Oranges

A few weeks ago, my mentor informed me of an opportunity to attend a research seminar - as a presenter!  I'd be presenting on a research project some of my fellow interns and I helped on over the summer.  I worked with him and a college intern who was the main researcher in the project to put together an abstract.  Early this week, the abstract was accepted!  The event is a Southern California Conference for Undergraduate Research open to undergrads and high schoolers researching anything, really, from engineering to poetry.  It will be held at Whittier College on November 23 - trade show style.  Thank you iPoly :')

Anyway, I'm pretty excited.  In this project, we exposed brine shrimp to varying plant extracts to determine their potency, indicative of biochemical activity and, thus, pharmaceutical potential.  

plant extracts

the SCCUR in all its citrusy goodness

oranges

10 Minutes

The 10 minutes presentation is around the corner and I am not sure what I will be focusing on, actually.

Deciding on an EQ that deals with the application of extremophiles research would allow me to connect the obscurities of microbial ecology in severe settings to the challenges we face today in medicine, technology, and environmental stewardship.  

Then there's technique, which is most relevant to my independent component so far.  Throughout my mentorship, I've learned technique - navigated through protocols, microfuge tubes, tough-to-deposit 4µl (micro liter, no mu-liter) increments of probe.  Delving into the techniques utlized to investigate the complexities of nature as it is - rather than using traditional pure culture - would help me with my I.C. [and, I'll admit, X) impress my mentor].

Both of these are tantalizing... maybe I can do some sort of 2-in-1 deal.  I talked to Pittman briefly and she recommended this route: the how and why.

Nanotubes between bacteria - an interesting form of communication that's just beginning to be studied

Now I just need to further narrow my focus.  Am I covering microbial ecology or extremophiles?  I mean, I could delve into how investigating interactions among microbes would reveal the secrets of global energy cycling, the development of biofilms (incluing those on our teeth known as plaque, and infections) , and the environmental application for this (how we can this knowledge to rid our environment of toxic waste like mercury).  I could also focus on extremophiles specifically, how they are studied and what we can learn from them.  What to choose?!  And what should my EQ be?  Can't it just be "What makes microbes so awesome?"?

Anyway, I've decided that my 10 minute will focus on the fascinating history of extremophiles.  This will hopefully make for an engaging presentation, if executed with enthusiasm and involving fancy pictures.  That's a good place to start, I think.

Research and Working EQ

1.  What is your working EQ?

How can the ecology of microbial communities be better investigated?

or

What biological process has best enabled extremophiles to adapt to the severe environments they inhabit?

2.  What is a possible answer to your working EQ? Please write the answer in thesis format. 

•With metagenomics, genetic material can be recovered directly from the environment being studied, the analysis of which provides insight into the interactions within and biodiversity of a community.  

• With 3-D microscopic cages, microorganisms are deposited into microcommunities that scientists have complete control over and are thus able to study the interactions that develop.    

or

•Horizontal gene transfer (HGT) - the transfer of DNA between microbes - has enabled extremophiles to work together and take advantage of functional genes that allow them to inhabit severe environments.

•DNA repair mechanisms allow extremophiles to constanlty respond to their environments, enabling them to withstand such stresses as extreme heat and radiation. 

3.  What is the most important source you have used that has helped you come up with an answer to your working EQ?

My mentor and his colleague, Marc Baum, have been important, as I was first made aware of the existence of metagenomics by them.  A Primer on Metagenomics, a review I am currenlty reading, also inspired my first answer.  The article 3-D Printed Microscopic Cages Confine Bacteria in Tiny Zoos for the Study of Infections provided my second answer.

The article How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions is most important in determining my answers to my second possibl working EQ.

4.  Who is your mentor, or where are you volunteering, and how does what you are doing relate to your working EQ?

My mentor is Manjula Gunawardana and I am a volunteering at the Oak Crest Institute of Science.  My mentor and his fellow researchers there actually developed a method for extracting DNA from tar samples, overcoming the Taq-inhibitors present in tar that make qPCR - and, thus, the investigation of microbial ecology and biodiversity - so challenging to carry out, usually.  It is their protocol that I will be using in my independent component.  This is relevant to my investigation into the techniques researchers use to assess the ecology and biodiversity of microbial communities.  As for relevance to by second possible EQ, we are using this protocol to look into the functional genes of microbes and thus how they survive in the tar pits they inhabit.  

Independent Component 1 Approval

1.  Describe in detail what you plan to do for your 30 hours.

I plan to participate in a research project at the Oak Crest Institute of Science investigating microbial communities in tar.  While the particulars are not crystal clear yet, I will most likely be repeatedly carrying a tar extraction protocol to isolate the DNA of extremophiles present in the tar.      
I will also be taking "Useful Genetics" - course offered by the University of British Columbia through Coursera.  

2.  Discuss how or what you will do to meet the expectation of showing 30 hours of evidence.

The extraction protocol I mentioned above is a multi-day process, so carrying it out multiple time should fill up my time requirement.  If it does not, I plan to join a science club at Cal Poly (BIO SCI, Microbiology Club), use MIT OpenCourseware to study organic chemistry, and attend any talks at CalTech and Cal Poly that relate to my topic.  These efforts will be evidenced by photos, primarily.  
The genetics course should take me about fours hours a week, not including the assignments I will complete in addition to watching the videos.

3.  And explain how what you will be doing will help you explore your topic in more depth.

I was inspired by this research project to choose microbiology as my topic, actually, as I learned about it during my summer mentorship.  It is a an environmental microbiology project dealing with extremophiles. 
The genetics course will help me understand biology more deeply - in more detail.  It will supplement what I am doing at Oak Crest and help me understand how extremophiles survive the way they do.    

4.  Post a log on the right hand side of your blog near your mentorship log and call it the independent component 1 log.

Done.