Cat Life is Happy Life

Amarillo relaxing with her paper ball

Securing Laboratory Rotations

Following the Rules

    UAB's GGB program requires that students select and participate in at least three laboratory rotations.  A fourth rotation is available, but many of the people who I have spoken with have assured me that most students know which lab they wish to join before that. Apparently the policy will change next year. Students will only be required to do two lab rotations before selecting the lab that they will work in for their thesis project. 

How to Plan to Join a Lab

    Before joining a lab, a student must contact and (usually) meet with the principal investigator (PI) of the lab which is of interest to the student. I looked through several different departments on UAB's School of Medicine website. Ultimately, I contacted professors in the Microbiology and Bioinformatics departments. This process took several months. Once I contacted a PI, I had to set up a meeting with him/her. However, I couldn't set up a meeting until I was sure I would be in town. All of this was arranged via e-mail. 
    Once I got settled into the apartment, I contacted the professors again and met with them. I have managed to secure two of my three rotations. During my first rotation it appears I will most likely be doing a project involving Streptococcus mutans, one of the key bacteria involved in cavity formation on teeth. Eventually, I would love to be involved in a microbiome project focusing on the mouth. I feel productive and safe knowing that I have labs to rotate in before the school year even begins. I don't think I could ever be ahead enough. 

My Future

    I have to sign the paperwork, but it seems that I will be joining a lab in the School of Dentistry. It may seem odd since I'm in the genetics, genomics, and bioinformatics program, but this rotation will involve studying my primary interest, bacterial genetics. My potential PI seemed very excited about the topic. I'm looking forward to "playing" with S. mutans. 
    Aside from that, another PI has told me that I would be welcome to work in his bioinformatics lab for one of my later rotations so that I can better learn how to analyze data that I might generate during my own experiments. He suggested that I learn Linux, so if anyone has any tips about learning Linux please feel free to share them with me in the comments section! I don't think I'll have much spare time to do this, but I will make the time for it. This PI also cautioned me. I have a very limited programming background. He told me that I wouldn't necessarily be the best candidate to do a bioinformatics thesis project, but I could certainly learn how to use bioinformatics tools to analyze data. This is definitely a skill set that I find vital for doing science in this era. I'm excited to have the opportunity to learn about computer data analysis. Lastly, this PI told me that if I wanted, I could combine my thesis project to be both something from my primary lab and the bioinformatics lab. If I chose to do a microbiome project this would be ideal. 
    As I get more solid details about where and when my rotations will be I will post that information in this blog. 

Tips

    The following lists tips for securing a rotation in graduate school. These tips were given to me by both faculty and other graduate students who have already joined their thesis lab:

1. Be courteous
2. Prepare ahead of time: Read papers the professor's lab has published, read his/her web page, do some of your own research on what it is that the PI of this lab actually studies
3. Bring a copy or e-mail a copy of your CV
4. Dress should be business-casual or business
5. Be a diligent communicator: Check your e-mail for anything sent by your potential PI; respond quickly to any messages sent by your possible PI
6. Ask lots of questions!!! Show him/her that you are interested.
7. Choose a PI with whom you think you will be able to get along. It's not just about whether or not you love the science. You will want to join the lab of someone with whom you are amicable since you will possibly be spending the next 4 or more years of your life working with this person. One of my professors in Indiana let me know that she still frequently works with her former PI.    

Surgery: Round Two

Not What I Expected 

    I previously posted about my medical condition with certainty about what type of operation I was about to undergo.  However, the day of my surgery the nurse let me know that plans might change depending on what the doctor found when he operated. And change they did! A stent was temporarily put in my common bile duct for about two weeks.
    I don't remember much about the events that took place before or after my first surgery. Vanessa went with me to the hospital. Before I went into the operating room, the nurses had her sign some paper work about being my emergency contact. I was extremely pleased (and surprised) that the hospital allowed Vanessa to be my contact. It had a solidifying effect for me. I've understood that our relationship is permanent for quite a while, but that felt like a milestone to me. I often worry about whether or not we will be permitted to legally do important tasks for/with one another. I'm truly grateful to be alive in America during a time that my relationship with Vanessa is more often viewed as equal to a relationship between a man and a woman. I honestly wouldn't want to be without her. I need all of the support and care that she gives me. My dad was there to support me as well during the surgery. It was surreal that he wasn't the primary contact in case of emergency.
    It took me about the whole two weeks after the stent placement to recover. The pain was extreme for almost one week. I was asleep most of that week thanks to some good painkillers prescribed to me by my surgeon. The second week was better, but I was still experiencing some spasms in my common bile duct. It almost felt like being shocked by electricity in the same spot over and over for long periods of time. There was also a constricted, full feeling on the right side of my abdomen. By the second week, the spasms decreased in both severity and frequency.
    The surgery to remove the stent was much less painful, and the anesthesia wasn't as strong either so I didn't feel as groggy or exhausted afterward. The surgeon let me keep my stent. He gave it to me in a biohazard bag before I left the medical center. In true science nerd fashion, I thoroughly examined and measure it when I got home. I didn't understand why it was so painful when it was inside of me until I figured out that it was 3.5 inches long. Here are some photos I took of the stent. This was inside my body!

Fig 1. Stent measuring 3.5 inches in length

Fig 2. Stent displayed next to a quarter

Fig 3. Side view of stent with some bile sludge

       Since the surgery I have only had periodic spasms, mostly when I'm very hungry or very full. I noticed that occasionally if I have too much caffeine I may also experience a small spasm. I'm not sure whether or not there is an actual correlation between the two.
    I suffered with this for seven months. Suffer is not an exaggeration. Sometimes the pain would be so great that I would fall to my knees onto the carpet in my home. Lifting anything above 5 pounds would generate violent spasms. I tried to work out two or three times during this time period, and each time I had to stop or slow down because of the pain. I'm so glad for modern medicine. I'm so happy to finally be free of this constant pain. I'm thankful to all of the physicians, assistants, family, friends, and everyone else who listened to my problem, made suggestions, and encouraged me to seek help. As far as I can tell, I'm still recovering, but I'm so much better than before. Maybe now I will be able to try to meet my weight-loss goals. 

Scheduled for Surgery

     This may seem like it has little to do with graduate school, but it's actually closely linked in the sense that you can only do as much as your health will allow. I feel like I'm still on track, but having health problems has been a challenge during all of the hubbub of preparing to move and attend a new college in a new town. I've been experiencing spasms, throbbing, and a varying range of pain in my upper right side since the end of January. I've been to multiple doctors numerous times. The consensus seems to be that I have Sphincter of Oddi dysfunction and costochondritis. If you don't feel like reading everything on the pages I've linked I'll give you a summary:

1. Sphincter of Oddi Dysfunction:

• Located in the duodenum, the Sphincter of Oddi is also known as the Major Papilla 
• It allows bile to flow from the gallbladder out into the digestive system
• Mine stays closed or nearly closed much of the time, causing muscle spasms and a build-up of bile in my biliary system.
• Can eventually cause liver damage

2. Costochondritis - Swelling of the cartilage around the rib cage

    I've had copious medical tests which means that I have copious medical bills. Hopefully, it will all be over this Thursday. My sphincterotomy is scheduled for 7 a.m. The gastroenterologist is going to cut through my muscle using a wire with an electrical charge passing through it. At least there won't be any incision. The technique he will use is called endoscopic retrograde cholangiopancreatography (ERCP). Try saying that out loud! It involves using dye, X-ray, and a small camera in order to visualize the Major Papilla and cut it. I will undergo anesthesia, and I probably won't remember anything about the surgery.

The Beginning of the Journey

Acceptance to a PhD Program

    I graduated with a Bachelor of Arts degree in Japanese and Asian Studies in May of 2010. I had no job prospects and I was confused about what I wanted to do after I graduated. Did I want to try to get into medical school? Did I want to put my resume on Monster.com and try to get a Japanese translating job? Or did I want to try to go back to school for something else? Regardless of what I chose, I knew I had to move back into my parents' house when my lease in Lafayette was up in July. It just so happened that everything fell into place so that I could go back to school at Indiana University Southeast for a different degree. But what would I get a new degree in? 
    After going back and thinking about my career desires, I decided to pursue a Bachelor of Science degree in Biology. I acquired that degree on May 11, 2015. Thanks to the tight-knit community at IUS, I also earned a certificate for undergraduate research that I did with a faculty member. The road has been long, extremely bumpy at times, and seemingly never-ending. But, here I sit, as a future student of the University of Alabama at Birmingham pursuing her Ph.D. in the Genetics, Genomics, and Bioinformatics program. I honestly never considered that I was capable of getting this far in my academic career. 
    I'll be moving to Birmingham in July. My fiance, Vanessa, is going to share in this adventure with me. I'm so excited to be able to start a new life with her in a new place. Our place. There are many people who have supported me along the way, but I wouldn't want to do this without Vanessa. She has her own wonderful, new plans for herself when we move. I'm just as excited for her as I am for myself. 
  Luckily, I have family living near Birmingham. I don't know what to expect yet, but I feel comfortable knowing that I'll have all of the support I will need there. Vanessa and I recently rented a beautiful apartment in the hills of the city. I'll be sure to post pictures when we have them!