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.

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