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: