My postdoc is in Alaska right now, and I will have to perform two full western blots by myself this week, but I am definitely ready for it. My time here is almost coming to an end, but I have definitely learned a lot about working in a lab.
Wednesday, August 6, 2014
Michael King - Week 8 - Loh Lab UCSF
Last week was a great week, as we were able to produce some very good results that were consistent with my postdoc's hypothesis. My postdoc will be on vacation for my last week, so we focused a lot this week on making sure I could do western blots on my own for the last week. Western blots are an important experiment in determining protein expression, and it really isn't too hard as my postdoc has already optimized his protocol. We conducted our final experiments on the cell cultures, and froze them down on Friday, as they will not be needed for this next week. Everything else has been going smoothly, and our lab also went out for lunch together on Monday. Next week a lot of people will not be in lab, though. When things are going well sometimes there is not always much to write about. I finally got a few more pictures of the equipment in my lab.
An example of the results from the experiments we conducted. Above is a graph representing a cell titer glo assay, measuring proliferation of different cell samples treated with drugs. The bottom is the western blot of the cells treated with drugs to identify induction of certain protein expression.
One of the three hoods in my lab, where cell culturing is conducted to ensure sterility. The large centrifuge is in the background, and this is where I spent most of my mornings in lab.
The setup for preparing the Vicell samples to measure cell viability. The flasks contain the various cell lines, and the small tubes in the front hold the samples. On the side are boxes of pipette tips, which we often run out of.
Something new we got at our lab, the metal beads replaced the water normally in our heater. It is used to warm up cell media and various things used in cell culturing. The metal beads will help prevent contamination that might have resulted from dirty water continuously being heated, but they do not heat up as quickly.
An important piece of equipment in lab, a microscope is especially important in checking for contamination in cell cultures.
My flasks among some others in the incubator, which regulates the temperature and CO2 content. Incubators should not have any smell, and a strange odor usually indicates some sort of contamination, which was an issue in one of our two incubators.
This is the lab bench I work at with my postdoc. Lots of pipettes and multichannels along with various chemicals needed to process cells for the various experiments he conducts. Although it might look a bit cluttered, we utilize pretty much everything in this picture on a fairly regular basis.
My postdoc is in Alaska right now, and I will have to perform two full western blots by myself this week, but I am definitely ready for it. My time here is almost coming to an end, but I have definitely learned a lot about working in a lab.
My postdoc is in Alaska right now, and I will have to perform two full western blots by myself this week, but I am definitely ready for it. My time here is almost coming to an end, but I have definitely learned a lot about working in a lab.
Monday, August 4, 2014
Colette Gazonas-Week 6-Shadlen Lab, Columbia University
This week was my last week in Dr. Shadlen's lab. Because we had already finished all of the paradigms by the end of my fifth week, I dedicated the entire week to creating my poster. Yul asked me to create a new set of visuals and to create a rough draft of the entire poster on the template. Each day I sent him a revised copy and he would respond with feedback each night.
On Tuesday Yul, You-Nah, and I met to discuss how the poster was coming along. You-Nah read it over and gave me suggestions on how to make it better. I generated a diffusion-to-bound model and a more intricate illustration of the experimental procedure. I also fixed the problems I had encountered when graphing the logistic predictions.
Because my poster was near completion by the end of Tuesday night, Yul assigned me another matlab exercise. I was to simulate drift-diffusion using the software. To do this I repeated adding some random Gaussian random value until the absolute value of the accumulated evidence reached or exceeded beta. I utilized a for loop and scaled the mean in terms of delta t(time).
I ran this simulation for various coherences, both positive and negative. I simulated up to 3 seconds and ran 1000 trials per coherence level. Then, I plotted a histogram of the decision times.
On Friday I attended my last lab meeting. Afterwards my PI asked me to meet with him for a brief discussion about my experience in the lab. He asked me about what I felt I had learned, accomplished, and asked what he could do in the future to better prepare students in my position coming into the lab. He admitted that at first he was skeptical about whether or not I would be able to contribute anything to the lab, but said that he was pleasantly surprised and would consider taking on another high school student in the future. At the end of the meeting he offered to write me a letter of recommendation and told me that the lab should feel like a second home to me, so if I was ever in the area again I should stop by.
Overall, working in the lab this summer was a great experience. I learned much more than anticipated and am overly satisfied with the fashion in which I was both welcomed and mentored in the lab. I will definitely miss working with Yul, You-Nah, and Dr. Shadlen and hope that we will stay in touch in the future.
On Tuesday Yul, You-Nah, and I met to discuss how the poster was coming along. You-Nah read it over and gave me suggestions on how to make it better. I generated a diffusion-to-bound model and a more intricate illustration of the experimental procedure. I also fixed the problems I had encountered when graphing the logistic predictions.
Because my poster was near completion by the end of Tuesday night, Yul assigned me another matlab exercise. I was to simulate drift-diffusion using the software. To do this I repeated adding some random Gaussian random value until the absolute value of the accumulated evidence reached or exceeded beta. I utilized a for loop and scaled the mean in terms of delta t(time).
I ran this simulation for various coherences, both positive and negative. I simulated up to 3 seconds and ran 1000 trials per coherence level. Then, I plotted a histogram of the decision times.
On Friday I attended my last lab meeting. Afterwards my PI asked me to meet with him for a brief discussion about my experience in the lab. He asked me about what I felt I had learned, accomplished, and asked what he could do in the future to better prepare students in my position coming into the lab. He admitted that at first he was skeptical about whether or not I would be able to contribute anything to the lab, but said that he was pleasantly surprised and would consider taking on another high school student in the future. At the end of the meeting he offered to write me a letter of recommendation and told me that the lab should feel like a second home to me, so if I was ever in the area again I should stop by.
Overall, working in the lab this summer was a great experience. I learned much more than anticipated and am overly satisfied with the fashion in which I was both welcomed and mentored in the lab. I will definitely miss working with Yul, You-Nah, and Dr. Shadlen and hope that we will stay in touch in the future.
Chris Oh Week 3 - Gabrieli Lab, MIT
My third week at the Gabrieli Lab was tough but productive.
On Monday, I continued searching for tutorials that would teach me how to use Python to manipulate Excel spreadsheets. Finding only few materials online helpful, I struggled for most of the day to figure out the basics. By the end of the day, I was able to create and format a new spreadsheet.
On Tuesday, I was learning how to read exisiting Excel spreadsheets. Because creating and reading Excel files require different libraries, I had to get used to the slightly different commands. As Zhenghan asked me to do, I wanted to add a column for the Subject ID to each spreadsheet. But again, editting existing Excel files require a different library, I was not sure how to convert to xlwt(editting) from xlrd(reading).
On Wednesday, Zhenghan was the speaker for our undergraduate/high school students weekly reading group. Her presentation focused mainly on ASD, Autism Spectrum Disorder, and why it is important to learn more about the disorder. She discussed the ongoing experiments regarding the language deficiency among ASD patients. Most of the studies done on Autism are still inconclusive, which made the topic more interesting. After much struggle that afternoon, I was able to come up with a script, but strange error kept occurring so I decided to seek Michelle's help. Michelle and I wrestled with Python for almost an hour, and we were finally able to fix the problem. When we opened the spreadsheet with xlrd and then copied the file with xlrt, we were able to write on the existing spreadsheet.
Finally on Thursday, I was able to write a script for overall average response time for each subject and add those numbers to the mastersheet. I was even able to write another script to find the overall average duration for each syllable group, which yielded quite strange results. In contrary to my previous assumption, the data showed that the longer the word lesser time it took for the subjects to respond. The difference between the average duration for two syllables and five syllables was about 0.08 seconds. After much thought as to why this was the case, I hypothesized that it must be because when subjects are presented with a longer word, knowing that they have limited time to respond, they rush not to get their responses cut off by the next scanner noise. Now the only task left was to find the average response time for each syllable group in each subjects.
On Friday, by noon, I was able to complete my task by adding numerous if statements to get average response time for each syllable group in individual subjects. I sent Zhenghan the finished products for her to look at. Impressed by my work, Zhenghan asked me to meet with her on Monday to go over plotting the data.
What my script looks like:
On Monday, I continued searching for tutorials that would teach me how to use Python to manipulate Excel spreadsheets. Finding only few materials online helpful, I struggled for most of the day to figure out the basics. By the end of the day, I was able to create and format a new spreadsheet.
On Tuesday, I was learning how to read exisiting Excel spreadsheets. Because creating and reading Excel files require different libraries, I had to get used to the slightly different commands. As Zhenghan asked me to do, I wanted to add a column for the Subject ID to each spreadsheet. But again, editting existing Excel files require a different library, I was not sure how to convert to xlwt(editting) from xlrd(reading).
On Wednesday, Zhenghan was the speaker for our undergraduate/high school students weekly reading group. Her presentation focused mainly on ASD, Autism Spectrum Disorder, and why it is important to learn more about the disorder. She discussed the ongoing experiments regarding the language deficiency among ASD patients. Most of the studies done on Autism are still inconclusive, which made the topic more interesting. After much struggle that afternoon, I was able to come up with a script, but strange error kept occurring so I decided to seek Michelle's help. Michelle and I wrestled with Python for almost an hour, and we were finally able to fix the problem. When we opened the spreadsheet with xlrd and then copied the file with xlrt, we were able to write on the existing spreadsheet.
Finally on Thursday, I was able to write a script for overall average response time for each subject and add those numbers to the mastersheet. I was even able to write another script to find the overall average duration for each syllable group, which yielded quite strange results. In contrary to my previous assumption, the data showed that the longer the word lesser time it took for the subjects to respond. The difference between the average duration for two syllables and five syllables was about 0.08 seconds. After much thought as to why this was the case, I hypothesized that it must be because when subjects are presented with a longer word, knowing that they have limited time to respond, they rush not to get their responses cut off by the next scanner noise. Now the only task left was to find the average response time for each syllable group in each subjects.
On Friday, by noon, I was able to complete my task by adding numerous if statements to get average response time for each syllable group in individual subjects. I sent Zhenghan the finished products for her to look at. Impressed by my work, Zhenghan asked me to meet with her on Monday to go over plotting the data.
What my script looks like:
Basic overview of my project (from Anna's PowerPoint):
Caroline Casey - Week 7 - Complex Systems Group: Edge Strengths, First Presentation, and Interference Distributions - University of Pennsylvania
This week was busy and exciting; I completed a lot of work and had my first presentation about my project, where I presented the PowerPoint that I was working on for the past few weeks! Dr. Bassett also invited me to present my project at the lab meeting on August 18, I am very excited and grateful for that opportunity.
Dr. Bassett was away on Monday and Tuesday. So, Monday I continued working on my paper; adding information and editing what I have so far. I also emailed Dr. Bassett a PowerPoint of what I completed the previous week when she was away.
On Tuesday, Dr. Bassett emailed me that she was intrigued by the community structure I got from the consensus partitions and suggested I look further into it. So, first, I completed community detection and consensus partitions on the brain coherence matrices (from the original fMRI adjacency (coherence) matrices in order to see if the community partitions were significantly different from the partitions from the networks where the edges of the correlation between interference and the scans (coherence matrices). I completed that and observed that the community partitions were significantly different than the consensus partitions indicating that interference plays a role in creating and changing the community structure. Dr. Bassett also wanted me to look at the edge strength of the networks. Since up until now I have been working with binary matrices, (containing only 0s and 1s) I went back and re-did everything using edge weights.
I continued working on re-doing everything with edge weights on Wednesday.
Thursday, Dr. Bassett and I met and decided that using binary matrices produced better results than using the matrices with edge weights, so we decided to stick to using binary matrices. Dr. Bassett and I also went over the PowerPoint that I would present to two other researchers on Friday. The rest of Thursday, I spent making changes to the PowerPoint.
Friday was a very exciting day. I prepared for the conference in the morning and at noon, I met with Dr. Bassett and we had a conference call with two researchers, Nicholas and Scott. I sent my PowerPoint to them and talked about each slide over the phone. Scott and Nicholas than gave us suggestions on what I could do with the results and data we have. It was really helpful to hear their thoughts and ideas! They suggested that I look at the distribution of the interference values for the different sessions in order to see if they follow a normal distribution, or if there are out-liars. I spent Friday completing the distributions for the sessions using interference values from the ANOVA and also using the difference between pre and post movement times for the sessions as interference values. After creating those plots, I went on to combining the interference values of the 20 subjects for both scanning sessions and splitting the now 40 subject group into 2 groups based on if the subject had interference or didn't have interference. I did that twice for the interference values from the ANOVA and the difference between pre and post movement times for the 2 sessions. For the ANOVA, if the p-value was significant, than the subject had interference. For the difference between pre and post movement times, if the difference was negative, than the subject had interference. I then completed a t-test between the two groups, for the two different ways I found the interference values.
I feel like I am learning so much at this lab, I am excited to see what else I learn and complete during my remaining 3 weeks at the lab!
Dr. Bassett was away on Monday and Tuesday. So, Monday I continued working on my paper; adding information and editing what I have so far. I also emailed Dr. Bassett a PowerPoint of what I completed the previous week when she was away.
On Tuesday, Dr. Bassett emailed me that she was intrigued by the community structure I got from the consensus partitions and suggested I look further into it. So, first, I completed community detection and consensus partitions on the brain coherence matrices (from the original fMRI adjacency (coherence) matrices in order to see if the community partitions were significantly different from the partitions from the networks where the edges of the correlation between interference and the scans (coherence matrices). I completed that and observed that the community partitions were significantly different than the consensus partitions indicating that interference plays a role in creating and changing the community structure. Dr. Bassett also wanted me to look at the edge strength of the networks. Since up until now I have been working with binary matrices, (containing only 0s and 1s) I went back and re-did everything using edge weights.
I continued working on re-doing everything with edge weights on Wednesday.
Thursday, Dr. Bassett and I met and decided that using binary matrices produced better results than using the matrices with edge weights, so we decided to stick to using binary matrices. Dr. Bassett and I also went over the PowerPoint that I would present to two other researchers on Friday. The rest of Thursday, I spent making changes to the PowerPoint.
Friday was a very exciting day. I prepared for the conference in the morning and at noon, I met with Dr. Bassett and we had a conference call with two researchers, Nicholas and Scott. I sent my PowerPoint to them and talked about each slide over the phone. Scott and Nicholas than gave us suggestions on what I could do with the results and data we have. It was really helpful to hear their thoughts and ideas! They suggested that I look at the distribution of the interference values for the different sessions in order to see if they follow a normal distribution, or if there are out-liars. I spent Friday completing the distributions for the sessions using interference values from the ANOVA and also using the difference between pre and post movement times for the sessions as interference values. After creating those plots, I went on to combining the interference values of the 20 subjects for both scanning sessions and splitting the now 40 subject group into 2 groups based on if the subject had interference or didn't have interference. I did that twice for the interference values from the ANOVA and the difference between pre and post movement times for the 2 sessions. For the ANOVA, if the p-value was significant, than the subject had interference. For the difference between pre and post movement times, if the difference was negative, than the subject had interference. I then completed a t-test between the two groups, for the two different ways I found the interference values.
I feel like I am learning so much at this lab, I am excited to see what else I learn and complete during my remaining 3 weeks at the lab!
Sunday, August 3, 2014
Shivani Gupta-Week 6- Reddy Lab
Shivani Gupta-Week 6-Reddy Lab
Unfortunately,
our colonies for the BirA-YY1 fusion did not grow. We determined that the
reason must be that we didn’t add enough DNA in our ligation reaction. We did
the ligation over, and grew the colonies on amp plates. Luckily, about 25
colonies grew on the BirA-YY1 plates. I then did the mini-preps over using
these colonies and then digested the BirA-YY1 with Xmal. After doing the
restriction digest verification, we found out that only one of our 10 samples
had the correct band length and we could send to sequencing.
We then
picked 10 more colonies from our plates and repeated the cloning procedure by
first doing mini-preps and then the restriction digest verification. Unfortunately,
I didn’t have enough DNA in my samples and had too much RNA, so I couldn’t see
the bands when I imaged my gel for the digest verification. We think that it
was because we may have lost some of our DNA during the mini-preps. Next week
we are going to grow new BirA-YY1 colonies on our plates, and hopefully we will
be successful.
Thankfully,
one of the sequences for the BirA-L2B matched the original construct, so I have
successfully made a fusion protein!
On Thursday, Dr. Crider came to visit my
lab. Jen and Dr. Reddy came to lunch with Dr. Crider and I, and we ended up
eating lunch in the newer part of the hospital. The cafe was so crowded, we
ended up sitting at a kids table, but it was still a great experience!
Jada Myricks-Chaiken Lab- Week 2 06/16/14
Week 2
I rode the bus down to the lab and arrived at 10 am. I went up to the eleventh floor of Drexel University's New College Building a met up with Charles. I had to review all my notes because today Charles was going to quiz me on ELISA, gradient purification, and fixing viruses. I still ended up taking a lot of notes. Then we went to the "hood" (which is a special machines that uses the powers of wind to force anything that could contaminate our samples out of the "hood" and into our regular air). Once we got to the "hood" we began virus fixation.
What does it mean to fix a virus (not be cause it is broken)? In order to make it stay put and not run wild and attach to things that wouldn't aid in our experiments it is important to fix the virus.
We added buffer solution to the virus in order to immobilize it so that when it is put on a plate for the next experiment it won't be able to move and block potential binding sites. It is most important for the next experiment that epitopes (highly specific binding sites for antibodies) be readily accessible.
After the viruses were fixed we put them on the super sticky ELISA plates which have 96 wells and put those plates in the 4 degree C freezer overnight.
I rode the bus down to the lab and arrived at 10 am. I went up to the eleventh floor of Drexel University's New College Building a met up with Charles. I had to review all my notes because today Charles was going to quiz me on ELISA, gradient purification, and fixing viruses. I still ended up taking a lot of notes. Then we went to the "hood" (which is a special machines that uses the powers of wind to force anything that could contaminate our samples out of the "hood" and into our regular air). Once we got to the "hood" we began virus fixation.
 |
| This is a "hood", but isn't the one in our lab because I couldn't get a nice angle. This image does the "hood" justice though. |
What does it mean to fix a virus (not be cause it is broken)? In order to make it stay put and not run wild and attach to things that wouldn't aid in our experiments it is important to fix the virus.
We added buffer solution to the virus in order to immobilize it so that when it is put on a plate for the next experiment it won't be able to move and block potential binding sites. It is most important for the next experiment that epitopes (highly specific binding sites for antibodies) be readily accessible.
After the viruses were fixed we put them on the super sticky ELISA plates which have 96 wells and put those plates in the 4 degree C freezer overnight.
 |
| ELISA Plate: ELISA stands for Enzyme Linked Immunosorbent Assay |
...Since the lab went to a conference in Florida and then Charles went to the Philippines for vacation I took a four
week break following this week.
-Jada
Friday, August 1, 2014
Jada Myricks -Chaiken Lab- Week 1 06/09/14
Week1
I rode the bus down to the lab and arrived at 10 am. I got another tour of the lab and Charles (my graduate student) explained every poster in the hallway to me. I took so many notes! Then I watched Charles do a gradient purification of the HIV virus.
Gradient purification is done to get different concentrations of a solution separated. Imagine a drink like the one below. In order to get its appearance liquids with different densities must be added. While our gradient was not a delicious beverage its display was very similar.
We treated the virus with a special compound called KR13. Its is a molecule that the lab developed in order to inhibit the infection of HIV virus, by disabling its Env (surface proteins), which make initial contact with cells. Charles' experiments are done in order to figure out what KR13 did to the virus and why it isn't infecting cells.
So in order to figure this out Charles put different concentrations of KR13 with the virus to see if particular proteins are being more or less disabled when exposed to the different concentrations. The samples with more KR13 were more dense and sunk to the bottom while the samples with less KR13 laid in the higher levels like the drink above.
Next Week we will fix the virus (not because its not broken) and begin some assays!
-Jada
Subscribe to:
Posts (Atom)