One day more...

...until the the first day of the last week of school (whether you consider that as being Sunday or Monday depends on what you consider "one day" being taking into account the time I posted this as well as what you consider to be the first day of each week - so that is open to interpretation).

I am right now sitting at the dining room table, drinking cinnamon coffee and listening to jazz, ruminating these last four years.  The slope of a line can be begotten by this formula:

Pretty much, the difference between the first point and last point.  This formula could be applied to my high school experience.  I can look at how I began - on that first day of school - and compare it to how I am now and find the slope of my growth.  It is most definitely a positive slope.

That was a less illustrative analogy that I hoped for it to be.  

Okay, to get the point - that I've grown a lot and thank iPoly for a great many things - across, I will define the first point and the last point.

First Point (first day of school):

I was distrustful of people my age, believing them to be foul-mouthed, sneaky creatures.  Around the end of first semester, I was determined to be a Loner, thus preserving my innocence and calm of mind.  My self esteem was a bit low and ordering things on my own usually proved to be an ordeal.  Those cashiers, man - fierce and demonic organisms.  Social gatherings and generally mixing with people I didn't know were uncomfortable necessities to me.  I was pretty set on physical therapy or naturopathy as the make-up of my future.  There's this college in Florida that has a naturopathy major.  UCLA is ideal, though.  I mean, it's UCLA.      

Ah, Passport Approved...

Last Point:

People my age are foul-mouthed, sneaky creatures - and that's okay!  It adds zest to the goings on of my everyday.  iPoly has taught me to deal with stress by having a sense of humor.  That nearly-all-nighter during Passport Approved was pretty funny, come to think of it.  Whenever I look back on it, I always laugh.  :)  I've come to realize that cashiers are humans like me and are there to make money and, some, to get a promotion.  They are not out to sabotage me!  Meeting new people is fun, but hanging out with any group of people from this Class of 2014 is always funner.  Academic shtuff is still a joy to me - but I'm not so sure what I will focus on.  I like my humanities - morals, literature, organizational goodness - as well as STEM - molecular biology, ecology, marine biology, physics, nano tech, green chemistry, engineering, maths.  I shall be going to Pomona College - chirp chirp - which I feel is way better than UCLA. X)  I now know how to appreciate a research paper, make an effective pie chart, organize a research presentation poster, use a micropipette, "network", shake hands properly, use Pixlr, fold a tri-fold brochure, play badminton, use a piñata as a presentation board, among other excellent things.  Risks are many times fruitful, and every experience is an opportunity.  Thanks iPoly.   

Behold, a delicious pie chart.

This post has a lots of "I" in it, which makes me uncomfortable.  That's okay, though.  This is blog is about me anyway, right?  I mean, it's called "vmachucan..."... (whoa, double ellipses).  Am I sad to see my four years come to an "end"?  YES.  I try not to be, telling myself that there is no "end", just a continuation, that many of my friends are staying in the area.  I won't see them as often, though, and some are going out of state!  But hey, we'll stay in touch, and I know I'll be coming back to iPoly.

Where am I now?

I've ended my mentorship, but Manji made me promise that I'd stay in touch with and update him on any significant developments.  I may start doing research at Pomona over the summer - perhaps on nano materials.  I'll find out if I've been accepted to the program this Monday.  I could have chosen a research project that mirrors my senior project - with Crane, on carbonoclastic anaerobes - but thought I'd choose something fresh and relevant to my blooming interest in the nano world.  At Pomona, I hope to hone my chess skills and maybe get into fencing, volunteer at the organic garden, do as much research as early on as possible, join the anti-fracking campaign, work on establishing a stronger connection between Pomona and iPoly, among other things.  In particular, I'll look into connecting the chess clubs, diversity efforts, and physics goodness at both schools.  Hopefully these efforts will bear fruit.   

So, I'm not saying "goodbye" to iPoly.  Rather, I'm saying "see you soon".  

This post is too sad - so here's a photo of my amazing dog and good friend: Kaia.

      

Senior Project Reflection

(1) Positive Statement

What are you most proud of in your Block Presentation and/or your senior project? Why?

I am most proud of my activity.  My audience seemed to really enjoy it - a few attested to this afterward - and I feel I made a clear connection between it and not only my best answer, but all three of my answers.  What's more, only one beaker was broken (and by a senior nonetheless)!  For it, I had them make apple juice from applesauce - some with the aid of pectinase, some with preheated pectinase, and some without any pectinase at all.  As we waited for the juice to filter into the graduated cylinders, we came up with a hypothesis as a class and, once they wrote the volume of juice their respective batches of applesauce yielded on the board and calculated the average for each type of batch, answer questions regarding both the experiment and my best answer.  I was impressed at how many answered correctly - they were listening!  A few juniors and seniors congratulated me on the quality on my presentation after, and one even said she understood everything I said!  That's a big deal for me.  My main worries were my activity and the challenge of explaining the complexity of my project.
As for senior project in general, I am proud of my audacity.  Going into Freshman, I will admit to having been "afraid of cashiers."  Standing in line at a Starbucks was a stressful experience for me, and stepping up to the counter, mumbling over my order was painful at times.  I've come a long way since then - learned to see each day, each person I meet, each coming experience as an opportunity.  Going to mentorship, seeking out interviewees, presenting at SCCUR - these were all adventures out of comfort zone and into the wild stretches of the science community and of my professional future.  It was a blast.

(2) Questions to Consider

a.     What assessment would you give yourself on your Block Presentation (self-assessment)?

P+      

b.     What assessment would you give yourself on your overall senior project (self-assessment)?

AE      

(3) What worked for you in your senior project?

What worked in my senior project...I feel I was able to score some very solid research, which added more than a helping of credibility to my iSearch paper, my presentation, and other tasks thrown at me during senior project.  My interviewees were also a great help.  Matthews gave me an insight into science, feeding me more encouragement and warning.  Manji painted the bigger picture of research for me, pulling from his years of experience to generate overreaching conclusions.  Mogul opened my eyes to another side of microbiology - astrobiology, soil crusts, etc. - sharing his opinions on my possible answers at the time.  Finally, Crane threw all sorts of information at me - from the fascinating history of the Salton Sea, to purple membranes, to Shewanella (which I mentioned in my second answer) - and helped me solidify my best answer as well as begin exploring branches of my topic which I might be interested in tasting.  I look forward to taking a class with him next at Pomona College.

(4) (What didn't work) If you had a time machine, what would have you done differently to improve your senior project if you could go back in time?

I would have done more research actually.  Yes, everything I used was quality, but I don't believe I took enough advantage of the tools before me - of Plos One, the Cal Poly database, Google Scholar, Scitable, Research Gate, NCBI.  Part of me want to continue research on my senior project over these next few weeks to find the ultimate answer...part of me (the other part wants to do maths, yoga, art, catching up on book series [Dune, The Vampire Chronicles, Heroes of Olympus, Hitchhiker's Guide) and get into making raw vegan desserts instead).  I would have prepared for my presentation more - a common sentiment among us iPolians - and sought out more interviewers.  Senior project has taught me that it doesn't hurt to ask - whether for clarification on a concept, how to autoclave tip boxes (my grand mess up), or for an interview with even the most highly regarded of people.  I would love to have interviewed Kenneth Nealson, for example, considered by many to many to be the father of geomicrobiology and premier champion of Shewanella.

(5) Finding Value

How has the senior project been helpful to you in your future endeavors?   Be specific and use examples.

Senior Project has made me closer to fearlessness than I've ever been, I feel.  Because of it, I've gained experience in research, presenting that research at an event like SCCUR, interviewing those with decades more experience than me, seeking out answers in as many places as I can find them.  There's one opportunity in particular that has popped up.  Last week, I was invited to apply for the High Achiever's Program (HAP) at Pomona College in which I'd spend four all-expense paid weeks on campus taking a writing and math course and doing research in a project of my choice mentored by the professor in charge of it - by an expert.  I'd receive a $3000 and $500 for books, as well as connections for the rest of my four years at Pomona.  The projects are all quite exciting.  One involves exploring the aerodynamics of seeds, another stochastic modeling of cell division, another - and this is with Crane - on metal reducing microbes, and yet another on revertant - immortal - hydra.  I will be submitting my application shortly, spurring the wait for notification of my acceptance or denial on June 2nd.  Because of senior project, I feel absolutely comfortable applying for a program like this, and have that bit of experience to cite in my application.
What I will "be" when I grow shall ever be a mystery.  I do not fear what is to come.  The classes I take, professors I befriend, connections I make will all carry me somewhere, guided by my personal compass and a curiosity I look forward to feeding.  

Mentorship

Literal

·     Done.

·     Manjula Gunawardana

      (626) 817-0883

      m.gunawardana@oak-crest.org

Interpretive

I gained insight into science in general - the thought process behind, the community engaged in it, the challenges it poses.  Manji often gave me pearls of wisdom I will carry with me into college and the lab, and his positivity, his eagerness to turn an obstacle into a learning experience inspires me.  The interns and employees I met showed me that there are many roads to success, that it is never too late to follow a passion.  Some of them just discovered a love for science, years into college.  Most are going to PCC with the hopes of transferring into a UC.  Before Oak Crest, I was under the impression that to be successful, one has to enter the "best" college, and right after high school.  This is not so!  Opportunity lies everywhere.  

My experience here also aided in my college choice.  I was in love with Pomona College as junior, but continually heard how the UCs are ideal for research, how going to a UC would better my chances of getting into my graduate school of choice.  My mentor and some interns at Oak Crest told me otherwise, opening my eyes to the benefits of a small college like Pomona in research - less competition, more one-on-one professor-to-student learning, close-knit environment.  Furthermore, Pomona is solely undergraduate - so I won't be competing with graduate students for spots in labs.

Overall, I feel I have a greater understanding of what it takes to succeed in science.  It takes social capability, a forward-thinking mindset, tireless inquisitiveness, and perseverance.  There's more to that list, but those are the four I've found to be most important.

Applied

I found my second and third answer through mentorship.  When Manji first proposed the tar extraction project to me, we discussed the long-term goal of it - to isolate functional genes coding for oil-degrading proteins.  Why?  To apply to bioremediation of course!  Running through the extraction protocol I realized how hard it is to extract DNA from tar and looked up reason why, chancing upon keywords that would later help me with research on bioremediation.  Quite a bit of pharmaceutical work is done at Oak Crest, inspiring me to venture outside of environmental applications for extremophile research into organic synthesis of pharmaceuticals in particular.  When I asked for details on this, Manji pretty much gave me the reasons for my answer in a nutshell, guiding the relevant potion of my iSearch paper.  Mentorship helped me with a my basic knowledge as well, with gathering intuition and getting a feel for key concepts in searching for my answers - the basics of needs and functions of the average microbe, enzymes and how they work - I know these seem simple, but embracing a broader picture of my topic, of biology, of how things work in general helped me "logic through" my EQ and the answers to it.

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.  

  

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?

February

I've changed the focus of my EQ to something broader - biotechnology.  This will allow me to look at biomedical and industrial application, which relates more to my mentorship and will give me some wiggle room with regard to answer development.  Any process involving high of low temperatures, pH - any "extreme" condition could use some extremophile research to guide its advancement.  

Let us visit Oak Crest.

Oak Crest will be welcoming new members soon - parasitic, nefarious members, namely Plasmodium falciparum.  What is Plasmodium falciparum, you ask?  It is the parasites found in the guts of mosquitos, producing malaria and using mosquitos as the vector for the virus.

Plasmodium falciparum

We will be exposing the Plasmodium to the natural products, the ones we used in the shrimp bioassay I presented on in SCCUR.  A few weeks ago, my mentor asked that I help with the task of helping find a proper assay to asses these parasites' response to the extracts, one that can be done in a high-throughput fashion, that is simple and inexpensive, giving me access to a plethora of papers to read to get started on the search.  So far, I've found that there are a few main methods widely used in determining the inhibitory concentration of antimalarials that can be used in the natural products project:

-isotope: radioactive substance uptake

-WHO: expose parasites to shtuff, wait a bit, visually count those alive and dead (like shrimp bioassay) 

-ELISA: gage parasite reaction to substance by measuring amount of certain proteins (reflective of parasite population health) produced (like HDPR2)
-SYBR Green I fluorescence assay: stain the parasites, measure how much light produced and use that to gage the number of parasite alive

Aside from this malaria business, some exciting drug-release work has been going, entailing that I press and fill many a pod.  I've believe I've explained the process already, so here is the picture to go along with it.  Behold, the pellet press:

Today, I read more papers and inputed some of what I found onto an excel sheet, then attended a meeting in which Manji went over the current projects with a few interns, an employee and me.  I will be working with two interns in particular on the tar extraction project.  The lab is such a bustling place!  I am amazed at how Manji can keep track of much of what goes on, at the energy here, the breadth of the research done, the constant change.

Speaking of constant change, Mr. Estrada has lent me his differential equation textbook.

With it, I shall prepare for the differential equations class I plan on taking at Cal Poly.  From what I've heard, it can be a beast.  Differential equations, according to a math professor I talked to a week ago, is the most applicable to biology of the math topics I now have the prerequisite to take a class for.  This won't be my independent component, just a little something to help me prepare for college.  I'll even keep a look out for those pesky equations around the lab...

the view from building 3, where the interview took place

Speaking of Cal Poly, I interview a professor there.  He was pretty chill, this Dr. Rakesh Mogul, and gave me an interesting possible answer for my EQ - well, more geared toward my original EQ.  From what he told me, biological soil crusts are of great interest nowadays...

It rained beautifully as I waited for Mom to pick me up from mentorship

An example of a USP2, where pods release drug into buffer

An intern and I cleaned the vats in two USP2s.

I am currently looking into biomedical applications and bioremedation.  I also read of this so-called purpose-membrane film used for, er, something important that was too science-jarga-filled for me to fully understand.

Advisory Meeting #2

EQ: What is the most useful application for extremophile research in biotechnology?

A2: One useful application for extremophiles research in biotechnology is in bioremediation      developments.   

1.) Cold-adapted lipase's from psychrophiles (cold-loving microbes) could prove to be invaluable in bioremediation in moderate to cold environments.  These lipase's have great potential in wastewater treatment as well as in depredation of lipids like petroleum oils. (a,b)

2.) Thermopiles are of particular interest in the bioremediation of oil-polluted desert soils.  Substrate utilization rates of thermophiles have been shown to be 3 to 10 times greater than those observed with the mesophilic - "normal" -  bacteria.  This means that these microbes would consume pollutants at a higher rate that other, mesophilic bioremediation candidates. (c)

3.) Marinobacter sedimentarum and M. flavimaris - two halophilic microbes - have proven to degrade hydrocarbons well at high salinities.  They may come to prove invaluable in oil bioremediation in hyper saline marine environments, like that found in the Arabian Gulf, where half of the marine-trasported oil in the world originates.  (d)

a.) Cavicchioli, R; Charlton, T.; Ertan, H.; Mohd Omar, S.; Siddiqui, K.S.; Williams, T.J.                                    "Biotechnological Uses of Enzymes from Psychrophiles" Microbial Biotechnology Volume 4 Issue 4(2011) : 449-460. Web. 23 Feb. 2014.
b.) Joseph, Babu; Ramteke, Pramod W.; Thomas, George. "Cold Active Microbial Lipases: Some Hot   Issues and Recent Developments." Biotechnology Advances Volume 26(2008): 457-470. Web. 23. Feb. 2014.)
c.) Ardestani, Sussan K.; Babanezhad, Esmaeil; Mohamadreza Masoumian; Vossoughi, Manouchehr; Zeinali, Majid. "Hydrocarbon degradation by thermophilic Nocardia otitidiscaviarum strain TSH1: physiological aspects." Journal of Basic Microbiology Volime 47(2007): 534-539. Web. 25 Feb. 2014. 
d.) Al-Mailem, D.M.; Eliyas, M.; Radwan, S.S. "Oil-bioremediation potential of two hydrocarbonoclastic, diazotrophicMarinobacter strains from hypersaline areas along the Arabian Gulf coasts." Extremophiles Volume 17, Issue 3(May 2013): 463-470. Web. Feb. 25. 2014. 

Extremophiles like the psychrophiles, halophiles, and thermophiles host great potential in bioremediation for their ability to degrade pollutants in environments like the arctic and hyper saline oceans.