2nd Part of Wk2

I'm really bad with the days and since my last post was the end of week one we'll just call this the end of week two because it has been a while.....

So in the last few days to be honest, not much has been done in the lab. My "advisor" Tiffany Tong went to her hometown Milwaukee for her high-school reunion and my PI is in Nigeria getting funding for his research. So for the past few days, (friday included) I have just been mixing solutions in preparation for creating my actual lab samples on Thursday. Everything is really expensive so I can't treat it like mixing gatorade in water and go for saturation; I have to be extra conscious to dilute all my practice runs by a factor of 10^-1 or 10^-2 before spin coating it on the glass slides.

Seems like tomorrow is a big day for me because I will be attending a SEM training session bright and early tomorrow morning (9:30 pm) and probably working until 7pm tomorrow night. After the class, I have to finish making P3HT:PCBM:Ti02 active layers on glass slides, meet with my PI to finalize project details and meet with my adviser to coordinate schedules for the coming weeks. I doubt I will be able to play for Peddie in the Summer League tomorrow and that hurts, but there are more to come.

Ala Viva

Santo Chen third week

I just keep forgetting to put up the posts. really sorry...
Um so not so much happened last week. Dr. Peretz came to the lab on Sunday and everything went well. I didn't get the access to the office so I only showed  her the insectary. Then on Monday I started to analyze all the data I have collected in the first two weeks. I have suggested this to Dr. Peretz that all the EXP students take AP Stats next year since my analyzing process involves so much statistics that I think it would be important for everyone to have a background of stats next year before they go to their summer lab. Sadly, all the data I have collected in the past two weeks only said one thing: NOTHING SIGNIFICANT. Doing all the ANOVAs (one-way+covariate)tests did not yield anything significant results, which rejects the hypothesis that Juvenile Hormone and 20E have played roles in the wing pattern development. This is actually unexpected..well so then my PI decided that maybe we will start another experiment to test the new hypothesis: 20E has developed a compensatory reaction to the level of EcR B1 in the male crawlers (there are a lot of terms in this hypothesis, hard to explain, but one thing: we have totally eliminated JH; the project is now entirely focusing on 20E)
So that is the first project I am participating in now. I have actually done all the work my PI expected me to finish in five weeks..she said I did the work a little bit faster than she thought. So now I am helping out with her other project, a project involves knocking down certain DNA by injecting antibiotics and mediums into the crawlers of another species Junonia Coenia. They have really pretty eyespots...so all I need is to do whatever I had done to all those Bicyclus Anynana to these butterflies and then collect data. Since this sample size is not that big (only about 30 a group), I guess I will finish it by the end of this week. Hope my PI will have another project for me next week hehe.

Santooooooooooooooo

Jack

My internet was out at home for the past week, so I haven't been able to post.\
I've finally begun my project. Over the course of the past week, I took the initial structure, solvated it, added ions, minimized it, and soon (if the queue ever clears) will begin equilibration. I started with a file called a .pdb file which contained information about the structure of the minimal length HHR I'm studying. I then modified this in a program called Amber by adding ions to balance excess negativity, solvating the system in a box of waters, and then bringing the solution up to .14M concentration NaCl, as well as updating it with new water and ion models. I then minimized the system using the program sander. When I and the researchers helping me took a look at the out put files, we discovered that all the ions had decided to clump up into a ball in one corner of our box (which makes sense to the model, but physically is not observed), so we had to use a program to manually randomize the ion positions. I then minimized the system again. That all took about a week (theses simulations take a very long time), during which time I also got another meeting with Dr. York where we discussed some of the theory behind the model I am using, and I had lunch with other high school and undergrad researchers in the physical chemistry department.
Before leaving for the day on Friday, I started running the equilibration. This essentially is a long warming up period for the system in which heat is evenly distributed across the atoms. Certain specific restraints and parameters have to be used to stop the system from heating unevenly or becoming unstable. When I came back this morning, the simulation was still running. As such, I've been set up with an account to access the super computer at UMN, and am at this moment waiting for my equilibration to clear the queue of idle jobs and begin.

End of Third Week- GR

I keep forgetting to post my end of week blogs...

The end of this week was pretty awesome (except for the commute home on Friday, which was a disaster). I got to synthesize a brand new compound! It’s called GR-1 and it's one of a series of compounds that the lab is planning to make.  The 40mg sample is going for a characterization on Monday.  I'm pretty excited about it.  Also, I will be going to a bio lab on Wednesday, Thursday, and Friday of this week to see the beginning steps of how the compound will be tested for efficacy.

I learned that if you mix dry ice and acetone, you get a -78 degree solution, which is what we used to freeze the solution of GR-1  and water because of the purification techniques.  It was necessary to freeze it because we needed to lyophilize it.  This process is the gentlest way to evaporate water out of your desired compound.  We were lucky that it started working again, because there was a problem with the vacuum for most of the week.  Good stuff.

Thanks,

GabRoss

My Second Week- Rahul Lakhanpal

So my second week was filled with a lot of interesting material. I feel like I am really getting into swing at the lab. After spending the majority of the first week following the lab graduate and reading documents, I fully began to understand my project. I revised my original proposal to correct it with the true project. I also finished my online models of Human Serum Albumin and TNF-a. I investigated how the Human Serum Albumin could be manipulated and how it could effectively bind to TNF-a. Dr. Li, my PI, sends me on searches sometimes to answer a specific question for the day. So usually it would take me some good time to try and tackle those questions and finding proof of my answer on PubMed. On Wednesday, I got to spend some quality time with Dr. Li and followed him around to see what he was doing. Dr. Li was working on a project which used Human Serum Albumin to help with Breast Cancer treatment. I watched Dr. Li culture cells and how meticulous he needed to be. Dr. Li used a new pipette for everything, and always made sure to steralize everything to make sure no unwanted materials would enter. I watched Dr. Li use the median and such to effectively do this. The biggest project I had for this week was to write a code for a primer that I could use to put the WP9QY peptide into the Human Serum Albumin. It was interesting because all the work I had been doing in the past week, all helped me to successfully write a primer. I found a restriction site that would only cut one site in Human Serum Albumin and had to add the enzyme within my primer. On Thursday I finished my primer and we ordered it online. Despite my sense of accomplishment, Dr. Li told me that primers many times don't work properly... so we will see. My primer is set to come in on either Monday or Tuesday, so once it comes in I will begin PCR and take another huge step in my lab.

Rahul Lakhanpal

End of Second Week - Kate Wang

Ok so this is the actual post that I'm supposed to post today.

As soon as I showed up to work today I was informed that there had been a water leak in Rob's lab that had spread throughout the building into the other labs and rooms as well. By the time I got there, most of the damage was repaired so it wasn't too eventful. Apparently Rob is the official "troublemaker" of the company since he has broken numerous things and also burnt polymer once without realizing it. I guess this makes sense since he is also the youngest employee (other than me but I'm not technically working for them).

Other than that, my week has been pretty un-eventful as I am still running tests on the polymers .

Oh, this might be interesting. So we order one of the proteins that I test from this company called US Biological and one day when Matt was ordering the protein, they suddenly asked if we would also like a jar of salsa and Matt replies, "what?" and so he agreed to try a jar of salsa and it was sitting in the fridge for quite a while since nobody brought in chips. But finally, yesterday someone did and it turned out to actually be quite delicious. Although, the ingredient list was very funny it said things like "tomatoes: not as many as peppers" " peppers: too many to count" and other funny things like that. Oh and it also mentioned that it was not to be tested on humans, etc. etc.

So yeah, that's it for me for this week. Please excuse my terrible grammar, but it's late and I'm tired. 

Half of Week 2 - Kate Wang

Hello there,

Ok so I originally wrote this post on Wednesday but I kept forgetting to hit post.

Anyways, so nothing too eventful has been happening. I've been doing the same things in lab everyday although I do rotate between three different proteins that I test. Rob has also been giving me different polymers to test so I'm up to 5 so far.

I brought in the cookies on Monday and made everyone very happy (brownie points for me). And then today (Wednesday) we had a pizza party as a sort of official meet and greet since the company hired quite a few people in the past three months. There are now 15 people working at CytoSorbents although they don't work for CytoSorbents. Rob was explaining this to me how they work for a company called JoulE and that's who pays them too. Anyway, the pizza party was really great and I finally got to meet everyone although we did have two people missing, because they only work a couple of days a week.

Other than that I don't really know what else to tell you. Also at the party we had a reminder about confidentiality stuff and now I'm getting really paranoid so I apologize that I won't be posting too much stuff about what I do in the lab and more about my lab experience.

Kate Wang

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

Timi Opeke (2nd Part of WK 1)

I started midweek last week, so this is officially the second part of my "first week" in the lab. Because my "advisor" has been working on other projects and running errands for the past week, we have met on Friday, Monday, and today.

Things are pretty good so far and I can't complain. Today was my first day working mostly independently in the lab, and was practically my final test before my "advisor" went to Wisconsin for her high school reunion. All in all thing went well, and with some help from a visiting researcher, I was able to get all the work done before my summer league basketball game at 7PM.

Although I would love as much help as I can possibly get in the lab, people are treating me like a visiting researcher so I am being pushed to do a lot of work in the lab independently (but mostly supervised). This is great because there is more pressure to be attentive to detail and take pride in your own work, but now I understand why everyone flocks for free coffee at 4.

Nonetheless it still is exciting and I'm happy to go into the lab even just to clean. Tomorrow I'll be going in to teach a post grad how to create her own active layer so I'm pretty suped. Professor Timi Opeke has a nice ring to it :)

Third Week, Post 1_GR

I can't believe that its already about half way through my time in the lab. It's going by so fast!  Things are basically the same as they've been for the past two weeks.  I keep getting more and more independent in the lab and everything is going well, save for a few broken pipettes and messed up TLC plates, of course.   

On a different note, I'm really liking the relaxed environment of the lab.  It's not at all what I thought it would be.  For example, one day, I came in at around 9:30, and one of the researchers said to me: "Why did you get here so early?"  Then I realized that the lab is pretty much dead until around 10am.  Everyone basically just makes their own hours because as long as your project gets finished in a timely manner, it doesn’t matter what time of day you do it! It's a pretty good system.

Also, I found out today that I will most likely be going over to the med school for a few days either next week or the week after to see how they will be testing one of the compounds that we are making in my lab, which should be pretty cool.

Thanks,

GabRoss

Pat Quinn - Day 8

I have gained a few responsibilities since a began. I have now taken on the role as mother chicken. Everyday I have to check that the incubators are at the right temperature of 38 degrees Celsius, I have to make sure the incubators have water so that it is the right humidity  and I have to rotate each egg 180 degrees so that the embryo doesn't get stuck to the shell. On Wednesday and Friday the new eggs come in. So I have to take them out of the box, check for any cracks and label each one with the day it goes into the incubator and the date. Then on the right day I will put the eggs into the incubator. I also dissect almost everyday and recently I have been dissecting the eggs at different stages of development. This week I will stain them in order to see the branching within the lungs at the different stages. 

Tomorrow I will be finding out what my specific research project is on lung development. The past week and a half I have been doing some of the basic steps in just seeing how the lung develops. I may not be doing the project I wrote my proposal on because it is a project the lab has done many times and is now writing a paper on it. So instead I may be working with a different aspect of lung development. In my spare time though I will continue to help the post doc in creating the pressurized system. 

End of Second Week- GR

This post is going to be about the end of my second week,  even though it’s a little bit late…

Reflecting on the end of my second week in the lab, I can say that I'm really starting to get a hang of how the lab works.  I'm getting used to the complicated lingo, figuring out how to do reactions, and just altogether learning a ton.  I have set up Gewald reactions, hydrolyses, neutralizations, etc. and I'm able to analyze the products. Over the next few weeks we will be continuing to make five grams of the final product and I also just found out that we are going to be making small scale amounts of a couple of other variations of the chemical to be tested.

I'm also learning a lot about Penn and West Philly as well.  I've walked around most of campus and have been asking Kevin (the undergrad in the lab) a great deal of questions about the college.  He's also been great at helping me find the best places to eat lunch.  Tomorrow morning, I'll be taking a tour of the school as Carlo has meetings all morning and I won't have to come in until the afternoon.  My experience here has made me want to come to Penn even more than I already did (which I didn't think was possible).

Overall, I'm really liking working in the lab.  Everyone is really helpful and it's been a great two weeks!

Thanks,

GabRoss

Rahul Lakhanpal- End of Week 1

So I forgot to do this last week because my parents picked me straight up from the train station on Friday to go to Maryland, but I wrote it on the train to Philadelphia and will submit it during one of my breaks at work.

The first week was a time where I learned more about my experiment and what I would be doing then I ever thought I would. After the spring term class, I thought I understood my project but in reality I understood everything wrong. Let me make some clarifications: we are NOT trying to cut the disulfide bonds, we are looking for them because they are one of the most stable bonds and securely hold the portion of the protein above it. This is the portion of the protein that we will be modifying in order for it to be modified with a peptide WP9QY (YCWSQYLCY). Another thing to note is when I was reading my primary literature, I had NO idea what YCWSQYLCY meant. But now I understand that each letter represents a different amino acid, its just written a cool/lazy scientific way. I can finally say I clearly understand what we are going to do now, and how we are going to go on with our procedure.

The second day in the lab I followed the graduate student, who was doing her own project. Although she has a different project it is similar to Dr. Li's. That day she was tagging Human Serum Albumin to see how it would react in contact with another protein. That day I perfected my pipette precision and watched her as she reviewed Gel Electrophoresis for me. The next three days, I focused solely on getting to know the two structures I would be working with. I made computer models of both the structures and found ways to tag the disulfide bonds, and the amino acids we were going to target. The models were tedious because I had to find the exact structures and make sure nothing else was attached to it. Once it got onto the program I could rotate the screen and easily modify it. It was a busy week, and I am looking forward to do even more work next week!

Rahul Lakhanpal

Jack

It's been a fairly boring and uneventful week; mostly I've been doing preparatory work. I downloaded VMD (a visualization program) onto the computer that I use, and spent a day and a bit figuring out how to work it. Most of the basic functions were pretty simple (changing the display options, measuring distance between atoms) but some of the analytically tools took longer to learn (free energy calculators, RMSD trajectories, etc.). Reading through the NAMD tutorial (NAMD is the program we use for actually simulating molecules) was death, as the prose was incredibly dense and boring. I also spent a little time familiarizing myself with the bibliographical tools used by the group, and made a mock entry to test it out.
I also had a meeting with Dr. York, where we discussed what primary research to read, what background to read up on, and more like that. I did finally get a concrete project, though-I'm going to be using novel methods to attempt to determine what causes the minimal sequence Hammerhead Ribozyme to switch from its catalytically in-active to its catalytically active state.
Since my last post, I had a chance to meet some of the other researchers in the group, including the three PhD candidates that moved here with Dr. York from Minnesota. They're very friendly and have taken me in, as it were, and even invited me rock climbing, which is a sort of group activity for the lab. I also got to go to a picnic for a recent PhD recipient and meet some of the people from the other labs in the building. All in all, a productive week.

Pat Quinn - Day 5

Things have been going well since my first day. Everyone has been very friendly and I am even getting my picture taken to be put on the website. I am still learning a lot about the different protocols within the lab but I am getting a grasp of many of them.

I learned that this summer I will be working on two projects. One project will be seeing the development of the lungs within chicken embryos. I will also be helping a post doc work on his project. He is trying to create a pressurized system that you can place mouse lungs into and you will be able to change the pressure so you can replicate a breathing pattern. The ultimate goal is to see what outside pressure has upon the development of lungs. We use mouse lungs instead of chicken lungs because mice are mammals.

So this week I practiced chicken dissections which I am getting better at. I can now successfully find the lungs but the tricky part now is separating the lungs from the digestive system because they overlap. With the lungs I have dissected I have begun the staining process which uses fluorescent tags to mark the epithelial tissue of the lungs. On the other project I have started making the parts for the system. I've cut glass, cut wires and made silicone molds for the system.

Pat Quinn

End of First Week - Kate Wang

So the first week went pretty well. I think. I mean I've only broken two things so far, a glass pipette and a glass funnel. Everyone in the lab is really nice and I'm starting to feel more and more comfortable with them. I mainly work in a lab with Matt but he's not there a lot of the time so I get to have the lab to myself and play music and whatnot. I've still been doing the same procedures for the past week although it is not completely identical depending on what I am testing. The only issue is that we have no way of seeing if my result is correct or not, because the beads that I am working on have not been tested before. And then, when I was going over my results with Rob, we realized that some of my numbers were negative when they definitely should not have been. I really hope I didn't do anything wrong although I don't think I did. At least it is only my first week there and I still have 4 more weeks to make it up and hopefully start getting better results.

I have yet to bring in any food to the lab so I bought cookie mix and am planning on making cookies today to bring into the lab tomorrow to celebrate my surviving one week in the lab. I also have regular meetings with Dr. Chan just to talk about what I'm doing in the lab and how things are going.

Also, the most embarrassing to happen to me, actually there's two of them. The first happened on the second day when I accidentally did not close the freezer door completely and the next morning apparently the freezer had frozen over and they had to throw almost everything in the freezer out! Luckily when I apologized to Matt he told me that they were supposed to have thrown most of it out a while ago but they just never got around to it so I gave them an excuse to throw it away. Phew! The second was that I was playing pandora while in the lab and suddenly, Teach Me How to Dougie came on. And I don't recall it being to bad swear-word wise except for some reason this one was terrible, every second word that came out was a curse word and Matt told me to turn it off immediately. I didn't even realize that it was playing because I was concentrating on my work. I quickly changed it to a Three Day Blind channel and hopefully Matt isn't too mad at me.

Anyways, I hope I have better luck next week and the cookies will hopefully earn me brownie points!

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

Santo Chen second week

Hey guys. Really sorry that I forgot to post my last one..I wrote it and saved it but did not post it.

One advice to everyone: do not try to impress your PI so that you work really really really hard. I mean work really hard is fine, but work really hard causes problems…health problems. It happened to me last week. I worked hard from Monday to Thursday, sitting there all day labeling butterflies, or photographing, or doing statistics tests without moving at all. And sometimes I just skipped lunch in order to get the work done ASAP. And guess what? I had a fever on Friday and diarrhea all day, so I had to email my PI explaining my absence... do not do that!

So starting from this Monday I started to do some real statistics tests on this program called PASW. It helps to separate the variables and factors and draw out clear diagram to show if there is any significant difference between two categories due to a specific variables. Sadly almost all the data I collected showed no significant results. Most of the differences in eyespot development were due to gender or season (dry season/wet season) instead of the injection of the hormones. However we did see some trends that show the potential significant differences, but we need more data to determine if these trends are really significant.

My PI is attending a conference this week and won’t be back until Sunday. So on Monday we talked about everything I needed to do this week: basically to collect all the data and put them on the spreadsheet. On Tuesday I finished clipping the allllllllllllllllllllll the butterfly wings, too many that I stopped counting at one point. On Wednesday I started photographing these wings using the digital microscope camera. And on Thursday I finished photographing them and started measuring and diameters. And today I finished doing all the measurements. Hopefully there will be some significant results this time.

Oh and Dr. Peretz is coming on Sunday. I will show her the insectary and the office if possible. I do not know what I am going to do next week. Maybe I will need to start writing some reports? Not an easy task for me…. 

Santoooooooooooooooooooo

First Day (Rotimi Opeke)

Yesterday was my first day actually working in the lab and it went pretty smoothly. Besides preparing sample active layers to get me accustomed to the techniques, it was a slow day because Dr. Soboyejo or my "project guidance counselor" had to help another PhD student get their project back on track after a one-week holiday. Nonetheless, it was a good day, and I only expect my involvement to increase.

Upon my arrival at the Engineering Quad, I crossed paths with Pat Quinn, who was taking a small break for Lunch in the E Quad Cafe. It's amazing that at least 3 Peddie students are working in the same building and we may barely see each other. We had a small chat and he told me a little bit about his work, but soon we both parted ways and headed back to our respective labs. Tiffany had just come back from picking up lunch so I ended coming back to the E Quad Cafe and keeping her company while she ate.

Soon after she finished eating, we went to have a conference call with Dr. Soboyejo in her cubicle. He was really helpful in finalizing some details of my project, but you can only get so much help over the phone compared to in person. I was soon kicked out by another Princeton PhD student who is also working on a project with Tiffany, so I went ended up sitting in the Coffee Room and using the Internet to research more about my project. I didn't know that the call was going to last for 1 1/2 hours, but I read as much as I could between accidental naps.

When she came back, she told me that we still had some paperwork to finish before I could enter the lab, so I had to copy some information from one form to another for multiple sheets before I was all set to work. By this time it was closer to 4:45pm and Tiffany was anxious to leave, but I reminded her that I hadn't even gotten the practice in the lab that I wanted. Though she was reluctant, she helped me rush through a procedure to prepare active layers composed of P3HT and PCBM. I actually was surprisingly accurate and efficient given the time constraints that she placed upon my work, and had three finished active layers (pre-annealed) in an hour.

She was impressed at my attention to detail, but after that 3 hour lab safety training session, I'm obsessed with cleanliness and precision in the lab. They don't wear eyeglasses in the lab, so I brought my own (THANK YOU WORTHINGTON LABS) and I wouldn't stop measuring and re-cleaning things until my heart was content. This may slow me down a bit in the lab, but I think its good for the long run.

By the time we had cleaned up and I had gotten all my things, it was closer to 7pm and we decided to call it a day. In conclusion, the day was not what I had expected, but it will only get better from here.

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

Second Week #1_GR

Today I learned what it is like to actually be a real scientist.  We tried to take a shortcut in the purification process… and it failed.  What we know will know have to be done is to purify the material after each step in the process.  While this overall takes a great deal more time, effort, materials, etc., it will overall make the final product cleaner and easier to purify. I also learned today that some things can take FOREVER if you don’t optimize the conditions.  And its not so fun to watch liquid trickle out of a column for 4 hours… trust me.  But, this was not in vain, because now we know that it needs a greater percentage of strong solvent to run in a reasonable amount of time.

One thing I'm having trouble with are the calculations that I need to do for some of the reactions.  I'm starting to learn how to do them more efficiently with the help of Kevin (the undergrad in my lab), but I'm still not getting them 100% right. I guess it'll come with more practice.

Other than that though, everything's going pretty well, I'm able to set up the HPLC and LC/MS machines by myself now and I'm pretty much a pro at TLC's ( I do a LOT of those).

Still no train stories… hopefully I won't ever have any…

Thanks,

GabRoss

P.S. There are a couple of corrections that I need to make regarding my first post: 1) Carlo is not the PI of the lab (I actually haven't even met the PI) and 2) the "grad student" I'm working with is actually a post-doc.  But hey,  it’s all a learning process...

Jack-1st Post, 1st Week

I started yesterday with a meeting with Doctor York. We outlined some basic goals and methods as well as sorting out some simple logistical matters, such as where I would park and what my schedule would be. This being Rutgers, there was also plenty of paperwork to fill out. We then took a tour to see the facilities; the conference room, a number of work spaces for the lab members, and a administrative office. There's not one "real" lab in the building, as far as I can tell (although there is a lonely eye-washing station outside my room, which as far as I can tell is completely ceremonial). We also met the members of the York group, including Georgie, the Eastern European RNA expert, and Ming, the Linux expert. I got my own cubical in a room with Ming, Kinyiu, and another man who I have yet to see, as well as a computer, which I'm typing on now before everyone gets here.

After the tour, I began with my first day's lesson-how to work Linux. Ming gave me a short tutorial on basic commands (ls-list directory, cd-change directory, etc.) and then pointed me to a more in-depth tutorial online. I spent the day just getting acclimated to Linux and copying over a few important files from GIT, an online library of sorts. Before leaving I had another short meeting with Dr. York where we went over the day's lesson quickly, and decided on a game plan of sorts for the next week. 

Oh, and I brought in bagels.

First Day - Pat Quinn

June 13
Today was my first day in the lab if you do not count the 3 hour training session. I am working at Princeton University in the chemical and biological engineering program under the Nelson Group. First off I was given a tour of the four rooms that the group uses: the main lab, the culture lab, the office and the cell freezing room. I was then given my own personal lab notebook that I can write all of my scientific discoveries in. I was also given my own section in of the lab which was a drawer that I can put the materials I'm working with and my lab notebook in. Quickly after that I learned how to dissect chicken embryos by watching a research specialist and a undergraduate. Soon enough I was able to take the embryo out of the egg and onto the petri dish. But the hard part is the micro dissection, you have to be able to look into a microscope while dissecting the embryo underneath of it. The lungs are hard to find in the chest cavity because of all the other tissues and organs in the way. Hopefully practice will make it become easier. Dissecting the lungs took up the first section of the day. For the second part I watched an undergraduate student do a part of her project. At the end of the day the post doc that will be looking over me showed me some of the mechanical engineering questions that his project was trying to answer. All in all, I thought it was a good start for the summer.

Patrick Quinn

Rahul Lakhanpal- First Day

Today June 13, 2011 was my first day working in an official lab.

My day started at 6 o'clock when I woke up to get ready to catch my 7: 27 train from Trenton to Philadelphia. My mom decided she wanted to go to the lab with me the first day, so she could see how my commute would work. We planned to leave early so we could get the donuts for my PI and the grad student! We reached Philadelphia and at about 9 o'clock we got to my lab. Unfortunately, Dr. Li was stuck in traffic and didn't get to the lab at 10. (We also decided from now on, I should come in at 10 too... more sleep!). Once Dr. Li got there, he showed me around the lab and where I would be working. Since Dr. Li's NIH grant and interview is due on Friday, he planned to finish it by this Tuesday. Thus, today and tomorrow, I would/will not be able to spend a lot of time working with him. So instead of sitting ideally, throughout the morning, Dr. Li and the Grad student, Michelle, gave me even more readings! I diligently finished the readings and learned even more about the protein, Human Serum Albumin, that I will be working with. When I was reading these articles I had massive déjà vu because of Mr. Brown's AP Bio Molecular Biology section. Everything we learned in AP Bio was essential to this project: cDNA, splicing, primers, restriction enzymes etc. The tour and readings took the majority of the morning and by...

12: 30, I was really hungry. The grad student had not moved an inch and was glued on fixing/modifying the protein Dr. Li sent her. Then my stomach let out the loudest grumble, and she started to laugh. She told me that I could eat lunch whenever I wanted to, I sighed in relief and quickly went to the cafeteria to eat. After lunch, Dr. Li came in and showed me how to use two programs: Omiga and Chimera. On Omiga I listed the nucleotide sequence for human serum albumin and it translated them into codons and proteins! After that, I used a feature on the program which allowed me to see all the possible cutting spots by going through each common restriction enzyme. As I left Dr. Li left me with a  message. He said in the next six weeks, I will learn how to go from step 0 to officially starting a lab. Today was Day 1 in that process. I look to learn more and have even more fun in the next 29 work days!

Its Always Sunny in Philadelphia,
Rahul Lakhanpal

First Day

Kate Wang, CytoSorbents Corporation

Hey guys,

So today was my first day at CytoSorbents and I think it went really well. I started off by meeting with Tom who works mainly in the polymer bead production side and we talked about how the polymer beads are actually made and it got really complicated with big organic chemistry words and such. Then I met Matt and Rob, who I will mainly be working with, and we went over what I will actually be doing in the lab. After that, Tom hooked me up with a lab coat and safety glasses and we went on a tour of the lab. I ended up in Matt's lab where Rob lead me through a sample trial. Okay so this is the tough part. I don't know what exactly I'm allowed to say about this since I can tell you that we were testing for the efficiency of the polymer beads in adsorbing a substance. But I don't know if I can tell you what the substance we used was, or how we did it. So let me tell you that it was pretty straight forward and not too complicated at all.

While we were waiting for the beads to adsorb substance, I ate lunch and then I had a meeting with Dr. Chan, the CEO and we talked about what I was doing and how my experience was in the lab so far. After that, it was back to work again. We finished of the rest of the day  by measuring the absorption with a spectrophotometer and then measuring the sizes of the polymer beads with a really high-tech microscope.

Andddddd I can't think of anything else to write so hopefully I'll have more stuff to share at the end of the week.

-Kate wang

End of First Week-- GR

I had written this on Friday while on the train, but forgot to post it...

Alright, so it's the end of my first week already.  I honestly don’t believe how much I've learned this week.  I can now going around saying TLC, THF, Rotavapor, LC/MS, Column Chromatography, Extraction, Filtration, etc. and actually understand what I'm saying!  My overall lab skills are already improving as well.  I'm learning how to be more accurate in my procedures as well as my documentation.  I can already tell that my experience now is going to make me a pro for Chem lab next winter.

So, what the lab is actually trying to accomplish is to make a drug that can eventually be tested in vivo as a possible Alzheimer's treatment… and this is way more complicated then I had previously believed it to be.  Creating the final product involves a number of steps that all need to be carried out efficiently. Also, five grams needs to be made, which is a fairly large amount. The catch is that its not as easy as scaling up the reactions to make the right amount.  The reactions don’t work at that large a scale, so there has to be many iterations of the same small-scale reactions over and over again.  What I also found surprising was that the actual reactions themselves aren't that complicated or difficult to carry out. The arduous parts are the purification and isolation of the product that you actually want from the garbage that results as by-products of the reactions.  Another thing that I thought was interesting was how imprecisely everything is done in the lab.  While there is an overarching procedure, much of the work done is by trial and error.  You try a bunch of different ways to carry out one reaction, and then figure out which one works the best. And because each step needs to be repeated many times, this is actually the most efficient way to get the job done.

My experience has been great so far! I can’t wait to start up again next week!

Thanks,

GabRoss

my first three days at yale.

Alright guys so I started my lab this Monday, and it's been three days. I pretty much started working on my project since the first day I got there..my PI forgot to get me a Yale ID and keys to the insectary, so we went to Yale Provost first and ended up getting nothing since my guardian and I needed to fill out some forms in order to get the ID and the key. Then my PI and I went straight to the insectary.

I thought since it was the first day I might just go around the lab and meet with the post grad student I am supposed to work with. Well, it didn't turn out to be that easy. My PI and the post grad first talked about the project with me: I need to collect data for butterflies reared in wet season and dry season injected with two different hormones in different phases before pupa. Each butterfly is kept in a small envelope and put into the freezer. So my first task was to label all the envelopes and put them into groups, for example 1-W-L-JH means the first sample in group reared in wet season and injected with juvenile hormone during larval phase. So I spent my first day in the lab labeling over 300 butterfly envelopes and transfer the data to Excel. It seemed easy at first but it was a lot of work..my hands were literally shaking after labeling over 200 butterflies.

So that was the first day, the second morning I finished transferring the data. My PI and was surprised that I finished the work. She thought it would take me a few days to label all the butterflies...after that I got a nickname "machine" because I do everything really really fast. My next work was to cut off all the forewings and photograph them in pairs using a really complicated equipment. So that's about 600 wings. These wings are really fragile, I broke several wings just by taking the butterfly out of the envelope. Anyway, that was again a lot of work, so I basically sat there cutting wings for the rest of the day and this morning I finished clipping all the wings. Then my PI came and told me that she had talked with her other partner and she suggested cutting the hindwings as well since studies had shown that mantis and other predators prey on butterflies with specific hindwing patterns. So I spent this afternoon clipping all the hindwings. And then...I got an email from my PI (she went back to her office, which is 15 minutes walk from the insectary) saying that she had thought about it and thought it would be better for me to just photograph all the forewings and leave the hindwings first...Well I guess that often happens in the lab.

So that's my first three days, kinda busy, but I guess more work is coming in the next few weeks. Since most of the people work from 9 in the morning and leave around 4pm or even before, I only work 7 hours everyday. Luckily the my PI said that I could come in during weekends, so I will spend weekends working in the lab as well so that I can get 40 hours a week. Nothing dangerous in this lab, no chemicals except hormones, so I guess no accidents will happen...hopefully

Santooooooooooooooo

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

First Day: June 7th

Alright guys, so today was my first day at "the lab." And since I'm relatively new at this whole "blogging" thing, you're going to have to forgive me if it sounds like I don't know what I'm doing... cause I don't.  I guess I'll figure  it out as I go along. So here it goes...

Yes, it was my first day at the lab, and yes, I was supposed to start yesterday, but my PI (Carlo) had a sudden obligation to take care of, so I started today instead.  When I got to the lab, I first had to get registered and obtain a "Penn Card" (an ID). After I got over the unflattering picture, I headed back to the lab where my PI gave me some articles to read while he went to a meeting (woohoo, more reading!). These articles were important though because, as I found out at the end of last week... my project got changed.  Nothing too catastrophic though, because the only thing that was really changed was the chemical that I will be synthesizing and purifying.

Then, After the articles were read (and lunch was eaten), I began to learn how to do my first reaction.  I was a little intimidated in the beginning, but after the first couple of steps, I realized that it was just like following a recipe or a procedure in science class, and that I would be completely fine.  Honestly though, I was awe stricken by some of the methods that I will need to use.  I will be using a high power microwave that is able to heat the reactants to 150 degrees Celsius in a ridiculously short amount of time.  I also saw a demo of thin-layer chromatography that I will eventually need to be able to navigate by myself. Some of you that took AP Bio probably know something of what this procedure is.  Remember when Mr. Brown (Hi, Mr. Brown!... if you're reading this) said that we weren't going to do a part of one of the labs because it never works properly? and then we had to look at the labbench for it anyway and we were so confused by Rf values?  Yeah, well that's basically what it is. (Sorry for the side bar.)  Alright back to about today: probably the coolest thing was the filtration method that was used to separate the solid precipitate product from solution.  A filtration flask was hooked up to a vacuum and when the suspended product was poured on top of some filter paper, the liquid was basically sucked out of it and into the flask. After reading that, I think that it was probably a lot cooler then it sounds. I'll most likely be learning how to do a bunch of other stuff throughout the week, so I'll say more about procedures in future posts.

I also found out today that I will be working with an undergraduate student as well as my PI and the grad student I met during my spring break visit to the lab.  I was sort of relieved to hear this because now I know that I'm no the only one in the lab who has only limited experience (plus I can ask him all sorts of questions about Upenn and college, in general). Oh, and one last thing is that my dad drove me into the city today, so I don't have any crazy train stories about how I was reading the wrong schedule or something (Alec, you know what I'm talking about)... yet.

Thanks, 

GabRoss

Preston Kung- Day 1

June 6th:
Since it's the first week, I'll update this blog a little more frequently than I have decided to. Most likely, I'll create a new post twice a week (hopefully on Wednesdays and Fridays).

So the first day. Because the general public might be reading this (eventually), I won't actually state how I already broke a rule and should be evicted out of Princeton University. Nonetheless, I went to the 3 hour and 7 minute training session. I attended the one that emphasized the dangers of chemicals. A lot of complex names were mentioned, and I learned a BUNCH of different ways one can get injured or be killed in a lab.  Fun, fun, fun. Apparently, even nanotechnology has a ton of potential to be hazardous too. A variety of chemicals can kill you even if only a drop lands on your latex gloves and you don't treat it in the next 2-3 minutes. Thankfully, I will not be working with those chemicals and therefore most likely will not be injured in any way. The worse thing that could probably happen is that I accidentally ingest some E. coli and get sick.

For whoever may be reading this and is like, "O_O ?!?!?!?!", I am Preston Kung, one of the first EXP-ers at Peddie. EXP (http://www.peddie.org/podium/default.aspx?t=127605) is a high school level program that allows "high level" students to explore, experience, and experience the life of a research scientist for at least 200 hours (5 weeks). I am working at Princeton University in Professor Shaevitz's laboratory (http://sites.google.com/site/shaevitzlab/). It specializes in studying the physical mechanisms of how bacteria move.

Since I haven't obtained my special high school student badge, I can't run any trials yet. So I am simply reading up on my experiment. [An attachment of my research proposal belongs here] The above link/attachment is my research proposal, created in the Spring of 2011. I can't wait to start actually running trials, gene sequencing, using big lasers to measure tiny objects, and programming. This summer will seem like a ton of fun.

Peace~

-PK