March Update!

Research and Other Good Stuff:

     What's great about the new focus of my EQ (biotech) is that my first answer still holds, as biofuel production is a very hot topic in biotechnology today - and so does my second answer.  I found this great paper on how psychrophiles can be used to improve biofuel production, allowing that lower temperatures be used.  Psychrophilic enzymes are very flexible, thermolabile, and can be inactivated with heat if need be.  Quite fascinating.  I've also been looking into purple membranes and organic synthesis (my third answer).
    The systems biology class I shall be taking via Coursera for my independent component began today. Take a look.  It's been challenge finding an online course related to my EQ, but this one looks promising.  It should familiarize me with how the data is collected that backs the papers I've been reading, familiarizing me with some terms that, knowing, will make my project run smoother, and prepare me for college for sure.  If I am to be on top and snag an internship as a freshman, I need to be able to speak science speak and prove my worth to professors involved in projects that interest me.   What I like about this course is that it involves paper-reading and lots of discussions to demystify those papers - which I shall appreciate greatly.  As much practice as I've had in reading paper, and as far as I've come in understanding their organization and jargon, I still feel I need more improvement in extracting as much value out of them as possible.

Huzzah.

This post is long, so here's some distraction along the way!  (my amazing buddy, Kaia/Kitty)

Interview 4:

Wednesday was great.  My mom dropped me off at the Seaver Biology Building at Pomona College at 3:30PM.

Brian Fung Photography

I spent the next twenty five minutes reading posters gracing the walls of the gorgeous place...

My hand must have been shaking a bit.

...then descended a flight of stairs into the basement, where I learned from a wild college professor in his natural environment that I was in the wrong Seaver Biology building.

(in his grey cloak and hat as he sat upon Collegefax, using an ornate staff to point the way) "Ascend those stairs a-yonder, past the Exit for Dire Situations, through the oaken door, down the spiral staircase to Tronjheim, and you shall be within a league of he whom you seek."

Within a minute, I was running past a door into a sunlit space lined with open doors, through some of which I could see professors talking to their curious students, and through others glimmered lab equipment.  Within five minutes, I was sitting in the office of E.J. Crane - a chemistry professor at Pomona College - interviewing him.

Behold, the right Seaver Biology Building...

...and the "spiral" staircase leading down to the well-lit basement.

Why post this in such a dramatic and descriptive way, you ask?  Well, this meeting was tremendous in many ways.  For one, I talked to a professor I may one day be taking a class with, as a student at a college I've been praying and hoping I'd get into - Pomona College!  It also signifies how iPoly has taught me to venture out of my comfort zone and grab at opportunities with the voracious fervor of a googolplex of stars.  Furthermore, it made me realize how far I've come in senior project, that I should be able to hold a conversation with a man who's life it dedicated to a field I'm only just scraping the magical membrane of.

Anyway, enough with the emotional, "I've come so far!" shtuff.  Our conversation swerved into such subjects as purple membranes, the Salton Sea, mud volcanoes, electrochemistry,  and the epic rivalry between the the Lord of the West and the Sire of the East:

• There are these halophiles that have purple membranes.  To live in the salty environments they favor, these feisty organisms often use a method in which they constantly pump out sodium - which takes lots of ATP, which they have evolved to generate using light.

Thank you, Google maps.  Along those shores lay mud volcanoes.

• The Salton Sea is located in the Coachella and Imperial Valleys and was created in the early 1900s when the Colorado River emptied into the Salton sink, and has increased in saltiness since (hence the purple-membraned halophiles north of the Sea).  Mr. Crane's lab investigates the anaerobes living in mud volcanoes along the Sea's shores.  Check it out.  Some of these guys may degrade hydrocarbons - future bioremedation application imminent.  You see, usually, microbes use up oxygen when degrading hydrocarbons, and so there lies the danger of the creation of dead zones should these little organisms be released into the sea to clean up oil spills.  Anaerobes don't use oxygen (those that Crane has investigated use sulphur), and so this danger is nonexistent.

Yum. 

• Electromchemistry is cool.  "It involves a lot of polishing" to paraphrase Crane, and those in his lab make all of the necessary electrodes themselves.  Pretty much, this science is chemistry involving electricity.  Surprise!  What happens in chemicals sandwiched between an electrode and electrolyte?  Think batteries in Mr. Pang's class.  

• Ah yes, epic rivalry.  The field of geomicrobiology owes its growth, according to Crane and, presumably, others, to two scientists - one of the West and one of the East of the USA - who have been one-upping one another for a very long time.  I will be reading a few papers written by the former - a Dr. Kenneth Nealson -  actually, and shall report on the nature of geomicrobiology once I get to them (though the name implies a lot...).  It's interesting how victim science is to such human tendencies, despite it being a field that prides itself on objectivity.  In this case, though, it wound up more as the victor than the victim (notice the poetic alliteration I used there).

I also learned of another answer to my EQ - fuel cells based on redox reactions!  Another vein of research lies before me.  I really need to get going on my independent RCs.  This week shall indeed be a busy one...

In summation it was wildly productive, over 40 minutes long interview, and this month has been a-okay.

I bid farewell to the door I had a really hard time finding at the
end of the interview...it's a maze down there...

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.   
  

Fourth Interview Questions

-What are the main mechanisms that researchers have found that enable extremophiles to persist in the environments they do?
-What enzymes specific to extremophiles have been of particular interest in biotechnology lately?
-What specific methods have researchers seen thermophiles use? Psychrophiles? Acidophiles? Halophiles?
-What methods do extremophiles use in protecting their proteins that differ from those used in protecting their genetic material?
-How can DNA and protein repair mechanisms found in most extremophiles be utilized in biotechnology?
-What are the main divisions of biotechnology at the forefront today?
-Which divisions can new developments in extremophile research benefit the most?
-What challenges are biomedical researchers facing that could be addressed with extremophile research?
-How can halophiles be used in biofuel generation and bioremediation?
-What challenges face industrial biotechnology?
-What are purple-membrane films?
-What are their biotechnological uses?
-How are they obtained from halophiles?
-What biotechnological applications for extremophiles that are resistant to radioactivity exist or are being developed?
-How exactly is Deinococcus radiodurans being used in bioremediation?
-What biotechnologies involve extremely low temperatures?
-Have there been any advancements in bioinformatics that involve or could involve extremophiles?
-How can extremophiles be used for long-term information storage in the future?
-How can the solvent tolerance of certain extremophiles be used in improving hospital sanitation?
-How are extremophiles being utilized in the development of antibiotics and diagnostic tools?
-How extremozymes improve food science, particularly wine and cheese making?