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.