Total Pageviews

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?)

Sunday, March 13, 2016

Q3 i2 Project Benchmark

Changes:
   Since I have temporarily taken a break from my research (which I will continue after finishing my experiment), I have finally decided what my experiment will be. I recently read a story on SF Gate that revealed that BART was the "germiest" subway system second only to NYC's Subway. This made me wonder which BART station had the highest bacteria diversity (aka which one is the "germiest") and what types of bacteria could be found there. I have decided to conduct an experiment in which I collect samples from select BART stations and compare them.

Revised Timeline: (see March-May)
Month
Actions
October
Begin planning research opportunities and finding resources that can help me achieve my goal
November
Begin research using mainly print sources
     ex. borrow most sources from libraries; take notes 
December
Continue research using sources
Finalize project plan
Winter Break
Continue research (begin notebook, finish Missing Microbes)
January
Annotate (articles & books)
February
Annotate/compile notes!
March
Begin conceptualizing/conducting experiment
(I'm tentatively planning to collect my samples over spring break.)
April
Complete experiment, do write up and compile/edit footage
May
Finalize my presentation (write up/video) 


Evidence of Progress:
     Since the second blog post in December, I have finished a couple other books. However, using library books as research isn't exactly the best method because you can't write in their margins and highlight. Therefore, I photocopied the four main books I read and added them to the growing stack of microbiology papers in my room (see below).

The photocopied books are at the top, and my random notebooks/papers make up the rest of the pile (because who needs one perfectly organized notebook when you can have ten haphazardly filled with notes?).
     In terms of what I've annotated in the books, I've mostly focused on things that could inspire other experiments/projects I could do later when I have more knowledge and better access to resources. A great example of this is the Winogradsky column, which I first found out about in Welcome to the Microbiome. If I happen to stop by Lake Chabot soon, I may even be able to present my column at the i2 showcase in May.

Each of these four books have provided the majority of my research, and I highly recommend each of them! (However, The Invisible Kingdom is probably the best for casual reading because of its more informal language.)
Photocopied page that first talks about Winogradsky-style columns (while this isn't exactly related to the human microbiome, it sounds like a fun side project)

Further detail on the Winogradsky column, which is a device used to culture a large number of microorganisms using pond water and sediment (to make it more effective, eggshells and shredded newspaper can be added)
     The farthest I've gotten with the BART project so far is coming up with the idea and ordering my supplies. All I can say as of now is that it will compare an undecided number of BART stations and their bacteria diversity. I also plan to document the project on paper and through video. (You can expect a blog post soon that will explain my project in further detail before April!)

Project Reviews:

Jessica Blelloch (2019):
     Jessica's project, which concerns bone data analysis (with a focus on osteocytes) is really interesting. It's great that she has such a specific focus and that she has an internship so early in her high school career. Her evidence of progress, which includes numerous microscope pictures of bones and a screenshot of her recently completed biology course is pretty impressive. I also appreciate and can relate to her candid confessions, especially when she states that she did not understand a lot of what was covered in the bio course she took, because I had a similar experience while reading the more technical books filled with confusing scientific terminology. To have a tangible project for the May showcase, I suggest compiling what she has learned during her internship into a presentation (such as Google slides) or video that she can have on loop. Overall, I like Jessica's project and wish her good luck!

Katherine Pan (2018):
     Katherine's i2 project is to get her junior HPR level one certification for rocketry. What she has posted so far for her evidence of progress shows a genuine interest in her project, which I appreciate. I like that she posted an interesting video of herself building a rocket since it provides concrete proof of her work. I wish her luck with completing the Bat Ray (the rocket she will use to get her certification) and I suggest that she make a specific long term plan and schedule that breaks up the rocket construction so that it is more manageable. 

Callie Boskin (2017):
     Callie's i2 project went from completing a short film to her position as the school's VEX robotics team manager. As a member of the team, I can totally say that she did a great job and provided some much needed organization to the club. What I really like most about her project is her decision to do something she wanted to do instead of something she felt she was forced to do, which is what i2 is all about. I can't really provide any legitimate constructive criticism. If possible, I would suggest promoting the robotics club to the entire SHCP community (especially to girls) if she chooses to be its manager again next year.

Tuesday, March 8, 2016

The One Where We Launch Even More Rockets (And Talk About Ovens)

"Reactions As Recipes"

Practice Problems:

     This cycle's practice problems were the most challenging ones so far. While the first few (with an excess reactant) were easy enough to understand, the other problems we did later were more confusing. Because there were so many different parts to the problem that I could (and did) mess up on, I struggled with these problems more than previous sets. My biggest problem was that I had no idea that every number in the "C" row had to be multiplied by the reference ratio. I also kept on making a bunch of simple mistakes, which included getting the wrong molar mass of substances with multiple elements and rounding wrong.
__________________________________________________________________________
Ex. of Understood Problems
If 0.25 moles of sodium metal, Na react completely with excess oxygen, O2 gas how many moles of solid sodium oxide, Na2O are produced?
_________________________________________________________________________
Ex. of Challenging Problems
How many liters of hydrogen gas must react with 4.0 grams of nitrogen gas to produce to produce ammonia gas, NH3 with no excess? Assume STP (1 atm and 0oC)
__________________________________________________________________________ 
Activities:

    One of our first activities involved making a mini version of our hydrogen rockets. We had smaller bottles filled with some water. After pouring in a bit of calcium carbide, we capped the bottle with a bandana. The reaction between the water and calcium carbide produced acetylene gas. We could prove this by lighting the bottle, and the small explosion that occurred after showed that the oxygen from the environment reacted with the newly formed acetylene gas .

Our two best mini rocket explosions

     Another activity we did was observe the reaction between potassium nitrate, sucrose, and fire in a "smoke bomb". This reaction creates carbon, the black substance left behind in the jar. 

A slightly sped-up clip of the smoke bomb

     We also placed a piece of magnesium in some hydrogen chloride to learn how to use the ideal gas law equation in stoichiometry. This lab taught us the difference between "limited" and "excess" reactants.
During the reaction, the magnesium in the test tube got warm enough to form steam.

     In an "enlightening" demo that involved dry ice and magnesium, we got to see another reaction that formed carbon. The magnesium was placed in a small hole carved in the dry ice then lit. An extremely bright light shone as we covered the magnesium with another block of dry ice. After we uncovered the magnesium, we found that carbon was formed! Mr. M applied this reaction to global warming, stating that this is one of the possible (albeit insanely expensive) ways to get rid of excess carbon dioxide in the atmosphere.

Two trials of the demo mentioned above, (one in the light, another in the dark)


     As another demo for this cycle, Mr. M made another rocket. However, this one relied on baking soda and vinegar to launch (yes, like the cliche middle school volcano science fair projects). This demo was done to reinforce the process we learned to treat "reactions as recipes" (the problem this demo represented is on the white board in the right of the video).
A brief slow-motion clip of the coke bottle-pens-baking soda-vinegar rocket

     Our final lab for this cycle involved us using 9-volt batteries to ignite steel wool. After burning the steel wool, we left it over the weekend and then poured water over it when we came back. The white iron oxide that formed when we burned the steel wool then turned red when we got it wet, which demonstrated a faster way of forming rust.

A few short clips of the rusting activity


Quiz (To Be Edited After We Get Tests Back):
     The quiz for this cycle wasn't devastatingly difficult, but I did get paranoid while solving the problems on it because of the numerous areas you could make simple mistakes in. The blimp question was especially daunting because of the huge numbers involved since we had only done problems with fairly small numbers before the test. In the end, this was probably the cycle test I spent the most time on, but I still feel confident in what I turned in.

Questions:
  • Does the technique for solving these types of problems change greatly when more than two reactants are present? Do those problems even exist?