Arnob #5 - Final Day and My Presentation

It's been about three weeks since I finished my lab. Within that time, I visited colleges, went to Chicago for my grandfather's 90th birthday, and then came back home and slept and did school work/college apps.
To sum up my experience in the lab in a couple words: "Extremely challenging, but interesting and rewarding". Everything from learning MATLAB to my PI Mike challenging me to think like a graduate student was difficult. But as I got more and more into the rhythm of my open-ended research, I started to slowly conquer these challenges.
I presented to my lab members on my last day at the weekly lab meeting. There was about 15 people attending my presentation, most of them post-docs. I was expecting my presentation to be no more than 10 minutes, but my 8 slide presentation ended up being 45 minutes long. This occurred because many of the lab members (mostly post-docs) were constantly asking me questions and seemed genuinely interested in my research. This made me happy but I also had be very focused and calm during my presentation. In the end it was a a great success (exceeding even my own expectations). Mike (PI) was going to bring everyone out to dinner to celebrate me leaving the lab (as he does with everyone) but he had to catch a flight to visit an ill family member. But nonetheless, my last day ended strongly and I'm glad I got this experience over the summer.

Soo Entry #5, Heading Back to School

My two-month-long internship in Dr. Bassett's Research Lab has ended, and now I am getting ready to head back to Peddie. I have learned so much working with her and it was an unforgettable, valuable experience. For future EXP students, I have made PowerPoint slides summarizing my EXP experience, and here is a glimpse of it:

I'm excited to share my story with my friends who are getting ready for their own EXP experience next summer :)

Jenny - Entry #5 at CHLA :(

I am sad to say that this will be my last week here in the lab and CA before I go back to school. I basically spent my whole summer here in the lab and in Mongolia with other CHLA staff, so I will definitely miss it! This past week has actually been pretty slow in terms of actual work. I technically finished my work for the 3D surface rendering, and all we had to do was see it on Imaris (3D imaging program) this week and see how it turned out. The final product turned out to look pretty awesome and I think we were all pretty happy with how it looked! There were some parts where the bronchi were all interconnected where they were not supposed to be (the program probably highlighted blood vessels accidentally) so we had to call an Imaris specialist to see where we can cut certain parts of the rendering.

Anyway, outside of my main project, I've been catching up on reading and work in the lab. Denise and Soula have been extremely busy lately because there is a lot of reading, writing, and experiments to do. I've just been helping out by making some solutions when they ask, and doing some washes for lung samples if they were busy. 

I also made a new friend which was pretty nice! In the last few days, I started talking to another girl who just graduated from USC, and although I've seen her around in the lab, we sat at computers that were in completely different areas, so I was never able to see her or talk to her. But we got along really easliy and went out for lunch a couple times after that - I wish I had talked to her sooner! I will really miss her when I'm gone because it can get pretty lonely and boring in the lab when you're alone doing the same thing over and over again.

On the last day, I was sad to leave, but I definitely had a fun summer with a super amazing team and project. I am planning on visiting whenever I am in California again and might even come back next summer depending on how everything goes. Words cannot describe how grateful I am to have experienced such a patient and kind lab. I hope everyone else has a great rest of their summer (which is almost over :(...) and I'm excited to see everyone back at school.

Bridgid, Entry #5, Getting Off the Hook

Hi Fellow EXPers!

Sorry it has been a while since my last post, it’s been a crazy few weeks since my time ended in the lab. (college visits, summer work, hopefully I'm not alone here......) I officially finished my time in the lab the first week in August.  The last 2.5 weeks in my lab were great, frustrating at times, but I ended up getting results for my project, which is so awesome to think about since I was only there for 6.5 weeks!

Lucky for me, these last two weeks were really the only time that I experienced some frustration in my project.  Since I had already extracted the DNA from all of my 18hpf and 24hpf samples, the only step left was to run a good PCR so all the bands were visible on the gel so that they could be cut and sent to be sequenced, with the ultimate goal of getting clean sequences back to genotype the fish.  Seems simple, right? Yeah that's what I thought, but Not exactly.  From the start there are a few things about this process that make it not exactly a piece of cake- 1. Because I started with single embryos that weren’t that developed to start with, there is limited DNA that I could extract in the first place which means that the PCR could easily be faint on the gel and hard to amplify, and 2. The entire process of running the PCR, making a gel, then running the samples, cut the bands, and preparing the sequencing reaction takes much more time that you think, so having to start from the beginning of the 2 hour PCR reaction every time is a bit of a pain, but nonetheless is very doable.  

It seemed that just about every time I ran the process, something went wrong- the bands were too faint to cut, the samples were some how contaminated, or worst of all I would get through the whole process, send the purified PCR off to be sequenced and have the sequences stop 150 base pairs before the mutation.  Between the last two weeks, I probably ended up running that whole process about 5-6 times (which is a lot, trust me).  The whole time, Patrizia and I continued to troubleshoot and figure out why we couldn't get clean sequences; adding more eth. brom. to stain the gel, running the gel longer, and even changing the sequencing core to Penn and not CHOP, and still nothing, for any of the samples.  We had just about tried everything, when Patrizia had one last idea- try centrifuging for longer during the purification to make sure to elute the DNA. So I ran the PCR one more time, cut the bands, and centrifuged for double the amount of time to make sure we had all the DNA we could possibly extract and sent the PCR off to CHOP (NAPCORE) for sequencing.  Both of us were so anxious about getting the sequences back, but when we opened the files, almost all the sequences worked for both time points, which meant that we could genotype the fish!!! It was really so exciting to finally know that I had a result and that I was able to help Patrizia confirm what she thought for her paper!! After looking at the pictures I took before and comparing the different straining of the 3 genotypes, we concluded that there was really no difference in the expression of the transcription factor, lmo2, in the mutant, heterozygous, or the wild type, which means that the mutation must affect something else further downstream.  Patrizia then helped me gather some pictures and graphs for my poster, which was so nice and extremely helpful!

Aside from my main project with lmo2, while we were waiting for the sequencing results, I started another project.  My second project involved going into the fish room, which so cool in itself and required me to cross an mll mutant fish with the new transgenic line to look at the expression of the hematopoietic stem cells.  On Wednesday night, Patrizia, Abby, and I all went to the fish room, where I learned how to prepare the breeding tanks.  Then, the next morning, I came in early to learn how to heat shock the fish (we heat shock them in order to make transgenic line expression MLL-GAS7, which has a heat shock promotor upstream from the gene).  I also learned how to sort the fish after the heat shock, based on the presence of a green heart (how we know that the fish are expressing MLL-GAS7).  Early the next week I helped Patrizia start the WISH, and although I didn’t get to finish it, she said that she would finish it and send me the results so that I could include them in my poster.  

Overall, my experience in the Felix Lab this summer was probably one of the best experiences I’ve ever had.  I learned so much in such a short amount of time and everyone in the lab was so welcoming and always there to help or answer any question whenever I needed.   I thought that my project was great, it was just the right balance between giving me freedom and feeling like I was doing something on my own, but at the same time, I never felt overwhelmed with not knowing where on earth to start or what to do next.  My post doc was a fabulous mentor and never really made it feel like I was working. Six weeks goes by amazing fast, especially when the days don't even feel like work. I don’t think I could have asked for a better lab team or environment to spend 2 months of my summer in!

I hope that everyone had a great time in their labs! Can't to hear about everyone's summers in person in just a few short weeks!! See everyone soon! :)

Emma, Blog #5, A close to the summer

After ten weeks in the lab, my summer at the Siegel lab has officially come to a close. It is so weird to be saying those words, as the last ten weeks have flown by so quickly.

I ended up finishing my two projects, one with the other high school student Meghan doing immunohistochemistries on ketamine and saline treated brain slices, and another running TMazes (a working memory paradigm) on mice with a Dexras1 abscission.

The results from both of my projects endeed up yielding publishable results which I am ecstatic about. I will not be an author of either of the two papers my results will be featured in, but I will be acknowledged in the reference section. The first paper I expect to be sent out for review will be the one about Dexras1 abscission's in mice, and whether this specific genetic manipulation cause schizophrenic-like endophenotypes. Below is the final report I gave to the post-doc writing the paper on what I found out about working memory in mice with the Dexras1 abscission.
Note: I couldn't paste the graphs I made on Statistica into this blog because they are not compatible.

T Maze Report

Dexras Mice

12 mice total

Wildtype Mice

14 mice total

Possible point of interest for future studies (?): Dexras mice on average ran 8.33 trials in T-Maze across 3 days, whereas the wildtype ran 10.067 during the same time period.

95% confidence interval for % of correct choices for Dexras mice: (.5, .65)

95% confidence interval for % of correct choices for WT mice: (.58, .72)

Null hypothesis: The % of correct choices is the same for Dexras and Wildtype mice.

Alternative Hypothesis: The % of correct choices is different for Dexras and Wildtype mice.

P-value: .104

With an alpha level of .05: Because the p-value is so high, we fail to reject the null hypothesis in favor of the alternative. Evidence to suggest that there is no difference in the % of correct choices in the T maze between Dexras and Wildtype mice.

This data supports the claim that there is no difference in working memory between Dexras and Wildtype mice.

My second project was about whether or not the number of neurons (measured by density and area) were different between the brains of ketamine treated mice and saline treated mice, This relates to schizophrenia because ketamine is an NMDA antagonist and produces symptoms in people similar to those that schizophrenics experience. We were in effect, trying to figure out if the cause of these schizophrenic like symptoms had to do with a difference in neurons in the prefrontal cortext. 

Immunohistochemistry Report

Ketamine Mice: 3429 (6 sections), 3425 (6 sections), 3418(6 sections). 18 sections total

Saline Mice: 3422 (5 sections), 3413 (6 sections), 3412 (6 sections). 17 sections total

Two ways we measured whether or not the amount of neurons differ in ketamine or saline exposed mice: Density & % Area of neurons in brain slices

Density: 

95% confidence interval for density of neurons in ketamine brain slices: (~.00018, ~.00026)

95% confidence interval for density of neurons in saline brain slices: (~.00016, ~.00023)

Null hypothesis: Density of neurons will be the same between ketamine and saline treated mice.

Alternative hypothesis: Density of neurons will be different between ketamine and saline treated mice.

P-value: .285

With an alpha level of .05: Because the p-value is so high, we fail to reject the null hypothesis in favor of the alternative. Evidence to suggest that there is no difference in neuronal density between ketamine and saline treated mice.

This data supports the claim that ketamine does not alter the amount of neurons in the brain in the long term (in this case 6 months after receiving treatment).

% Area:

95% confidence interval for % area of neurons in ketamine treated brains: (~5.2, ~9.5)

95% confidence interval for % area of neurons in saline treated brains: (~3.1, ~7.75)

Null hypothesis: % Area of neurons will be the same between ketamine and saline brain slices

Alternative hypothesis:  % Area of neurons will be different between ketamine and saline treated brains.

P-value: .195

With an alpha level of .05: Because the p-value is so high, we fail to reject the null hypothesis in favor of the alternative. Evidence to suggest that there is no difference in % Area of neurons between ketamine and saline treated mice.

This data supports the claim that ketamine does not alter the amount of neurons in the brain in the long term (in this case 6 months after receiving treatment).

Jenny - Entry #4 at CHLA

Hello everyone, I'm back for my fourth blog post. This past week and a half was pretty ordinary. I've still been working on the imaging of the lungs, and it's taking much longer than I thought it would. The process is pretty tedious, as I'm basically sitting at my desk,staring at 283 slides of similar images on the computer for hours. I'm not complaining, though! I am super grateful that I am able to help out my lab so that they can use this for their grants in the future - and hey, someone has to do the work, right? My PI has been super busy writing her grant and going to conferences and I've pretty much been working alone.

Last Friday, though, I was pretty so close to finishing up my slides (only about 10 more out of 283) and then the worst possible thing happened - the program crashed. I thought that it wasn't a big deal because I had been saving so frequently, but unfortunately, when I opened up the file, nearly all my data from the week was gone. At first I was kind of in disbelief that basically all my work had been erased, and then I just got very annoyed. Not only did we never figure out why the program crashed, but I never retreived the data back. But no matter how upset I was, I reazlied that this is what research is about. Not everything works out the first time, and you have to keep trying and troubleshooting to get results. Since it was the end of the week, I was just told to go home and rest so that we could figure it out the next week.

Thankfully when I came back to the lab, the situation was looking a little better. Although my data would never be recovered, our imaging specialist came up with another method so that the process would go by much faster. Instead of me individually circling each cell, he manipulated the image so that nearly everything, even dimly stained parts, of the lung would be highlighted. All I had to do was erase the "fuzzy" spots, since a lot of the marks were not significant and would just be background noise in the final product. This method was much more efficient than before, and I was able to finish it in 3 days instead of a whole week! I just had to keep going at it, with Spotify by my side.

And as I mentioned before, I had been testing out a new protocol for clearing human lung tissue for antibody staining. A 15 week sample was mostly cleared so the goal by the end of the week was to mount it in primary antibody. Unfortunately, because my PI was not directly here with me and her assistant, we were unsure of exactly what antibody she wanted and there was a lot of confusion. Eventually, everything was figured out and I washed and blocked the sample, while the assistant mounted it in the primary antibody. Next week will be my last week at the lab, and even though I haven't even left yet, I know I'm going to miss everyone so much! I hope everyone's having a nice summer!

Julius, Post #4, Turn up for Biology

The sample tested was a new compound (described in previous post), which I had synthesized the day before. Part of the "triazolopyrimidine" family of compounds, it is structurally similar to previously tested compounds. We tested the compound for its "MT (microtubule) stabilizing" ability. A common symptom in Alzheimer's patients is the destabilization of neuronal cell microtubules. This leads to cell death, as the microtubule plays an important role in intracellular transport. Thus, compounds with the "MT stabilizing" properties are at the focus of Alzheimer's research.

When I got to the lab in the morning, I met Jane. Jane had been a post-doc at the lab for a year and a half, and had done her graduate work at Temple on cocaine drug studies. The first thing she did was show me around the lab, which was a pretty big surprise to me. The lab was only 3 years old, compared to our 42 year old chemistry lab, with a beautiful view of the campus and spacious, clean work spaces Despite my love for our chemistry lab, I had to admit that the medical lab seemed much nicer, an opinion that my other lab-mates agreed with. 

While Jane showed me around the lab, she explained the steps of the experiment. In her words, we were to "test the microtubule stabilizing" effects of the compound on "QBI-293" HEK kidney cells through an "ELIZA test". In order to do that though, we would first have to conduct a "BCA protein assay" in order to determine the concentrations of the proteins in advance. I did not understand anything she was talking about, until she explained it to me in laymen terms.
"So basically", she said, "we're adding the compound to the kidney cells, then using a lysis buffer to open the membrane and collect the proteins."
(Wait...so the cells die in the process)
"Yeah, the cells die when you add the buffer. That way it prevents degrading and accumulation of protein."
"Then we'll add BSA to the cells, which will help change the color of the cells for the BCA protein assay.
(Wait, what's BSA).
"Bovine Serum Albumin. Write that down. It's important for determining protein concentration."
(Got it).
"So, using a BCA protein assay, we can find the concentrations of the proteins. Basically, depending on the concentrations of protein, the cells will change color. So by measuring the color change of the cells, we can then quantitatively determine their protein concentration."
(And that's it?)
"No, that's actually the preparation for the ELIZA test itself. We need to know the concentrations of protein to conduct the ELIZA. You'll have to come in tomorrow to finish that."

So, for the rest of the first afternoon, I shadowed Jane as she conducted the preparation for the ELIZA test. It being my first time in a biology lab,  I had a lot of  questions for her, which she answered patiently. There was a lot of precise pipet work and centrifuging involved, but I was just waiting a large portion of  the time. I was definitely surprised by how much down time there was between the different tests and assays. (In the chemistry lab, there are often several different reactions and purifications occurring at once, meaning that we're at work more frequently).

So the next day, I showed up early for the ELIZA test.
"So today, we'll be conducting the ELIZA test."(Alright).
"By any chance, do you know what it might stand for?"(No, I'm not really sure).
"Alright, thats fine. It stands for Enzyme-Linked immunosorbent assay. What we've doing is we're adding capture and reporter antibodies to the kidney cells from before. These antibodies will bind to two types of microtubulin, and have HRP "tags" that will change color depending on the protein concentration."(So kind of like the BSA?)
"Yeah"(Alright, and why is this important?)
"Well, that's what this experiment is all about. This color change allow us to detect the concentrations of two substances: acetylated tubulin and alpha tubulin. And after we collect this quantitative data, we can use it to see the microtubulin levels, to see how effective a stabilizer the compound is".(Ahhh).(By the way, what does HRP stand for?)
"It stands for horseradish peroxidase. You might want to write that down".

Similar to the BCA assay from before, the ELIZA test worked based on color change and concentration. The two different antibodies changed color based on tubulin concentration, thanks to the HRP tag; this meant that by measuring this color change, using a specialized machine, we could quantify the microtubulin levels.

To sum the entire test up, we added the compound to the cells, first checked the protein levels using the BCA assay (which was needed to set up the ELIZA test), then used the ELIZA test to find the final concentration of microbutulin present in the cells. Gathering this data then, we were able to determine whether the compound was a potent microtubulin stabilizer based on the level of acetylated microtubulin present and whether the compound was harmful towards microtubulin levels in general (which is a negative characteristics), based on alpha tubulin levels.


When we finally performed the statistical analysis on the data (Dunnett Test, Nova test), we were able to see that the cells treated with the compound had a statistically significant increase in levels of acetylated tubulin (indicating strong microtubulin stabilizing properties) and no decrease in levels of alpha tubulin (indicating that it is not harmful to tubulin in general), meaning that the compound shows promise for further testing. 

Jenny - Entry #3 at CHLA

Hey all, I hope everyone's having a fun, research-filled summer in their labs. I got back from my trip to Mongolia with a few doctors and girls associated with the guild that fundraises for the research institute in CHLA. It was probably the best experience in my life - I learned so much not only about global healthcare and medicine, but different cultures and lifestyles! Although I am sad the trip is over, I'm glad to be back in California and continuing my project. I am in the middle of my fifth week and there have actually been a few changes in the lab when I came back. Before my trip I mainly worked with my PI, Denise, and another undergraduate, Emily. When I came back, Emily couldn't come to the lab anymore, but instead there were two other research observers, Alex and Winnie. Although we don't work together, it's nice having more people walking around on our side of the lab because it's usually so quiet! I am also working with Soula, who is like Denise's sidekick. Everyone is super friendly like I remembered and I felt right at home when I came back!

Me, Emma (a medical student from Holland), and Dr. Warburton (my lab director) sipping on tea in our Mongolian gear!

My project of imaging the human lung continues! Before I left, my main task was to wash and stain the samples. I did this for about 10-12 lung samples, and the whole protocol took a while. We were able to get 2D images images under the fluorescent microscope which was pretty cool, but the main goal was to get a 3D image where we can trace cells and see how they branch and grow. We were able to get that done with outside help so this is where I step in! (I'm sorry about the lack of pictures from the lab - I don't think I'm allowed to share them just yet!)

The 3D imaging is basically a video with around ~280 frames of the whole lung lobe that we had stained beforehand. Although just the images themself look amazing, the whole goal is to trace cells to get a better understanding of how lungs develop. Focusing on one particular antiody, our imaging specialist had already used a computer program to highlight very prominent stains. However, there are a bunch of other cells that have been stained, just not picked up by the program. So for the past few days, I have basically been tracing these undetected cells with ImageJ. It's not the most exciting thing ever, just because there are 280 frames and they all look pretty similar. I don't mind too much, however, because in the end, someone has to do it. 

On the side, I've also been testing out a new protocol on clearing tissue. Although the method to clear our lung samples was effective, some of the solution actually had melted the plastic and leaked out onto one of the microscopes - eek. When clearing tissue, methods that are shorter are usually more effective, but I am testing out the CLARITY clearing method, which takes a few weeks. I am currently waiting on an embryo and lung. I hope this method actually works! 

Michael, Post #6, A Glimpse of the Future?

Due to some misfortune (aka contaminated cells), I could not complete my final experiment by last Friday, my original last day at Drexel. Instead of calling it quits, I decided to come in for a few days this week to finish up one last experiment. Although I haven't had a ton of individual lab work over the past two days, there have been other important things going at the Bouchard Lab.

Today was Jason's thesis defense. It was the first (and last) one during my time in lab this summer, and it was interesting to see how the Ph.D process concludes. Jason came in to lab today dressed up in his suit, and at 1:00, the entire lab filtered downstairs to meet him in the Geary auditorium for his thesis presentation. Also attending were members from other labs on our floor, as well as Jason's family and friends. The talk lasted until 2:15, and he did a great job summarizing all of his work into that period of time, though his heavy use of bioinformatics was a little above my level of expertise (Dr. Bouchard even commented that he learned many new techniques as a result of Jason's work).

After the talk, Jason met with the five members of his thesis committee (including Dr. Bouchard), who questioned him while he defended his thesis. This process was supposed to last until 3:00, at which point there would be a celebration upstairs.

We set up for this party while we waited for the defense to come to an end. We hung streamers and decorations from the conference room where lab meeting is normally held and set up the food. However, we had to wait until 3:45 for Jason and the thesis committee to conclude their meeting and for the party to begin. Dr. Bouchard made a toast while Nikhil and I stood there with no champagne in our hands. The food was pretty good, and there was pizza, salad, and cake from all different places in Philadelphia.

Setting up for the party

Jason will still be in lab for a few months to finish up some work, but tomorrow should be my last day. I plan on running my final experiment tomorrow, assuming my transfection went well today. It's been a long ten weeks in lab, but I'm excited to see what results I get tomorrow!

Ally, Entry #5, how are they still marketing Olaf I mean it's been years

I'm finally on my last week.  I say finally, but I think it went by rather quickly, so seems the trend for the entire summer.  So little time left, but I still have so much work to do..

This being what I believe to be my last post (I think we're supposed to write 5?  No one answers me when I ask them how many there are supposed to be), I thought this would be a good time to talk about what I learned.

1. It's ok if you break glassware, and when you do, dispose of it properly.
Three broken test tubes, an 1000 mL beaker, and a mercury thermometer later, somehow I'm still alive.  You see, when cleaning test tubes with a wand, it might not be best to use so much force that the wand physically breaks through the bottom of the test tube.  It took me a couple to figure that one out.  There should be a sharps container somewhere in your lab, safely dispose of such glassware broken in a fit of kultzy-ness and stupidity in the box.

2. Ask questions.
If you don't you're going to end up mixing two toxic chemicals and blowing something up, and as much as Mr. Park does it for fun, it's not the best way to use your chemicals.

3. You're not always going to have something to do,
Sometimes you're going to sit around and have nothing to do.  Enjoy your free time and catch up on that summer reading you probably should have done by now.

4. Lab work can be very boring.
Sometimes you're going to have to spend 3 hours at a time cleaning test tubes.  Deal with it, it's got to get done.  Just think that if that test tube doesn't get clean, someone's experiment is going to be contaminated, so you're going to put the damn time in the make sure that test tube is squeaky clean.

5. If you read your Enviro book in the lab and your PI walks in and you're working in a marine biology lab, he will be very impressed.
Enough said.

6. Washing glassware is a tedious and over the top process.
I washed a lot of glassware.

7. The fish tank in Mario's office is cursed.
There were 6 fish in there and then 5 of them died, leaving Andy,  Steph and I bought 2 more, Owen Wilson and Creamsickle Joe, and then Creamsickle Joe died, so we bought 2 more, the Winklevoss twins (the Winklevi), and then the three remaining died.  Except Andy.  Andy is still alive.  I don't think Andy is ever going to die.

8. Listening to music makes everything go by faster.
This is a general rule for all of life.

9. If your PI is named Olaf, take full advantage.
The lab computer background is this (tiled):

And my thank you card has a picture of Olaf drawn inside:


10. Dress comfortably.
It makes such a difference when you're sitting in the same spot for hours at a time.

Until later.

Jay Ha #4 disinfection efficiency test

Final part of my research was to understand inactivation trends of E. Coli based on different disinfection methods and to assess the method with highest disinfection efficiency.

Three sets of disinfection experiments were being conducted; 1) UVC only, 2) Hydrogen peroxide only, 3) and UVC enhanced by filtered hydrogen peroxide.

Each set of experiment required all the lab skills I learned throughout the summer such as agar plating and using photoreactor.







The data turned out to be rather straightforward as both UVC only and H2O2 enhanced UVC killed over 99.99% of E. Coli within 1 minute of the experiment, and it turned out that inactivation by hydrogen peroxide only is rather negligible.

So, the 6 sets of 4watt UVC lamps that I used was way too strong to compare the effect of OH radical enhancement.

Although supposedly, I should have reduced the watt of the UVC lamp by half or so and conducted another set of experiment, unfortunately, time ran out, and I could not really do that part.

Anyways, still, I showed that the UVC lamps are super strong and effective in killing the E. Coli bacteria and I hope that the Korean Condo company would be satisfied regardless that their lamp will successfully disinfect the surface of their condos.

I had decent amount of fun doing lab at yale this summer and i hope rest of you guys would finish up your lab stuffs stronk.

Michael, Entry #5, Philly Bucket List

I'll be finishing up my time in lab this Friday. While thinking to myself on my long commute to Philly every morning, I realized that there are a few things that I wanted to do during my time here that I hadn't done yet. Striving to make some memories, I called up my friends Sidney and Jalen, who presented for their program yesterday, but won't be going back to Texas until Saturday morning. Jalen said that he was down to play some basketball at a park near his dorms (Sidney was tired), so I told him I'd meet him there at 2:00 since it was a pretty easy day in lab.

I took the Drexel shuttle to University City, then walked for ten minutes until I reached the park, which bordered the Schuylkill River. I arrived a bit before Jalen and noticed that the two courts were pretty crowded for a weekday. Jalen came with his friend, Dhruv, a few minutes later, and we headed for the courts. They forgot to bring a basketball, so we asked a group of four older guys if they wanted to have a larger game. They were willing to, so we got set up for a 3-on-3 (one sub for them) game. 

I was a little rusty since I hadn't played basketball in a while, but I regained my touch pretty quickly. We won the first game pretty easily and to the delight of our "coach," a local adult who was in the park and came over to watch the game and give (multiple) tips while reminiscing on his glory days. In the second game, our opponents gained a lead late in the game, but we made a comeback and won that game, too. 

The third and final game was probably the best of the day. It was a close game all the way through, but the other team pulled it out due to their height advantage. We were all pretty winded, and all three games took a little over an hour to complete. The three of us relaxed for a bit in the shade, then headed over the bridge and back towards University City. I said goodbye to Jalen and Dhruv, wished them luck, and walked towards the train station. I picked up a much needed Gatorade on the way, boarded the train, and arrived home at about the same time as usual. 

It was nice seeing the University City portion of Philadelphia. Although I thought I would be working there until about a week before I began at Drexel, I've only been to that part of the city once, when the Philly EXP students met Dr. Peretz for lunch at Shake Shack. It was one more thing I can cross off of my bucket list. 

Conor, Entry #5, If Only Our UAVs Could Fly By Like Time

It seems like whenever I am off 3D printing one of my parts, I always tend to miss the good stuff. In my last blog entry I mentioned the quadcopter catching on fire. Recently, I missed the event of one of the blades tangling in the supposedly fail-safe line which resulted in the quadcopter flipping upside down and crashing into the ground. This event also broke two of my 3D printed parts, which resulted in more 3D printing from me. But not all that I miss is catastrophic. Most recently, EJ and Ben finally cleaned up wall following. This means that all of the different controllers that we made are done, and we can now finally piece them together to finish our whole project! This however is easier said than done.

This diagram is what I made the first week I was here. This is supposed to simplify all of the nodes that are happening by visualizing which topic publishes to which subscribing topic. Obviously there is a lot going on so it is by no means simple. 

I however have been occupied by a different project recently. I am now designing a charging station that will lie on top of the segbot for our UAV's to use. This charging station opens up new possibilities for further research, such as increasing autonomous exploration for the drones. A typical exploration project with a uav is limited to the relatively small flight time that its batteries supply, which is under ten minutes. With this charging station, the uav's can recharge by harnessing the segbot's power, whose batteries last for a surplus of three hours.

I have finished designing all of the components for the charging station, and now it is time to 3D print, lazer cut, and vacuum form all of the parts. This should assuredly keep me gainfully employed here during my last three days. This week for me is not only my last, but also the most exciting. I will be leaving with a boom, but all of us in the lab are hoping that it won't be a crash landing.

Arnob Entry #4 - Monkeys next to my lab that I didn't know about

Wrapping up the second to last week in my lab, and it's definitely crunch time. On my last day I will give a presentation at the weekly lab meeting about my research. Hopefully I can finish my research by the end of this week so I can have all of next week to prepare and edit my presentation. My graduate student, Yul, has been helping me with my research the entire time and I am sure that he will also give me feedback on my presentation. My PI Mike has also given me pointers about my presentation and ideas on what areas to focus on. In my meeting with Mike last Monday, he challenged me to think more deeply about the concepts of my research and also to think about areas which I haven't really been focusing on (for example, to analyze the failed trials much more than I have been doing). The 'thinking' aspect when confronting these deeper conceptual ideas has been very difficult, but I also need to create the proper graphical representations on MATLAB which will also be challenging. However, Mike did hint that a high school student usually wouldn't be able to properly analyze research to this extent. I have been motivated by his challenge and hopefully I will be able to overcome it. 

On a completely different note, I was pretty surprised by the news I found out the other day. Many of the lab members work with monkeys for their decision-making experiments. What I didn't know until 6 weeks into my lab was that the monkeys lived in the room across the floor from my lab. Of course I wouldn't be able to work directly with the monkeys but NaYeung, a fellow lab member, said that I could be able to watch the monkeys through some glass wall when she performs one of her experiments. Looking forward to that and will definitely post some pictures (if she lets me take some). 

I don't have any good pictures from the lab this week, so here is a picture of this concert I went to with Jesse. It was the free concert at the Lincoln center that we happened to come across and there was this Brazilian band performing. Their most memorable song was about an experience the band had. They were in Japan on one of their tours and they had a cab driver whose name was Charlie, and the whole song was about their conversation in the cab with Charlie.

Katie Entry #4: Transduction

My fifth week in the lab was very busy and exciting. At the beginning of the week,  I was told that I would present all of my work from the past few weeks to my lab during lab meeting on my last day so I began working on my presentation.  I also finished my growth curves from the previous week and streaked and grew cultures of the wild type and two mutant strains of S. aureus  that I would be using later in the week for transduction.
Over the next few days, I made two phage lysates that would each carry a mutated region from a mutant strain that exhibited cold sensitivity in the primary and secondary screen.  I did this by mixing a phage lysate that was previously grown on wild type cells, each mutant strain, TSA and TSB. Then, we plated the mixtures on hard agar and incubated overnight.  The next day, we scraped off the soft agar and sonicated and filtered it, resulting in the two phage lysates.  We then repeated this procedure using the mutant phage lysates and the wild type cells and plated the mixture on TSA with erythromycin.  Since the transposon insertions in the NARSA mutant library strains contain a plasmid encoding macrolide resistance, only the wild type bacteria that were successfully transduced and carry the mutated region would be able to grow on the plate containing erythromycin.

These are the plates of the wild type cells transduced with the mutant phage lyates.

This is what happens at the cellular level during transduction.  We used a phage lysate grown on wild type cells to infect mutant bacteria cells, incorporate part of the bacterial genome containing the mutation into their own DNA, and infect and pass on this mutation to wild type cells.  The resulting wild type cells will then be tested for cold sensitivity by measuring the growth rates through ODs like in the secondary screen.

Unfortunately, the transduction did not work very well and only one plate of the transduced wild type cells had a few colonies growing.  This may have been because we did not use enough bacteria or we did not incubate the plates for long enough. So I grew more cultures of wild type and mutant strains for transduction the following week.

Also, Mrs. Terhaar visited the lab midweek, which was really fun.  I got to show her my work and explain what I have been doing so far, which was also great practice for my presentation. 

Ally, Entry #4, Excessive Test Tube Washing

This week has been pretty routine.  During the mornings, we work on extracting FA, or dissecting crabs, something along those lines.  During the afternoon, Steph and I clean out the crabs' tanks.  It's a pretty nasty process, and usually we have Mario or Mike to help.  It's definitely at least a two person job, better with three.

I generally take the food the crabs didn't eat out of their individual tanks before they get a water change to make cleanup easier.  Steph and Mario or whoever is helping out drains the water from the tanks and put the crabs in a separate container while they rinse out the container and scrub the sides.  The crabs are uber aggressive and I'm very easily startled.  I mean I yelp whenever they snap at me.  Or when someone walks up behind me and surprise me.

The room smells like clams all the time, and I swear if I never see another clam again it'll be way too soon.  Every time I smell clams I get the war flashbacks of cutting them up.

Mrs. Terhaar visited on Monday and confirmed by beliefs that our test tube washing process seems excessive.  The test tubes are soaked in soap and water, then scrubbed with a wand for at least ten seconds.  The tube is rinsed out with tap water 8-10 times, or more if there's still soap in it.  Then the tube is rinsed out a few more times with distilled water, before being wrapped in tin foil and put into the muffler furnace where they're heated to 550 degrees.  Then after that, they're solvent rinsed with methanol chloroform.  All done with gloves, even the washing before the test tubes get heat blasted.  It all seems very wasteful.  I mean I'm using so much water to clean test tubes, while in California Tom Selleck has to steal public water for his avocado farm.

Also here's a crab that died on Friday: