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Short Intel ISEF Recap

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I wanted to put this here for recordkeeping, debriefing and future planning purposes before I dive again into the end-of-junior-year workload. Thank you so much for your help with scheduling and makeup work and all your help this year as my mentor, journal-accesser and patient proofreader and listener. Thank you!!

Intel ISEF 2014 was probably my happiest, not because I won awards (although earning the recognition of esteemed scientists is a true honor!!) but because I was able to connect with so many old and new friends and discover the huge potential of interdisciplinary scientific collaboration. THAT is what I remind myself of every year as I walk out of the convention center and think about on the plane. I have a feeling these peers will stay with me for years to come.

And Nikhil! Phenomenal! I cheered until I got a sore throat :)

Now, for me, I'm listing the following purely for recordkeeping - I don't want to come across as self-absorbed, so please realize that (!!!). I was honored to receive

  • 4th Place Grand Award in Physics & Astronomy
  • 3rd Place Internationally & 1st Place Nationally, SPIE International Society for Optics & Photonics
  • Certificate of Honorable Mention (Top 6 Nationally), American Association of Physics Teachers & the American Physical Society
  • New American University Provost Scholarship to Arizona State University (Awarded to 22 Nationally)

What this really means is that many judges thought I was worthy of recognition. That is the highest award. Thank you for your support all these years, without which I honestly could not have dreamed of getting to the level I am at now.

I look forward to a summer of hard work and reconnecting as a 2014 Research Science Institute Scholar at MIT. I will be sure to keep you updated all summer, because I've forecasted for Science Research next year. Truly, deeply excited!!

Thanks so so so much, Veronica. I wore a Catlin Gabel sweatshirt to the international pin exchange and a selfie that New Yorkers took with me showed up on the big stage of the opening ceremony, so CATLIN GABEL! :)

Thanks again Veronica. So many thanks. Talk to you tomorrow.
VD

National JSHS

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Apologizes for the lack of blog posts recently - as you know, I have been swamped with concerts, performances etc.

An update - the National JSHS is next week. I have edited my PowerPoint slides per your recommendations - thank you - and plan to fully cut my speech down to 12 minutes by this weekend.

Thank you,
-VD

Friday's Science Fair and Upcoming Presentation

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Friday's Intel Northwest Science Expo was fun, engaging, and rewarding. Thank you Veronica for preparing our class so well!

The conclusion of this science fair is just the beginning, and I look forward to much more research and experimentation.
My project involves data that is real and meaningful, but hard to get. When I perform an experiment and wait for results, I cannot control the outcome, and most of the time, I don't get the results I want. It takes repetition, troubleshooting, and discussion to figure out solutions to a problem. In my research, I did find a potential new target for cancer treatment by identifying a driver of a particular cancer. But as I said before, this is just the beginning--the key that opens many more doors. There are many directions I can follow, much more evidence to obtain, and I plan to pursue those paths to follow up my findings.

My research here is by no means "complete." I will continue to investigate and work on this fascinating and thought-provoking project. I believe that it is important to conduct more experiments and build upon this study, because findings and discoveries for the future of targeted cancer therapy can tremendously benefit society.

My next presentation of "Novel Targets for Personalized Medicine: Identifying Oncogenic Drivers of Cancer" is May 6. I have been invited to present at Oregon Health and Science University's Research Week, May 5-9, 2014. The poster session is from 1:00 pm to 2:30 pm. I am thrilled for this enrichment opportunity to share my research. I'm also eager to see the graduate students and faculty's research projects and talk to them about the research they are doing in different subjects as well as observe how they conduct their projects.

If you are interested, please go to https://www.conftool.pro/research-week-2014/sessions.php

Presentation prep

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To prepare for tomorrow's Intel Northwest Science Expo, I met with Aline yesterday to go over my presentation and hear her feedback. I printed the poster to the size of an 8x11 piece of paper. First, she read over the poster, and then asked me questions about it. She said my poster is very clear and that there is a nice balance between graphs/diagrams and text. Then, I went through my whole presentation, inviting her to ask questions as I went through the poster. Her comments were positive; she said I was very formal and fluid, the presentation came naturally and not forced, and that I showed a deep understanding throughout. 
 
Some questions and interesting points came up, and she gave very helpful feedback and suggestions to improve my presentation and help me connect my results to the bigger picture, personalized medicine.
 
In addition, this morning I presented my poster to Chris' 8th grade science class, which went quite well. I did my best to explain the science in simple terms, and it seemed like the class understood well the concepts and the science behind my work, as well as the significance of my results. It was a fun experience! 

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Neat; this sounds like great

Neat; this sounds like great preparation for how to communicate to a wide variety of audiences! I look forward to seeing the finished product tomorrow morning.

Western blots this week

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After running the gel, transferring the gel, blocking, and probing with primary antibody, I washed the primary antibodies with TBST, then probed with secondary antibody corresponding to whether it was anti-mouse or anti-rabbit (see below). Afterwards, the western blots were imaged.
 
Which antibodies did I probe each blot with?
 
293T17 cells:
  • 4G10 (mouse)
  • Total TrkA/TrkB pan (rabbit)
  • pMEK (rabbit)
  • cyclin D1 (mouse)
SF BaF3 cells
  • TrkA/TrkB at specific tyrosine residue (rabbit)
  • TrkA/TrkB at another tyrosine residue (rabbit)
  • pMEK (rabbit)
  • pAKT (rabbit)
 

Comments

Picture?

How did the Western turn out? Can you post an image or otherwise describe your results?

Western blot images

Welcome back, Veronica!
The blots are on the computer at the lab, so once I get the files transferred to my computer, I will share them with you.

Lysates and protein concentrations

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Preparing for another western blot: From the Bradford assay of the BaF3 serum-free (SF) lysates, I calculated 50ug/ul per well (for each sample) and enough for 5 gels. With the protein concentration calculated, I determined how much lysis buffer to add up to a volume as well how much sample buffer (dye) to put in each sample. I kept these samples in the -80 freezer. 
 
Last Thursday, I lysed the 293T17 cells. Since the media had already collected virus, I also kept the media. 
Lysing the 293T17 cells was a similar process to lysing the BaF3 cells; the only difference is that 293T17 cells are surface-adherent, so it involved scraping the cells of the bottom of the dish. The cells were pelleted after the buffer was applied, and the supernatant was kept (the lysate). Lysates and media went into my box in the -80 freezer.
 
On Monday, I did the Bradford assay with the 293T17 cells to determine how much lysate to use for each well of the western blot. Like for the BaF3 cells, i calculated for 5 gels and did corresponding calculations for lysis buffer and sample buffer concentrations.
 
With all samples ready, I prepared and performed the western blots this week. More info in the next post!

Busy in the lab!

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Some updates from the last two weeks!

 
My checklist:
 
1. Sequence NTRK1 WT
I have sequenced the NTRK1 WT, and found that there were no extraneous mutations and that the construct was correct. Follow-up ideas: maybe move the plasmids into another vector, called MIG, in order to correct for different levels of expression. MIG is tagged by GFP (green fluorescent protein). Looking at the fluorescence of cells expressing the genes of interest, the idea is to sort the cells into groups with equal levels of expression.
 
2. Get more antibody
Ordered and arrived, NTRK1/NTRK2 sampler kit
 
3. Bradford assay and Western Blot with serum free (SF) BaF3 NTRK-expressing lysates

-Cells were cultured in serum-free media and lysed using cell lysis buffer

-Bradford assay: protein assay comparing sample concentrations to a standard curve with known concentrations of BSA protein

Bradford assay data in lab notebook--this allows me to calculate the right amount of lysate and buffer to load in each well.

Today's western did not turn out so well--there was some kind of misconnection between the current and the gel box or a general problem, but the two gels ran really slowly and ended up being warped.
I plan to redo the western tomorrow. 

 
4. Look at NTRK receptor signaling in 293T17 cells through a transient transfection 

-Transfect samples (NTRK1 WT + mut, NTRK2 WT + mut)
-Wait 48 hours (I transfected today, the cells will be ready to lyse on Thursday)
-Lyse cells
-Western blot (probe with phospho tyrosine antibodies)

 
Future questions/experiments:
-Check NTRK1 WT behavior in 32D cell lines--a murine bone marrow cell line (literature and past research have shown that the WT did not transform in these cell lines), and move all mutants to this cell line system
-Look into performing a western blot at different times during an IL-3 withdrawal assay 
 
Meanwhile:
-I have been working on another NTRK2 mutation (I transformed the PCR and then made overnight cultures)
-In addition, I looked at more batches of patient samples and found some interesting NTRK mutations in NTRK1, NTRK2, and NTRK3 to work on in the coming weeks.
 
 

More Research

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Yesterday, I started on my next steps to further investigate the unexpected behavior of the NTRK1 wild type and continue my research. 
First, I prepared the plasmid sample and sequencing primers to do a full DNA sequence of the NTRK1 WT construct. The sequence should come back tomorrow. 

Also, yesterday I had the opportunity to listen to a talk given by Dr. Kimberly Stegmaier from the Dana-Farber Cancer Institute. Her talk was great and she described her lab's work on studying small molecule targets for cancer therapy as well as their work in looking at cell differentiation and transcription factors--the small things and details that happen in the nucleus. 
She shared findings from her lab about acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and neuroblastoma. In the AML and ALL research, the lab primarily focuses on pediatric patients. By profession, she is a pediatric oncologist, and that makes her work even more special. 
In addition, their lab looks at known hits and tries to find out more about them. For example, in neuroblastoma, a particular gene called MYCN has been well known to be overexpressed and amplified in neuroblastoma tumors. Instead of looking for other targets, they examined closely how MYCN interacts with other proteins. 
They also use a mouse model in their lab, and study different chemical compounds that may inhibit certain gene expression or activity of oncogenes. Additionally, her research has passed on to significant clinical trials. 

Many survival rates in both children and adults can be better, and that is what makes the research I am doing, the research Dr. Stegmaier is doing, and the research other labs are doing so meaningful. 

I was inspired by her great depth of knowledge across all cancers and thoughtful answers to the questions asked at the end of her presentation. 

Comments

Friday reflection

It's great that you're observing how other scientists communicate their findings with each other and engage in dialogue about their significance. Now that you've shared your work with several more people who are scientists, but not experts in your field, what are your thoughts about how that process went? What sort of ideas for how to successfully present your project (what worked well, what didn't) came out of your experience last Friday? Ideas for what to change/maintain/refine for April 4th?

Before April 4th

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Debriefing Gresham-Barlow. Preparing for the Intel NWSE & ISEF.
- Poster design was inefficient. Next time, I have resolved to just use rulers and tape instead of the fancy metal screws I bought from Home Depot. (Read that on the internet) I'm not as worried about efficiency in poster setup for the state fair because I will go the night before to setup, but the screws also forced me to bore the holes, which were imprecise. Thus, rulers and tape, rulers and tape, all the way.
- The judges checked off everything on the comment sheet, so at this point I am just looking to fine-tune my oral presentation. No concerns about the content of my project. The written criticism was to eliminate the bibliography from my poster. I already printed my poster, so I'm caught between redesigning to address this concern and paying another $100 to print my poster, or just leaving my references on there at the state fair and ISEF. What do you think?
- I need to revise my research paper. As I was talking to the judges, I noticed that I could improve my JAVA program by incorporating an automated design process, e.g. instead of identifying each solar panel design manually (as I did before), I am now thinking about coding a secondary and refined process that will pick those designs and write some algorithms that will enable the highest-efficiency designs to be automatically reported to the user instead of manually identified. Does that make sense?

Again, thanks so much. I really, really do appreciate it.

-VD

Comments

Rulers and tape, all the way!

Even so, I was impressed with your fancy engineering, and the whole thing stayed vertical, which counts for something. You're right, setting up the night before will be an enormous time saver.
I think the references are not enough of an impediment to warrant reprinting before April 4. We can see whether you want to reprint before ISEF, at which time you can reconsider the usefulness of the references.
I'm interested to hear more in our next class about the automation you're considering (I confess I don't quite follow the idea just yet.). A change of this sort might be enough to warrant reprinting your poster; we'll see.
I'm glad that the conversations with the judges got you thinking and a potentially useful idea for improving your project came out of the whole experience! This, plus positive feedback on the clarity of your presentation, are both great outcomes.

Presentation Things

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  1. I printed out a paper copy of my poster board for more convenient practice.
  2. Looking forward to a run-through with you (using my mini-poster OK with you?) tomorrow!
  3. Yay!
  4. Thanks!

Comments

5. looking forward to it!

6. and let's see if we can find another available person or two who don't know anything about your project to also give you feedback.

another set of eyes

I am a new to your project and am interested in your presentation if you would like another set of eyes and feedback let me know.

Would love that! Science

Would love that! Science Research meets during block 7. Thank you so much!

A Working PPT & Talk!

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I spent the weekend writing my speech and editing my JSHS PowerPoint presentation to my satisfaction! (For your viewing ease, my speech for each slide is in the notes in PowerPoint. There are some animations and GIFs that won't play unless you enter slide show mode, though. Either way, you'll see the whole collaboration during my presentation practice!)

I would love to hear your feedback, if possible!

Thanks so much! :)
-VD

Comments

Oscar for best QDSC presentation!

This is quite impressive. Very nice logical organization throughout. I am wondering if this truly fits into the time frame indicated on the slides, or if you calculated that using warpspeed Dingspeak. We can talk more in depth in person, but here are some initial thoughts:
Slide #8, point #1 - the potential has already been stated in previous slides, and this first point doesn't seem to fit under the "challenges" heading. As such, is it worth keeping here, or is it redundant and expendable?
Wise of you to have prepared both technical and non-technical versions of your model descriptions.
Slides 15, 16, 17, graphs of 1, 2, and 3 QDSC are fuzzy, but the 5 and 9 stack on later slides are much more clear. Can the first 3 be improved in resolution to match the last two?
Slide 20: I can't figure out why the percent of incoming usable solar energy starts out higher than the percent of incoming photons absorbed by each stack, but then the green bars gradually surpass the blue. Should I not even be attempting to compare these to each other?
Slide 22: is it worth somehow highlighting the most important numbers via color/bold, etc? I'm sure you'll be able to point with a laser pointer, but it might help to do something visual on the slide to call attention to the appropriate spot.
Slide 24: silly question - what does interdisciplinary mean, in the context of describing this model? JAVA + Monte Carlo?
Is the drop in price over the last few years exclusively due to an increase in efficiency? The increase on slide 32's graph doesn't seem sufficient to explain the dramatic decrease in price in the graph on slide 5.
Whatever is happening in slide #30, I love it.

Hi, Leo

Thank you so much for your detailed feedback! I actually timed myself speaking each slide in regular (slower than I normally speak) Dingspeak because I know I get too excited sometimes.

Slide 8: It's redundant. At the time, I thought it was necessary for stress and context. I have now modified my talk and the slide to eliminate point 1.
Yes, the fuzziness is because I ran the first three through another software to slow down the GIFs (while I deemed 5 and 9-stack to be at reasonable speeds because they have more parts to the animation). I can't improve the resolution without remaking the GIFs, so I will look into that. Thank you.
Slide 20: That's a critical distinction I should make clearer, and perhaps re-graph. Number of photons does not equal energy absorbed. Usable ENERGY thus "surpasses" percent of PHOTONS absorbed in the first few data points, but note that it is always lower than the yellow (energy absorbed).
Slide 22: I'm not sure I totally follow you - which numbers are you referring to? I suppose I could highlight the more important designs, though.
Slide 24: Interdisciplinary = Quantum Physics + Earth Science + Power Engineering
Slide 30 is a backup slide, peripheral information I found interesting during my treks of the interwebs. Kardashev scale!

Oops.

Must have accidentally clicked twice. Now I can't delete. Just know that these two replies are the same. Thanks!

Hi, Leo

Thank you so much for your detailed feedback! I actually timed myself speaking each slide in regular (slower than I normally speak) Dingspeak because I know I get too excited sometimes.

Slide 8: It's redundant. At the time, I thought it was necessary for stress and context. I have now modified my talk and the slide to eliminate point 1.
Yes, the fuzziness is because I ran the first three through another software to slow down the GIFs (while I deemed 5 and 9-stack to be at reasonable speeds because they have more parts to the animation). I can't improve the resolution without remaking the GIFs, so I will look into that. Thank you.
Slide 20: That's a critical distinction I should make clearer, and perhaps re-graph. Number of photons does not equal energy absorbed. Usable ENERGY thus "surpasses" percent of PHOTONS absorbed in the first few data points, but note that it is always lower than the yellow (energy absorbed).
Slide 22: I'm not sure I totally follow you - which numbers are you referring to? I suppose I could highlight the more important designs, though.
Slide 24: Interdisciplinary = Quantum Physics + Earth Science + Power Engineering
Slide 30 is a backup slide, peripheral information I found interesting during my treks of the interwebs. Kardashev scale!

Let the Storm Rage On

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Yes. I was so desperate for a clever blog title that I turned to Disney. ("Let It Go")

I am looking forward to practicing my presentation this coming week. I have completed and polished about 80% of my talk for the JSHS, which I will modify and condense for Gresham-Barlow. 

I ordered my poster papers. I have two boards at home from years ago, so I think I will use them in constructing my poster.

Thanks for reading! More coming soon.
-VD

Running out of blog title ideas

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  1. Thank you for reviewing my JSHS slides with me today. I'll continue to edit up to March 9th.
  2. We discussed my oral presentation for all forums. I plan to write it this weekend and practice next week.
  3. Thank you for sending me Stephanie's comments regarding my paperwork. I would really appreciate it if you could forward me her response (if and whenever) to your response with my 2013 abstract, if only so I can rest in ease / be nervous about SRS approval beforehand. :)


Darn Near Completion!!!!

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 IT'S SO DARN CLOSE
WORDS CANNOT EXPRESS
Right now, my paper is approaching it's penultimate form.  I need to create a graph to show the differences (along with actually inserting all of my graphs into my paper), and then I can focus solely on my presentation, footnotes, and refining refining refining!!!  I will go into more depth in class tomorrow (as I am dead tired because of a combination of extracirricular factors), and I can answer more fully Veronica's questions.  But, anyways, here!
-Nick P.
<3
<3
<3

Another Poster Draft

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I am also working on my general oral presentation as well as presentation slides for JSHS.

Thanks very much!
-VD

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Poster is looking good! The

Poster is looking good! The font size on graph titles and labels is improved, still not uniform. I'm sure you're working on this, along with everything else. Tomorrow, we can look at places you can reduce/streamline your text (i.e. "This project attempts to find a new path to achieve breakthroughs" is simultaneously vague and obvious)
Let's look at your JSHS slides tomorrow and schedule a practice presentation.