Yet Another Update

    On Tuesday, I met with Dr. Gaines, the chair of the geology department at Pomona College, at 1:30PM.  Mom dropped me off and, as with Mr. Crane's office a few weeks ago, I found myself frantically searching for Edmunds Hall.  Finally, I ended up at the front of the hall and made my way up to the geology department.  Dr. Gaines proceeded to walk me around the department,  introducing me to faculty, students, and iron reducing microbes alike.

Behold - Edmunds Hall

     The earth has a long and tumultuous story to tell, and it is up to the geologist to read that story.  This entails going out into the field, collecting samples, and manipulating them to extract the most meaning out of them.  To put it simply, this requires that rocks ground and split into factions according to characteristics like magnetism.  Speaking - or, rather, writing - of magnetism, Gaines showed me this super cool...thing in the basement.  I don't recall what it is called and I have yet to Google it (funny how "google" has replaced "look up"), but what it does is strip samples of magnetic field they've caught over time until the original field is recovered.  You see, when a rock comes into being, its structure aligns latitudinally with the earth's magnetic field.  By reading this alignment, geologists can tell where a rock originally was.  In this way, they can tell how parts of the earth have shifted over timing, drawing a picture of our world as various points in time.
     Pretty cool, huh?
     Gaines also showed me this small vial containing iron-embedded clay, lactate rich media and a culture of iron-reducing anaerobes, which is kept in a cabinet, waiting.  The point of this arrangement is to gage the iron-reducing capacity of these little guys.  I'm not sure what microbes these were exactly, but they are like the Shewanell that Crane mentioned and which Kenneth Nealson specializes in.  Metal-resistance has proven to be quite valuable in radioactive waste processing, as with a study that Crane referenced in which the Shewanella were more able to immobilize radioactive compounds than Deinoccocus radiodurans - known for being THE radioactivity-resistant microbe - because of its metal-resistance.

This post needed another photo.  Behold - the lunar eclipse that occurred a week ago!  
Actually, GIS is a geological tool that can used to determine the composition of
such heavenly bodies as our moon and Saturn's moon - Titan.  

     In the aforementioned basement lay mechanisms for grinding down rock into super-fine (fresh, and fly) dust, whence it can be melted down into glass, ground, melted, ground, melted, until the sample is adequately homogenous.  Then, it can be placed in an x-ray spectrometer used to determines how much of certain elements are present within the sample.  With a diamond pencil, classifying information is inscribed onto each glass disc and it is stored away.
     By the end of the tour, Gaines had given me a nice taste of geology, a paper he wrote a few years ago on a main cause for the Cambrian explosion (fascinating), and an acquaintance with members of the department.  I hope to take an intro to geology course at Pomona.  Will I become a geologist?  Time will tell.  Gaines reminded me time and time again to "keep an open mind".  Freshman year will be about laying down my foundation (chemistry, physics, biology, math) as well as exploring my interests.  At Pomona, I can take as many leaps as I want with the assurance that a safety net will be there to catch me.

Exit Interview

1.) What is your essential question and answers?  What is your best answer and why?

EQ: What is the most useful application for extremophiles research?

1st: Extremophile research can be used to improve biofuel production, thus addressing fossil fuel depletion.

2nd Answer: A useful application for extremophiles research in biotechnology is in bioremediation developments.

3rd Answer: An application for extremophile research in biotechnology is in improving organic synthesis.

My 1st answer is my best answer. It is the most "useful" of the applications I've explored in that it addresses an immediate and pressing issue - the energy crisis. Furthermore, biofuel synthesis is a hot topic in biotechnology, being feverishly researched and of great interest to many parties beside the scientific community. Extremophiles, of all agents in, are the best option we have to improve current biofuel synthesis processes and develop new ones.

2.) What process did you take to arrive at this answer?

It began with Google Scholar.  Late last year (as in, 2013), I activated a Google Scholar Alert for "extremophiles" - meaning that the engine would send me papers on extremophiles each week.  When time permitted, I'd peruse through the titles of these visitors to my inbox a take note of the their themes.  One theme I found coming up again and again was biofuels - inciting me to set up an Alert on biofuels.  I began reading these papers and looking into how biofuels are made and what problems face the major forms of synthesis used today and in development.  The more I looked into it, the more I came to like this answer.  I found robust research, solid reasons, and I happen to deeply care about the energy crisis facing today's world.  Solar and wind energy are long term - the world needs an intermediate step.  

(3) What problems did you face?  How did you resolve them?

Sifting through the plethora of sources has proved to be troublesome.  At times, I felt quite inundated - a victim of information overload.  The jargon proved to be a challenge as well.  Transesterification, lignocellulose, E factor - becoming familiar with these alien but common terms in the subject I was exploring constituted much of the battle.  Reviews were my best bet, but I could not seem to find many.  I decided to leave my qualms behind and just READ.  Also, I found that NCBI includes a paper search engine, on which there is an option to search ONLY REVIEWS.  I should have known!  I'd come to associate NCBI with papers I'd have to pay to access and, belatedly, integrated it into my research toolbox.  Taking "Intro to Systems Biology" - the first assignment of which involved writing about databases - and exploring BLAST at my mentorship helped me to finally embrace the full potential of NCBI.  
I also struggled with defining "useful" and "important" in my EQ.  This took some thought, ruminating on my senior project.  I decided to base usefulness on relevance and immediacy.  Importance came down to ease of finding research.  Biofuel synthesis is the hot topic in biotechnology and is under rapid development.  Extremophiles will play a huge role in this.  

(4) What are the two most significant sources you used to answer your essential question and why?

The following functioned as guides to this answer, forming a basis from which I could branch out to other, more specific sources.  The first, "Genomic Evaluation of Thermoanaerobacter spp. for the Construction of Designer Co-Cultures to Improve Lignocellulosic Biofuel Production.", a paper by  TJ Verbeke et. al and published in PLoS ONE in 2014, provided me with an overview of how microbes are used in biofuel synthesis and what challenges remain which must be overcome to replace fossil fuels with biofuels.  The second, "Molecular Adaptation Mechanisms Employed by Ethanologenic Bacteria in Response to Lignocellulose-derived Inhibitory Compounds" Omodele Ibraheem and Bongani K. Ndimba and published in the International Journal of Biological Sciences in 2013, focused on lignocellulose derived biofuels, which is where extremophiles seem to be the most useful.  It details the specific challenges facing this development, giving me an idea of how the unique capabilities of extremophiles could be used to address them.  From this basis, I was able to intelligently seek out specific examples supporting my answer, looking into thermopiles and halophiles in particular.  

Independent Component 2

LITERAL:

a.) I, Vanessa Machuca, affirm that I have almost completed my independent component which represents nearly 30 hours of work.  I have yet to complete my independent component 2, as both classes end past tomorrow's due date, but will report on my final grade in each.

b.)  I am taking this Systems Biology course via Coursera.  Ravi Iyengar, PhD of the Icahn School of Medicine at Mount Sinai teaches the course, which he designed along with Evren Azeloglu, PhD, Jens Hansen, MD, and Joseph Goldfarb, PhD.  The course involves reading multiple papers covering such topics as differential equations in chemistry and the basics of systems biology.   I did a research check on one such paper recently:
Iyengar, Ravi. "Lecture 2: Quantitative Representation of Enzymes and Receptor Action." Introduction to Systems Biology. Icahn School of Medicine at Mount Sinai (online course). 4 April 2014. Web.
The CHM 121 class I am taking at Cal Poly is taught by Dr. Gagik Labadzyhan. I refer to my notes, course documents he posts on Blackboard, and the course textbook - "Chemistry" (very creative) by John E. Murry and Robert C. Fay, to complete the homework.

c.) My independent component 2 log is posted to the right.

d.)  So far, I have watched and taken notes on videos for the Systems Biology course, while also diving into some of the required reading.  For the Cal Poly chemistry class, I attend and take notes during a one hour class on Monday, Wednesday, and Friday and complete homework on Mastering Chemistry.

INTERPRETIVE and APPLIED: 

"Introduction to Systems Biology" has, so far, helped me gain a deeper understanding of life at the molecular level.  What I've found as I've gathered and read research is that there are certain bits of intuition I need to develop in order to better appreciate and learn from them.  How do extremophiels interact with their respective environments at the most basic level?  How are these interaction analyzed and quantified?  I now understand how an organism can have a range of capabilities but only display a few, and how outside stimuli are translated into a physical response in cells.  In bioremediation, understanding these interaction is extremely important.  How can we be sure that a microbe we place in an environment to remedy it will integrate well into the the native microbial ecosystem?  How are substrates process in biofuel synthesis?  Something else that I've gained from taking this course so far is to see life as information.  We all information, split up into compartments - flows of information.  Extremophiles just so happen to hold information we can use to develop biotechnology further.

Each video is quite lengthy - averaging about 15 minutes each - and I often pause them to take notes, hence the hour I recording it having taken me to complete each.  The assigned reading and peer assignments take a few hours each.  

Here are four sample pages worth of notes I took for the Systems Biology course.

The other part of my independent component is the CHM 121 class I am taking at Cal Poly.  My project has become largely a chemistry-based one - especially with my third answer involving organic synthesis.  In fact, it was investigated by third answer that made me realize my shortage of chemistry prowess.  Taking this course refreshes what Pang taught us juniors last year and forces me to "think chemistry".  Reading papers on organic synthesis with this mindset makes them much more digestible, and I know I will better equipped to explain the concept - especial when it come to C-C bond formation - for my senior project presentation thank to this class.

Dr. Labadyhan posts a plethora of class materials on Blackboard.

Behold, the homework I have completed thus far.
I aim to get that percent up to 100% (which is  possible, actually).

So fierce, So Fresh, So Fly

Mentorship:

Last Thursday, I went to mentorship.

You see, I've begun taking a MoWeTh Chemistry 121 class at Cal Poly, so now mentorship shall take place on either Tuesday or Thursday.  Upon talking to a certain inter at Oak Crest, though, it has been decided that I shall only come on Thursdays.  You see, from 1:30PM to 6:00PM on TuTh, interesting things happen at the lab, which will more likely than not last at least 4 hours.  With everything going on, tackling this beast two times a week is a bit much, so I shall just tackle it once a week.

By "beast", I mean RNA extraction from tar samples.  The project is fully underway now.  In fact, last Thursday, I helped the intern out in finding primers for genes coding for certain cell functions characterizing a thriving population of microbes.  What in the world am I talking about, you ask?

Let me remind of this tar extraction business and how it works:
1.) Collect tar samples
2.)Extract RNA with fancy, magical protocol
3.)Convert to cDNA and run PCR on genetic material
4.) Analyze.

Recall that PCR stands for polymerase chain reaction and is used to amplify DNA - meaning that the DNA multiplies into many times more than what you began with.  You don't just amplify ALL of the DNA, though - you must choose certain genes to amplify.  In fact, PCR tells us whether a gene we are interested in is there or not.  What we are looking for in the tar extraction project (which I shall now call TEP), is genes coding for functional proteins that indicate whether microbes in the tar are thriving or not - like cell division.

The computer I used to work my magic, and some researchers in the Fish Tank.
That guy to the left has amazing facial hair...

A primer is a a strand of nucleic acid that specifies a certain gene.  When mixed up with the genetic material from a sample and placed through PCR, it acts as a sign saying "Hey, polymerase, amplify this gene right here!".  You can make your own primer Primer-BLAST, or use one made by some other lab.  This requires that you sift through paper upon paper, searching for the best primer - and that is what I did on Thursday.

I found of bunch of primers and ran them through Nucleotide-BLAST to see how general they are.  BLAST tells us how what organisms the primer was found in, and according to which papers.  Ideally, we wanted a primer found in E. coli, since that would mean that it is a general primer found in many organisms.

What we do, then, is run PCR on the cDNA and analyze our results.  Are these organisms still multiplying?  If so, they must be thriving.  Upon establishing that, we can continue to investigate these "bugs" as Dr. Crane puts it.  HOW are they thriving?  What unique proteins do they produce?

Independent Component 2:

I'm kind of behind on that Systems Biology class, but am frantically catching up!  There is so much complexity at the cellular level.  I mean, look at this:

And that's a fairly simple one!

Life is filled with self-sameness across scales.  You see it in snowflakes, economics, and here in biological relationships, whether it be in a network or a food web.

Other:

On Monday, I attend the Admitted Students Day at Pomona College - and finally mailed my acceptance of their offer of admission the next day!  It was a fantastic day - and I made two friends.  What a relief.  The aspect of college I had been the most nervous about was the prospect of having to make new friends...

Anyway, I talked to a plethora of interesting people with lots of information to give.  The geology department representative we're pretty cool and one, the chair of the department, actually, agreed to give me a tour of the facilities at some point before early May.  Hopefully, that shall happen next week, but we shall see.

It's funny: if not for senior project, I would not be in this position.  I would not have known about geomicrobiology or Kenneth Nealson, and perhaps would not have engaged Dr. Gaines enough for him to give me this amazing opportunity.  I wouldn't have felt confident enough to approach the molecular biology table, or even the PPE table.  Senior project - and iPoly in general, actually - has allowed me to find a level of comfort, of courage, of audacity I don't think I would have achieved elsewhere.

For me, it wasn't the candy sales that these last three four have prepared me for but, rather, this Monday.  See you next year, Pomona College.

The mascot of Pomona College - the majestic sagehen.
So fierce, so fresh, so fly.

"You're mom is really nice."

     I shall be taking chemistry at Cal Poly this quarter - CHM 121: General Chemistry, to be exact.  Huzzah.  Good-bye for now, math.  I shall revisit you frequently, though, I promise.  Taking this class will prepare me to enter a higher chemistry class at Pomona and allow me to better understand the papers I am reading for senior project.  I hadn't anticipated how chemistry and molecular biology-based the answers to my EQs would end up being - all this talk of synthesizing organic macromolecules, transesterifying biomass in biodiesel production, and redox-based fuel cells.

It can be a bit lofty at times.  

Oh Bird of Knowledge, give me a feather.

     For that reason, this chemistry class shall be a part of my independent component, accompanying the systems biology class I am taking on Coursera.  It's going well, by the way.  I'm almost done with the first assignment, which entails that I give short answers to questions regarding short papers on biology databases like PubMed, Gene, and UniProt.  The videos this week covered what systems biology, bottom-up and top-down approaches to viewing a system, and doe detail on cycle adenosine monophosphate (cAMP) and its role in certain signaling pathways.  

     You see, cells and constantly responding to stimuli that one can think of as new information - just as us humans respond to new things were learn.  If I learn that one college is giving me more financial aid than another, I will act accordingly.  In order for the cell to respond, though, that information must be translated into intercellular language that components in the cell can understand.  This is done via signaling pathways wherein information is passed on down the line in a "bucket brigade" manner - like a bucket of water passed form hand to hand until it reaches the fire.  This process is called "transduction" and is a hot topic in biochemistry, according to this cool blog post: http://sandwalk.blogspot.com/2007/05/regulating-glycogen-metabolism.html.  

This shows the path from hormone to cellular response,
found and explained more thoroughly on the blog I mentioned. 

     This is how hormones affect our moods.  The hormone binds to a receptor on the cell, the signal goes down a signaling pathway until it is an an intracellularly (meaning "inside cell") understandable form, whence it affects a physiological function and elicits the results it is meant to.

     I shall attend my first class with this professor (having tried to add myself to another professor's class at the time Labadzhyan's class took place on Wednesday) tomorrow at 2:00PM.  Mentorship shall now have to take place on Tuesdays and Thursdays.  Things are looking good - 'tis now a matter of juggling core, Cal Poly, Coursera, my independent endeavors regarding differential equations, and getting the paperwork in for college and scholarships popping up.  When May rolls around, classes at Pasadena Community College will open up, so that shall add another scintillating layer to my life.  Gosh, it's all moving so quickly - kind of hard to not get swallowed by "the machine" (On the Road reference - that book is quite a trip, and not just figuratively).  

   Mom, Robert and I went to the bookstore together to buy my chem. book.  As she paid for it, the cashier guy turned to me and said, "You're mom is really nice."  As we walked away, he iterated his comment with a smile.  Yes, she's awesome, actually.  I realize more and more each week how she's much of why I am who I am - her and my Dad.

As I near graduation, I find that realizations like these are important.