Last week was when we started the analysis of our data. At the end of the week, Nick said to me "it's one thing to collect all the data, but then it's another thing to actually ask 'what does this mean'?" which pretty much sums up my entire week. At the beginning of the week I met with Nick and Dr Lewis a couple times to see how we wanted to classify some of the questions and each time we met, he changed how he wanted us to organize the data. For example, there were a couple questions on the forms like "hobbies" or "AP classes" and if someone wrote down something that didn't fall into one of the pre-established categories, I had to put them into an "other" category. The other category ended up being too large so I spent most of the week re-sorting through all of the raw data to come up with a way to classify the data that we put in the "other" category. As I said in probably all my previous posts, it's kind of ha...
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My final week went by very quickly. I began testing my task on other undergraduate and graduate students in the lab. However, I quickly noticed that the questions were extremely difficult and therefore lowered the difficulty to receive better results. After lowering the difficulty, I performed this test and was able to determine connections between creative thought processes and mind wandering due to time and accuracy of the answers. In all, I have had a great time at my lab in working and collaborating with the undergraduate students and Post-Docs. However, similar to my first day at the lab, I did not get to see my Post-Doc on my last day.
At the beginning of the fourth week, I started working on my third project with Charlotte, a PhD student at the Tomasello Lab. For the first part of the study, the child watched a pre-recorded Skype video in which three different adult experimenters name three toys (a dog, a book, and a dump truck) in their own ways. The first two people name them “a fish”, “a spoon”, and “a shoe” respectively, which is obviously wrong. Then when the third person came and was about to name the toys, there was a buzzing sound in the video and the experimenter would ask what the child participants expected the third person to say. After the children answered, the experimenter would take out three toys with different shapes and colors and l et the child play with them for a while. After that, the child would watch another pre-recorded Skype video in which the first person in the previous video assigned three names to the three toys respectively. As she left, a new person who did not appear in th...
These two weeks, I decided to keep myself open to new opportunities so I could get the most out of your lab experience. Though I have been working primarily with SERT in staining slides, I got to try several new things this week that I am really excited about. First of all, I began working with another protein (tryptophan hydroxylase) that produce 5-HTT in an attempt to explain the high levels of serotonin in Giardiasis and IBS. One interesting thing that came from this slide production was that though SERT levels are higher on the outside of the intestine, trp levels are found to be higher on the inside of the intestine. This was very surprising to me because I assumed the reverse would be true. As for my continued work with SERT, levels in the distal colon still seem to remain higher than any part of the small intestine. This was an unexpected result that we first thought was a fluke, but now is presenting itself more and more. We will continue to look into that as we keep analyzin...
This week's mostly been about statistical analysis, which was great at first until we realized that we didn't have enough rat subjects for our data to be statistically significant, which means...more scoring!!(yay) I'm not complaining, but I really would have loved to see some solid results. No one else was as disappointed, so I guess this pace at the lab is the norm. This means, however, that I probably won't be able to be there when the statistics actually end up being significant enough to establish a conclusion. Other than that, I found a really great Thai restaurant just around the corner of where I've been living, but I'm leaving on Wednesday, so I think I'm just gonna pig out every day until I actually have to leave :(
My mentor's other research assistant, Isabel, and I have begun consistently testing at the Bing nursery school on Tuesdays and Thursdays. By now, we've already had the script memorized and have many times had to improvise when the child doesn't follow our script. An example was one incident when Isabel, following our usual protocol, presented the child with a picture of me and asked him if I could come in to watch him play with the toys. The child casually responded, 'No,' and I could see Isabel starting to panic a little since the whole point of our experiment was to have a stranger observe the child play. Isabel questioned the child as to why he did not want me to be inside of the game room, and it turns out the child doesn't want to share his toys with me. As a result, we had to compromise with me observing him from the doorway instead of sitting right next to him. Other than that, testing has been hard because none of the children wants to go to the...
My main project is working on creating an accurate vector map of the entire Richmond Field Station by using the relatively inaccurate GPS coordinate from google earth/maps. I'm working on this project with Devin who is a local rising senior and Heiru who is a graduate student originally from Taiwan but attends the University of South Carolina. A vector map is the defined area that a vehicle knows it is allowed to operate in. The benefit of having a vector map is that an autonomous vehicle can still function in areas where there may not be GPS connection due to interference from buildings or trees. The vector map is also considered to be more accurate than GPS, but the trade off is its high creation cost and time requirement, as there is no public software that can accurately make a vector map from raw collected data. The data that will be used to construct the vector map was collected from the test vehicle as it was driven around the facility. Here is a picture of the raw data in...
It is now coming to the end of my third week in lab. Life was great here except that there was a major problem popping up in my research in past two weeks. What I wanted to do was to try to spin coat gold nanorods onto the surface of polystyrene film. Yet, most of the nanorods cannot stay on the film after spin coating since the polystyrene film was super hydrophobic. To solve this problem, numbers of solutions were thus proposed. I first tried to let the gold nanorod solution sit on PS film for 5-10 minutes before spin coating. Further, I applied plasma treatment to PS film which allowed the film surface to be hydrophilic shortly. However, these methods still did not offer me desirable nanorods dispersion. In addition to spin coating, I also tried drop casting. Through dropping the gold nanorods solution and allowing it to evaporate naturally, the gold nanorods can be preserved on film surface. Though I did detect lots of nanorods on the drop casted film via AFM scanning, they were ...
Week 7 has certainly been a whirlwind. For our experiment, we essentially wanted to compare the DNA damage in the muscle stem cells (MuSCs) of injured mice with those of non-injured mice. However, our experiment which tested for DNA damage using the biomarker 53BP1 didn't quite work out. When my postdoc Elisia imaged the MuSCs in the microscope room, she looked at the DAPI (nuclei) staining and the 53BP1 staining to see if they overlapped; an overlap of the two stains would indicate DNA damage. While the DAPI staining successfully indicated the nuclei of the MuSCs, the biomarker 53BP1 had stained both the cells and their background. 53BP1 therefore proved to be ineffective at indicating the DNA damage we were looking for. Subsequently, Elisia decided to perform this experiment using a different biomarker, one that would reliably indicate DNA damage. I then spent the first half of Week 7 repeating this experiment using the biomarker Gamma-H2AX, which stains for double-...
Due to some miscommunication and scheduling problems, I got my UCSF ID badge at the start of my second week. Now, I could go to the bathroom without being locked out of the lab and finally start my online training. I successfully completed the training within a day since Nino (my mentor) had to go to the hospital to retrieve thyroid glands and a few other organs from a human donor. These samples were frozen and stored in the cold room, which is what lab members call the giant walk-in fridge. The next day, we thawed the thyroid cells and placenta cells to sort them using the fluorescence-activated cell sorting (FACS) machine. The steps required to use this machine is quite long, but I was able to master it after preparing over a hundred samples and repeating the protocol about five times. First, the cells need to be transferred to well plates and centrifuged for five minutes at 1200rpm. Then, I get rid of the supernatant with a shar...
For the first two days of last week, I finished my last batch of hot-water extraction. My data turned out well for the majority of the samples, but there were some samples that had TOC concentrations over the measuring range and one sample that had a negative number. I planned to dilute the over-range samples but had no idea what to do with the negative one. I might rerun the negative sample just to see if it's an analysis error. It is unsatisfying to see such a result, but as Dr. Dmochowski said during our lunch meeting: no progress is progress, so I hope to learn something from this negative number. Since both Kyle and I were using mid-range kits for our TOC analysis, we ran out of kits and needed to wait for more to come, and I used this time to do some data calculation. I used the total carbon amount/percentage data from Liz and calculated the percentages of TOC that were extracted by hot-water extraction. The results turned out interesting: even though there is more ...
So, change of plans on receiving the human islet cells for live testing. I talked to Charlie and he said that the human islet cell supplier might not be able to have any cells in stock for the foreseeable future. The problem with obtaining human islets is that they’re extremely hard to come by, since they have to be sourced from recently deceased, young, healthy organ donors. It’s understandable that there aren’t many “in stock”. I asked Charlie about subbing in mouse islets since those could be harvested at will, but he explained that each mouse only has a small fraction of the islets that a human does, so we would need to sacrifice 80-100 mice for just this project – an ethical choice that I am happy to avoid having to make. Fingers crossed that I receive them before I leave California though! After the past two weeks, I successfully fabricated a few more hollow fiber cartridges that were suitable for in vitro tests. I tested them all for water flow rates with this pump setu...
I began week 5 by using the microscope to view the cell plates that I had previously stained. It was really exciting both to have results and to also see that I had followed the procedure correctly. I was a little bit nervous that something that gone wrong along the way and that the microscope but be unable to see the neurons, but I was able to view the red, blue, and green stains. I then had to set points in the center of each well and then focus the image and change the brightness, in order for the microscope to, hopefully, capture. However, I was a little unlucky and had to keep restarting the process because the microscope kept crashing, and was not able to take the 25 images needed of each well. Instead, Claire was able to take a single image of each well by zooming out, leading to a larger picture. We were happy to find that the results were as expected, with cell death occurring in wells in which it was predicted, and the cells in the veh...
This week was very busy. I started out each day watches two or three fin print videos. I have been seeing a lot of brown-banded bamboo sharks and lemon sharks and I even saw a couple of green sea turtles. I spent three afternoons in the wet lab processing my vertebrae and so far I have managed to get through about half of the samples. After I finish all of them, my next step will be to bleach and bake them. The other two afternoons I spent collecting data for a spreadsheet on the life history of guitarfish. I have about fifty-five species to get through, many of which are data deficient. After the spreadsheet is as complete as it can get with the data that is already available, I will finish aging the vertebra and getting the DNA samples back so it will hopefully fill in some of the blanks and provide data about this fish that has not yet been provided. I also got to help another student feed the epaulette sharks this week. She is working on determining the temperature pre...