Science Project Blog

Syndicate content
Send by email

Upper School students publish their progress several times weekly.

Blog authors choose whether to mark items public or limit them to the Catlin Gabel community. Please log in to see more posts.

National JSHS

posted in
Send by email

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

posted in
Send by email

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

posted in
Send by email
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! 

Western blots this week

posted in
Send by email
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)
 

Lysates and protein concentrations

posted in
Send by email
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!

posted in
Send by email

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

posted in
Send by email

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. 

Before April 4th

posted in
Send by email

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

Presentation Things

posted in
Send by email
  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!

A Working PPT & Talk!

posted in
Send by email

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

Let the Storm Rage On

posted in
Send by email

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

posted in
Send by email
  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!!!!

posted in
Send by email

 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

posted in
Send by email

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

Thanks very much!
-VD

Poster Updates

posted in
Send by email

I have completed a first rough draft of my poster for the NWSES system. It still needs work, but I have attached the draft here for reference.

In other news, I am closing in on a first draft for my JSHS PowerPoint presentation as well.

Thank you very much!
-VD