My 20 New Friends

I emailed my mentor a few days ago, asking for some papers for me to read in preparation for the tar extraction project - to commence in about a month.  I thought,  "Excellent.  I shall have a few more sources of inspiration.  These will count for a few more research checks or so."

"I have added 20 papers to your file server."

20 papers.  Yes.  This is awesome.  I now have 20 new friends.  Things are looking better now that I have these new sources of information.  I always feel as though I should ask more questions at the lab, but don't feel informed enough to.  In writing, that makes no sense, but it is real fear in the shadowy realms of my mind: asking uninformed questions.  

I've been going to mentorship about once a week and partook in a pico green assay the week before last.  This is another method for gaging the concentration of something in a sample and involves applying a stain to the sample which attaches to the genetic material (double-stranded DNA [dsDNA]). As little as 25 pg/ml of dsDNA can be detected using this method - that's 25 picograms (one trillionth of  a gram) per ml (1 thousandth of a liter).  Science!

I have no pictures to post but hopefully will soon.

Updates

SCCUR
It was enjoyable, to say the least.  A day of presentations on everything from pancreatic cancer to chaos , poster sessions with passionate people, and a sandwich - you can't beat that!  There was this one presentation on bouncing droplets on a vertically vibrating fluid bath.  Here is a video of bouncing droplets to give you can idea of what I am talking about:

There was another presentation on green fuel production, another on TCR recognition in T-cells, and I caught the end of one on "plasmods".  It's "between a dielectric and metal", whatever that means.  That is a subject for research at another time...

I can explain the T-cell freshness, though.  TCR stands for "T-cell receptor".  Recall that T-cells are lymphocytes - proponents in the body's immune system.  They differ from other lymphocytes in that they have the aforementioned TCRs that are responsible for recognizing and binding to antigens.  In TCR gene therapy, anti-tumor TCRs are placed in a patient.  The goal is to induce the T-cells in the patient to attack a certain virus or cancer specified by the type of TCR they are "transduced" with.  The problem is that, sometimes, the introduced TCR's "chains" sometimes "mispair" with the the endogenous - this means, original - TCR's "chains".  The point is, the transduced TCR doesn't get to do its job and make the patient's T-cells attack the target virus or cancer, and, sometimes, the T-cells become autoreactive and attack the patient's tissues.  The point of the research project presented was to develop a way to detect the extent to which this mispairing occurs.

Pretty cool.

my poster, and a very nice fish tank through that door over there

Then there was my poster session, from 4:20 to 5:15.  It was the end of the seminar, and I was set up at the end of on the side aisles, so I didn't get as many visitors as I would have liked, but those who did come by were all very interested in what I had to say.  The prospect of the development of a new pharmaceutical excited them and they wished my good luck in my future.  It was very encouraging.  The undergraduates around my area were vaults of advice, giving me insight into their respective colleges, how they found their research opportunities, and insisting that I continue getting involved in research once I go to college, snatching every opportunity to further my expertise, including study abroad.  This one student from Occidental College traveled to Costa Rica to study the effect of sunlight on the pH of the liquid in bromeliads.  Another from UC Riverside was looking to carry out some mechanical engineering research, but found himself researching how salmonella attaches itself to the wax on spinach leaves.  A UCLA senior told how nervous she was about getting grad school.  Apparently, the applications are due this week on next.

One day, I will be one of these people, perhaps taking part in SCCUR next year or the year after - perhaps talking to a excited high school student during the last poster session of the day.

Coursera

The Coursera is going smoothly, though I've found that I much prefer in-person instruction.  Dr. Redfield's optimism is contagious, though, even if she is all the way in eastern Canada.  The making of life are unfolding theirs secrets to me with each lesson, and I've found another purpose in life: find the Romanesco cauliflower.  It is a mutant of cauliflower, sometimes referred to as a broccoli, and featuring a partial fractal pattern that, according to Wikipedia, has been "modeled as a recursive helical arrangement of cones", whatever that means.  I shall look that up some other time...
Dr. Redfield has attempted to procure one of these beauties at a farmers' market in her city, but to avail -  motivating me to see one for myself!

Romanesco Cauliflower

Dr. Redfield is a magical woman.

Last week

This week

EQ
My EQ is now "What is the most useful application for extremophile research in addressing global climate change."  I have a few answers in mind.  Judging from the google scholar alerts I get, quite a bit of extremophile research has been focused on biofuel production.  Methanogens actually consume methane - a more severe green house gas than carbon dioxide and byproduct of cattle ranching and rice production.  Perhaps methane can be used as a fuel source in the future.  There's are oil spill clean-up by oil-degrading extremophiles.  There's also the prospect of creating a better climate model by analyzing how deep-sea extremophiles cycle nutrients and produce nitrogen.  

EQ

1.   The Rule of Three Criteria:

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

I reviewed the rule of three for writing an EQ.

2.   

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

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

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

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

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

Summation: meets all but last criterion.    

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

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

Summation: doesn't meet the criteria.  

     d. How can an Anesthesiologist best treat chronic pain?

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

Summation: meets the rule of 3 criteria

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

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

•Why should microbiologists continue to research extremophiles?

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

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

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

Of Revenge and My Perfectly Good Finger

Going to Oak Crest each week, I always leave feeling that there is so much I have left to learn.  It's a bit frustrating at times, actually.  I've decided to exact organized revenge upon this frustration for causing me hassle in previous learning experiences.  You shall not conquer me this time!  My main weapon in this stage of the battle is Coursera - home to a plethora of excellent online courses, hence the name Course - ra.
Ha, ahe, he.  That's clever.
In particular, there is the "Useful Genetics: Part 1" course taught by Dr. Rosemary Redfield of the University of British Columbia (the Canadian accent shines through every once in a bit) that commenced Nov. 1st but which I discovered Nov. 8th, so I missed the first graded quiz.  Grrr.  I've been rushing to consume as much information as I can to get caught up - upon enrolling the class -, leading up to this very busy weekend of finishing two weeks worth of work in two days by the time the second graded quiz is due - about 2 hours from now at 11:59 PM.  Wish me luck.
This course will reacquaint me with biology and familiarize me with its molecular aspects - a focus of my independent component.  It will also force me to keep my toes in the pond, so to speak, to think about biology everyday, to be born back into it, mounded by it.  Also, genetics is cool.

Proof

Hopefully, this course will be to me what Sam was to Frodo and help me reach Mount Doom to cast my worries into its fiery depths - and  I am NOT wasting a perfectly good finger fighting Gollum for it.  I need that to pipette stuff and things (in the words of Rick Grimes).

Well, if it's not the whole Sam, than his super fresh head of hair.

Did I mention that Dr. Rosemary Redfield has blue hair?

Nice plant

It's Christmas!

Today, I learned how to operate an ultramicrotome.  This may seem like a fancy device, but it is actually quite simple.  "ultramicro-" implies that the instrument deals with the very small, while "-tome", comes from the Greek "temnein" to cut.  Thus, it can be inferred that an ultramicrotome cuts stuff into extremely thin slices - and that is exactly what it does!  The "stuff" it slices is sample - some bacteria perhaps - so that it can be viewed under a transmission electron microscope.  In transmission electron microscopy, a beam of electrons is shot at the sample, and the microscope detects the electrons that passed through, thus creating a detailed image of the sample.  

C. elegans embryo - example of a TEM image

    
The samples must be fixed, dried, and set in a resin.  My teacher for today, Paul, a microscopist and senior faculty member at Oak Crest, had prepared some samples years ago and used them for today's instruction.  It was a rectangular block of resin with some sample at the end of it.  He fixed it onto the segment arc of the ultramicrotome and first trimmed some resin off with a metal blade, looking through the lenses on this apparatus (it is much like a microscope, but with the added slicing capability), until the section of resin with sample in it was jutting out from the rest of the pod.  He moved on to the glass blade, fixing the segment arc onto a special port and the glass blade onto its throne beneath the ultramicrotome lens, and manually cutting the resin until the top of the bit of resin with sample in it was flat and some sample was exposed.  Behold a graphic to make more sense of this.  Hopefully it helps.

I was allowed to cut some resin myself.  The slivers that curled off looked like tinsel, with worms of pink and cotton candy blue wiggling around their edges, like the surface of a soup bubble.  It was marvelous.  The top of the jutting sample/resin block was "polished" by the glass blade, creating a very flat surface.  Next, Paul took out a small, clear, plastic box.  inside of it was a foam holder and inside of that was a blue block.  At the edge of that  block was, what other than, a diamond blade.  :'D It was beautiful.  He replaced the glass blade with this glorious instrument.

After operating it manually for a bit, he filled the trough behind the blade with water so that the slices made by the blade could float off, waiting to be collected later for TEM, and automated the slicing process.

The blue thing is the trough filled with water, and the gray rectangle is the diamond blade.  Floating on the surface of the water are the slices of sample from the resin block.  There are only a few nanometers thick.  That golden thing is the resin block, held in the segment arc.  The diamond blade is caught in mid-slice.  You can barely make out the sample - the dark spot on the edge of the resin block.    

It was at this time that I watched the diamond blade working its magic through the lens.  Here is a short video of this excellence.  Excuse the bad quality.  

It was like Christmas!  Each delicate sliver was a present, a snowflake, a bit of tinsel.  There you go - the connection between the title of this post and the post itself.  Got that over with.

Anyway,  once the slicing was done, the water was thrown out - slivers included - sadly.  They were only for demonstration, after all.  It was a pretty cool experience.  I remember Mrs. Matthews explaining electron microscopy to use, holding up a diamond blade that I could barely see.  Little did I know that I'd be getting a good look at such a blade one fine day...

Oranges

A few weeks ago, my mentor informed me of an opportunity to attend a research seminar - as a presenter!  I'd be presenting on a research project some of my fellow interns and I helped on over the summer.  I worked with him and a college intern who was the main researcher in the project to put together an abstract.  Early this week, the abstract was accepted!  The event is a Southern California Conference for Undergraduate Research open to undergrads and high schoolers researching anything, really, from engineering to poetry.  It will be held at Whittier College on November 23 - trade show style.  Thank you iPoly :')

Anyway, I'm pretty excited.  In this project, we exposed brine shrimp to varying plant extracts to determine their potency, indicative of biochemical activity and, thus, pharmaceutical potential.  

plant extracts

the SCCUR in all its citrusy goodness

oranges

10 Minutes

The 10 minutes presentation is around the corner and I am not sure what I will be focusing on, actually.

Deciding on an EQ that deals with the application of extremophiles research would allow me to connect the obscurities of microbial ecology in severe settings to the challenges we face today in medicine, technology, and environmental stewardship.  

Then there's technique, which is most relevant to my independent component so far.  Throughout my mentorship, I've learned technique - navigated through protocols, microfuge tubes, tough-to-deposit 4µl (micro liter, no mu-liter) increments of probe.  Delving into the techniques utlized to investigate the complexities of nature as it is - rather than using traditional pure culture - would help me with my I.C. [and, I'll admit, X) impress my mentor].

Both of these are tantalizing... maybe I can do some sort of 2-in-1 deal.  I talked to Pittman briefly and she recommended this route: the how and why.

Nanotubes between bacteria - an interesting form of communication that's just beginning to be studied

Now I just need to further narrow my focus.  Am I covering microbial ecology or extremophiles?  I mean, I could delve into how investigating interactions among microbes would reveal the secrets of global energy cycling, the development of biofilms (incluing those on our teeth known as plaque, and infections) , and the environmental application for this (how we can this knowledge to rid our environment of toxic waste like mercury).  I could also focus on extremophiles specifically, how they are studied and what we can learn from them.  What to choose?!  And what should my EQ be?  Can't it just be "What makes microbes so awesome?"?

Anyway, I've decided that my 10 minute will focus on the fascinating history of extremophiles.  This will hopefully make for an engaging presentation, if executed with enthusiasm and involving fancy pictures.  That's a good place to start, I think.

Research and Working EQ

1.  What is your working EQ?

How can the ecology of microbial communities be better investigated?

or

What biological process has best enabled extremophiles to adapt to the severe environments they inhabit?

2.  What is a possible answer to your working EQ? Please write the answer in thesis format. 

•With metagenomics, genetic material can be recovered directly from the environment being studied, the analysis of which provides insight into the interactions within and biodiversity of a community.  

• With 3-D microscopic cages, microorganisms are deposited into microcommunities that scientists have complete control over and are thus able to study the interactions that develop.    

or

•Horizontal gene transfer (HGT) - the transfer of DNA between microbes - has enabled extremophiles to work together and take advantage of functional genes that allow them to inhabit severe environments.

•DNA repair mechanisms allow extremophiles to constanlty respond to their environments, enabling them to withstand such stresses as extreme heat and radiation. 

3.  What is the most important source you have used that has helped you come up with an answer to your working EQ?

My mentor and his colleague, Marc Baum, have been important, as I was first made aware of the existence of metagenomics by them.  A Primer on Metagenomics, a review I am currenlty reading, also inspired my first answer.  The article 3-D Printed Microscopic Cages Confine Bacteria in Tiny Zoos for the Study of Infections provided my second answer.

The article How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions is most important in determining my answers to my second possibl working EQ.

4.  Who is your mentor, or where are you volunteering, and how does what you are doing relate to your working EQ?

My mentor is Manjula Gunawardana and I am a volunteering at the Oak Crest Institute of Science.  My mentor and his fellow researchers there actually developed a method for extracting DNA from tar samples, overcoming the Taq-inhibitors present in tar that make qPCR - and, thus, the investigation of microbial ecology and biodiversity - so challenging to carry out, usually.  It is their protocol that I will be using in my independent component.  This is relevant to my investigation into the techniques researchers use to assess the ecology and biodiversity of microbial communities.  As for relevance to by second possible EQ, we are using this protocol to look into the functional genes of microbes and thus how they survive in the tar pits they inhabit.  

Independent Component 1 Approval

1.  Describe in detail what you plan to do for your 30 hours.

I plan to participate in a research project at the Oak Crest Institute of Science investigating microbial communities in tar.  While the particulars are not crystal clear yet, I will most likely be repeatedly carrying a tar extraction protocol to isolate the DNA of extremophiles present in the tar.      
I will also be taking "Useful Genetics" - course offered by the University of British Columbia through Coursera.  

2.  Discuss how or what you will do to meet the expectation of showing 30 hours of evidence.

The extraction protocol I mentioned above is a multi-day process, so carrying it out multiple time should fill up my time requirement.  If it does not, I plan to join a science club at Cal Poly (BIO SCI, Microbiology Club), use MIT OpenCourseware to study organic chemistry, and attend any talks at CalTech and Cal Poly that relate to my topic.  These efforts will be evidenced by photos, primarily.  
The genetics course should take me about fours hours a week, not including the assignments I will complete in addition to watching the videos.

3.  And explain how what you will be doing will help you explore your topic in more depth.

I was inspired by this research project to choose microbiology as my topic, actually, as I learned about it during my summer mentorship.  It is a an environmental microbiology project dealing with extremophiles. 
The genetics course will help me understand biology more deeply - in more detail.  It will supplement what I am doing at Oak Crest and help me understand how extremophiles survive the way they do.    

4.  Post a log on the right hand side of your blog near your mentorship log and call it the independent component 1 log.

Done.

Second Interview Questions

1. Who is your mentor and where does he work? 
Manjula Gunawardana is my mentor and he is a senior research scientist at the Oak Crest Institute of Science in Pasadena.

2. What five questions will you ask him about his background?
1. What degrees do you currently hold and where did you acquire them?
2. When and how did you become employed by Oak Crest and why did you decide to continue your work here in particular?
3. When did you become involved in research, how, and what were you working on?

4. What excites you about the research you do?

5. Within microbiology, what fields would you say are the most active, and where do you see microbiology in general heading for in the future?

Tar is Beautiful

I encountered another "first" today, namely my first tar extraction.  We ran through part of the protocol for extracting DNA from tar, and while I can't reveal the details, I can say that it was magical and awesome.  The reason why we do this is so that we can assess the biodiversity of and relationships between the microbes present in the tar.  How do these guys survive in such a hostile environment?  Do they work together?  How biologically diverse is this environment? Here are a few pictures:

 Tar (and my glorious, gloved hand) 

More tar (don't you love how the light sparkles against the black mass?)

  We dumped out leftover liquid nitrogen at the end of the day.  Most people think of Halloween and dippin' dots at the mention of liquid nitrogen, but it can be quite useful in a lab.  For one, it is used in lyophilization - the drying of materials like DNA or liquid culture (bacteria in liquid media) for later use.  What happens is the liquid nitrogen freezes the liquid in the sample, which is placed in a freeze drier and exposed to low pressure and temperatue, which causes the now frozen liquid to enter the gaseous state directly from its solid state (sublimation), migrating from the high pressure of the sample to the low pressure of the surrounding area.  

   

It Has Arrived

As I completed my Blog 5, my father dramatically walked up to me and held out the one and only "Manual of Environmental Microbiology: Third Edition" (the fourth edition is currently being drafted)  and waited cooly for my reaction.  I will admit to "oh my gosh"ing more in that minute than I have in the last week.  Those crisp, white pages.  That table of contents.  The cover is embossed with shining, copper-colored renditions of microbes!

I just thought I should blog on this tremendous event - the acquisition of my first "Manual of..." and textbook with far more text than pictures (as in, WAY more.  I've only found one little picture of bacteria under a fluorescence microscope so far).

Blog 5 Project Reflection and Working EQ

behold... The Pentagon: 

1. Positive Statement: What positive thing happened as a result of what you have completed so far?

     Overall, I'm just more familiar with science and the skills needed to succeed as a scientist.  My mentorship is giving me a taste of research and the nature of the science community, and has revealed the glorious field of microbial ecology to me (I believe environmental microbiology is a subset of it).  I'm beginning to explore an exciting and purposeful field I never would have otherwise, having previously convinced myself that multicellular organisms, expecially marine ones, are far more interesting than archaea and bacteria.  From my interview with Mrs. Matthews, I gathered more inspiration and an encouragement to be adventurous, network, and EXPLORE.  This is the essence of research science.  Aside from all this goodness, I just feel more confident and comfortable with my abilities.  Being trusted and talked to as an equal at Oak Crest, and encouraged by my family, friends, and teachers has convinced me that my lack of self-esteem is not an unsurmountable hurtle.  The future is still one, huge cloud of probablility, but now it's a sort of opalescent, smiling cloud instead of a dark and stormy one.      

2. EQ Content:  Pick a piece of research or your interview.  How has it helped you improve your understanding of your topic?

     My reading of "Microbial Ecology: Fundamentals and Applications" has given me a nice introduction to microbiology and the origins of life on earth.  Life began with progenotes, which split up into bacteria and archaea, and from archaea came eukaryotes, which evolved into us.  What's more, mitochondria and chlorophylls may just be permanent symbionts in eukaryotes, meaning they began as independent prokaryotes but are now reliant on their hosts for survival.  Isn't that awesome?!  Mind you, I haven't taken a close look at microbiology after my first taste of it in Mrs. Matthew's class two years ago, so all this is fairly new and consumingly exciting to me.  I like it that way.  

3. What has worked for you so far in the senior project?

     Gaining access to a lab so early on in my senior project is what is especially working for me.  My mentor and the opportunities he has provided me with have made my mentorship a joy and indispensable learning experience.  I've always been a fairly indecisiveness person, so even having a clear topic and overall direction is a relief to me.  Whether I go with a focus on extremophiles or ecology, a variety of interesting pieces of research lay in wait for me to sink my teeth into, and there exists a noble purpose in both to indulge my more idealistic side.  It's clear to me that senior project has a slew of obstacles up its sleeve, but being sure of my direction will help me get through them.  

4. What hasn't worked so far?  

     Finding current, reliable, satisfyingly detailed works on general information on microbiology has been a challenge.  The textbook I found up at Cal Poly was published in the 1970s, and I haven't been able to get a hold of a copy of "The Manual of Environmental Microbiology", written in 2007.  According to WorldCat, there a few copies floating around in colleges near and far, but none are accessible.  Fortunately for me, I have awesome parents whose priority is my education and have agreed to purchase said book on Amazon - at half off, thanks to our committed relationship with the site. ;D
     I also just need to work on my confidence in the lab and become informed more expediently.  This will take practice, as you can imagine.  On with the chase.  

5. Finding Value:  
5b. What is a potential question you would like to study this year?  (working EQ)

-What is the most useful application for extremophile research?  I'd have to define "useful", "application", and "extremophile research" for that one.  Possible answers are the astrobiological, pharmaceutical, and environmental applications.  
-What has been the most important advance in microbial ecology/environmental microbiology?  I'd have to decide between those two disciplines for this one and define "important" and "advance".  Both fields are fairly new (microbial ecology was first really recognized in the 1970s, I believe) which may narrow my options for answers.  I was thinking of asking a question having to do with the future or history of one of these disciplines.  

5a. What do you plan to do for mentorship?  If you haven't found a mentor yet, then discuss where you are currently looking and who you are talking to to find it.  

I will continue with my unpaid internship at the Oak Crest Institute of Science for my mentorship.  

Blog 4: Interview Preparation

1.  Who do you plan to interview?  Why?

I plan to interview Dee Ann Matthews (a.k.a. Mrs. Matthews).  Before becoming a teacher at iPoly, she received a Ph.D. at UC Irvine in Neurobiology and took part in research primarily dealing with the hippocampus.  She has so much advice to give, especially when it comes to research.  From what I've heard, research can be a dog-eat-dog world, and I'd like to get more insight into why that is and how I can deal with it.    

2. You have to ask 5 questions.  What additional questions do you plan to ask?   

What was the first research project you participated in, and how did you become involved? 

What exactly did participating in that project entail?

How did you first become interested in the hippocampus?

How did your research regarding that region of the brain turn out?

What part of your education prepared you the most for research?

What kept you going during the harder times?

Why did you decide to get your Ph.D. in Neurobiology?  

What was acquiring that Ph.D. like?

What general advice can you give me as I become more involved in research?

What do you know about extremophile research and its general standing in the science community?

Mentorship and Research Update

Friday was an exciting day.

I made it to Oak Crest at 2:00 pm and stood gawking at the bizarre BSA readings until my mentor ambled into sight.  He ushered my fellow unpaid intern and me into the conference room along with the CEO of Oak Crest and three paid researchers.  Thus began an hour long chat about "what's cooking."  In the end, I found myself officially involved in that very cool extremophiles project, a continuation of one carried out last year.  Thanks to this development, my topic is definitely microbiology and I know my EQ will most likely have something to do with extremophiles.  Being part of this project means I will have to brush up on some bacteria and archaea basics and read the paper written on the novel methods used by Oak Crest last year.  That's all I can say about the project for now - don't want to spoil it for the world.

As far as research goes, I'm currently reading a review from the Journal of Extremophiles that details DNA transfer among hyperthermophilic (super heat (>80ºC) loving) bacteria and archaea.  DNA is exchanged across species and domains and enables these microbes to evolve according to their extreme environments.  One important find was the presence of a gene coding for reverse gyrase - an enzyme that prevents DNA degradation due to high temperatures - and is now, thanks to ages of DNA transfer, a commonality among all hyperthermophiles.  

Last thing:

Amid shining equipment and receptacles of volatile fluids (including 

liquid nitrogen), a single flower sits softly under a sky light... :')

Blog #3: Topic Choice and Semester 1 ESLR Goals

1.) List your topic here: 

Microbiology

2.) What do you plan to do this year to show growth in each of the ESLRs?  Be specific and use an example.  Examples can come from senior project, model assembly, core, and/or participation in senior class ASB or other organizations on campus (clubs etc).

• As an Effective iPoly Citizen, I will participate in more community service opportunities including beach and natural habitat clean-ups with TreePeople and Amigos de Los Rios, the feeding of the homeless at the Union Station near my house, and the Wiggle Waggle Walk next month.  I will also be more active at school mostly through the Blood Drive committee, but also through HOPE club and Christian Club.  If any of my classmates need help with anything, from a physics problem to the challenges of Senior Project, I will be there to give it.    

• As an Effective Learner, I will take full advantage of the opportunities that my mentorships  provides, helping out around the lab as much as possible and not being daunted by topics or techniques that I find challenging.  I will also put in more study time for each core subject than I have in previous years and step up to the plate whenever somebody needs academic help - a.k.a. tutoring.  After all, teaching is learning.  Cal Poly and Cal Tech provide an array of presentations on various topics throughout the year, so I hope to take advantage of those as well.       

•As an Effective User of Technology, I will take advantage of sites like ProQuest, JSTOR, and Academia.edu to provide me with reliable pieces of research, especially since my topic is a scientific one.  If there is a topic I feel I need a deeper understanding of, I will consider Kahn Academy, Coursera, and MIT OpenCourseWare as sources for it.    

•As an Effective Communicator, I will work on becoming a clearer communicator and improving my projection.  During core classes, I will step up to whatever role is given to me in group work and not let fear or self-consciousness prevent me from expressing my ideas.  Neither will I let my conviction in my ideas cloud my attention to the ideas and opinions of my group mates.  Being a member of the Blood Drive committee will definitely give me the opportunity to improve my verbal communication skills, as I will have to make class announcements regarding upcoming blood drives, and ensure that everybody understands the donor requirements.  

Summer Mentorship Component

1. Summer Mentorship Log 

2. Manjula Gunawardana 
(626) 817-0883 
m.gunawardana@oak-crest.org 

3. What questions were raised because of the 10 hours of experience?  List them.  
- How are the symbiotic relationships between microorganisms determined?
- How are functional genes isolated?
- What is the nature of the competition that occurs between labs researching similar topics?

4. What is the most important thing you gained from this experience? Why?
I gained a detailed insight into biological research and a deeper understanding of science as a whole. Scientific fields are far more interconnected than I previously thought.  In fact, my mentor made it quite clear to me that biologists often do more chemistry than biology, and I learned that there is such a thing as a microbial ecologist (ecology + microbiology) and laser chemist (laser physics + chemistry).  When I voiced my interest in marine biology, he also exposed me to how techniques used in a lab like Oak Crest are transferrable to a marine biology lab.  I've also realized how foundational group work is to a research lab.  There is a great sense of community at Oak Crest and people from varying fields work together to accomplish common goals.  Furthermore, I see now that research science is a way of life.  My mentor lives and breaths what he does.  It's a constant learning experience and no question is too dumb to ask.  I think I've gained a measure of intellectual freedom and fearlessness from this realization - or, rather, confirmation of what I've known, but not fully understood, for a while. 

5. How did what you did help you choose a topic?  Please explain.
I've decided to choose microbiology as my topic, as my mentor has agreed to include me in an extremophile research project.  I'm considering making my EQ something along the lines of "What is the most useful application of extremophile research?"  I haven't decided how to define "useful" yet, but this is a good start and there exist three possible answers to this EQ...  Microbiology is a fairly diverse - and interesting - field with so many applications, from pharmaceutical to environmental to astrobiological (hint hint).  It also helps that my mentor is a microbiologist himself.      

2013 2-Hour Presentation Reflections

1.)  The presentations I viewed are as follows.

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

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

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

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