Week 10 Final Post-PK

YAY!~ wow... it's I can't believe summer is over and my EXP experience comes to close. So sad, but it was extremely fun, interesting, and overall, great! 

I assume I won't be going back to the lab regularly, but I still have to analyze the data and come up with a conclusion. I actually had to go back to the lab for one extra day to get the software to analyze the data. I expect I will be going back so that Teuta can help me with my conclusion.

So ever since the last day, I could never tell whether Teuta actually like me or not... I guess that's something I shouldn't be writing. Well, whatever. On the planned last day, I brought in bubble tea to the lab right after lunch. Everyone minus my PI, Josh, wanted one (apparently they like it more than doughnuts)! Then Teuta said something along these lines: Preston, you can come back again! You're very useful... and you bring nice treats!~

LOLOL after working in the lab for over 400 hours, all I'm good for is bringing the lab treats. Hahahaa

jkjk Teuta has complimented me quite a few times over the past two years. It's just that the way she said that was funny. 

Well, I doubt I'm gonna spend 3 summers working in Dr. Joshua Shaevitz's lab, so I'd like to thank him so much. Not many would take a short, pimply sophomore kid in their lab for two summers. He and Teuta really made a huge difference to my experience. Also, I'd like to thank Teuta and the other members of the Shaevitz group. The environment was extremely pleasant and I had a great time working with and next to all of them. Once again, I'd like thank them all SOOOOOoooooo much for making my past two summers a great experience. 

Wait... I don't think any of them are going to read this... whatever~

Anyways, this is my last post (if you didn't get the hint from the title), and I'd just like to say EXP was expecially awesome!

Peace!~

-PK

Week 9 Post 2 -PK

Lahh only 3 more days!~ I'm so excited yet sad. I'm excited because I'm almost done with all of my trials. I'm sad because, well I'm almost done working in Shaevitz's lab. Hahahaaa I mixed feelings seem very weird when explaining them.

So everything I've done up till now essentially was just gathering data. I haven't had any time to analyze it really. I did a little bit in July I think, but while I'm in school. I have to do that. So I still have yet to download the software for analyzing and plotting the data. That always seems like it's a problem huh? The truth is I'm technically not supposed to get ANY software since all of it belongs to Princeton and I'm not a student. As I mentioned in a previous post, I am a "visitor". If I didn't make it clear in my other post, I'm very sad. I get the same status of a 1-day visitor despite working in a lab for 10 weeks, walking in and out of signs that say "restricted access" (or something like that), and walking through doors that require a swipe of a key card! Plus, when I buy food from the campus center, I get charged tax :'(
So coming back from my digression, I will be getting the program I use for analyzing the data on Monday. On  Tuesday, I learn how to use it. On Wednesday, I use it a bit and ask Teuta a lot of questions. Then for the next month, I'm supposed to plot, analyze, and interpret the data all by myself. Hopefully I'll be able to come to the lab during some days in September to get help, but the vast majority of it is going to be done by myself. Truthfully, this is going to be a huge challenge for me. One because I don't know statistics very well. Two, I don't know biology very well, so I may not have the best interpretations. Three, essentially I have to teach myself this program. Four, I have a bunch of other stuff going on in September that I'm supposed to do.

But so far, I think I'm going to be getting enough data to be meaningful. Data is data, but meaningful data is better. We'll see. Only 3 days left and nothing major broken. I'm keeping my fingers crossed, but we'll see.

Oh and apparently someone in the lab is working with Cholera so now whenever he's in the lab, I have to wear a lab coat. No one else does... just me :(

Peace~

-PK

Week 9 Post 1 -PK

OMGSH!~ I only have 1.5 weeks (ish) left! Overall the experience was pretty cool, but there are so many things I still want/need to do! Largh, why is there ALWAYS too little time? Well I guess part of the reason is that I'm limited by the number of trials I can do each day. Since I have to grow the E. coli that day, I can only run two trials, regardless of how fast I am at running the actual experiment. Pity...


So I just got back from my two week Bible camp retreat and I was told that once again, I am going to be doing a slightly different experiment. I still am studying the effects of osmotic shocks on the same strains of bacteria; however, I am going to be looking at a different mechanism the E. coli employ when coping with the osmotic shock. The first mechanism I studied was that certain pumps transferred materials (it depends on which pump one is looking at) in and out of the cell. The mechanism I am beginning to study now is the synthesis of materials, one of which is trehalose.


This is going to be pretty awesome, but there are two downsides of this. One, I don't get as much data on the first mechanism as I would be able to if I concentrated all my efforts on the first mechanism. Two, I have to read a lot more primary articles. It's not really that I mind the second one, but I'd really like to keep my brain fresh for the Peddie homework and college apps I do at night. (Yeah... I've been procrastinating a lot lately :( )


I can't wait for the next two weeks to come. Not just because I'm done, but I finally will feel like I accomplished a lot. Hopefully, it won't end and I'll be able to come to the lab during the school year. I don't know how that'll work out, but I got my fingers crossed that it does.


Peace~


PK

Week 8 Post 1 --PK

It's great to be back in the lab!... well sort of. I definitely don't miss the delectable aroma of E. coli. But it's nice to work with awesome equipment and know that you're doing something actually productive and brand new.

So, after my break from the lab, I returned today to find out that the next three weeks are going to be extremely  busy for me. So basically I have been running one 3+ hour experiment every day. I've done that for three different E. coli strains for different magnitudes of osmotic shocks. Now, I have to run 6-9 20 minute experiments AND the one 3+ hour experiment every day. It's a lot harder to increase my output by 600-900%! However, it should definitely  be worthwhile since I'll be able to collect a ton of data.

Sadly, I only ran one experiment today. :( This was due to technical difficulties with the optical trap. It took more than two hours to fix and recalibrate. Also, I made a few errors in the slides I prepared. Good thing I have 3 more weeks to practice.

Also, I finally got the installation CDs for a program I need to analyze the data. So hopefully, I won't be needing to analyze everything in Matlab. Matlab is really convenient for data in matrices, but it's a bit tedious and annoying to put the data into the correct format and laying it out as graphs or other such things. The program I will be using is called Labview. I'm pretty sure I won't need to learn another programming language, which is a bit nice. So towards the end of August, I'll be analyzing data while running experiments. So I'll be SUPER busy. Can't wait... seriously.

Also, I'm very happy to say that so far, I haven't broken anything despite the fact that I am constantly rushing around trying to get the timing of my experiment perfect. The problem is that timing the growth of E. coli is hard since they are living organisms and grow at slightly different rates (even if they part of the same colony and strain).

Can't wait to finish! I'll try to keep you, the general public, updated on my most current activities, but it might be hard since I literally will be working 9.5 hours a day with only a 30 minute break for lunch. :( I like breaks.

Peace~

-PK

Week ???-PK

Yeah... It's been along time since I've "talked" to you guys. A lot has happened in the past few weeks. First off, Dr. Peretz and Ms. Rodrigue came to visit my lab. I took a day off for July 4th (yay!) and am currently on a week vacation. I actually started the week vacation the day before I was supposed to give a talk with Teuta, my supervisor, and Steven, the senior undergraduate. Most people would say that good, but in reality, it's very bad. Firstly because I have to give my presentation without any help from Steven (I probably would have looked better with him presenting before or after me). Secondly  because when I come back and give the presentation, I'll forget most of what I did these past few weeks.

I have done a lot of things these past few weeks. I'm almost done with the program, I just need to edit a few lines. I've read a lot more literature simply because I am actually planning my experiment now. Based upon what I read and what I expect, that's what I am probably going to be studying. I also get to make my own primer with the help of Teuta; however, I'm not done yet. I'm really excited to start on that part of the project! Also, there's been some pretty interesting things with the results. I'd love to attach it here, but right now I can't since I need to be connected to Princeton's network.

Since my last post, I've been much better with the tricky procedure. I'm actually doing the whole procedure by myself. Teuta just does her thing and only randomly peeks in to make sure I'm not messing up any lab procedures. The only thing I don't know how to fix is the really big, complex, and expensive optical trap. It's basically an inverted light microscope that focuses light to "trap" and control small particles (less than 1 um!). It can even be used to play tetris! Too bad I don't have time for that :(

Another thing I need to do when I get back is making growth curves because I have been working with different strains and each strain has a different incubation time. It's very annoying to find out that after 4 hours of work, you can't continue because you waiting too long. So I have plenty to do in the next few weeks. I can't believe summer is almost 1/2 over!~

Peace~

-PK 

Week 3-PK

Let me start off with an apology... I was way too lazy and tired this week to write two posts. I'm sorry. 
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A lot has happened this week. I got a Princeton Net ID so I can work at home! That makes me feel a little bit better after having been reduced to a VISITOR. However, I can't actually work at home. I'm gonna try to figure this problem out, but as of now, I still can't access the programs and the websites I need to when I'm connected to a different network other than the Princeton wireless. Speaking of programs, I was able to download ImageJ, but I still am not allowed to get Labview. I might be able to get a CD that installs it from another lab, but that's unlikely.
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So throughout this week, I've been practicing and learning how to do the whole procedure safely. The biggest problem is not setting up the experiment, but setting up the optical trap. It is literally the most expensive equipment in the lab, and obviously, no one would want a  mere high schooler to be touching that unless that high schooler knows what he's doing. Thus, I've been slowly been learning each step, such as what to turn on and initialize, what settings to turn everything to, what order I press the many buttons. Surprisingly, even where to save all the data points is a bit confusing at first. Thank goodness I'm good with computers, 'cuz if I wasn't, it would take me a long time to get just this part of the procedure correct.
Recently (as in just yesterday), I experienced the largest obstacle in [is that the right idiom?] the way of me becoming one of the top three ophthalmologists in NY/NJ (one of my many life-long goals xP ). So there is this one part of the procedure that requires UBERLY steady hands and... I learned that my stead hands aren't too steady. :( I need some more practice. Instead of macro-movements, I should do something that requires small movements. Something like... model making! I think... v?v
http://www.showcasemodels.com/resources/E1/3297/picture/08/16967432.jpg
or maybe those anime ones :D
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I got really disappointed one day. I don't know if others have the same problems, but on Tuesday (I think), I basically wasted that whole day. This is because I incubated the E. coli too long. Then, the population grew to a different stage in the growth curve. Because we want to see the response of E. coli at a specific phase in their growth curve, I couldn't use that flask of E. coli. AND, it was too late to make another flask :( I wasted a WHOLE day :'(
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I've done a ton of things that I wouldn't have expected I would need to learn how to do. For example, I learned how to check if a pipette is working precisely as it's supposed to. Also, I've learned how to autoclave various things. It's been a pretty chill experience so far, but I imagine as the experiment moves on, it'll get busier. I also am able to analyze the data, but just a cursory glance suggests that I might need to switch strains due to the lack of interesting things.
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Peace~
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-PK

2nd Week Part 2 --PK

Alright. A lot of good news, and some bad too.
Bad news: I almost broke a micropippette that costs 300 dollars.
Good news: I almost broke a micropippete, but caught it like a ninja.
Bad news: Teuta (my supervisor) saw that the micropippette slipped out of my hand due to carelessness.
Good news: Teuta saw my lightnin' fast reflexes and good coordination.
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Yea, so I was doing the first half of the procedure for the experiment all by myself when Teuta called my name. I had a 200uL pippette in my hand right before she called my name. After my name was called, it wasn't in my hand. I quickly squatted and grabbed the pippette right before it hit the ground. Before that Teuta always thought that I was uncoordinated and kept saying that I should do some yoga/ballet. =.=''' Not any more! I was so happy (most scared actually) that I caught the pippette. Thank goodness I play enough computer games so my average reaction time is less than .2 seconds. :P
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Okay so I've been doing really well with the first half of the procedure, and so Teuta started showing me the second part. Although she's been really hard on how I do things (don't lean, make sure this doesn't touch that, etc.) she actually complimented me. Yay! The optical trap has been fixed, so I can start on my experiment again. The problem was never really diagnosed; the machine just magically fixed itself one day. Pretty cool.
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Yesterday, the undergraduate, who is doing a similar project to mine for his Senior Thesis, and I cleaned out some beakers that had "dangerous" bacteria in it. We had to wear lab coats. Since I don't stand or sit completely erect, I look more like I'm 5'5'' than 5'7''. The undergraduate is like 5'4''. The labcoats were long... they went past our shorts. It literally looked as if we were wearing the labcoats as a dress. Hahaa Everyone in the lab took one look at us and chuckled. Haha I'm actually taller than some of them!
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Alright so basically, my average day is pretty boring. This is because I haven't obtained the correct programs to analyze the data. So whenever I have time that is designated for analyzing data, I'm watching movies and reading books. I just got my Princeton Badge, so hopefully, I can obtain some programs in the near future. I really need to get started and analyzing my data. Oh one more bad thing, despite the fact that I'm supposed to be paid 10 dollars an hour and by the end of the summer, I would have worked in the same lab for more than 500 hours, my Princeton Badge fridgin' says VISITOR in big, bold font. :'( wahhhh
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Oh almost forgot the best news of all, by the end of  next week, I should be able to run the entire procedure all by myself. I am so happy and excited. I finally get to feel like a researcher. (Instead of being babied and stuff... which I probably still will be [my PI called me a toddler hahaa])
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PS. I brought in doughnuts and everyone was very happy. Maybe next time I'll bring in bubble tea. After all, half of the researchers are Chinese. Lawl

Peace~

-PK

First Half of Week Two --PK

Alright, so like Gab. Ross, the beginning part of my first week was pretty depressing. This is due to multiple reasons:
1. A rising senior joined the lab and Teuta, who thought I did wonderfully last week, decided that I should attempt to do the whole experiment basically without her help. This was after I ran the experiment with her ONCE. She ended up correcting me approximately 20 times in less than one hour... Yeah... now that undergrad who's from Princeton thinks I'm a fool. Great.
Sidenote: we're seriously taking a lot of precautions for working with something as harmless as E. coli. It makes sense for all of these things to be in place though. [point, there are a lot more than 20 things to keep in mind when doing this experiment.]
2. The trap (huge mechanism that records videos essentially) for some unknown reason, doesn't work. So basically, 3 days in the lab are wasted. The problem is still trying to be fixed, but I can't run my experiment because I need 3 to 4 hour long videos!
3. Because of the nature of my experiment, I have to miss lunch. That means from the usual 4 meals and 3 snacks I have just dwindled down to 2 meals and 1 snack. :'(
4. I still don't have the proper software due to regulations. I'm not allowed to get the disk that allows me to install this program called LabView since my computer that I use doesn't belong to Princeton. This essentially means that it's gonna take a lot longer for me to analyze the data, and my programming skillz are put to the test.

Okay, that's depressing and pathetic enough. So heading towards the good part. I essentially ran the whole experiment today without a mistake (I actually made a tiny one, but it was easily fixed.) So that made up for Monday's work. Too bad Steven, the undergrad student, didn't see me.
Also, my supervisor said that she'll try to get the installation disk of LabView tomorrow, so I can analyze my data much quicker. It's a pity that all the work I did might go to a waste, but it was extra practice!
So depending on how the next set of E. coli behave towards a 620 mM sucrose shock, I may start looking into two different strains of E. coli. If that happens, then things can get interesting and very busy. However, that would mean that I don't think the original amount of time I planned to put into working in the lab will be enough. I might have to cancel my trip to Florida ...  x( ...all in the name of science

Other than that, my experience is going pretty well. I'm not too challenged in terms of difficult concepts, but the precision I need with my hands can be a bit taxing. I guess this is good training for eye-hand coordination for gaming and surgery. I'm not sure if it's just me or if it's just because my experiment is just getting starting; however, I have a lot of free time. Sometimes, Facebook and Tetris seem pretty tempting... :D

Peace~

-PK

Preston Kung- Day 3

So apparently, I can't link my lab notebook to this blog, but I'll describe what I did today. Essentially, we're getting initial and broad readings to see if the mutant form of E. coli  without this certain osmoregulatory pump (TrkA) is going to react differently than the wild type strand of E. coli. So the standard procedure of preparing the materials and recording data was implemented.

Because I haven't done this procedure in a long time, I had to be walked through the process by Teuta. So there are three main processes that must occur before any data analyzation can take place.
1. Incubating only the E. coli strain of interest
2. Preparing the special slide and attaching the E. coli strain of interest on to the special slide
3. Obtaining Data.

Today's focus was mostly review, especially with processes 1 and 2. Something similar is going to be taking place on Monday (It would be Friday, but I'm going on a college visit xP [I really dislike the whole college process]) today I watched Teuta do all three steps and she had me do steps 1 and 2 by myself. I will do step three all by myself on Monday. I think tomorrow is analyzing the data we obtained today.

Speaking of which, since I recently recloned my computer all the softwares I had got deleted. So now, I have to reinstall a ton of software, including the three programs I need to analyze this data. Plus, because I don't have a Princeton netID, I can't just install them from the network. Paperwork is such a hassle!

Coming back from my digression... umm... Today was pretty awesome. It's pretty much an insight to what I am going to be doing most days. It was fun. I broke a piece of a slide that cost less than 2 cents. Nothing like beakers or expensive equipment yet xP (come to think of it, I haven't been that much of a problem to Josh [my PI] in terms of breaking things in the past 1 and 1/2 years YAY!~)

Teuta, the person in charge of me, got pretty mad. See, she just came back from nearly dieing (which is why she didn't respond to my emails as quickly as she usually does) so a lot of stuff has happened in the lab which she wasn't aware of. Things like people using her materials and misplacing them. People using up materials and not telling others or restocking. There were just some bad, careless mistakes. Something wasn't even labeled!~ We, the "strong science kids" of the Peddie School of Excellence, would never do such a thing. Hahahaa   But in all seriousness, it was kinda scary. She's sent like 5 angry emails to the shaevitz email group in the past 24 hours. I usually never get any angry emails due to being part of the lab's email group!

Anyways, today was eventful and fun. So much so that I couldn't go and get a full size lunch.

I'm hungry...

Peace~

-PK