The purpose of this application is to diagnose an individual’s seasonal allergies. It does this through correlating allergy symptoms to the daily local allergy index. Each day that the user experiences symptoms that may be related to allergies, they will input their symptom data along with location and date. The app then gets the local allergy index information for the day, and correlates the symptoms to the index. Then, over time and use of the app, a correlation will be established, and determine the likelihood an individual’s reaction to various seasonal allergies. This app currently only works within the city of Austin, due to the locality of the allergy index.
For almost two years now the DIY Diagnostics Research Stream has been monitoring Waller Creek along campus in the lookout for bacterial hotspots and attempting to identify the sources of these. I had the opportunity of joining the DIY Diagnostics Stream in 2014 and have been one of the Waller Creek investigators since then. I had honestly never really thought about Waller Creek before, even though it is right there in our main campus. Nevertheless, my time working on Waller Creek has made it clear to me that it deserves more attention than it currently gets. I’m honored to have received a Waller Creek Conservancy / Winkler Family Foundation fellowship through the Freshman Research Initiative to continue my research on Waller Creek.
The sites that we mainly focused on were located in the northern part of campus, where testing had proven high levels of fecal bacteria. Our tests consist of two stages; first we determine whether there is bacteria at any given site by using culture dependent techniques, which is basically giving bacteria nutrients and food and generally an awesome environment for them to grow. If the first stage proves that bacteria are present then we move on to the second stage. The second stage consists of determining where the bacteria came from, as of now we have the ability of telling whether the source of the bacteria is human fecal matter or dog fecal matter. It might sound kind of unpleasant and maybe almost kind of creepy, but think about it. These techniques allow us to identify contaminated water and point to the problem, which can then be fixed and prevented in the future. When talking about urban watersheds, such as Waller Creek, identifying sources of pollution is crucial. Waller Creek is surrounded by the city of Austin and the chances of people coming into contact with the water are pretty high, not to mention that Waller Creek eventually discharges its water into Lady Bird Lake where we like to paddle board and kayak, some of us also like to fall off of the kayak or paddle board into what we assume is water mostly free of human/dog “you know what.”
This summer we made some pretty amazing findings with the help of a group of high school students. The DIY research crew came together to lead high school students from the UT High School Research Academy to sample simultaneously at different sites along Waller Creek. We expected the results to show the usual happy bacteria, thriving in the very polluted water of Waller Creek. To our surprise, however, our usual joyful fecal bacteria were gone at the southern sampling sites. Where did they go? I’m talking about a huge drop, one that could mean two things: we messed up the experiment or something was making the bacterial levels drop fast.
These are the values of bacteria (E.coli and enterococci) at each of the sites sampled by the high school students. The purple line represents the point at which the bacterial levels dropped.
In attempts to find an answer we searched the creek for anything that could potentially explain the drop in bacterial levels. The search was a success! Right in the area of bacterial drop there was water flowing into the creek. We went ahead and collected water from the mysterious outfall to determine if bacteria were present. And the results said: NO. The culture dependent tests indicated that the bacterial levels were zero at this suspicious outfall. We returned to sample a second time and the amount of water coming out of the outfall was still high considering it hadn’t rained in more than a week. In addition, the temperature of the water from the outfall was almost 5C higher than the creek. Finally, we mixed some of the outfall water with water from a site further north that we know had high levels of bacteria. The bacterial levels of the contaminated water were cut in half!
Mysterious outfall.
We were now convinced that the mysterious outfall was somehow lowering the bacterial levels. We contacted Environmental Health and Safety and let them know about our findings. They were extremely responsive and within two days we met with them to show them the outfall. They conducted follow up tests and contacted utilities and facilities who were able to stop the outflow of water!
DIY Diagnostics Stream and EHS collaborating to protect Waller Creek.
Overall, this is a bittersweet story: Sweet because through scientific research we found a hazard to Waller Creek and with the help of EHS were able to stop the problem. Bitter because bacterial pollution is still a major issue in Waller Creek and needs to be addressed, especially since Austin’s population is growing. The next step for us is to determine the source of pollution, which I described before as stage two, and use this information to aid in the restoration of Waller Creek and ultimately prevent future contamination.
Blog Post by Ava Ibanez:
Ava Ibanez is a student from Mexico City completing her Bachelors in Science degree in Marine and Freshwater Biology at the University of Texas at Austin. Currently, she is on her third year and expects to graduate in the Spring of 2016. She has experience with experimental design, conducting independent research, and research presentation. During 2014 Ava worked as a mentor and researcher in the DIY Diagnostics Research Stream at the University of Texas at Austin. Her research focused on assessing bacterial levels in Waller Creek and determining the source of the bacteria through culture independent techniques. Ava was then accepted into the Semester by the Sea undergraduate research program at the University of Texas Marine Science Institute in Port Aransas, where she worked on another independent research project focused on fisheries ecology in the Northern Gulf of Mexico. Most recently she took a field research class through UT at the Yucatan Peninsula in Mexico, where she led a group research project and studied the effects of tourism on the feeding behavior of herbivorous fish. In the future, Ava wishes to continue her education in graduate school as a field biologist with a focus on natural systems, such as Waller Creek, that are increasingly affected by anthropogenic and environmental factors.
In the Spring 2014 semester, 34 freshmen along with 7 upper-division mentors completed a series of skill development exercises that produced authentic data on a wide range of topics including the diversity of the student’s oral microbiome, the public health of the creek on UT campus, and the diagnostic potential of molecular techniques on saliva.
LAB-WIDE PROJECTS 2013–2014
Oral Microbiome Metagenomics
Students designed ethics board approved study linking bacterial diversity/abundance in saliva with health and behavior
Generated 81 sequence libraries of oral microbiomes
Authored online survey with 114 questions to characterize health/behavior
Found tentative correlations between bacteria levels and sleep/gum chewing/hand washing
Molecular Diagnostic Development
Successfully implemented a diagnostic PCR for P. gingivalis
32 diagnoses made based on PCR results
Adapted P. gingivalis PCR protocol to novel qPCR diagnostic
107 assays run leading to 31 diagnoses
Public Health Water Quality Assessment
Sampled campus creek
28 water samples analyzed
3 different bacteria levels quantified
3 site locations analyzed
Surprisingly high bacteria levels found indicating possible sewage leak
Diagnostic Apps Development
Students developed “survey style” apps
Brainstormed ideas, developed apps independently
Diagnose a wide range of conditions
tinyurl.com/diyappgallery
FOCUSED DIAGNOSTIC PROJECTS SUMMER 2014
Dehydration saliva diagnostic
Ear wax (cholesterol) diagnostic
LAMP PCR development: next-gen tool for diagnostic development
Frack water diagnostics: Working with industry partner to develop molecular diagnostics to quantify sulfate reducing bacterial contamination in water produced by hydraulic fracturing
Texas Memorial Museum collaboration: Two summer students received a Joseph Jones Life on Waller Creek fellowship to continue work on creek bacteria
Diagnostic industry collaboration: Negotiated summer internship with local startup diagnostic company to optimize a patent-pending diagnostic device
Summer App Development: Students unable to stay in the lab working remotely on diagnostic app projects
My interest in the DIY Diagnostics stream was actually sparked long before my knowledge of the Freshman Research Initiative, and long before my enrollment in UT, and, if we’re being very specific, long before my acceptance to the university at all. As a senior in high school, my AP biology teacher offered us extra credit to attend Hot Science: Cool Talks at UT. The “Cool Talk” I ventured to was hosted by Dr. Andrew Ellington and it was all about self-diagnosis. Or rather, diagnosing yourself at home, made to be as simple as the at home pregnancy test. You do it at home and if you realize you have an illness that needs medical attention you can get to a doctors office. If you just have the common cold, you stay at home and save you and your doctor time. This was really interesting to me and it made lots of sense; finding something that saves time and money – I’m in! I’m also constantly looking for things that interest me, because it seems I have this chronic state of boredom I am trying to shake.
So, I did my one page write up of this extremely “hot” science, turned it in, got my five points of extra credit and moved on. Over the next however many months I ended up out of high school and at UT in the Freshman Research Initiative and was a few months away from having to apply to streams. As soon as I saw DIY Diagnostics I was reminded of that talk that had so caught my interest. I realized I couldn’t make any of the open houses and scheduled a meeting with the RE, Dr. Tim Riedel. And after that I was pretty sure there wasn’t another stream I wanted be in.
Being in the DIY Diagnostics lab is like being a real researcher, because you are a real researcher, which feels very hard at first for someone who has never been in a “real” lab before. You do everything on your own, and if you are me, you do it with a serious lack of confidence the first go around. By the end of the year I had mastered skills I didn’t even know existed before this class and was performing tasks that had taken me half an hour in the beginning of the year in half that time. The first time I felt like an actual scientist was during our weekly meetings when we were having a discussion that sounded like science and I understood all of it, and had responses and we were all formulating things together that would have sounded like garble to me three months prior.
One of my favorite diagnostics we did was using dog saliva. Now before I get into it, we did not get any valid results from experiment, not one person out of the 35-40 students. But I am starting to learn this is less about being distraught about failure and more about learning what to do differently the next time around. Those of us with dogs had to swab the dog’s mouth, fill out a survey on the dog’s behavior, then extract the DNA in the dogs mouth and see if we could link any of the DNA to behavioral characteristics. Pretty cool, I know, but it didn’t work. This semester I would like to figure out why it didn’t work, or at least how to get it to work. I love this stream because I am able to make my own decisions like that. And I’m sure if I suddenly develop a hatred for dogs and their saliva I have no doubt Tim would help me figure out something else to benefit the stream but also keep me from being totally miserable. DIY is a well-run, very interesting lab. I highly recommend it to anyone who wants to feel like a scientist and really have a integral part of their research experience. I will now refrain from making any puns involving Labrador retrievers and research labs, but I will include a picture of my photogenic dog whose saliva I have and will be testing.
CH 204 (Intro to Chemical Pract-FRI) OR BIO 206L (Lab Exp Bio: Strc/Func Org-FRI)
Fall Semester: BIO 377 OR CH 369K OR CS 378
Who is this stream for?
Science majors looking for computer experience
Computer Science majors looking for wet lab experience
Creative students comfortable with undefined open-ended projects
What will you do?
Students can expect to learn about the design process (how do I brainstorm innovative ideas that solve a problem in a new way?), biochemical detection (how do I develop a test that indicates the health of the patient?) and interfacing with the virtual world (how do I make a website or app to interface the diagnostic output to a computer?).
Going to open houses can have an affect similar to that of an approaching avalanche. But don’t panic! Despite the wealth of streams available and all of the information to be absorbed, it’s completely possible to fall in love with a few research topics.
To help first semester freshmen here at UT with their FRI stream decisions, we’ve asked our Fall 2014 student researchers to write about their time with the DIY Diagnostics stream. Most of our researchers are sophomores, but we have several upperclassmen too, as well as mentors who have already finished their FRI coursework.
Our researchers have worked to extract bacterial RNA from saliva samples, find sulfur-producing microbes in fracking water, and search out chemical signatures in olive oil using TLC plates. By working to place diagnostic power in the hands of the consumer, we hope to help create more personal and safe health care and industrial diagnostic systems.
If you like what you read, make sure to stop by the DIY open houses.
I chose to be in the DIY Diagnostic stream because we have a diverse selection of opportunities available for research and lab experience. There are a variety of group projects available to become a part of, like the FRIome, frack water, and Waller creek projects, but we are also given the opportunity to develop our own research projects. I think it is also really cool that we learn how to code, because without this stream, I’m about 85% positive I would have never learned to code, and I’ve always wondered how it works.
I think I am most excited about the FRIome project simply because I’m a biology major and this field interests me. I have heard many times over here at UT, that there are more bacteria cells in/on your body than there are your own cells, so I definitely believe that these bacterium have to be affecting humans in some way, and FRIome could possibly help to determine how.
Being part of the research community at UT has helped me succeed because you get to meet a tone of ridiculously smart and friendly people and you also learn a lot of techniques that can help you in your future research or labs. I actually went into my Chemistry Lab course with a great understanding of techniques, lab protocols, and tools simply because I had a great learning experience in the DIY Diagnostic stream.
I think the funniest part of the stream was that many of us students would be so completely lost at times and think that everyone else knows what they are doing, but when you talk to students you realize we’re all on the same page. After the first couple of weeks, when all the students were settled in and friends were made, that is when the serious work went down because there was a great sense of community and everyone collaborated to achieve success and spread the skills we had just learned. I think that was a major experience of the stream.
Compared to other undergrads who have done research outside of this stream, or FRI in general, the DIY Diagnostics stream definitely puts a lot of emphasis on student participation. We are the ones collecting samples, analyzing data, and the results. I think it is very important to be a part of every step in the research and we are given every opportunity to do so. I see diagnostics as moving in the direction of primarily “at-home” diagnostics because they will generally be faster and cheaper, and guess what, this stream is called DIY (do it yourself) Diagnostics, and I see this DIY diagnostic stream as a way to force upon the world a more stringent focus on accessibility to technologies we have to capability to produce and help accelerate the production of “at-home” diagnostics.
What appealed most to me about the DIY Diagnostics stream was the way it combined biology and chemistry with computer science. I really liked the idea of learning to code and create an app that could actually be useful. When I went to the presentation during open house, Dr. Riedel was the most genuinely enthusiastic of all the research educators I heard speak. After hearing the pregnancy test example as a DIY diagnostic, it got me thinking of the many new diagnostics that would be useful to the public, such as a reliable at home strep test. Plus, I was excited to work in a stream that was just starting.
The diagnostic ideas I am most excited about is the ones that can come from the FRIome project, in which we are testing saliva samples to find correlative data between various health factors and bacterial abundance. I hope to help enlarge the database of samples so we can a large amount of samples sequenced. Then we can look at abundance of specific bacteria, and develop experiments that can lead to new diagnostics. In my Microbiology class, my professor briefly discussed how there are ongoing studies that are looking at the relationship between subjects’ microbiomes and obesity, autism, and immune response. The more I hear about the significance of the microbiome, the more excited I get for the FRIome project.
Being part of the research community has helped me with my time management skills in that I had to always get enough hours of lab time in each week. Also doing research has taught me that not getting expected results does not necessarily mean failure, and that I should always keep working to find solutions to problems I encounter.
I came into this stream with very limited knowledge in coding. The bit of coding we learned during the spring semester has been quite helpful. This summer I started working on an app that helps to speed up the process of which foods specifically are causing widespread food poisoning to hasten the recall process. Most of this app is not completed though.
My biggest “aha” moment so far was when I used the Qubit correctly. It took me several tries to get the technique right, so I was very excited when I got the machine to properly find the concentration of dsDNA in my samples.
I’m glad I have been able to start research so early in my undergraduate career. I hope this opportunity will open doors for me to receive internships in other labs in the next couple of years. Hopefully in 20 years, we will be able to have our entire microbiomes sequenced, which would mean we would quickly be able to diagnose ourselves with things discovered to be related to or caused by the bacteria that live in us. I hope to be part of this process of discovering how the microbiome affects the health of humans.
Ava Ibanez is a student from Mexico City completing her Bachelors in Science degree in Marine and Freshwater Biology at the University of Texas at Austin. Currently, she is on her third year and expects to graduate in the Spring of 2016. She has experience with experimental design, conducting independent research, and research presentation. During 2014 Ava worked as a mentor and researcher in the DIY Diagnostics Research Stream at the University of Texas at Austin. Her research focused on assessing bacterial levels in Waller Creek and determining the source of the bacteria through culture independent techniques. Ava was then accepted into the Semester by the Sea undergraduate research program at the University of Texas Marine Science Institute in Port Aransas, where she worked on another independent research project focused on fisheries ecology in the Northern Gulf of Mexico. Most recently she took a field research class through UT at the Yucatan Peninsula in Mexico, where she led a group research project and studied the effects of tourism on the feeding behavior of herbivorous fish. In the future, Ava wishes to continue her education in graduate school as a field biologist with a focus on natural systems, such as Waller Creek, that are increasingly affected by anthropogenic and environmental factors.
