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.

Second Interview Questions

1. Who is your mentor and where does he work? 
Manjula Gunawardana is my mentor and he is a senior research scientist at the Oak Crest Institute of Science in Pasadena.

2. What five questions will you ask him about his background?
1. What degrees do you currently hold and where did you acquire them?
2. When and how did you become employed by Oak Crest and why did you decide to continue your work here in particular?
3. When did you become involved in research, how, and what were you working on?

4. What excites you about the research you do?

5. Within microbiology, what fields would you say are the most active, and where do you see microbiology in general heading for in the future?

Tar is Beautiful

I encountered another "first" today, namely my first tar extraction.  We ran through part of the protocol for extracting DNA from tar, and while I can't reveal the details, I can say that it was magical and awesome.  The reason why we do this is so that we can assess the biodiversity of and relationships between the microbes present in the tar.  How do these guys survive in such a hostile environment?  Do they work together?  How biologically diverse is this environment? Here are a few pictures:

 Tar (and my glorious, gloved hand) 

More tar (don't you love how the light sparkles against the black mass?)

  We dumped out leftover liquid nitrogen at the end of the day.  Most people think of Halloween and dippin' dots at the mention of liquid nitrogen, but it can be quite useful in a lab.  For one, it is used in lyophilization - the drying of materials like DNA or liquid culture (bacteria in liquid media) for later use.  What happens is the liquid nitrogen freezes the liquid in the sample, which is placed in a freeze drier and exposed to low pressure and temperatue, which causes the now frozen liquid to enter the gaseous state directly from its solid state (sublimation), migrating from the high pressure of the sample to the low pressure of the surrounding area.  

   

It Has Arrived

As I completed my Blog 5, my father dramatically walked up to me and held out the one and only "Manual of Environmental Microbiology: Third Edition" (the fourth edition is currently being drafted)  and waited cooly for my reaction.  I will admit to "oh my gosh"ing more in that minute than I have in the last week.  Those crisp, white pages.  That table of contents.  The cover is embossed with shining, copper-colored renditions of microbes!

I just thought I should blog on this tremendous event - the acquisition of my first "Manual of..." and textbook with far more text than pictures (as in, WAY more.  I've only found one little picture of bacteria under a fluorescence microscope so far).

Blog 5 Project Reflection and Working EQ

behold... The Pentagon: 

1. Positive Statement: What positive thing happened as a result of what you have completed so far?

     Overall, I'm just more familiar with science and the skills needed to succeed as a scientist.  My mentorship is giving me a taste of research and the nature of the science community, and has revealed the glorious field of microbial ecology to me (I believe environmental microbiology is a subset of it).  I'm beginning to explore an exciting and purposeful field I never would have otherwise, having previously convinced myself that multicellular organisms, expecially marine ones, are far more interesting than archaea and bacteria.  From my interview with Mrs. Matthews, I gathered more inspiration and an encouragement to be adventurous, network, and EXPLORE.  This is the essence of research science.  Aside from all this goodness, I just feel more confident and comfortable with my abilities.  Being trusted and talked to as an equal at Oak Crest, and encouraged by my family, friends, and teachers has convinced me that my lack of self-esteem is not an unsurmountable hurtle.  The future is still one, huge cloud of probablility, but now it's a sort of opalescent, smiling cloud instead of a dark and stormy one.      

2. EQ Content:  Pick a piece of research or your interview.  How has it helped you improve your understanding of your topic?

     My reading of "Microbial Ecology: Fundamentals and Applications" has given me a nice introduction to microbiology and the origins of life on earth.  Life began with progenotes, which split up into bacteria and archaea, and from archaea came eukaryotes, which evolved into us.  What's more, mitochondria and chlorophylls may just be permanent symbionts in eukaryotes, meaning they began as independent prokaryotes but are now reliant on their hosts for survival.  Isn't that awesome?!  Mind you, I haven't taken a close look at microbiology after my first taste of it in Mrs. Matthew's class two years ago, so all this is fairly new and consumingly exciting to me.  I like it that way.  

3. What has worked for you so far in the senior project?

     Gaining access to a lab so early on in my senior project is what is especially working for me.  My mentor and the opportunities he has provided me with have made my mentorship a joy and indispensable learning experience.  I've always been a fairly indecisiveness person, so even having a clear topic and overall direction is a relief to me.  Whether I go with a focus on extremophiles or ecology, a variety of interesting pieces of research lay in wait for me to sink my teeth into, and there exists a noble purpose in both to indulge my more idealistic side.  It's clear to me that senior project has a slew of obstacles up its sleeve, but being sure of my direction will help me get through them.  

4. What hasn't worked so far?  

     Finding current, reliable, satisfyingly detailed works on general information on microbiology has been a challenge.  The textbook I found up at Cal Poly was published in the 1970s, and I haven't been able to get a hold of a copy of "The Manual of Environmental Microbiology", written in 2007.  According to WorldCat, there a few copies floating around in colleges near and far, but none are accessible.  Fortunately for me, I have awesome parents whose priority is my education and have agreed to purchase said book on Amazon - at half off, thanks to our committed relationship with the site. ;D
     I also just need to work on my confidence in the lab and become informed more expediently.  This will take practice, as you can imagine.  On with the chase.  

5. Finding Value:  
5b. What is a potential question you would like to study this year?  (working EQ)

-What is the most useful application for extremophile research?  I'd have to define "useful", "application", and "extremophile research" for that one.  Possible answers are the astrobiological, pharmaceutical, and environmental applications.  
-What has been the most important advance in microbial ecology/environmental microbiology?  I'd have to decide between those two disciplines for this one and define "important" and "advance".  Both fields are fairly new (microbial ecology was first really recognized in the 1970s, I believe) which may narrow my options for answers.  I was thinking of asking a question having to do with the future or history of one of these disciplines.  

5a. What do you plan to do for mentorship?  If you haven't found a mentor yet, then discuss where you are currently looking and who you are talking to to find it.  

I will continue with my unpaid internship at the Oak Crest Institute of Science for my mentorship.