Third Answer

EQ: What is the most useful application for extremophiles research in biotechnology?
A3: An application for extremophile research in biotechnology is in improving organic synthesis

1.) Organic synthesis is the construction of organic molecules via organic reactions.  It has been used to generate pharmaceuticals, dyes, cosmetics, high-technology materials, agricultural chemicals, among others. Carbon-carbon bond formation is central to organic synthesis (recall that "organic" indicates that carbon-based molecules are being synthesized).  C-C bond forming reactions are carried out in conditions of high temperature, generally.  (b)


2.) Aldolases have been greatly investigated for their potential in C-C bond formation - fundamental to organic synthesis.  They have not become widely used because of their fast inactivation under industrial conditions (high substrate concentration, elevated temperature, presence of organic solvents).  Aldolases from hyperthermophilic pose a possible solution to these issues, as they are highly thermostable.  DHAP-dependent aldolases (those which use dihydroxyacetone phosphate as a donor) are of particular interest, like those found in Thermus ther- mophilus and Thermo- anaerobacter ethanolicus.  (a)

3.) Laccases are another type of enzyme that have potential in organic synthesis of certain molecules, especially those from Myceliophtora thermophyla - a thermophilic fungus.  

(a) Falcicchio, Pierpaolo; Franssen, Maurice C. R.; Oost, van der John; Wolterink-Van Loo, Suzanne. "DHAP-dependent Aldolases from (Hyper)thermophiles: Biochemistry and Applications." Extremophiles: Life Under Extreme Conditions: Volume 18, Issue 1 (2014-Jan): 1-13. Web. 10 March. 2014.

(b) Nicolaou, K.C. "Organic Synthesis: the Art and Science of Replicating the Molecules of Living Nature and Creating Others Like Them in the Laboratory." Proceedings of the Royal Society: Volume 470, No. 2163 (2014-March). Web. 20 March. 2014.  

(c) Nicotra, Silvia; Cramarossa, Maria Rita; Mucci, Adele; Pagnoni, Ugo Maria; Riva, Sergio; Forti,  Luca. "Biotransformation of resveratrol: synthesis of trans-dehydrodimers catalyzed by laccases from Myceliophtora thermophyla and from Trametes pubescens." Tetrahedron: Volume 60 (2004): 595-600. Web. 20 March. 2014.   
  

Senior Project: The Holiday

1. I read two of the papers that my mentor gave me and went to mentorship on January 3.  I also updated my independent log and began looking into some professors at Cal Poly Pomona and Pomona College who could perhaps be future interviewees of mine.  

2. I know, I know - that's only 10% of my "20 friends", but hey, I was busy tide pooling at Cambria.  In fact, it reminded me of the complex ecologies that exist in our world.  In one little pool, there were hermit crabs fighting over a shell, anemones chilling, a sea snail struggling to reach water with another sea snail attached to its back, a tide pool sculpin flitting about - just the general give and take of nature.
The same exchanges can be seen at the microscopic level.

tide pool sculpin

Also present on those rocks were smudges of oil, perhaps from leaks from the S.S. Jacob Luckenbach - a cargo ship loaded with 457, 000 gallons of bunker fuel.  Cambria marks the southern tip of the Monterey Bay National Marine Sanctuary - governed by tight regulations and home to a marked perfection I've had the privilege of being witness to many times.  THIS is what all coasts should be like.  They don't deserve oil spills.  THIS is why I chose an environmental focus for my senior project.

I couldn't find any photos of my own, so here is the next best thing.  Behold: moonstone beach.

Anywho...
At mentorship, I worked with a community college who was pipetting for her first time.  I showed her how to tap the 96-well plate to pull droplets off the sides of the wells, and operate the UV Vis.  My mentor helped out as well, showing us his wicked pipetting skills and giving tips on how to deal with bubbles (the bubbles were from aspirating the liquid - that means pumping it up and down to mix it (in this case, 'twas a mixture of BSA and sodium azide)).    

Such fashionable pipette tips.  Behold their glory!

Reading "Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits" and "Advantages and Limitations of Quantitative PCR (Q-PCR)-based Approaches in Microbial Ecology" exposed me more to terminology I will become familiar enough with over the course of my project.  It's all about gaining intuition and becoming comfortable with my topic.
There are a few Cal Poly professors who may be of some interest - sort of.  At Pomona College, there's this one professor who has a special interest in the microbial ecology of mud volcanoes.  He might be a future resource... 

3. I would talk to my mentor, and perhaps the aforementioned E.J. Crane of Pomona College.  There's also CalTech (only a few minutes from my house, actually), home to a geobiology department and Victoria J. Orphan (whom my mentor mentioned over the summer).  She's a molecular microbial ecologist, primarily, and another potential interviewee.

EQ

1.   The Rule of Three Criteria:

• Provide a framework for studies (It calls for breadth and depth of research, Is not a yes/no question)
• Takes a stance (Allows you to argue some point, Cannot be a recitation of facts or a list)
•  Format (It is specific, The wording makes sense)

I reviewed the rule of three for writing an EQ.

2.   

     a. What is the most important factor in healthy weight loss?

The criterion that this EQ meets quite well is the second one - as it is very arguable.  Experts debate on how to loose weight healthily, the value of fad diets, etc. The author just needs to decide on whether to focus on the "how" or "what".  How to loose healthily, or what makes a weight loss plan healthy?   

Summation: This EQ meets criterion 2, partly 1, and does not quite meet 3.  

     b.  What is most important to securing a conviction in a criminal investigation?

Perhaps "what" should be specified - maybe "technique".  A who should be included as well.  How can a, I don't know, lawyer best secure a conviction in a criminal investigation, maybe.  

Summation: meets all but last criterion.    

     c. What is most important in creating a hairstyle that best satisfies a customer?

This EQ doesn't seem to meet criterion 1.  "Listen to the customer" seems to be the answer.  The EQ could be worded to allow more wiggle room - perhaps focus on the most important skill for a hair-dresser to have.  

Summation: doesn't meet the criteria.  

     d. How can an Anesthesiologist best treat chronic pain?

This EQ meets the three criteria.  It calls for the author ti research medical papers, secure credible sources, explore opinion and find evidence.  Answering this EQ means settling on an opinion - no doubt an arguable one, as medical method varies out there.  Finally, the EQ is nice and specific.  The profession it involves and the condition being treated is included.  Even the use of the word "treat" adds specificity in a crucial way.  

Summation: meets the rule of 3 criteria

3.  Based on your review of the rule of 3 and your experience with assessing four EQs, please write another draft EQ for your senior project.

•What is the most important advancement in microbiology that extremophile research has facilitated.

•Why should microbiologists continue to research extremophiles?

•What is the most useful application for extremophile research in the context of the world today?

•What is the most important development that extremophiles research has to offer?

The gist of my EQ drafts is "Why extremophiles?".  I just need to get the wording right.

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.  

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.  

2013 2-Hour Presentation Reflections

1.)  The presentations I viewed are as follows.

Gina T. - Consultation Pharmacist
Clara A. - Special Needs Behavioral Consultant
Teo C. - Real Estate
Elijah A. - Marine Biology
Nicole D. - Forensic Photography
Valeria N. - Dance Choreography
Amanda M. - Film Directing
Taylor M. - Scope Surgery
Rachel H. - Deaf Culture
Gohan Q. - Mexican Folk Art
Alissa M. - Microbiology
Hanna S. - Theoretical Physics
Jesus A. - Teaching Algebra
Alexis C. - Violin

2.) I only wonder what school life with the senior project at its center will be like, but only time will tell.  These last two weeks of presentations have given me a pretty wholesome feel for the project and I now know, logistically, what to expect.  My only questions were answered weeks ago by my designated senior inquirer.

3.) Based on what I witnessed during these past two weeks of senior presentations, one of the most important parts of the senior project is the mentorship component.  Most of the presenters decided on an EQ and found three answers to it through their mentors.  For example, Gina Thi found her three answers largely through the expertise of her mentor Robert.  The same can basically be said of every presenter I watched.  My summer mentorship will most likely be the main determining factor for my senior project. 

4.) I am considering doing my senior project on ecology.  Mrs. Cancino first turned me on to ecology -  marine ecology in particular, an interest I put into action by becoming a volunteer at the Aquarium of the Pacific.  I began considering focusing on riparian ecology this year when I read an interesting article on the effects of pharmaceutical residue on biofilms in Californian rivers.  I also found a research opportunity at Oak Crest Institute, one that focuses on freshwater ecology.  Land ecology is also a possibility, taken that I live so near to the Eaton Canyon, found a few plant societies I could join in LA, and met a presenter at Adelante Mujer Latina who was inspiringly passionate about Californian native plant life and community gardens.