that environment. In our opinion, her direct experience was one of the best ways to investigate the issue. She discussed how the device must be relatively simple to use and be fast, as often people leave the clinic before they get the results back. The more we spoke to people, the more evident it was that a quick and simple kit was something that was an actual necessity. More details on these investigations can be found in the “Engaging with Experts” section of this page.'),
    p('We also engaged with people who are vital to the process of HIV-1 diagnosis and an integral part of that community. We spoke to someone involved in HIV policy in order to help us understand the complexities of building a kit and how to ensure that it was truly beneficial in diagnosis. We also spoke to a biological safety officer in order to understand the disposal techniques and packaging methods in order to ensure that our kit would be used responsibly and have no negative effects that were preventable. More details on this HIV and safety community engagement can be found in the “Engaging with Experts” section of this page.'),
    p('We chose this approach of interviewing people who had actually traveled to locations where our kit was needed because we thought that it would be the best way to get feedback that was personal and genuine. We feel as if we were successful in this, as the information they provided us was seemed much more personal than information gained from papers or other resources. We also interviewed safety and policy officials, as we felt like they would be able to provide a fresh perspective on our project. The team ourselves would not be able to catch every single minute detail that may have a negative impact considering we are not experts in the field. Therefore, we talked to experts who were able to make sure that our work was truly responsible and would have a positive impact.')
  ),
  h(g.Section, {title: 'GOLD MEDAL CRITERIA'},
    p('Utilizing the information that we gained from various experts, we were able to finalize our laboratory protocols and decided to focus on protocols that did not require specific machinery. By doing so, we were able to divert from depending on large central labs, to doing detection within small rural hospitals, thereby increasing communication between the technicians and family. In response to sterility, we created a resource to establish a standard for universal precautions. To see a more detailed description of the designing and implementation please refer to the Integration section.')
  ),
  h(g.Section, {title: 'BEST INTEGRATED HUMAN PRACTICES SPECIAL PRIZE'},
    p('Our project directly targets one of the most vulnerable groups to the HIV infection, infants in rural countries, and aims to provide a seamless solution to detecting this infection early on by using synthetic biology techniques. In doing so, we not only familiarize ourselves with local hospitals in order to understand common issues and better adapt, but we have considered implementation of our project from the viewpoint of a stakeholder. Thereby, all the protocols and materials used in this project were chosen with a specific goal in mind, more information on how our project best integrates the interest of all parties can be found in the “End Result” section.')
  ),
  h(g.Section, {title: 'CONSIDERED TOPICS'},
    p('Our project was related to the detection of HIV-1 in infants. This gave us a lot of room to work with human practices topics. One of the major topics we wanted to look at was the education of the general public about synthetic biology. We considered numerous educational opportunities about synthetic biology and genetics with younger children, which we followed through with. Another topic we considered was informing ourselves about how people diagnosed with HIV in the United States feel about the process and general experience. We pursued the option of going to HIV-1 clinics, but unfortunately this was not possible for us due to the sensitive circumstances surrounding such an institution. Along with this, we wanted to focus on the topic of the struggles of HIV diagnosis and other low resource diagnoses. This led us talking to experts who have experience diagnosing HIV in the field and safety protocols, since we wanted to make sure that our kit would be safe.')
  ),
  h(g.Section, {title: 'ACTIVITIES'},
  h(g.Section, {title: 'Education and Outreach'},
    h('p', null, 'Our team was very active in reaching out to our local community, particularly to younger children. We’ve listed out below everything we’ve done.'),
    h('ul', null,
      h('li', null, 'The LASA iGEM Team spent time volunteering at the AHA 2018 Stem Event (7/21/18)',
        h('ul', null,
          h('li', null, 'The second annual Austin STEM Day, led by the American Heart Association, Abbott and Texas Mutual Insurance Company, will engage 40 high-school students in a day-long conference. The program aimed to inspire students, encourage innovative thinking and demonstrate that not only are STEM careers critical to the health of our communities but also, they can be fun!'),
          h('li', null, 'Volunteers engaged with other students during the conference from 8:30-12 p.m on July 21, 2018 and participated in various STEM related activities with mentors to to help inspire future students.')
        ) 
      ),
      h('li', null, 'The LASA iGEM Team led mini science experiment-labs at The Thinkery Museum (8/10/18, 8/25/18, and 9/15/18)',
        h('ul', null,
          h('li', null, 'Members led 3-4 hour workshops in the Thinkery Museum, a children’s museum created to  help the new generation of innovators and creative problem solvers.'),
          h('li', null, 'Workshops included the following the ', h('a', {href: 'https://www.genome.gov/pages/education/modules/strawberryextractioninstructions.pdf', className: 'link'}, 'procedure'), ' of the classic Strawberry DNA Lab'),
          h('li', null, 'During the lab, members discussed basic science concepts with children and parents and mentioned the field of synthetic biology to adults. This event was extremely successful as there were over 30 participants each session. The LASA iGEM team volunteered here for a total of about 8 hours each.'),
        ) 
      ),
      h('li', null, 'The LASA iGEM Team volunteered at the Summer Mad Science Camps in Austin (8/6/18-8/7/18)',
        h('ul', null,
          h('li', null, 'Austin Mad Science is a well known establishment with the goal of delivering unique, hands-on science experiences to children.'),
          h('li', null, 'From 1:30 p.m. to 4:30 p.m. members of the LASA iGEM team helped the camp run by facilitating activities with kids and interacting with them about synthetic biology.'),
          h('li', null, 'Activities are attached ', h('a', {href: 'https://austin.madscience.org/locations/austin/pdf/SummerCamp2018IAAAustin.pdf', className: 'link'}, 'here'), '.')
        ) 
      ),
      h('li', null, 'The LASA iGEM Team conducted a short lab experiment with Clayton Elementary School on (10/5/18)',
        h('ul', null,
          h('li', null, 'LASA iGEM members went to Clayton Elementary and met with an afterschool science group to perform a simple DNA lab. Students had a great time learning about new scientific concepts and having hands-on experience with scientific tools.'),
          h('li', null, 'Workshops included the following the ', h('a', {href: 'https://www.genome.gov/pages/education/modules/strawberryextractioninstructions.pdf', className: 'link'}, 'procedure'), ' of the classic Strawberry DNA Lab')
        )
      ),
      h('li', null, 'The LASA iGEM Team went to a local elementary school, Laurel Mountain Elementary and talked about DNA, genetics and did the strawberry DNA extraction activity (the protocol in one of the sections above). The kids were super enthusiastic about the activity and even knew what the acronym DNA stands for at the end.',
        h(g.Image, {src: 'https://static.igem.org/mediawiki/2018/1/1f/T--Austin_LASA--Strawberry1.jpg', position: 'center'},
          h('p', null, 'Here’s some of our team members in the classroom, before performing the experiment with the class.')
        ),
        h(g.Image, {src: 'https://static.igem.org/mediawiki/2018/5/50/T--Austin_LASA--Strawberry2.jpg', position: 'center'},
          h('p', null, 'Will helping a student filter their mixture in order to remove chunks. The kids enjoyed seeing the DNA form after rubbing alcohol was added.')
        )
      )
    )
  ),
  h(g.Section, {title: 'Engaging with Experts'},
    p('In order to learn more about the diagnosis of HIV and biosafety, we interviewed several experts in the field and have included the information they gave us below.'),
  h(g.Section, {title: 'Dr. Veronica Leautaud, Ph. D.'},
    'Director of Education',
    h('br'),
    'Rice 360 Institute for Global Health',
    h('p', null, 'Dr. Leautaud is a professor at the Rice 360 Institute for Global Health and was able to provide the following feedback on our project and kit.'),
    h('ul', null,
      h('li', null, 'Discussion Regarding Blood Sample to LAMP Procedures',
        h('ul', null,
          h('li', null, 'Dr. Leautaud recommends that for the LAMP assay to start with white blood cells. If we begin with plasma, after lysing we will still want to have white blood cells present, but she adds that “The good thing about LAMP is that it is a robust amplification so you can still get away with lysing the WBC with a small amount of detergent or high temperature or some other mechanical approach without killing the LAMP enzymes. And without having to purify so much, normally [compared]  with PCR you need to clean it so much before the Taq polymerase works.”'),
          h('li', null, 'Overall the initial starting point would be to start with whole blood, with both red and white cells, then lyse the white blood cells (what we are after for the double-stranded DNA template)')
        )
      ),
      h('li', null, 'Blood Sample to Amplification Procedures/Advice',
        h('ul', null,
          h('li', null, 'Dr. Leautaud’s advice, “It is not trivial, but there are papers… There is one professor, David Kelso, he takes whole blood, takes a finger prick on a wet mount, flushes it with a bit of sodium hydroxide (diluted) which destroys the cells and even denatures the DNA a bit, but in the end results in clean DNA for easy sample prep.”'),
          h('li', null, 'Overall, the means of procuring a blood sample and processing it until it is usable in amplification studies has its own challenges. In terms of our team, it would be in our best interest to focus on one part of the planned kit. Generally, in a larger lab, different individuals would work on various parts of such a kit, so it is not realistic to plan on developing a fully functional kit (in theory) with such limited resources and time. This part is best suited for a collaboration with another lab.')
        )
      ),
      h('li', null, 'Dr. Leautaud’s Experience in Malawi',
        h('ul', null,
          h('li', null, 'Dr. Leautaud was developing a detection assay for HIV RNA in 2012 in which she focused on plasma (since it dealt with RNA).'),
          h('li', null, 'She describes the workspace as follows, “In Malawi, there is no lab. They had a separate room with a fridge, centrifuge, agar plates, did not have pipettes or a vortexer; Eppendorf tubes and gloves were scarce.”',
            h('ul', null,
              h('li', null, '“There are centralized locations that will look at PCR, made out of blood spots that will be taken when a baby is born, it is analyzed by a large microbiology lab with all the staff and materials needed. Two types of locations, local labs with no or minimal resources and large centralized national lab.”'),
              h('li', null, '“One major problem in Africa or Malawi is that there is no communication and follow up with patients and the hospital, so even if a child is diagnosed the parent will not know. The hospitals don’t have the manpower to do that.”')
            )
          ),
          h('li', null, 'She describes various parameters that should be considered, “The test needs to be under 3 or 4 hours for the mother to stay in the hospital.',
            h('ul', null,
              h('li', null, ' You also need to keep in mind cost.'),
              h('li', null, 'The third parameter is your user which would be the nurse or lab technician, who is not as highly trained as they are in America. Instead, they have technical degrees. You need to teach them to not contaminate the test. You need to be aware of the level of literacy and skill of the user. My test in Malawi was a fail, it was too sensitive and was always contaminated.'),
              h('li', null, 'Dr. Leautaud sent materials with visiting staff to Malawi, used lyophilized reagents.',
                h('ul', null,
                  h('li', null, 'She mentions considering that most products will be kept at room temperature, so to keep that in mind when designing the project.')
                )
              ),
              h('li', null, '“Be aware of the resources: whether you need electricity or will use battery powered machines?”',
                h('ul', null,
                  h('li', null, 'One research fellow that works with Dr. Leautaud mentions that she is planning on conducting a usability study to see if people in the area are willing to take time out of their schedule to learn how to use the technology/ device she created.'),
                  h('li', null, 'important to consider public interest and involvement')
                )
              )
            )
          )
        )
      ),
      h('li', null, 'Precautionary Measures to Prevent Contamination (Other than sending material directly)',
        h('ul', null,
          h('li', null, 'Dr. Leautaud mentions, “A good option is to aliquot your products or enzymes. You also need to make sure that when you are running your tests that you have a negative control, positive control, and sample.”'),
          h('li', null, 'When she conducted her tests, Dr. Leautaud used synthetic oligos as a positive control  and plasma as the negative control. She would follow through the entire process with the controls, not just add it in at a certain step to make sure there was no contamination of the data.')
        )
      ),
      h('li', null, 'Advice for Project Planning',
        h('ul', null,
          h('li', null, 'Dr. Leautaud recommended ordering LAMP immediately as it will take a while to arrive.'),
          h('li', null, 'She recommends to focus on the sensitivity of assays (explains method on how to do so).',
            h('ul', null,
              h('li', null, '“Start from the beginning, when you are receiving a blood sample from a baby you most likely will do a heel prick which is no more than 50 microliters on a good day, if you do a venous draw, no doctor will allow you to have more than 0.1 mL. So how many white blood cells will be present? Assume that there will be 10 HIV copies in that 50 microliters of the blood sample, then you must look at LAMP; you have 20 microliter LAMP reaction and 50 microliters, so you can identify how much the HIV copies are present. From there you can identify how many copies you will need for the CRISPR assay to work and how many for the fluoresce to work (find the limit of detection of the LAMP assay).”')
            )
          ),
          h('li', null, 'Dr. Leautaud recommends doing the experiment with the fluorophore specifically because even if it says that it is visible to the naked eye, it is important to identify the concentration that must be present for it to be visible?'),
          h('li', null, 'She recommends to focus on the CRISPR assay with a really clear limit of detection and characterize the assay (do a dilution series of the assay).'),
          h('li', null, 'Dr. Leautaud adds that we can consider a paper test instead of a test tube if that is better suited to our goal.'),
        )
      )
    )
  ),
  h(g.Section, {title: 'Jessie Anderson'},
    'Research Fellow',
    h('br'),
    'Rice 360 Institute for Global Health',
    h('p', null, 'Ms. Anderson visited Malawi as preparation for her own validation study but was able to provide valuable insight into the conditions of the hospital and staff in other parts of the world. She was able to provide insight into the functionality the neonatal wards at two tertiary, referral hospitals and was able to give us the following feedback.'),
    h('ul', null,
      h('li', null, 'Would you be able to describe the setting of the hospitals that you visited? What were the conditions? How many staff and how well trained were they?',
        h('ul', null,
          h('li', null, 'The neonatal wards for both QECH and KCH seemed understaffed, even for this season which is not the busiest of the year. There were two short (10-30 seconds long) power outages within 20 minutes in the KCH ward. KCH had more equipment available to them than QECH (much more incubators, radiant warmers, blue-lights, etc; I think also a higher proportion of the room heaters was working), but the flow and size of space available seemed better at QECH. Still not ideal at either location. Both wards were segmented off into low-risk, high-risk, and isolation/quarantine areas or rooms. Every 2 hours the mothers come for feeding at both sites, and once every morning nurses go on rounds to check up on every patient (a doctor accompanies at QECH; they only come if called at KCH).'),
          h('li', null, 'Overall the initial starting point would be to start with whole blood, with both red and white cells, then lyse the white blood cells (what we are after for the double-stranded DNA template)')
        )
      ),
      h('li', null, 'Blood Sample to Amplification Procedures/Advice',
        h('ul', null,
          h('li', null, 'Dr. Leautaud’s advice, “It is not trivial, but there are papers… There is one professor, David Kelso, he takes whole blood, takes a finger prick on a wet mount, flushes it with a bit of sodium hydroxide (diluted) which destroys the cells and even denatures the DNA a bit, but in the end results in clean DNA for easy sample prep.”'),
          h('li', null, 'As far as training, I am not able to know how well-trained the nurses are; every nurse in Malawi must go through a training provided by the COIN Manual, but I don’t know how often (if ever) it is repeated. For diagnosing of jaundice, talking with two different nurses at KCH yielded two different procedures in using the transcutaneous bilirubinometer (one answered us “I think everyone should be trained on it now..” and when asked how often it was calibrated “I have never seen it calibrated” – if it is supposed to be used the same as a very similar device, t is supposed to be calibrated every use).'),
          h('li', null, 'KCH is better staffed 24/7. At QECH, there are 3-4 nurses during the weekday, and 2 overnight and on weekends. The study nurse who was there told us 75% of deaths occur overnight.')
        )
      ),
      h('li', null, 'Are the hospitals equipped to handle diagnostic studies? How knowledgeable were the staff or patients on diagnostic testing/ how willing are they to get them done?',
        h('ul', null,
          h('li', null, 'Both of these central hospitals have partnered with various universities and organizations throughout the years to complete studies. Rice itself has primarily partnered with the neonatal and maternity wards of QECH over the past 10 years (starting with bubble CPAP), and other organizations (like Baylor and UNC-Chapel Hill) have done some work at KCH, though I’m not sure exactly what studies they’ve done. UNC has a permanent building at KCH, as does Rice and the Liverpool Welcome Trust at QECH. There is also currently a sepsis diagnostic study occurring at KCH as with another group funded by Greater Challenges Canada.'),
          h('li', null, 'The staff is knowledgeable at both locations of diagnostic tests; both QECH and KCH are very supportive of the BiliSpec jaundice-diagnostic study (we’ve met with the department heads of both locations as well as other clinicians). Also, because the grant that funds our study provides stipends for the nurses who work with us, they are willing to work beyond their normal work hours to have another source of income.'),
          h('li', null, 'Are there any problems with sanitation, resources, or communication that is present?',
            h('ul', null,
              h('li', null, 'The sanitation and resources at both central hospitals are not the same that’s present in the US (or most western) hospitals. That being said, nurses are supposed to use available hand sanitizer before and after each time they interact/touch a patient, and gloves and biohazard bins are used when drawing blood or performing heelpricks. As far as communication, the data management is not consistent or as thorough as in western hospitals. I think that is one of the biggest obstacles in performing studies in such an environment. For the BiliSpec study (and most studies should do this anyway), we will be providing all our material resources (i.e. devices, consumables like gloves and needles among other, computer, desk/chair, wifi dongle as wifi is not available, etc).')
            )
          )
        )
      )
    )
  )
  )
  ),
  h(g.Section, {title: 'Human Practices in Our Kit'},
    h('p', null, 'We integrated human practices into our project throughout the iGEM season. Below we’ve summarized how our integrated human practices fits the requirements for the Gold Medal Integrated Human Practices criterion and the Best Integrated Human Practices Award.'),
    h('p', null, 'For a much more detailed reference on the development of our kit and how our human practices played a role in that, please see our Kit Considerations page. For a much more detailed reference on how our human practices impact our wet lab work, please see our Design, Development, and Results page.')
  )
);