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.

Independent Component 2 Approval

1.  Last semester, half of my independent component was taking part in a tar extraction project at the lab I mentor at - the Oak Crest Institute of Science.  I will continue on with it this semester.  The project involves using a protocol developed by my mentor and his colleagues to extract DNA from tar samples.  We have yet to collect fresh samples, but should soon.  There are multiple directions for the project to go in from there, all involving analyzing the DNA, most of which will be of extremophiles (anaerobes, etc.).  The details of the project have yet to be sorted out, and I am not permitted to disclose them once they are.  I also plan on taking an online class, though I have not yet decided which.  Coursera offers a few on the science behind global climate change that could be helpful - one of which is "Global Warming: The Science of Climate Change." offered by the University of Chicago - but all of which begin in March.          

2.  Each tar extraction takes a good four hours from start to end, and multiple extractions should take place.  Add that to the collecting of the samples - which is an all-day affair.  As for the time it would take to carry out analyses, that is to be seen and cannot be detrained as of now.  The online class I plan to take will account for remaining thirty hours.   

3.  Being familiar with what enables extremophiles to thrive in the environment they do will help me better assess how extremophile research can be used to address global climate change.  An example most relevant to the tar extraction project is bioremediation - the use of living organisms to clean up environmental pollution, like oil spills.  To use oil-degrading bacteria for these purposes, much needs to be understood about the nature of their interactions with their environment and with each other before they can be utilized.  The tar extraction project involves this seeking of understanding.  The online course on global climate change will familiarize me with the other half of my EQ.  Together, my independent component 2 will allow me to gain a broader and deeper understanding of how my EQ can be answered by further exposes me to its two facets: extremophile research and global climate change.          

4.  It hath been done.  

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.