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.

 

Nitya Talreja #3: Cancer Trials Part 1

Three dogs at the Penn Working Dog Center are currently being trained to detect ovarian cancer at various stages. Those three dogs are McBaine (spaniel mix), Ffoster (yellow lab), and Tsunami (german shepherd). As you can see, the list above is not specific to any breed of dog, which concludes that the ability to detect cancer (and other diseases) is not based on the dog's senses, but on it's ability to be trained.


The cancer training trials were conducted promptly at 9:30 am every morning and ended around 11:30am. All three dogs were trained on a scent detection wheel such as this one here:




There were 12 ports on the wheel and the cancer team would watch all 10 trials from a dark room where the dogs could not see us (to prevent any distractions). Three of the ports were filled with blood plasma samples in which there were malignant, benign, and normal samples stored in glass containers from three different people. The other 9 ports served as controls and were filled with either blank glass containers or miscellaneous pieces of plastic or rubber bands.  All the ports were covered with a metal case so that exterior variables (such as human saliva or dog drool) do not interfere with the scent of the sample. I was specifically told to treat the 3 experimental samples as powered sugar and to be extremely careful when handling them to prevent its scent from spreading. Data was collected on the cancer trials through a flase/true negative/positive basis. For instance, if a dog signaled at the malignant cancer port, it would be labeled as a true positive. If a dog signaled at a benign, normal, or control sample, it would be called a false positive. If a dog passed a benign or control sample, it would be a true negative. And, so on. It was a bit tricky for me to grasp at first, but it did not take long for me to get accustomed to.

Which ever dog began first, the dog had to be walked before and after each cancer session to prevent any accidents and limit and variables of the data. Also, the cancer team had to clean each of the ports between every dog with rubbing alcohol (70% concentration) and after cancer trials were completed each day.

As far as the actual people on the cancer team concerns, there had to be one person collecting data, one person spinning the wheel (with a stick) in-between each of the 10 sessions, and one person clicking when the dog sat at the correct cancer port. I was lucky enough to have tried all three tasks, and from experience, I can say that collecting data is by far the most difficult. You have to be alert at all times and observing the dogs and all of their reactions. But just in case, all cancer sessions are video recorded to refer back to in times of doubt.

I am genuinely enjoying my time at the Penn Working Dog Center and cannot believe my time here is almost over! I have had a great time with Dr. Lorenzo and am going to miss the puppies so much! Shortly after I had been accustomed to the cancer trials, Lorenzo and the rest of his team had abruptly changesdit to improve the study. Stay tuned for the interesting change in task :).

Tiffany Budiman, Entry #5, Last Week

This week Reem and I finished conditioning the mice on Monday and on Tuesday I post conditioned the mice and analyzed the videos on Ethovision. I spent most of the day in the computer room and adjusted the arena and detection settings for the Coc vs. MS mice. The next day Reem and I used Prism to analyze the data from the second group of mice the way we did last week on the first group of mice (Ms vs. Oxy). 

Adjusting the arena settings of the boxes on Ethovision

When we analyzed the combined data of the two trials, the outliers were already identified in the first trial by Chris but Sarah and I couldn't figure out why the specific mice were chosen so I spent the day watching the state dependent videos from the first trial of the Oxy vs. Ms mice. Then, Sarah thought me how to use excel to identify the outliers in our trial. 

The mice in box 1 preferred the stripes side as seen on Ethovision using the track visualization setting

The mice in box 3 only stayed in the stripes side and we had to figure out which drug ti received on the that side

The plan was for my PI Dr. Cahill to go over the combined data with Sarah, Chris, Reem and I by the end of this week since it is my last week here however she was busy and we didn't have the time to do so. However, since Reem and I analyzed most of the data ourselves I have an idea of what the final data and graphs would look like and will be able to work on my poster. Dr. Cahill also sent me the grant for the study so that I have additional information that i can work with. I will be in touch with most of my lab mates since they are going to send me the finalized data and results for my poster.  On my last day I bought doughnuts from Sidecar doughnuts, a popular chain in Southern California for my lab. 

I was surprised that my six weeks here went by so quickly and it was sad to not be able to come back next Monday. I am thankful that Dr. Cahill allowed me to work in her lab and for the opportunity to have been able to work with all the people that I have met there. I have learned so much during my time here and I wouldn't have been able to do it without Dr. Peretz and Dr. Venanzi. 

Tanvi Dange, Entry #5, The End

On Friday, August 19, 2016, I officially finished my 6 weeks at the Franz Lab at Duke University. During my last week, I made one last checkboard assay, but this time I tested more metals than copper (iron, zinc, and silver), and I also tested lower concentrations of copper.

Last time in the cell lab :(

I updated my poster with the data from my new experiments during the last couple days and before I knew it, it was Friday afternoon, and it was time for me to pack up my stuff and drive down to Georgia. I can't believe it's been 6 weeks since I first stepped foot onto Duke's campus. I guess time flies when you're having fun because time went by too quickly. I want to thank Dr. Peretz and Dr. Venanzi for accepting me into the EXP program and for always believing in me. I would also like to thank Dr. Franz for allowing me to join her lab and making me feel so welcome. Finally I want to thank Lizzie White aka the best graduate student mentor I've ever had. Thank you for always answering my questions, being patient with me, and showing me the best pizza place in Durham! I've learned so many skills and met so many great people in the Franz lab that I feel so confident for what the future holds!  

Lizzie, Abbey, Jacqueline and I i front of the BEAUTIFUL Duke chapel. I'm going to miss seeing it everyday.