Nitya Talreja #5 Ovarian Cancer Part 3

To my disappointment, my last few days at my lab, most of the dogs became mysteriously sick. Dr. Otto, Dr. Ramirez, and other PennVet externs predicted this mysterious illness may have been passed on from a human-canine contact or may have been due to a patch of mushrooms growing outside. The first to get sick was baby Hoke (a 3 month old yellow lab). He was quarantined in the women's restroom to avoid the other dogs becoming sick too.

Also, one of the more advanced interns, Camden, was leaving the same day as me and was also fostering Quigley ( a black lab) at the time. To celebrate the completion of our internship, she asked me to meet her in Princeton one day to walk Quigley around for public access purposes. I met her Wednesday morning at the Princeton Train Station and we walked all around Princeton University's campus and Nassau Street. Camden trained Quigley for public access walking for a few hours while I recorded her with a video camera and filled out all the necessary Environmental Exposure data. Quigley did quite well; he was seldom tempted to greet other people and was not distracted by all the construction conducted on Princeton's campus. Unfortunately, he also got sick during out outing and we had to shorten our walk and head back to the PWDC.



     My last few days at the PWDC, the cancer trials changed once again. Dr. Lorenzo promised that these new trials would be the new norm from now on at the PWDC.

  Originally, there were three experimental ports on the scent detection wheel at all times: a malignant, a benign, and a normal from 3 different people. From now on there would still be 3 experimental ports, but those three ports would alternate between 6 different samples instead of 3 from 6 different people. In other words, there would be 2 benign, 2 malignant, and 2 normal samples alternating between 3 ports in-between the trials . There would also be 5 trials per dog instead of 3 due to the addition of samples.
 
  This new change made the first day of trials extremely stressful and hectic because no one was used to the new method yet. Worst of all, Dr. Lorenzo was not overseeing the trial and put a PennVet intern in charge of so great a responsibility. The first day of testing the cancer was shuffling to maintain the correct samples in the correct ports. Between all 5 trials we had to distract the cancer dog, with just enough time to place all the samples in their specific port numbers after cleaning all the samples. The task required at least 6 people in the back room. I was extremely surprised that we didn't break anything of mess up the samples after the trials that day. All three dogs took about 4 hours to run on the wheel instead of the normal 2 hours. The second day of testing, we began to develop efficient methods to help differentiate the 6 samples and we assigned each person to one task to avoid any possible mistakes. The purpose of using 6 different samples instead of 3 was to avoid dogs from alerting on the specific scent of the person. By implementing 2 different malignant samples, we were teaching the dog to alert of the scent of the cancer, not the person. The success rate of the dogs dropped drastically, from an unwavering 98% to a mediocre 50%. Despite the drop, Dr. Lorenzo still has high hopes for the trial and for improvement within the cancer dogs. He predicts that with time, the dogs will get used to the new setup and improve their success rate on the malignant sample.

Jay Swarup, Entry #6. Last Days

Hey everyone,
I just finished up my last few days at the Ramachandran Lab. During these days, we finished reading all 315 vials using the UV-Vis. This took a long time because we needed to make sure that the cuvette was 100% clean on the outside and there were no powders (fines) inside of it. But, we managed to finish the job. Afterwards, we plotted the points in excel, and the results turned out really good! Since today was my last day, we all decided to go out to lunch to a really good restaurant named Mamoun's (I highly recommend going to this place if anyone is in the mood for really good Middle Eastern food). Nevertheless, it was great having lunch with the crew one last time.

My time at Rutgers went by so fast, but I learned so much during my time at the lab. Thank you to Dr. Venanzi and Dr. Peretz for connecting me with Professor Ramachandran and one of the most interesting labs I could imagine. Also, shout-out to the crew, Vinod, Raje, and Shashank, for being some of the most interesting and affable people I have ever met. I wish them the best of luck in their future endeavors. Although my time is up at the Ramachandran Lab, I have gained invaluable knowledge about the work that is done in pharmaceutical engineering.

Emmy Wang, Entry #5, Final Week

My last week at the lab was a little more quiet since I had finished my project and was just working on my presentation and poster. On Tuesday I presented to my lab and afterwards we had a little cake and coffee to celebrate. I was a little nervous talking about a topic that I had been learning about for a couple months to people who had been studying it in depth for years, but everyone was very receptive and supportive of my work and data. There are four new masters students in the lab and the students from last year have come back to teach them the techniques and help get their projects started, so I have been observing them. Their projects include calcium imaging and odor stimulation, which have been very interesting to watch.

Working with the images from the confocal

One of the things I will miss the most from my time at the lab will definitely be eating lunch every day around the big table in the lab and talking. On Thursday the guest researcher from Russia played us some songs with my PI's guitar which was really nice to hear. It is sad that my 6 weeks have quickly come to an end but I have definitely learned a lot and really enjoyed my experience. It was quite a small lab so I got the chance to get to know everyone, especially my PI. I will for sure come back and visit if I get the chance and my lab is excited to hear about my future plans. I'll also miss Trondheim, although the day I left it started pouring rain and the temperature really dropped so I think I got out just in time. 

My PI Dr. Berg

Nitya Talreja #4 Ovarian Cancer Trials Part 2

The first few weeks into my EXP, Dr. Ramirez decided a change was necessary for the cancer trials to improve. His concern was based upon the issue that the dogs were trained to detect something during each of the 10 trials. There was a malignant blood plasma sample from a person with ovarian cancer in the scent detection wheel at all times. The issue was that it wasn't a very life-like circumstance. Everybody the dog encounters will not have ovarian cancer. We needed to train the dogs for scenarios in which there wasn't something to alert on.

Dr. Ramirez's solution was implementing a blank trial among the 10 normal cancer trials each dog was trained on. The other 9 trials remained the same, but on trial #4, a blank glass container was substituted for the malignant cancer port. This ensured that the dogs would not always find what they were trained to look for ( or in this case sniff for).

These blank trials made the lab environment a bit more stressful than usual. In the middle of the trial, we had to collectively take out the malignant port, clean out the empty port, and put in the blank trial all in the matter of a few minutes as to not make the dogs restless. It took a lot of teamwork but we somehow managed to complete the task without any mistakes.

All three dogs were successful on the blank trial and did not alert on any of the port on the scent detection wheel as they usually would on the malignant port. :)

Since we were changing the course of the trial, a new excel spread sheet was to be made to log in the new data. Dr. Ramirez gave me the honors of making the new spreadsheet. It was a bit challenging to grasp the image Dr. Ramirez had in mind, especially since I had not had much experience with excel nor had a made a spreadsheet of this kind in the past, but I eventually got the hang of it, and towards the end, logging in data came easily to me.



This week Dr. Ramirez also put me in charge of the Environmental Exposure data. Environmental Exposure is recorded on a data sheet that every trainer must have with him/her when taking a dog in a public environment(there was a copyright issue, otherwise I would be able to include the data sheet on the blog). These sheets record a dog's reactivity to object/noise/people around them and they note the specific environment of the dog. For instance, the sheet require the trainer to note whether if there are dogs in the environment or if there are high/low value treats being used, etc. Every time, a trainer had completed a Environmental Exposure sheet, I would be responsible for its entry into the excel spreadsheet. It was not an easy task at first. I had to become accustomed to the specific language used to the spreadsheet. But after I did, it came easily to me. There were some days this week where I would come in and there would be about 30 sheets for me to complete at once, but it wasn't too difficult after I got used to it.

We enforced this new aspect of the cancer trial for about a week before Dr. Ramirez decided it was time for another change. I will learn more about it in the beginning of next week right before I leave. This week was also the start of the new journal club meetings where we discussed the history of scent detection based on the very first paper published on dog scent detection of ovarian carcinomas. We discussed the pros and cons of the trial and how far the scientific community has come since that paper was published. Dr. Otto joined us on the journal club meeting and we had an informative session about the volatilome and the future of scent detection by dogs.

Jessica Cha, Entry #5, The Final Week

I have finished my 6 weeks at my lab, and although I have learned so much and am so grateful for being given this opportunity, I can't help but feel a little regretful. I have really gotten to know all of the horses involved in the research, so I will really miss seeing them each morning. I also wish that I could have stayed at the farm a little longer to see the end results of the research. I feel as if I am leaving when there is still work to be done, but I am still thankful for the 6 weeks that I have experienced.

During the final week, we focused mainly on the pastures. We continued to identify the grasses and collected the herbage mass in a couple of the rotational fields. This is done by walking diagonally around the pasture. We step 50 times, then we place down a wooden square and cut all of the herbage down to about grazing height (about a 1/2 inch above the ground). On the larger fields, about 16 brown bags of herbage are filled while on the smaller fields, only about 4 bags are filled. We then drive over to the lab and place the bags in the dryer. Once all the water is out, we carefully put the herbage inside the grinder and then ship it to a lab in Ithaca where it is processed.

Collecting herbage mass

While the research is still not over, there are clear distinctions between the continuous and the rotational fields. In a couple of the continuous fields, the trampling had caused patches of bare ground where grass will not grow. Also, in the continuous fields, there are large sections of weeds and manure that the horses will not graze on. Although there is not a stark difference between the continuous and rotational horses, there is a slight difference in the amount of fat (continuous horses tended to be fatter). I am expecting these results to stay the same until the research is over at the end of fall. 

On a side note, I was finally able to see the birds that hatched in the barn. On my first day, I had noticed that there were a lot of birds flying in and out of the barn. When I asked my PI about it, she told me that every year, the birds come into the barn to lay eggs. Although she wasn't very happy about letting the birds stay (sometimes she knocks the nests down with a broom since the birds leave a mess of poop and straw in the barn), she left them alone. On the last week, they hatched which was a perfect ending to my last few days at the farm. 

Two baby birds sitting in the nest

I want to thank my PI, Dr. Williams, for this experience. Last year, I would have never even thought about studying equine nutrition, but this research has really broadened my perspective of both animal health and agricultural sciences. I will forever be grateful to her for letting me under her wing, and for taking the time to teach me. I also want to thank Dr. Peretz and Dr. Venanzi for preparing me to take on this research. It was a hard process, but I am so thankful for everything they have done. 

Oliver Crane, Post #5, Last Week

My final week at UCLA was busier than all the previous weeks combined. Dr. Walwyn is trying to publish one of the lab's projects as soon as possible so everyone was working overtime. Most days I would stay till 6 or 7 pm to finish all the work I had to do which was a wide range of things. When I would arrive in the morning I would feed all the mice then make more food which involved crushing the regular mouse food with a hammer and blending fish oil pills into it (which made me and the entire room smell like a fish factory). Normally in previous weeks I would then go and do some work labeling brains on the computer, however Dr. Walwyn asked me to help prepare a few sets of brains, which have been recently sliced, for viewing under a microscope. This is truly a painstaking task as each brain has hundreds of thin slices in little wells which must all first be filled with PBS (a buffer that prevents them from drying out). Then the PBS must be removed from each well using a pipette and replaced with Triton (a mixture that contains a sort of soap and is used to clean the brain slices). After 10 minutes of leaving the plate on a shaker to mix, the Triton must be removed and then more Triton must be added again. This step is repeated many times along with other mixtures being added to the brain slices. The brain slices are then left overnight in a special solution which must be removed and then replaced with other solutions the next day. Anyways, this multi-day process involves pipetting thousands of times but finally prepares the brain slices to be moved onto a microscope slide.

An example of the well plates which are filled with brain slices in each well.

Once the brain slices are ready they must each be moved very carefully with a sort of tweezers onto a microscope slide. This roughly takes a few hours per well plate because of how fragile the slices are and must be completed in a dark room due to the slices being light-sensitive. Nevertheless, it felt really good to be able to see all the brain slices I had prepared by my last day at UCLA. On Friday, my PI took me and the new lab manager to lunch which was a lot of fun. I found out that the lab manager is actually applying to medical school in the fall which was cool. Back at our house, we all started packing up our things and cleaning everything which also was quite a task. I learned so much from my 6 weeks at UCLA in Dr. Walwyn's lab. Before this experience I really did not properly appreciate all the grunt work that goes into these massive publications. It really does take a village to put research grade papers together. Looking towards the future, I still have to write up a report of the history of drug advertising in the United States for Dr. Walwyn which should take a good amount of research. It's been a great summer and really amazing learning experience.

Jay Swarup, Entry #5

Hey everyone,

I just finished up a couple more week at the Ramachandran lab at Rutgers University. As mentioned in my previous post, I have been doing a residence time distribution experiment these past couple weeks. To do this experiment, you need to granulate the powders using different parameters on the continuous granulator. But, you must also add 80 mg of the nigrosin dye to the hopper on the continuous granulator right as you are about to collect the granules from the granulator. So, to summarize, when the granules are at steady state, you must add the dye and then directly after, collect the samples in weigh boats every three seconds for one minute. This procedure was done fifteen times. A picture of the granulator is below.

A picture of what the granules looked like after they were collected with the dye added is below.

After all the granules were collected and we finished using the continuous granulator, we transferred the granules from the weigh boats into vials. After this, we added 10 mL of deionized water into the vials and sonicated the vial for two hours. After the sonication, the powder and water are separated into two layers in which the powder is below and liquid is on top. Currently, we are using the UV-Vis to measure the liquid in the sample. A picture of what a sample would look like is below.

However, when doing UV-vis it is absolutely necessary that no powders enter the cuvette in which the UV-vis will read the sample because it will mess up the reading. So, in the case of a dark liquid, such as the vial above, we dilute the sample with deionized water either 100 times or 10 times depending on the color and how much liquid is present. For the sample above, we would dilute it 100 times because it is a very dark sample. Because we have over 300 vials, this process is taking a long time. But, hopefully it will be finished soon.

Aside from doing research at Rutgers, I have been enjoying my summer vacation by playing a lot of golf with my brother and father.