New Project about plant

As we have finished our 3D printed bionic ear, our group is starting a new project. We are basically preparing for the new one, which will be about plant and energy harvesting.

In this project, I need have more reading since I need to contribute a lot to the experiments design and performing, which includes the material choosing and methods design. As I am pretty familiar with the knowledge of plant photosynthesis (thanks to my great AP Biology class), I will be more specifically in charge of the mechanics part of the leaf, while I will learn more about the electronic part.

What’s more, instead of alginate and bovine cells, we will use totally different material for this time, which means we need to design new setting for our lab. These days, through the information we have, we are deciding the material and other electrical components of the project, while the material needs to be reconsidered. We are also preparing for the interview from MIT’s Technology Review, which records the whole process of our 3D printed bionic ear. So a new fresh ear is coming.

One of the most exciting things taking place these past two weeks is the presentation of the new project in our group meeting. This is the presentation that I have longest talk about our idea, in which I explain how our research would go. In the presentation, I first mentioned the necessity of plant energy harvesting and the general information about photosynthesis including photosystem and electron transaction way. Later, I talked about the idea of combining nanotechnology and plant biology, and the specific methods that we were going to follow. The presentation went well.

In the next week, we will start the new project and I cannot wait for the experiments with plant.

Making Sense of Scents - Week 1 at Duke

I thought I was done with the visa stuff the moment I had sent in the forms to Jason, the human resource manager, but first thing I had to do Monday was to meet with Visa Services. This building was pretty far from my apartment so my dad and I took the bus. After that we went off to the International House (IHouse) for a "scholar orientation". It started pouring while we were walking there so we waited for the rain to die down under a tree. When we got there, I had to fill out some forms. Lisa came to talk to us about how to get around Duke and the Durham area as well as student activities. She gave me a whole stack of information which was really helpful. The first time she talked to me, she called me "my dear Jocelyn" which actually made me feel uncomfortable at first but I got used to it because she kept on referring to and talking to "her dear Jocelyn". It started pouring again and the thunder kicked in too. My dad and I didn't know how to get to the Duke Eye Center from here, but Lisa was so kind in offering to drive us there. She was like a "grandma-you-would-want-to-meet-in-the- woods" as PJC so refers to, although she wasn't too old. She was just really nice.

I called Hiro (my PI) from the Duke Eye Center and he said he would walk over in a bit. Next thing, we're walking to the lab just having a conversation about the summer. We walk into the building and I finally meet Jason! I still have yet to give him a present! Anyway, we have a lab meeting and one of the grad students presented a paper that she read. I realized after a minutes into the meeting that the whole lab was Asian. Not one single non-Asian. I thought that was pretty funny.

After the meeting, I was introduced to the grad student I would be working with: Neha. She showed me around the lab and I was introduced to the other lab members. I talked to Natalie, who is the only undergrad, about her research. I also talked to Mingshan about her topic of research. Then Neha brought me and another high school student to get our Duke cards. Neha also described her project to me.

For the remaining hours of my first day, I counted glomeruli in the olfactory bulb from pictures that Neha had taken with the microscope. Pretty eventful first day. Then the remainder of the week I read some review papers on the olfactory system. Our project investigates the difference in number of glomeruli in the olfactory bulb of wild type mice and knock out mice. The wild type (WT) mice have two proteins: RTP1 and RTP2. The knock out (KO) mice have neither of the proteins. Neha did 6 mice crosses and we genotyped the mice with the gel results we got. She told me that RTP1 and RTP2 genes are linked so if one mice had RTP1 the chance of it having RTP2 would be very likely.

Neha already had the DNA sequences ready for the gel so we made the mix and the gel. Each mice would have 4 columns in the gel: 1 WT, 1 M (mutant/knockout), 2 WT and 2 M. The numbers are the protein RTP1 and RTP2. She told me that they had designed the primers for the sequences so if the band is visible on the gel that means the sequence annealed to the primer. If in one mice, there are bands for 1 WT and 2 WT, that means the mice is homozygous WT, having both RTP1 and RTP2. If bands are all visible for 1 WT , 1 M, 2 WT and 2 M, then the mice would be heterozygous.

Then another experiment she did was put mouse 1 in a paper bucket as the control. She put mouse 2 in a paper bucket, then another paper bucket with a smell (acetophenone). We had four slides of the cross section of their olfactory bulb after the experiment. We did RNA in situ hybridization. For slides 2 and 7, she had a cFos probe that would bind to cFos that has DIG. For slides 3 and 8, she had a Gs probe that would bind to Gs which is present in all the cells. Slides 2 and 3 were from mouse 1 and slides 7 and 8 were from mouse 2. She also added a primary antibody which would bind to DIG. Then a secondary antibody that binds to the primary antibody, which has properties that allow for fluorescence. If the probe has cFos to bind to then there would be a lot of staining (purple in our case).

Apart from these 2 major experiments, I also got to section paraffin blocks of tissues for cross sections to put on slides. I got to use this really cool machine. I thought it was awesome when I first saw Neha use it but now that I have sectioned 4 blocks onto 20 slides of at least 10 cross sections each, it has become pretty tedious and actually somehow painful because the machine is at -20 degrees.

The lab members Mingshan, Ting, Neha, Jianghai, Jessica, Natalie and the other high school students are all very approachable. Yesterday when I was reading review articles, Jessica, the lab technician, asked me if I had plans for the weekend and I had absolutely none. That's why I'm writing this right now! But she gave me a bunch of recommendations to go to Chapel Hill, 9th street and other places in Durham. So far first week has been going well! Hope to do even more hands on work though!

Worms, Bombs, and Everything in Between

My first day was a bit of a surprise.  After extensively studying and ultimately writing my review on the insulin-like growth factor 1 (IIS) pathway and its roles in aging in C.elegans (a nematode), I learned that the project which I would be undertaking had nothing to do with the pathway.  But I'm actually glad that Dr. Murphy pushed me in a different direction.  Before coming to the lab, I couldn't really decide which of the various components of the aging process, including reproductive aging, oxidative stress, and learning and memory, I wanted to focus on, so I simply said that I wanted to do something on general longevity regulation, which, in hindsight, was probably the least attractive of my options.  I was assigned to work with a grad student, Geneva, who focused specifically on learning and memory.  We came up with a project in which I would train wild type, egl-4 (which functions in the AWC neurons), and egl-4 crh-1 double mutant worms to develop an association between a specific odor and food, and then examine if such an association is still present after a certain amount of time.  Unlike the IIS pathway, which is so well documented, the pathway in which EGL-4 acts is not, so it'll be really cool to study something which isn't as well understood.  And since I'll be working for 9 weeks, I might get to make more double mutant strains to test.

So basically, the rest of that first day consisted of some basic training of techniques, i.e. how to bleach the worms to obtain the eggs (which sucks for the worms because their bodies get completely dissolved), seeding plates (putting bacteria on them); a 2 hr long lab meeting, during which I was hopelessly lost; and reading 2 articles.

Tuesday was weird, to say the least.  Geneva, who is six months pregnant, needed to get some sort of test from a doctor, so she wasn't coming in until 12.  I arrived at 8:30 as always, and got cracking on reading those last 2 articles I was supposed to.  Some time between 10 and 11, I overheard two people in the lab I was in (not the Murphy lab because Geneva's office is in another lab) mention a bomb threat.  I thought this was simply a drill, so I just sat at my desk and turned to Gunnar, a postdoc in Dr. Murphy's lab who, like Geneva, has his office outside the lab, asking what to do.  He wasn't sure either, but a lady told us all to get out, so we did.  It wasn't a chaotic scene, however.  There was no sense of panic among everyone, and once we got outside we saw a mass of people walking towards the parking lots.  Thank God Gunnar was there, because he was able to drive me home.  Otherwise I would've been wandering around like an idiot.

Wednesday wasn't too eventful.  I learned how to 'chunk' worms (cut out a piece of agar on a plate of worms and transfer it to another), but other than that, I didn't have much else to do in the lab, so I mainly sat in Geneva's office reading articles and learning more about C. elegans.  In the afternoon Geneva and I went to another building, because she needed, for her project, to use a biosorter (a very fancy, intricate machine) to separate her worms which fluoresced under UV light (due to expression of GFP) from those which did not.  There aren't too many low points when it comes to research, but this has to count as one of them.  We essentially sat there doing nothing for three hours just waiting for the machine to count the tens of thousands of worms she had in her samples. And by the time I left about three hours later, the process still wasn't over.

The next day I attended safety training and I learned how to pick up individual worms, by using an extremely thin 'spatula' to scoop the worms up while I observed them under the microscope (these things are only about 1 mm long).   At first I couldn't pick up a single one as I didn't want to puncture the agar on which the worms grew, but after a few minutes something just clicked and I was able to pick them up with ease.  The funny thing is, on Friday, after I picked up the worms, they wouldn't get off the spatula, so I tried to scrape them off, but when I did that I would get agar stuck onto the spatula, which made it even harder for the worm to get off. There were several instances in which, after approval from Geneva, and a bit of guilt, I stuck the spatula into a gas flame and burned the worm to a crisp. Yes, I feel terrible about doing this, but I really had no other choice.

The rest of Friday was spent preparing for my first STAM (short term associative memory training) on Monday with wild type worms.  I needed to bleach my worms (dissolve their bodies; keep the eggs to make sure all the worms I use are the same age), and seed my plates with E. coli.  I also set up a mating of an egl-4 hermaphrodite and a crh-1 male so that I get heterozygotes in the next generation, from which I can ultimately select double homozygous recessive mutants.

So far I've enjoyed my time in the Murphy Lab.  Next week will be busy, as I need to run three STAMs and  do the necessary preparation for each (bleach worms, seed plates, chunk plates), but I'm looking forward to it.  If there's one thing I'd say I don't like about the lab, it's that I have to work extensively with E. coli, and that stuff just smells terrible.

Computer Networking Lab: Week 1

My first day at the lab, we had a conveniently planned lab meeting. I had taken the train and subway before to go to Columbia, but since I didn't want to be late on my first day, took a very early train and arrived about 1 1/2 hours before the meeting started. I loitered around the area around Columbia until the meeting started. I got to meet everyone in the lab and learned quite a lot about their projects. Since I found my lab during the last week of school, I spent my first week of summer reading as many articles about my phd student's project as I could. I felt that I had a sufficient understanding of his project and had a grasp on the terminology and concepts being explored. However, when he went to present his project to the group, he presented something completely different. I became concerned that I had spent time reading all the wrong papers, and learning the wrong concepts and terminology and that I was not fully prepared for the lab.

We left the lab meeting and my phd student -Varun- showed me around the building, took me to the lab - which is undergoing renovations, and then took me to the new work area where he had taken the time to set up a desk for me with a computer and four large textbooks all about programming in different languages. Our lab area doesn't look very "sciency," but it is a very comfortable working enviornment. We began talking and fortunately, the first thing he said to me was, "the project I presented is not the project you will be working on." This surely calmed my nerves and the more I talked to him, the more comfortable he made me. He made sure that if I needed anything or needed nay help at all, he would aid me in any way possible. He sent me copious emails explaining different parts of his project to me and sent me several articles and power points to read in order that I have a solid understanding of his project.

I read quite a lot about computer networks in general and WiFi network specifically and learned that they are far different than whatever I read about before. Nonetheless, I was very intrigued about how layered computer networks are, and how servers relay messages to clients. My phd student's research centers around creating an algorithm so that when on a WiFi network, the algorithm can effectively select a "feedback node" - essentially a device which can send information back to the server - so that the server can transmit the data better to all the nodes in the network; this is simply a broad and general explanation.

Over the next few days, I spent most of my time reading the papers and powerpoints, and experimenting with ORBIT - a testbed located at Rutgers that has 400 nodes set up. We access ORBIT remotely from Columbia and can upload Varun's algorithm onto the nodes and evaluate how effectively the algorithm is working. Varun spent a great amount of time explaining his project thoroughly to me and in the most basic terms since he knew I didn't have much experience with computer networks before. He courteously answered all my questions, regardless of how time consuming or basic they were drawing vivid diagrams on the white boards. I got to meet an undergraduate student - Josiah - whom I will be working with. He is an undergraduate student studying electrical engineering at North Arizona University. We both bad quite some trouble accessing ORBIT and were trying to problem solve together but to no avail. I worked on it that night when I returned and, unbelievably, I got to show him how to access it! So far, I've been having a great time and have learned so much. Looking forward to the next week!

The First of Many 12 Hour Days - Week 1

At 5:00 AM on the dot a sharp ring echoed through my room signaling the beginning of my time working in The Children's Hospital of Philadelphia (CHOP).  Two hours, two train rides and a taxi ride later I walked through the doors of the hospital.  Immediately the impact this experience would have on my life began to show.  All around me hung posters and images of the patients and doctors involved in this life saving institution.  Through the EXP program I was now a part of CHOP, which I think is pretty cool.

Because my lab is not soley research based there are a few unique protocols I had to follow before I started any work.  I was trained in the safetly regulations for the hospital and I took a tour through the different sections of the lab.  As the main Virology lab for the hospital, technicians are constantly running samples and testing patients who are waiting for their diagnosis.  As if that weren't enough work, several of the techs are responsible for validating new diagnostic modalities and equiptment that will be implemented in the future.  And just in case that didn't cover it, they were (are) now responsible for a 17 year old high school student from Peddie (me). 

After my first three days in the lab I have seen several steps of the process of diagnosing patients.  From processing to analysis each step must be done with care and accuracy EVERY TIME.  If not the results could be dire.  As a minor and not an official employee of CHOP it will be a while before I am cleared to do substantial work in the lab.  With that being said, there has not been a moment in the lab where I haven't been learning something.  Each member of Dr. Hodinka's team is about as knowledgable in their field as it gets and they always have something new to share. 

After my two week introduction to the lab is over I will recieve my project for the remaining four weeks. SO far the name of the game has been patience... learning how to take my time and STAR (the background of every computer in the lab) S-top T-hink A-ct R-eview: make sure all of your actions are well intended and appropriate.  I am excited for the remainder of my time in the lab and what new challenges await me.