Sophie Kennedy: B.I.O.S. Week 5

For my final week in Sam’s lab it was definitely the busiest one. For starters, Kevin was away all week- making our lab feel nearly empty but also giving the three of us a lot more work to do! Lea started her certification process and dove a few days that week while Annie and I caught up in the lab. It’s a funny feeling to leave people working in the lab and go diving; it was nice to see others doing it as well. Most of the week I continued collecting growth data pictures for Kevin’s maps and also collected and settled the planula from the porites. This week was exceptionally busy because of all the settling we needed to do in addition to all the growth and settlement checks. We were definitely caught off guard that the corals did not spawn in as high of numbers as the previous month. Sam thought this could be because they spawned quite a large amount in June. Our wet lab had also had a flooding problem that week, so we could have lost a lot of planula if the water was high enough to allow the planula to float out of the mesh containers.

Also this week Sam asked me to present what we do in our lab to all the other interns. I wish I could have presented our data but since Kevin and Annie presented before me, it would have been too repetitive.  I was happy to even have the opportunity to practice my presenting skills. Taking the pictures and videos that I had collected over the 5 weeks I was at B.I.O.S., I combined them into a short video. I wanted to speak during the presentation however, an intern the previous week used a video to present her data and that was what all the others raved about. So I went with a video instead. Listening to the other presentations really helped me understand what can grab the audience’s attention so I am looking forward to showing the future EXP students some tricks and my video!

Lab selfies 

Porites astreoides

Dr. Sam swimming to get the boat

Jada Myricks- Chaiken Lab- Week 6 08/18/14

Week 6 Final Week at the Chaiken Lab

This is my final week at the Chaiken lab. I saw a very interesting presentation from a graduate student at the lab on how the cholesterol that makes up the lipid membrane on HIV was influenced when treated with various peptide triazole entry inhibitors. Even though his results were unexpected he figured out a new approach for his experiment when he opened up the floor for questions.

This week was shorter because I had a doctor and dentist appointment scheduled for the last two days so my last day was on Wednesday. I worked on my poster and watched Charles try to figure out what is wrong with the KR-13 we were using.

It was a valuable experience being in a real professional lab setting. I learned so much! When I entered the lab all of the equipment was foreign to me and I felt a little out of my element. Everyone at the lab helped me along and were patient with me. I am so thankful for everyone who has supported me and given this amazing opportunity. I also want to wish the Chaiken Lab a good luck in all their future experiments and endeavors. Their research is going to save a lot of lives.

Here is a picture of my lab (it's a tad outdated, but for the most part its on point)!



Thanks to everyone especially Dr. Peretz and Dr. Crider!
-Jada

Jada Myricks- Chaiken Lab- Week 5 08/11/2014

Week 5 Back to the Drawing Board

Viral Gradient Centrifugation and p24 ELISA plates

Since our previous work wasn't as successful we are going to repeat the same processes in hopes that our results will be more predictable. We began the with the viral gradient centrifugation. I established a gradient using two liquids of different densities One was at 20% and the other at 5%. I began to fill the centrifuge tubes slowly with the 5% and then little by little added the 20% liquid. This produces a steady increase from 5% to 20% by adding a higher concentration in increments until it reaches the 20% concentration. After 12 tubes of these gradients were made I moved to pipeting the virus just on the surface of the liquid so that it wouldn't mix before centrifugation. I loaded all 12 of the tubes in the centrifuge and let them spin for 2 hrs.

After the centrifuge I took out the tubes and removed the first two layers of liquid. These first two levels would most likely not be useful because they would almost entirely just be virus that didn't distribute throughout the tube. Next I pipeted just below the surface of the solution and filled the wells on the plate making sure I kept track of which levels I added to each well. It was really important that I didn't pipet too far down in the tube because that would disrupt the gradient and then the tube could not be used.

Then these plated samples were put into the freezer overnight for the p24 ELISA plates I would be doing. It is best to have them sit overnight because you want as many of the viruses as possible to stick to the ELISA plates for a clearer reading.

The next day I did the usual ELISA process. I block all sites not occupied by virus with BSA. After that I added the primary antibody and that was placed on the shaker of 1 hr. After that I went off to lunch with Dr. Crider and Alex!!!!! Yum :)

Then I did 3 washes to rid the plate of any thing besides what was to be detected. Then I added the secondary antibody which is conjugated to an enzyme. This enzyme produces a colormetric detection when its substrate is added to the sample. I put the results in the plate reader and this is what I got! This is a much better reading than the one before, but there are some mysterious inconsistencies that need to be figured out.

In the rows with the green corners are the averages of each set and then by column the are grouped by kind. They should be similar from top to bottom and should dwindle from left to right excluding the last two columns which are controls. So while this assay shows a slight trend there must be something going on with the KR-13 molecule itself and not just the virus.

Thanks!
-Jada

Jada Myricks- Chaiken Lab- Week 4 08/04/14

Week 4

The results were not what was expected at all. There must have been multiple errors along the way because there was only one set of assays that showed any kind of trend! After some error analysis we concluded it was most likely due to the heavy washes and the abuse that the viruses endured during the gradient concentration procedure and ELISA. These procedures can prematurely destroy the virus and then it cannot be detected in the final step of the assay which gives the colormetric detection. Below are the results of the 2f5 epitope ELISAs which showed the most promising results despite the large margins of error.

In this assay ist seems that as the concentration of KR-13 increases so does the absorbance relative to the control. This means that HIV was inhibited more at higher concentrations of the KR-13 molecule which supports how effective it may be.  Next week we will have to go back and repeat the previous experiments beginning with the baseline assay of p24 which will cancel out any infectivity being attributed just to the number of viruses in the sample.

Thanks!
-Jada

Caroline Casey - Week 10 - Complex Systems Group: Lab Presentation, 'Donut Day,' and Continuing my Project - University of Pennsylvania

This week was very eventful! On Monday, I prepared to give my presentation on my project at the lab meeting. It was an amazing experience, I received a lot of helpful input from the other lab members. Monday was also my 'donut day,' I brought in homemade cookies for the lab members during the lab meeting and they all loved them!

On Tuesday, I worked on identifying the differences in the community structure between the interference and non-interference groups. I computed a z-Rand score for the community assignments for the two groups and got a score of 0.0180. This result is very good, it means that the community partitions of the two groups are significantly different from each other. I was very excited by that result. I then went on to plot the community assignment of each node onto brain surface plots, where the nodes were colored according to community assignment. I continued working on that on Wednesday.

Thursday was my last day physically being in the lab, however, Dr. Bassett and I met and decided I would continue working on my project throughout the school year. I am very excited to continue with the research. I will be touching base with her every week or so to discuss the progress of my project. We also discussed the new paths we plan to take in my project. We decided to dig further into the differences between the interference and non-interference groups. We think that focusing on using those two groups is better than the four scenarios I was working with previously because we don't have to explain how learning is involved in the process. After we discussed the new path I will take, I realized that the 'paper' I was writing before is more like a collection of all the steps I took, a lot of steps that we won't mention in the actual paper we will send for submission. We will be writing the true paper as we explore more and start to see more results. Dr. Bassett and I had a very nice conversation where she told me that I am seeing what true science is like because we we are exploring many different paths in order to get the results we want and we are forced to think critically about every step. My project is difficult to see results in immediately because we are looking for a very specific sub-network that predicts the interference effect. Dr. Bassett said that we should eventually have enough information to write a paper and she also told me that she would be using my project and results in her grant proposal later in the year. I am so happy to know that I will be helping the lab in this way! At the end of the meeting I asked Dr. Bassett if she could write my college recommendation and she said she would be very happy to write one for me.

Although I am sad that my time in the lab is over, I am very excited to continue working on my project throughout the year. The prospect of having my own research published is amazing! This experience in the lab was eye-opening and made me realize how I really want to continue with research in the future. I really enjoyed getting to know the lab members and learning what it is like to be in a lab.

Chris Oh Week 5 - Gabrieli Lab, MIT

On Monday, I had a brief meeting with Zhenghan to discuss further analyses of the data.  She introduced to me some advanced statistical terms such as OLS Regression and ANOVA that I can use for data analysis.  She also suggested that I try plotting graphs that look at the correlation between the out-of-scanner phonetic scores and the average duration of just the 5-syllable words.  At the end of the meeting, I asked Zhenghan if I could get a chance to observe a scan this week, and she said I could come to a scan on Thursday.  For most of the week, I spent most of my time trying to familiarize myself with the statistical concepts that Zhenghan had mentioned.
Excited to observe a scan for the first time, I came to the lab on Thursday morning to hear that the scanner we had reserved was shutdown due to technical difficulties.  The scan was postponed to the following day.
On Friday, there was a lab meeting at noon primarily due to a new member of our lab.  After a series of brief announcements from Dr. Gabrieli, the new postdoc gave a presentation on her research.  Her topic was functional specializations of emotion and memroy processing using MEG.  Although I couldn't understand everything from the presentation, the topic was fascinating.  Around quarter to three, I had a meeting with Dr. Gabrieli.  It was my first formal meeting with him, and I was initially a bit intimidated by his imposing stature.  But soon, he turned out to be very, very friendly and funny.  We briefly discussed my work so far at the lab, and he thanked me for all the hours I put in for the research.  We then moved on to talk about several other topics.  Shortly after the meeting, I went to the first floor where the imaging center is to meet with Zhenghan for the scan.  Madlyn, another high school intern, volunteered to be our participant as it was her last day at the lab.  For Josh, the new technical assistant taking over for Michelle who is leaving in a week, it was his first scan.  Before we got into the scanning room, Madlyn had to fill out a form to make sure she doesn't have any metal in her body and Josh brief explained to her the task.  Then we got into the scanning room, and the amount of prep work before the scan stunned me.  Before we began the task, we had Netflix on for Madlyn so we can get a rough scan of her brain.  Then, we started the functional scan.  Because the new scanner did not have a microphone, we did not conduct the Non-word Repetition and the only task for Madlyn was syntax task, where she pressed left or right button depending on the correctness of the phrase presented to her.  After the three trials of syntax task, we turned on Netflix again while we took Diffusion Tensor Imaging, or DTI.  As Josh was still going through the learning process, Michelle and Zhenghan's hints and instructions taught me so much about brain scans.  The task only took about 5 to 10 minutes, but the time we spent in the scan room was almost 2 hours due to much prep work and post-scan work.
It was probably the best moment I have had at the lab so far.  Here are some pictures from the scan:

Josh preparing the machine before the scan

The scanner that we used

During the syntax task

Caroline Casey - Week 9 - Complex Systems Group - University of Pennsylvania

This week, I spent a majority of my time preparing for the PowerPoint presentation on my project that I will be giving to the lab group on Monday, August 18.

On Monday of this week, I completed finding all the interference values from the ANOVA of the four scenarios with the before, within, and after scanning session movement times that I started working on last week. I then plotted the distribution of the interference values. The distribution was not normal (not much of a surprise since the ANOVA values from the original pre-post scanning session data were not normal either). I then began finding interference values from the difference between the movement times at the two time points for the four scenarios, for each of the 20 subjects (pre-scanning session 2 movement time - within scanning session 2 movement time, and so on). If the value from the difference is negative, then the subject has interference, if the value is positive, then the subject does not have interference. This took a while, I continued this process through Tuesday. Monday, we also had our weekly lab meeting where two undergrads presented their work in the lab this summer. The presentations were very interesting, one undergrad spoke about networks in materials, specifically sand. I enjoyed learning about how networks can be applied to fields besides neuroscience.

The interference values distribution using interference values from the ANOVA. This is the third scenario: ANOVA between pre-scanning session 3 and within scanning session 3.

The interference values distribution using interference values from the difference between the two time points. This is the third scenario: difference between pre-scanning session 3 movement time and within scanning session 3 movement time.

Tuesday, I completed finding the interference values from the difference between movement times at the two time points for the four scenarios, all 20 subjects. I then plotted the distribution of the values for the four scenarios. These plots were much more normal than the ones from the ANOVA interference values. I spent the rest of the day adding and editing my paper with my new findings. I also found out on Tuesday that Dr. Bassett was not going to be in the office for the rest of the week. I created and sent her a  PowerPoint of the work I completed since our last meeting.

On Wednesday, Thursday, and Friday, I worked on my paper, read more relevant papers, and worked on the PowerPoint that I will present on Monday, August 18. I am excited to present my work to the lab and hear what suggestions and ideas the lab members have about my project. I cannot believe that I only have one more week in the lab, I am both sad and surprised that that my experience is already almost over. I hope to continue working on my project throughout the school year, finding more results and finishing the paper. This has been an amazing experience so far!