Emmy Wang, Entry #4, Nearing the End

My time at the lab is coming to an end with one week left. This past week my work has mostly consisted of working on my laptop and observing the other members of the lab in their projects. On Monday I showed Dr. Xi how to prepare, stain, and dissect the brain, which was a little daunting since it had been four weeks since I last did any of those steps, and even then I wasn't too confident. After spending about 20 minutes trying to catch the moth while the postdoc looked on, I definitely felt a little flustered, but soldiered on. Fortunately the rest went more smoothly.

Dr. Berg and I also returned to the other campus to try out the new confocal microscope and scan two more of my preparations. The new confocal is smaller and faster and basically better in every way. While the first two scans at the old confocal took about 40 minutes each, the new one only took 13 minutes.

The new confocal

The past couple days I have been working on a short presentation that I will present to the whole lab next Tuesday, including the new masters students, about what I have done and the data I've obtained. Also a little daunting, but Dr. Berg is always ready to answer any questions I have and tell me more about the images I have. In addition to this, I have also been helping with some housekeeping tasks around the lab since the lab doesn't have a technician. This includes moving around the pupae and insects, diluting more ethanol for the dehydration process, and cleaning and organizing the microscope area and equipment.

Moving newly delivered pupae into the containers

My mom had to fly down to Stavanger for the rest of my EXP time so I'm now staying by myself. After I finish at the lab I like to go down to the city centre and walk around and maybe grab a bite to eat. School has officially started so there's a lot more bustle. It's strange that I will be done in one week but I have enjoyed my time here thoroughly.

Jessica Cha, Entry #4, Diets for the Horses

My fifth week at my lab has come to an end, and I cannot believe that the time has flown by this quickly. We had to take a few days off from the research, because my PI sprained her ankle over the weekend, but we were quickly back at work once she could properly walk again. We continued our herbage mass collecting and step-point in the fields, and checked up on the conditions of the horses. Similar to last time, we weighed, took an ultrasound, and recorded body condition scores of all nine horses.

Ultrasound machine

We take three horses at a time and walk them over a scale as we lead them into the stalls. Once each one is groomed, we take them one by one to the ultrasound machine and measure the fat in the tail head area. We then run our hands over the major areas of fat, and give them a score from 1-9.

One of the students feeling the fat on the neck of the horse

Last time we did this, some of the horse were scored 7 and 8. Although they are still not in the best condition, this time, it was easier to feel their ribs as we ran our hands over the fat. We will still have to put some of the horses into stress lots once the research is done, but they did lose a bit of fat. 

While their body condition scores did improve, the horses didn't seem to have been eating less. In fact, they seemed to have been eating more. The horses in one of the rotational fields had eaten all of the grass over the span of a week, and we had to put them into their stress lot where they were on a measured diet of hay until the grass grew back. One of the horses in one of the continuous fields also ran over to the area of grass we were supposed to collect, and started to eat our data. So, they must be exercising in the fields to lose weight since their appetites seem to have increased.

Next week, we will continue our work in the fields and on the horses.

Tanvi Dange, Entry #4, Trying New Things

At the beginning of the week of August 8-12, I had a one-on-one meeting with Dr. Franz. I showed her my research from the first four weeks and told her my future plans for the last two. I told her I wanted to test Fenpropidin and Flu-TSCZ against all the S. cerevisiae strains and look at Cu+ binding instead of Cu2+ binding, which is what we had been doing on the UV-vis instrument. Dr. Franz was impressed with the research and the ideas for the future, and even made some suggestions on what plates I should make. So after my meeting with her, Lizzie and I decided that for that weeks biology experiments, we were going to make 6 checkerboard assays: 5 fenpropidin plates, one for each strain, and one Flu-TSCZ plate against the clinical Saccharomyces strain since it has a low azole-resistance. So I went through my normal biology experiment routine: streak a plate on Monday, make an ON Tuesday, plate on Wednesday and keep incubated for 48 hrs (and take time points in between).

the ON for the Oak strains

In addition to working with the new strains, I also had my first experience in the glove box. The glove box is oxygen-free, so it is the perfect place to work with Cu+ so that it won't react with oxygen and become Cu2+.

The Glove Box, aka a sauna for your arms

In the glove box I made oxygen-free azole-antifungals dissolved in DMSO and did what I usually do on the UV-vis to test for binding, but this time it was in a box with my arms very restricted-- the gloves were too big on me, and I barely had a grip on anything that I held. But regardless, I was still excited to have the opportunity to work inside of it: I felt like a true scientist!

I had no shame taking this selfie by the glovebox. Also my thumb is not actually that long...

And while the glove box was a cool experience, I did experience one of the traumas of working in the constricted, oxygen-free space with large gloves. At one point, I was trying to put the cap back on the bottle of DMSO, and I accidentally knocked down the flask. Thankfully, none of the DMSO touched any wires in the box (that would've been AWFUL), but I did have to step out of the glove box and let the graduate students clean up my mess.

Kimwipes covering my spilled DMSO. S/o to Lizzie and Steven for cleaning this, you guys are the best!

 Once I finally finished the scans, it was time for the Chemistry Dept's Happy Hour! I had never been before, and since this was the last one they were hosting while I was at the lab, I decided to check it out for a little. It was so fun! I met some students from other labs, drank water, and played Jenga! It was a great way to end my second to last week, and it's crazy that by this time next week, I will no longer be in the Franz lab. :(

Bob (honorary Franz-lab member) setting up Jenga; Steven is photobombing, and Lizzie didn't know I took a picture. 

Tiffany Budiman, Entry #4, Analyzing Data

This week Reem and I continued conditioning the second group of mice (Coc vs. Ms) and finished testing on the first group of mice (Ms vs. Oxy) by running the state dependent tests. On Monday before we started conditioning on the second group, Sarah taught Reem and I how to analyze the pre-conditioning data to determine which compartment each mice would get the drugs in. We use the program Ethovision to analyze the video and determine whether each mice had a bias towards a certain side in the CPP box. Before running the videos we have to adjust the box settings and make sure the mice are tracked properly bu ensuring the 'subject not found' number is below 1%.

Running the pre-conditioning videos on Ethovision

After balancing out which mice would get the drug in which compartment and on which day, we turned the data into a table so that it will be easier for us to prepare the boxes and injections during the conditioning days. 

Condensation of the pre-conditioning data

The table tells us which drug the mice is going to get and on which side of the box. We alternate day 1 and day 2 of conditioning for 8 days in a row and then a post-conditioning test is done before the two state dependent tests. While we condition the second group of mice we started to analyze the data from the first group of mice. After repeating the same settlings for the boxes, the date is converted into an excel sheet and analyzed using Prism. In Prism we can enter the data and acquire different tables that show whether or not the data is significant for the study. Since this is the second trial of the study we still need to combine and compare it to the first trial done. We also had a lab meeting, the first one since my PI got back from vacation. We used the time to get everything on track and determine what needs to be done in the coming weeks.

The setup of the CPP boxes

Megan Gabruk, Entry #10, Last Week

I have had the most amazing experience over these past 10 weeks and am sad to leave the lab and Palo Alto in general. I will miss all of the great people I have met this summer, the nice weather, and Stanford’s beautiful campus. My last week in the lab has been a bittersweet one because I don’t want to leave, but everyone has made this week so special. Kate took me out for lunch on Thursday and talked to me for quite a while about past experiences and my future aspirations. Vivian, the BABIES study project coordinator, also took me out for lunch today to say goodbye. It was so great that everyone in the lab cared so much about others. I did work until the end, making sure there would be clear instructions for the next RA and that my tasks were either finished or transitioned over to someone else in the lab.

            Also, I presented on Mendeley, the reference management program, to Kate’s RAs and anyone else in the lab that wanted to know how to use it. The presentation went well and helped people either learn about the program for the first time or understand how to use more in-depth features. I hope to be able to share this program with students at Peddie because it would really help with writing research papers that have a lot of references.

The lab meeting this week consisted of talking about retention for the Early Life Stress study and recruitment for the BABIES study. Dr. Gotlib was very happy that we have already scheduled 20 participants in just a few months. It is very difficult to recruit participants and get them to take part in all of the data collection which can be up to 10 hours of time commitment. Another difficulty the BABIES study may encounter soon is that we are soon adding more stages of the study. We now want to recruit mothers at 20 weeks gestational age and follow up at them when they first have the baby, when the baby is 6 months old, when the baby is 18 months old, and when the baby is 36 months old. So, retention will soon become a major factor for the BABIES study as well.

            My other tasks this week included editing an article written by some of the lab members about irritability and researching sex differences in irritability. Also, I read a dissertation involving similar tasks to what I created and took notes to identify their findings. I sent the tasks I coded to the group that had sent us stimuli as well. They were very appreciative that we pointed out the error in the morphing faces task. Another task included making an instruction sheet for the next RA. I also helped to create figures for a paper.

            Outside of the lab, I am packing up my apartment and enjoying my last days living alone in California. I have grown up so much this summer and have learned so much. This was truly one of the best experiences of my life. I want to thank Dr. Peretz, Dr. Venanzi, Kate, Vivian, Dr. Gotlib, the other lab members, and my parents for making this amazing experience possible.

Sharanya Entry #5-Final Two Weeks!!!

Even though I had to stay an extra week, I still can't believe that my EXP experience has officially come to an end. While I am sad that I won't be seeing my lab partners and friends anymore, I am still very satisfied with our group's results and most importantly, I am so grateful to have learned SO MUCH during my time there. During the two weeks, my group performed our last two sampling days and have been finalizing our results for my lab partner Anxhela's poster, which she had to finish and present on Monday of the next week. One of the major things I did was average out and plot the FIRe data, specifically the AL and MT measurements. The trends demonstrated that under light conditions, both Al and MT were increasing at a faster rate from 0 to approximately 300W/m^2 in irradiance, but then plateaued between 400 and 1000 W/m^2 and finally decreased from 1000 to 1400W/m^2. After discussing the resulting graphs with out PI's, we concluded that Noctiluca does prefer lighter conditions since the prey culture bottles in the light had way more cells (as indicated by the cell counts on the poster-image 2) than the ones in the darker conditions. Additionally, we also analyzed the final ammonia and chlorophyll measurements, which are an indicator of how much photosynthesis the cells were participating in. Initially we were confused as to why the cells were behaving this way but our PI soon determined that this was due to the cells dividing and therefore distributing the chlorophyll amongst two cells. Looking at the cell's preference for lighter conditions, we assumed that the cell preferred performing photosynthesis instead of phagotrophy since there was more light available and no need for it to feed on another organism. However when we looked at the prey counts, for which we used the FlowCam (image below), we noticed that the prey numbers were on the decline and that some culture bottles had very little to no prey at all. This is where it got interesting.

A VERY large clump of prey caught on the FlowCam!

Anxhela's poster (with my name on it;))

With its mixotrophic characteristics, Noctiluca is able to perform both photosynthesis and phagotrophy. Of course we all knew this but what we didn't know was that the two processes are not separated and are in fact interdependent, making it even more difficult to categorize this unique organism. Its ability to photosynthesize depends on its ability to feed and vice versa. I have personally never seen or heard of an organism behaving this way so this was definitely mind blowing.   The organism was thriving under light replete conditions not only because it had easier access to photosynthesis but also because easier access to photosynthesis allowed it to feed on the available prey species.

One of the many obstacles we faced while analyzing our data came from the FlowCam, which takes ten minutes to analyze each sample. This proved to be challenge when we had 120 samples of prey culture to filter through. Basically, the instrument is designed with a laser that detects individual prey cells and allows a tiny camera to capture images of them. Since there are thousands of prey cells in only 5mL of culture, it took a day and a half to get through one species of prey. While I did enjoy looking at the images of the prey, I eventually found this process, which mostly involved waiting for the culture to run through, the most boring part of the experiment. For one of the prey species Peridinium, we were afraid that we may have cross contaminated bottles since were were not seeing any Peridinium-like structures on the monitor. Instead, we were strange, round, spindle-like structures which were neither prey nor Noctiluca. After doing some research, our PI found out that the structures are actually Noctiluca, but in the form of cysts. Other dinoflagellates also form cysts usually when they are not reproducing during the winter seasons (image below). We are not yet sure on why the cells transform into cysts since there hasn't been much discussion about them in the marine biological community.

A dinoflagellate-Gonyaulax cyst

Finally after an entire week of sampling, averaging, and plotting (graphs), it was time for Anxhela and other undergrads to present their results to the entire observatory. The presentations themselves were only a minute long and took place in the Monell Building Auditorium. Afterwards, our lab and other students flocked to the Comer Geoscience building where the presenters would stand in a sort of Peddie Science Night configuration and explain the details of their findings.

Monell-the swankiest building at Lamont :)

Anxhela during her presentation 

Me, Anxhela, Kali (our technician), and Yen Sheng (another undergrad in our lab) during presentation night

After presentation day, we only had one more major sampling day on Wednesday. Since we didn't have time to go out to lunch, our PI surprised us by ordering sushi and BonChon chicken (I've never heard of it) takeout. We all sat together as a group and since another one of my PI's former grad students was visiting, he was able to join us for lunch too. Overall, our last sampling day went smoothly and we finished up what was left of the FlowCam prey cultures. Realizing that I was about to miss the shuttle (again), I said goodbye to my PI's and lab partners but promised to visit them later this month or in the fall.

I would first like to say that this has been an incredible learning experience for me. I am so grateful to Helga and Joaquim for welcoming me in to their lab and giving me this opportunity. I also realize how lucky I was to be a part of such a friendly and knowledgable group. I definitely would not have been able to accomplish what I did if it weren't for my fellow high school student Alexandria's friendship and my partner Anxhela's positivity and guidance. I realize that not everyone is lucky enough to truly bond with their lab groups but I am glad that I was. Going in, I was very shy and didn't really know much about this particular field or any of the methods that we were implementing. I was also making quite a few mistakes during the first few weeks and though my lab partner was more than understanding towards my inexperience, I was frustrated with myself. The first sampling day was probably my biggest challenge but it was also the most rewarding experience since that was the day I learned the most about our lab's procedure. However towards the end of these eight weeks, I was able to fully implement the protocols of the methods but also fully comprehend their purpose and the big picture of our study. Additionally, I was learning from my mistakes not only in the lab but outside of it as well. By getting lost in Harlem more than once, I learned how to travel in NYC's subway system. I also became a commuter for the first four weeks, traveling four hours a day through NJTransit, the Subway, and a forty minute shuttle. Ultimately this experience is something that I will always remember especially during my future scientific pursuits.

Last but not least, I would like to thank Dr. Peretz and Dr. Venanzi for giving me this amazing opportunity and for guiding me through to success. I would once again like to thank my PI's Joaquim and Helga for letting me be a part of their lab. Also, a BIG thanks to Kali our technician and go-to person for everything Noctiluca. I would also like to thank Alexandria, Yen Sheng, and Anxhela who helped make this an fun and unforgettable experience!

The Group-Yen Sheng, Alex, me, Kali, and Helga

David Alvarez, Entry #5: Week 7, El Gran Final

That's a wrap! It's hard to believe that 7 weeks have already flown by and my time in the Wireless and Mobile Networking Lab is over. It didn't really hit me until I sat down to write this after I had lunch that this really was it. It's definitely a bittersweet feeling to be leaving today. Part of me is going to miss coming in every day and seeing everyone here, as well as continuously learning more about computer networking, a field which I knew nothing about but now am so fascinated with. Another part of me is feeling so glad that I emailed this lab, by some miracle survived the 7 weeks here, and am now accomplished in completing my work here.

My last week here was actually one of the slowest. The direction in which to take the WebRTC experiments was a little unclear, but we figured that it would be better to just re-run the scenarios that we'd already gone through, but with one wired machine in order to have a more stable set of results to look at. Rodda and I went through the usual routine of running the experiments while taking .pcap traces on Wireshark, uploading all of the traces onto one machine, and generating .xml files to parse through in order to generate graphs for data rate, throughput, packet size, time delta, and CDF for all three machines. We've begun to see some interesting results on the receiver side when we add traffic to the channel, which I both love and hate because I like that progress is being made on the project, but hate that it's being made just as I'm leaving. I wish them the best as this project rolls along.

My experience here has been absolutely incredible. When I came in 7 weeks ago, I was really nervous because this wan't a field that I knew a lot about, and I knew that this was a small lab, so every person here would have a certain expectation of them. However, the guys have been extremely helpful and I now feel very good about the work I've done and the things I've learned. It's been more than just learning about computer networking; it's also been about learning how to commute, how to get around New York City, and getting a good feel about what life in the city is really like. It's an experience that I'm so grateful to have had, and will carry with me in all of my future endeavors in science.

I'd like to thank Dr. Peretz and Dr. Venanzi for helping me through every step along the way through EXP. I'd also like to thank Varun, the PhD student who guided me through my time here and made sure I didn't crash and burn. Also, a quick nod to Rodda, the other high school student here who knew way more about networking than I did and who was a great partner to have, and friend I hope to keep in touch with for a long time. To everyone who hasn't finished yet, good luck and have fun! And to everyone else, until next time.