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Saturday, September 30, 2017

2017-2018: (almost) Q2 Benchmark

Goals:
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.

Resources:
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).

Questions:
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?

Timeline:

Month
Goals:
September
- Finalize Big Goal (Q1 Post)
October
- Find sample sources (friends, family, etc.)
November
- Collect samples
- Send samples
December
- Sample analysis
- Research R
January
- Research R, begin coding
- Get results (hopefully)
February
- Coding
March
-Finish coding
-Begin preparing showcase presentation
April
- 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

Progress:
    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.   

Timeline: 
Month
Goals:
September
-Finalize Big Goal (Q1 Post)
October
-Begin Compiling Research (Library, Print/Web Articles)
November
-Continue Collecting Resources/Research
Check in #2 (Q2 Post)
December
-Narrow Down Topics/Determine Focus
January

-Continue Collecting Resources/Research
February
-Contact New Resources (Emails w/ Mr. Carey & Mr. H)
March
-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)
April
-Begin Sample Analysis
-Continue Preparing Presentation (Board/Video TBD; using any resources available)
-i2 Showcase Presentation!

Sunday, November 27, 2016

Q2 Benchmark:

Progress:
     Since the first blog post in October, I have continued to collect and annotate resources (mainly articles and books) on the gut-brain axis and microbiology in general. Portions of two of the most interesting/my favorite/most easily understood articles are shown below (excuse the messy annotations!): 

"A person's genes can influence the gut microbiome's composition..."- Ruth E. Ley, "The Gene-Microbe Link"
"In the not too distant future each of us will be able to colonize our gut with genetically modified 'smart bacteria' that detect and stamp out disease..." - Justin L. Sonnenburg, "Microbiome Engineering"

I have yet to find any main sources (see last post's timeline), so I may have to reduce the number of sources from three to just two and rely on many more smaller sources. 

Updated BIG Goal:
     Now that I have gotten more time to think about my final goal, I realize that there are three different microbiological subcategories I am interested in: the gut-brain axis, microbial engineering/synthetic biology (which is technically its own field), and the relationship between ones' genes and microbiome. As pictured above, I have already begun research concerning these three topics. However, juggling schoolwork and this extra research isn't as easy as I hoped it would be when I set my goals earlier this year. My final goal has changed little compared to what it was before. I intend to compile my research (as I did last year) in some sort of presentation, using another tri-fold and possible video. I also still plan to learn about my own microbiome using the resources provided by a company like uBiome and include this info in either the same or a separate presentation.  

Timeline: 
Month
Goals:
September
-Finalize Big Goal (Q1 Post)
October
-Begin Compiling Research (Library, Print/Web Articles)
November
-Continue Collecting Resources/Research
December
-Narrow Down Topics/Determine Focus (Choose Btwn. 3 Above)
-Contact uBiome 
-Get Microbiome Kit/Submit Samples
January
-Contact New Resources (Mentors/Companies)
-Compile Research (Digital Doc)
-Receive Sequencing Results (Hopefully!)
February
-Receive Sequencing Results (If not in Jan.)
-Finish Research Compilation
March
Prepare Presentation (Board/Video)
     -Using Research Comp. & Sequencing Results
April
-Continue Preparing Presentation (Board/Video)
-i2 Showcase Presentation!

Resources (Doesn't Really Need A List):
     The only resource I need for this project, besides the research (which I can get on my own/already have), is the kit needed to learn about my microbiome. I plan to order a kit from uBiome before the end of the semester.

Monday, September 26, 2016

Q1 Benchmark



Big Goal:
     For this year, my goal is to further research and explore the human microbiome. Last year, the books and articles I read were mostly broad and covered microbiology as a whole. Now that I have a better idea of what exactly interests me, I can focus on the gut-brain axis and how this relationship affects our bodies. I would like to gain a solid understanding of this specific topic by the end of this school year. In addition to this, I would like to sequence my own microbiome to make what I am learning about more relatable. With the help of a kit (like the one provided by uBiome), I would see what microbes are in my body and research them as well.

A simple explanation of the gut-brain axis (the focus of my research this year)
A SF-based company that sequences people's microbiomes
Resources: 
What I Have: 
     Just like the previous year, my main resources will consist of the past research of actual scientists and experts in the field. These resources include books, scientific papers, and news articles (print and digital). I have many articles from last year that I have yet to read, so these papers are what I have for my project at the moment.

What I Need: 
     Gathering new research resources is a major part of my project. A good amount of my time will be spent looking for and compiling the information I need to learn about the subjects listed above. However, I will need to a microbiome sequencing kit from uBiome to complete the second half of my project.

uBiome's microbiome sequencing kit
Timeline (expect revisions!):

Month
Goals:
September
-Finalize Big Goal (Q1 Post)
October
-Begin Compiling Research (Library, Print/Web Articles)
-Main Source 1: TBA (Gut-Brain Axis)
-Contact uBiome
November
-Main Source 2: TBA (Gut-Brain Axis)
-Get Microbiome Kit/Submit Samples (?)
December
-Main Source 3: TBA (Personal Microbiome)
-Contact New Resources (Mentors/Companies)
January
-Compile Research (Digital Doc)
-Receive Sequencing Results (?)
February
-Receive Sequencing Results (If not in Jan.)
-Finish Research Compilation
March
Prepare Presentation (Board/Video)
     -Using Research Comp. & Sequencing Results
April
-Continue Preparing Presentation (Board/Video)
-i2 Showcase Presentation!

Tuesday, May 10, 2016

Friday, April 29, 2016

Intro to Batteries: Little Bits Challenges


Challenge 1: Manually Adjustable Buzzer


Challenge 2: Light Sensor Controlled Fan


Challenge 3: Motor


Challenge 4: 2 Motors


Challenge 5: Remote Controlled Buzzer



Mini Battle Bot Challenge:

Unfortunately, we forgot to take a picture of our bot before we took it apart. In terms of design, we figured that protecting the front and back of the bot from the opposing robot was the most important. However, we realized that the sides of our bot were vulnerable way too late. This weakness caused us to lose our first match. (But at least we had fun?)