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Saturday, September 30, 2017

2017-2018: (almost) Q2 Benchmark

This year's project will still involve learning more about microbiology, but improving my programming skills is my "BIG" goal this year. More specific goals this year include: successfully collecting samples, getting the samples analyzed in a lab, learning how to visually display this analysis, and (hopefully) creating this visualization.

Some of the resources I'll need include:

  • a means of analyzing the samples I collect (through a lab, like uBiome)
  • a software to statistically analyze the data I get from aforementioned lab (most likely R).

What are the best ways for me to display these data online (how should I sort them)?
On average, how long does it take to analyze samples in the lab?


- Finalize Big Goal (Q1 Post)
- Find sample sources (friends, family, etc.)
- Collect samples
- Send samples
- Sample analysis
- Research R
- Research R, begin coding
- Get results (hopefully)
- Coding
-Finish coding
-Begin preparing showcase presentation
- Finish presentation

Thursday, September 14, 2017

2017-2018: Q1 Post

Reflection: Dog Ownership & The Microbiome

For last year's project, I researched more about the microbiome and later designed an experiment to observe the effects that pet ownership might have on the human microbiome. I enjoyed learning about all the different factors that could alter our microbiomes, including diet and location. Being able to actually pitch my experiment and getting positive feedback was one of my biggest successes last year. I should have planned my project more thoroughly so that I could have gotten farther. If I had done this, I might have been able to conduct the experiment during the school year. I would like to explore this same topic this year, with an added focus on computer programming. All of the research I have done since sophomore year would play a role in my final project this year. In addition to this focus on the human microbiome, I would like to improve my programming skills and learn how to analyze the genetic data(from the experiment) independently using software.

Broadening Scope & Building Upon Past Work:

Since last year, I don't really have any new questions regarding the microbiome. I would like to know how to combine programming and the microbiome however. This is what my final project will focus on. Collecting and analyzing microbiome data in a lab are the steps for this year's project that will definitely require the most guidance. Ultimately, I would like to develop solid programming skills and gain more insight into how our microbiome affects our everyday life (and how our everyday life affects our microbiome). 

Change in the Broader Community:

By showing people how pet ownership positively (or negatively) affects our microbiome, I could promote lifestyle changes that people can make to be healthier! Sharing the results of this project would increase awareness as well because the microbiome is a relatively foreign concept to the general public. 

Sunday, March 5, 2017

Q3 Benchmark

    At this point, the progress I made can't be photographed since I basically rehashed my entire project. The best summary I can include is the project proposal I wrote up this quarter (it includes a personal anecdote, statistics, and mentions of poop; basically everything you'd want in a pitch):

A Look at the Effects of Dog Ownership on the Human Microbiome

As a sophomore faced with the challenge of choosing a year-long project, I was seriously intimidated. The freedom to choose whatever topic I wanted was daunting, but I finally decided to explore microbiology after a realization I first documented on my blog post:  

“This year, I have decided to pursue an interest that I have wanted to work on for years. Ever since being introduced to the world of microbiology through a PBS game show episode that premiered when I was 6, I have wanted to conduct some sort of research concerning this field of study. But as the years passed I believed that I would never get the opportunity to do so. Until now!” -Q1 Project Benchmark October 15, 2015

The aforementioned episode explored the bacteria present in homes and had contestants conducting their own experiments in the lab. They swabbed toilet seats, fish bowls, and telephone key pads to see what kinds of bacteria were present on these surfaces. Seeing kids my age learning about microbiology and the countless invisible microorganisms that can be found everywhere really resonated with me as a first grader and now, as a junior, I have realized that I am passionate enough about this field to want to conduct my own experiment.

From sophomore year till now, I have done some broad research on microbiology by reading several books and articles with focuses ranging from how the microbiota in our gut "talks" to our brain and helps control our behavior to the connection between genes and the microbiome. Last year, I also conducted my own experiment that looked at the microbial diversity of the fifteen busiest BART stations. I documented my progress with two different videos. This year, I’d like to gain more formal experience and conduct an experiment to look at the effects of dog ownership on the microbiome.

According to the American Veterinary Medical Foundation, 36.5% of households in America own at least one dog. That’s over 43 million families owning nearly 70 million dogs! This is might actually be a good thing, since the benefits of owning a dog have been supported by several studies in recent years. Past studies have shown that people who own dogs are happier, less-stressed, and even less likely to die of heart disease. But, does this exposure to dogs result in changes in the the gut microbiome (and are dog owners healthier for owning dogs)?

Project Overview:
In this study, the gut microbiomes of dog owners and non-dog owners would be compared. The difference between the gut microbiomes of these two groups would be assessed to speculate the effects of the transferring of bacteria from dogs to their human owners.

  • Collect fecal samples from subjects (possibly from the SHC student body, ideally randomized)
    • ½ dog owners
    • ½ non-dog owners (Comparison group)
    • Record data on subject (ex. age, sex, zip code, general health)
    • Record data on dog (ex. age, breed, level of closeness with owner)
      • "level of closeness with owner" defined by
        • 1. Approximately how many times a day do you let your dog lick your face?
        • 2. Does your dog sleep in the same bed as you?
        • 3. How often do you personally walk you dog each day?
    • Also collect fur samples (from under neck) to provide a point of comparison
  • Analyze diversity of gut microbiome samples
    • Check for significant differences between two groups
    • Possibly use results of another study on the microbiome of dogs to see what types of bacteria transferred from dogs to owners
    • Discuss effects of dog ownership on asthmatic kids (i.e. is it beneficial for them to own a dog?)

Hopefully, the results of this experiment support the idea that dogs are both cute and good for our health!

Updated BIG Goal:
     Since I'm not entirely sure how long this entire experiment will take, I plan to present whatever progress I've accomplished during the i2 showcase in April regardless of whether I have completed the project by that date.   

-Finalize Big Goal (Q1 Post)
-Begin Compiling Research (Library, Print/Web Articles)
-Continue Collecting Resources/Research
Check in #2 (Q2 Post)
-Narrow Down Topics/Determine Focus

-Continue Collecting Resources/Research
-Contact New Resources (Emails w/ Mr. Carey & Mr. H)
-Finalize Project Outline
-Finalize Project Proposal
-(Everything depends on ^ now! Everything below is just a projection)
-Begin Collecting Samples
-Prepare Presentation (Board or Video? TBD)
-Begin Sample Analysis
-Continue Preparing Presentation (Board/Video TBD; using any resources available)
-i2 Showcase Presentation!