Independent Component 1

LITERAL

a.) I, Vanessa Machuca, affirm that I completed my independent component which represents 30 hours of work.

b.) Dr. Rosemary Redfield of the University of British Columbia taught the online genetics course I took for my first independent component on Coursera.  Here is a link to a an overview of the class.  My mentor, Manjula Gunawardana, introduced me to the other part of my independent component - the tar extraction project - and has been my main source of information regarding why the project is being carried out, project protocol details, etc.

c.) My independent component log is right above  my mentorship log on the right side of this page.

d.)  For "Useful Genetics Part 1", I watched nearly thirty videos and took notes for all of them.  For the tar extraction project, I went through the protocol twice with others in the lab.  It took 5.5 hours over two days to complete it the first time, as we took the extra step of preparing the samples for amplification by PCR - to see if we had successfully extracted DNA from the tar.  The second time took two hours, as we stopped to complete the 10 Things To Do List.

INTERPRETIVE and APPLIED

Taking "Useful Genetics" gave me a refresher on my biology basics.  I found myself asking simple questions at mentorship that I should have known the answers to.  Knowing how genes are passed down, mutated, expressed, stored in DNA then RNA - how life works is imperative at my mentorship, and relearning this has enabled me to be more confident around the lab.  I knew these concepts before - thanks Mrs. Matthews and Cancino - but the specifics, the names, the order of things - this little bits were what I had trouble with.  Here is a link to a sample of the notes I took.  It includes my first page of notes, some on mutations, and some on cancer.  As you can see in the image below, most lecture videos are around twenty minutes and I watched about thirty of them - that's 10 hours there.  Add onto that the six quizzes I took, each lasting around 1 hour, plus that the times I paused the videos to take notes, the re-watching of parts I hadn't caught the first time around, the problems Redfield included in the videos, and you have the 24 hours I've recorded on my log.

The green checks indicate that I watched those videos. (5 Modules in total)

There there's the tar extraction project.  On my log, I recorded the time I was assigned to the project, the conversation I had with Manji regarding it, the and the two extractions themselves that I took part in.  I wrote about both of these times here and here.  All of this has familiarized me with how microbiology works: plan, collect samples, store, run tests, gain knowledge.  Learning the tar extraction protocol, carrying it out, getting this hands on experience has helped me become more comfortable in the lab and familiar with my abilities.  I've enjoyed learning from those around me who have far experience than I do.  Pipette diagonally and against the well wall; when in doubt, throw it out; balance out any samples you place in the centrifuge; pound that tar like you mean it! - I will carry these bits of guidance with me into mentorship this year as well as any lab I intern at in the future.  As for justifying the hours I've logged, I'll just say that, as you can imagine, crushing tar to a fine powder and transforming it (quite magically) into a clear liquid takes a while...        

photos of my first tar extraction

Lesson 2 Reflection

1. Positive Statement

What are you most proud of in your Lesson 2 Presentation and why?

I am proud of the clarity with which I presented my first answer, as evidenced by my classmates' ability to complete the worksheets with such ease.  Upon typing up the worksheets, I that the the long words and science jargon would dissuade them from conquering it - but this was not the case.  I am also proud of my powerpoint.  It seemed to follow the rule of three, with relevant bullet points and pictures.

2. Questions to Consider
       a.     What assessment would you give yourself on your Lesson 2 Presentation (self-assessment)?

       P+  

       b.     Explain why you deserve that grade using evidence from the Lesson 2 component contract.

I fulfilled all of the requirements on the contract and then some.  My powerpoint, I believe, was very well put together and added to my presentation rather than detracted from it.  The font was large, the pictures plenty, and it followed the rule of three.  Furthermore, the activity went well and involved everybody.  The answers those I picked on gave indicated that they understand what I had presented.  As for research, I neglected to directly reference the three papers I indicated on my lesson plan, though my activity worksheets were based on them and I indirectly referred to them in my second to last slide.  I believe I made up for this my referencing more than one quality piece of research throughout the presentation, including for the two graphs on the fourth slide - which I created myself. 

3. What worked for you in your Lesson 2?

My powerpoint worked well for me.  I wrote my script in speaker notes to ensure that each slide added to what I was talking about.  The activity went better than I thought it would, so that worked for me as well.  What also worked were my explanations of biofuel production processes.  Originally, my explanations were more detailed and complicated, but I was able to trim them down to their bare bones.  I also articulated well, I believe, not stuttering and speaking clearly, albeit a bit quickly.     

4.  (What didn't work) If you had a time machine, what would you have done differently to improve your Lesson 2?

I would have practiced weeks in advance.  Holding any sort of aid - as I did - is not professional, in my opinion, and neither is referring to the powerpoint as regularly as I did.  I don't believe I did either of these often enough to have distracted my audience, though.  Plus, It was necessary, in my case, to have carried that aid, since I hadn't memorized the names of the sources I planned to cite.  I also neglected to refer to the sources indicated on my lesson plan - a mistake that could have been prevented had I prepared more thoroughly.  From what a few classmates indicated to me, I spoke a little too quickly.  Again, this has to do with preparation.  Finally, I would have chosen a different hook.    

5. Finding Value

What do you think your answer #2 is going to be?

I plan on my second answer involving bioremediation.  It will go something like this: One application for extremophile research is to develop new bioremediation strategies, thus addressing the presence of pollution in pristine environments. I'd have to make a connection between bioremediation and global climate change, as it is a result of the phenomenon rather than a cause of. I would just have to define terms in my EQ carefully to make this answer's relevance clear.

Microbial Constellations

On Monday, we viewed the aforementioned epithelial cells under a fluorescence microscope.  These cells were grown to express green fluorescence protein (GFP), which can be viewed under the microscope, as seen below.  Pictures need to be taken quickly, lest the cells begin dying and deform/burst.  To achieve a desirable picture, you must navigate about the slide using knobs attached to the stage below the screen until you reach a patch that displays a good amount of GFP expression.  Take a picture (there is a feature for that on the screen).  You must then turn on the regular trasnmittance so that a picture of the cells as they are (not lit up) can be taken.  This is layered over the previous GFP picture and settings are adjusted to get as clear a picture as possible.  Looking at these clusters of cells, seeing them twinkle, reminded me of what I see when I look up at night (in Cambria, where little air and light pollution exists).

There is great contrast between the expressing cells and the background.  If you were to see the image up close, you'd see that the nucleus of the cell is lit up, with dull cytoplasm surrounding it and the dark outline of the membrane surrounding that.  The nuclei on these are large, since these are mammalian cells, so the bright green takes up most of the cell.

There is quite a bit of background noise in this one.  The contrast should perhaps be adjusted.

This is as good as my mentor could this picture to be.  There is a clear difference between the background and the lit up cells.  If you look closely, you can see microtubules stemming from the cells.  There are some going through mitosis as well.  Pretty cool.

Today, we pressed drug pellets.  I weighed so-and-so milligrams of powdered drug onto a folded wax paper sheet and handed it over to the college intern working with me to press it into a pellet.  it was repetitive and sometimes frustrating work, getting the weight to be within .2. milligrams of that desired. It gave me time to think about time and black holes... thank you Mrs. Pittman and Brian Cox.

After that, I worked on the microtome and talked to Paul about a biofilms project he is working on. Quite fascinating.  

 The glass knives are at top, the resin blocks below them to the fight, a bunch of parts below those, and a package of razors below those (the one with the yellow label.

January Update

I went to mentorship twice this week: Monday and Friday.

Monday was a 9:30am to 3:00pm day beginning in the tissue culture lab, where mentor was handling a flasks of epithelial cell culture under the ventilation hood.  A little bit about tissue culture: you cannot keep your cells in the same media for too long lest they die.  As the cells grow, it can get a bit crowded, as you can imagine, and the cells must be split up.  Furthermore, the cells tend to start sticking to the walls of their flask after a while.  To detach them, they are treated with trypsin, which hydrolyzes the peptide bonds in the protein attaching the cells to the flask wall.  The trypsin must be deactivated with a neutralizing medium, as prolonged exposure to it will damage the cells.  The cells are then spun down, resuspended, and split.  In this case, my mentor split the cell into three flasks, giving them fresh medium to feed on.

cells in growth medium

After this culture business, we attended a meeting on general lab safety, then began on tar extraction.  It was glorious, magical, fantastic - like the last I participated in it.  We pounded tar to a powder!  Upon completing most of the process (we ended at a lengthier step and never proceeded to the next), I cleaned up at a lab adjacent to ours, had a chat with Mr. Webster, and worked with an intern as she pressed pellets of a drug we are looking into.  It's another sustained-drug-release project.  She, in turn, showed me how to operate the solicitor.  It's quite simple.  You must place whatever you are sonicating into a falcon tube, fill the tube with water, simply place it in the solicitor (pretty much a container of water) and turn the thing on.  Low frequency sound is generated.  This is one form of maceration - the breaking up of something.  Maceration can be chemical (ex: acid) or mechanically (ex: metal pestle, sonication).  

My day ended, then.  

On Friday, I worked the microtome.  I took some pictures with my cell-phone, which I shall add here shortly (upon figuring out how to transfer photos from my phone to this computer…).  I mounted a resin block onto the segment arc, which I attached to the trimming block, and that onto the stage trimmed the block with a metal blade first, then a moved on the glass, fixing the segment arch onto the cantilever arm.  The actually cutting of the resin was a challenge for me, though, and it came out all messy and rough.

End of the day surprise: free books!  There were just piled there at the end of the hallway by the microtome.  I 'd heard that best ones were taken days ago… but I managed to find Shakespeare!  Hopefully there are still some left for me to rummage through next week…    

As far as independent learning goes, I found a courses on astrobiology and climate change on Coursera.  The latter is a possible independent component idea.  We shall see.

Third Interview Questions

Here are my 10+ questions.  

1. What is the most useful application for extremophile research in addressing global climate change?

2. What are the most pressing problems in the addressing of global climate change today (roadblocks, etc.)?

3. How can these problems be solved?

4. What is it about extremophiles that makes them particularly useful for the aforementioned purpose?

5. What possibilities are there in bioremediation?  How about in hydrocarbon pollution clean-up in particular?

6. Which extremophiles in particular that have proved to have potential in such advancements?

7. How could extremophiles be used in biofuel production?

8. Which extremophiles in particular that have proved to have potential in this field?

9. What do we need to understand more in order to tackle global climate change?

10. How could extremophile research contribute to the development of this understanding, perhaps of a clearer global climate model?

11. What extremophiles show particular interest in this development?

12. How far has extremophile research come? Is there is still a long way to go before any of it can be applied?

13. What papers or journals you would recommend I use to stay up to date on developments involving the application of extremophile research to addressing global climate change?

14. What people or organizations in particular are involved in work related to my senior project?

Blog 11: Mentorship 10 Hours Check

1.  I am mentoring at the Oak Crest Institute of Science in Pasadena.

2. Manjula Gunawardana, my mentor

3. I have completed 30 hours of mentorship.

4. Mentorship always holds surprises for me.  I began with culturing shrimp with an undergrad who interned over the summer.  From there, I received the opportunity to extract the RNA from my very own cheek cells, converting it to cDNA (otherwise known as ssDNA (single-stranded)) afterwards.  Next came OD readings and DNA extraction from yeast, preparing samples for electron microscopy and operating an ultramicrotome, autoclaving trash, coating pods, and, finally, witnessing a fellow aspiring scientist pipette for the first time.  There was also SCCUR and the thrill of presenting an exciting shrimp bioassay on potentially pharmaceutical plant extracts.  We'll see what 2014 at Oak Crest holds.

5. I will do that soon.

Senior Project: The Holiday

1. I read two of the papers that my mentor gave me and went to mentorship on January 3.  I also updated my independent log and began looking into some professors at Cal Poly Pomona and Pomona College who could perhaps be future interviewees of mine.  

2. I know, I know - that's only 10% of my "20 friends", but hey, I was busy tide pooling at Cambria.  In fact, it reminded me of the complex ecologies that exist in our world.  In one little pool, there were hermit crabs fighting over a shell, anemones chilling, a sea snail struggling to reach water with another sea snail attached to its back, a tide pool sculpin flitting about - just the general give and take of nature.
The same exchanges can be seen at the microscopic level.

tide pool sculpin

Also present on those rocks were smudges of oil, perhaps from leaks from the S.S. Jacob Luckenbach - a cargo ship loaded with 457, 000 gallons of bunker fuel.  Cambria marks the southern tip of the Monterey Bay National Marine Sanctuary - governed by tight regulations and home to a marked perfection I've had the privilege of being witness to many times.  THIS is what all coasts should be like.  They don't deserve oil spills.  THIS is why I chose an environmental focus for my senior project.

I couldn't find any photos of my own, so here is the next best thing.  Behold: moonstone beach.

Anywho...
At mentorship, I worked with a community college who was pipetting for her first time.  I showed her how to tap the 96-well plate to pull droplets off the sides of the wells, and operate the UV Vis.  My mentor helped out as well, showing us his wicked pipetting skills and giving tips on how to deal with bubbles (the bubbles were from aspirating the liquid - that means pumping it up and down to mix it (in this case, 'twas a mixture of BSA and sodium azide)).    

Such fashionable pipette tips.  Behold their glory!

Reading "Microbial Diversity in Natural Asphalts of the Rancho La Brea Tar Pits" and "Advantages and Limitations of Quantitative PCR (Q-PCR)-based Approaches in Microbial Ecology" exposed me more to terminology I will become familiar enough with over the course of my project.  It's all about gaining intuition and becoming comfortable with my topic.
There are a few Cal Poly professors who may be of some interest - sort of.  At Pomona College, there's this one professor who has a special interest in the microbial ecology of mud volcanoes.  He might be a future resource... 

3. I would talk to my mentor, and perhaps the aforementioned E.J. Crane of Pomona College.  There's also CalTech (only a few minutes from my house, actually), home to a geobiology department and Victoria J. Orphan (whom my mentor mentioned over the summer).  She's a molecular microbial ecologist, primarily, and another potential interviewee.