Author Archives: Ayana Paul

The End

Summer 2018 is one of the most memorable summers I’ve had in my whole life. I’ve gone to Disneyworld, travelled abroad for a couple of weeks but I can never say I recieved as much as I did from this Summer compared to the past. More imporantly, I feel that I have changed personally and that I have a better understanding of what I want for my future. As of today, I can’t imagine being fully satisfied with myself without investigating some sort of question. As much as I’d like to claim that I’m going to apply to medical school or graduate school I’m not sure where I’ll end up. I do know for sure that I will performing research whether that be in a wet lab or dry lab.

In consequence to this, I’ve agreed to continue to participate in the lab I’ve worked in for the summer. My mentor, Jenny, has been supportive and helped along my mistakes and taught me how to learn from them. Moreover, I was surprised at how willing other members of the lab were to help me when I needed it. In a way, I had something to learn from everyone in the lab-not just my mentor. I am very pleased that they asked me if I wanted to continue to work with them because there was a part of me that felt I was a nusiance for having no idea what I was doing. It was through this that I learned that part being a scientist means being willing to train others in your science or trade. Otherwise, the story that you’re attempting to construct cannot possibly be continued.

In terms of me changing personally, I will attribute this to Dr. Greenwald and the program itself. I feel that I’ve become more open-minded to things such as animals and public speaking. After volunteering at the Eno Festival, I have more empathy towards snakes and feel a need to defend them when someone speaks ill of them. I have also come to understand the relevance of presenting data verbally in the science community. To be honest, I’m naturally very shy and I’ve been waiting my whole life to understand why having public speaking skills was relevant to me. After doing my chalk talk earlier this month, I understand why being able to present effectively is useful and essential for my career.

In short, the BSURF program met my expectations and more. It has opened my mind up to the possibilities research provides and the many pathways I can take to getting there. I have an understanding of what research is and what it means to be involved in discoveries. I have learned biomolecular skills and background knowledge. Furthermore, I know what role I want to play a science. Thank you Dr. G, Jason, Jenny, Dr. Perfect and to my peers for making this a truly memorable Summer.

My Favorite Seminar

Besides the immense amount of training I have recieved this summer, I have learned a lot about what I want for myself in the future. This is in part due to the seminars that I have witnessed in the last two months. I had expected to learn skills and techniques used in molecualr biology research but I didn’t expect to completely change my goals for the next couple of years. Hearing about the multiple paths that some Duke’s accomplished faculty took to get to their careers and the things they had to overcome in life really helped me in understanding the role I wanted to play in research and in the science community. I found all of the seminars intriuging but I believe my favortite was Dr. Bob Levkovitz’s.

Honestly, I was able to pull messages from each faculty member, but Dr. Levkovitz was the most personable in my opinion. What stood out the most to me about him was that he was honest about some of the career decisions he made. For example, he said that he joined the yellow berets solely because he didn’t want to be sent into the Vietnam War to most likely die. Whereas, the nice answer would have been: “I joined the yellow berets because I wanted to use clinical expertise for a greater purpose.” I learned that some of my decisions in life may not all be based in selflessness and I may have to take actions to for  myself one day. In addition, I appreciated that he had spoke with a concise attitude and didn’t “sugar coat” his advice. He talked about the changes in demographics at his school over time, how important the lab you work is and is minimal interest in research initially. It made me realize how vulnerable your goals are for the future. I may set a goal for myself today but as I’m progressing towards it or after I achieve, I may come to find I don’t actually want thing I was chasing. This scares me but at least I know this is a possibility and that I need to be prepared to be wrong.

This speaker was the last clue that I needed to truly figure out what I wanted to exactly. I am still a biology major so that hasn’t changed-if anything, I actually love Biology more because of this program. I realized that in terms of conducting research in the future, it doesn’t matter extensively if I pursue a MD or a PhD. Whether I pursue either one, my work life will be surround by people with varying degrees and level of expertise. These people will be there to bring new ideas and perspectives to the project. Most importantly, others will make up for the things you don’t know, so it isn’t imperative that you have a MD for clinical research or a PhD for general research. So in a way, you aren’t restricted no matter which path you choose. This was my main conscern in terms of figuring what I wanted to do with my life. In short, I am very greatful for these seminars.

Ayana’s Abstract

Cryptococcus neoformans is a fungus that is most commonly responsible for the disease meningoencephalitis, an infection of the central nervous system, and is potentially fatal in immunocompromised individuals such as those with AIDS. In addition, research related to C. neoformans has concluded that melanin production allows the fungus to cause disease and that the transcription factor, BZP4, is associated with this phenotype. This data leads one to question whether BZP4 actually has an influence on the fungus’ ability to cause disease. In order to test this theory, a strain of C. neoformans H99 with BZP4 absent was restored with the BZP4 gene via biolistic transformation and used to inoculate a 30 mice along with the deletion strain and wild type and observed  for 42 days for virulence and fungal burden. By the end of the experiment, it is expected that the reconstituted strain and wild type will present the most cell counts in the mice on average compared to the deletion strain. These two strains may also be able to cause disease and kill the mice they infected. Based on previous data, one can predict that the transcription factor, BZP4, is crucial  for C. neoformans virulence.

 

*The data does not exist yet but will in a couple of weeks

How things are going so far

My activities have slowed down in the recent couple of days because the lab is starting its mice experiments. All that is required is to grow my cultures out and prepare them into an innoculum for the mice. After that I simply inoculate the mice and watch them for days and record what I see. To be honest, this week has mostly consisted of me trying to get building and ID clearance so I can actually check on the mice for days to come. I have been able to get ID clearance but I’m waiting on going through orientation for the animal facility next week in order to actually observe the mice on my own. I did however innonculate 3 mice on my own, so I am proud of that.

I am a little worried in terms of time because I don’t actaully harvest the mice until the week of the poster session. As a result, I will probably be scrambling to collect the data from the dissection. In fact, we dissect on the day I’m supposed to submit my final draft poster for printing. So in short, I’m a little stressed as to how this is going to play out. I’m prepared to at least explain what the results appear so far in the poster.

Other than this, my experiments last week were successful for the most part. Although, I did make a mistake last week while doing  a PCR.

I was so confused when they came out. I didn’t think it was physically possible, but I made it happen. Basically, I screwed the canister that holds the tubes in the machine too tight and they melted. I couldn’t even get the pipette inside some of the tubes. So I had to do some of them over.

My favorite Chalk Talk from Last Week

I really enjoyed all of the chalk talks from last week. To be frank I felt a little proud of everyone because from what I could understand everyone had fairly complicated subjects and projects. To see that everyone could effectively explain what their projects were about and what they were doing was impressive despite out lack of experience. In addition, I thought everyone had demonstrated effective public speaking even though I noticed some were nervous (I was nervous, too). However, I really enjoyed Christine’s chalk talk because it was so different from everyone else’s.

Most if not all of us are working at the microbe or molecular level but Christine’s project has to do with quanifiying the amount of stress disctributed amongst different ranks amongst baboons. When I was first listenin to the premise of the study, I was first thinking that it was obvious that the alpha and lower-ranking baboons would have the most stress but then I realized that this was assumption based on bias and observations. Christine’s work is actually quantifies the stress by measuring the amount of stress hormones excreted by the animals. I also liked that the types of stress expressed by the varying ranking baboons were identified. Alpha baboons were marked with energetic stress, having to defend or fight for their position in the group. Low-ranking baboons were marked with psychological stress, meaning their stress originated mainly from their inability to access resources and isolation due to their percieved weakness. I guess I enjoyed her chalk talk the most because it involved a combination of behavioral science and molecular biology. Moreover, (she stressed that this was a stretch)I found it interesting about the implications that this project has on Homo sapiens. I am primarlily interested in microbiology/infectious disease but I do have a keen interest in society and how socioeconomic status affects people in an abundance of ways because the two topics interconnect in several ways.

Life in the Perfect Lab

My work in the Perfect Lab varies from day to day. The day may start with me immediately working because at this point I know what I’m expected to do. Nevertheless, on days where I have no idea what I’m supposed to do, I sit and talk with my mentor, Jenny, about the next experiments I need to complete to finish my construct*. Most days consist of me performing PCR’s on particular segments of gDNA to make the constructs for biolistic transformation. However, every week I learn something new in order to move further in the project. Jenny primarly introduces different techniques and approches to solving problems in experiments. Besides performing PCR’s and gel electrophoresis, I have learned to cut bands out of gels, extract DNA from gels, innoculate microbes, isolate DNA from cells and a plethora of other tips and procedures. I’m usually doing 2-3 of these things in a single day.

In addition to this, I have also learned from my mistakes and through those mistakes learned more about myself. For example, I have noticed that around 4 or 5pm, I am more prone to making simple mistakes compared to the beginning of the work day. Nowadays, I avoid performing complicated procedures at that time of the day and simply prepare to do it the next day. In doing this, it forces me to be more congnicent of time and prioritize my responsibilities for the day.

Fortunately, I have been able to produce sufficient yeilds with my PCR’s and DNA extractions to be able to transform the C. neoformans fungi. The next couple of weeks will be a little more stressful because my mentor will be leaving and I have to prepare/start mice experiments.

*construct: DNA that is to be put into an organism’s genome

My Work with Crypto

The lab that I work in (Perfect Lab) focuses in further understanding fungal Cryptococcus strains and how it utilizes its genes and proteins to function. My project specifically deals in further studying the fungal strain, Cryptococcus neoformans, that causes meningitis in immuno-compromised individuals. The ability to produce melanin in this fungus is an important factor in determining its extent of virulence. Further, I’m working with a transcription factor, BZP4, that was previously found to be associated with the expression of melanin production. The goal of my project is to demonstrate a relationship between the presence or functionality of this transcription in C. Neoformans and virulence within a host via genome deletions, additions and replacements of BZP4. I will speak more in depth during my chalk talk next week.

My Interview with Dr.Perfect

During my interview with Dr. Perfect, we discussed numerous topics related to his education, science/research, medicine, his kids, etc. My most memorable moments in life are the times when I give people the oppurtunity to speak freely and simply tell their story.

In school, a guidance counselor told him he could be anything he wanted to be. So he decided to become a doctor. He continued along the pre-med course in his undergradute career and revelled in the complexity and ability to help people as a doctor. Further, he continued to specialize in infectious disease in his mdecial career because he appreciated the simplicity of infectious disease: it normally requires a diagnosis and treatment. He added his conscern that this fact is changing given the surge of antibiotic-resistant bacteria but it has not affected his work immensely (his top world coscerns were also nuclear warfare and global warming). However, he would find himself falling in deep interest in a particular yeast involved in causing meningoencephalitis.

On February 14, 1978 at 11pm, Dr. Perfect recieved a severley ill patient infected with Cryptococcus neoformans. At the time, he found the situation very intriguing and decided to study the fungus thoroughly. As a result, his lab and research over the years has contributed to the understanding of meningitus and mycology. Unfortunately, he did have many conscerns about how research is conducted even today. He believes funding for research is minimal and that PhD research and MD research is too polarized. Moreover, he attributes this to the public’s and government’s attitude toward science. People don’t fully understand the importance of the “silly little experiments” that take place in the lab and how they directly affect the people. He proposed one example in relation to molecular biology. Without the establishment of basic molecular biology data and techniques, doctors/scientists would be unable to even identify the cause of an individual illness, let alone treat it.

Also in my discussion with him, he gave me advice on considering a medical degree and his personal experiences. Dr. Perfect feels that the field of medicine is a rewarding career and appreciates that he is able to help people everyday. Upon asking him how he deals with a patient he is unable to cure, he said you must first distinguish between sympathy and empathy when in medicine. Essentially, doctors have to learn to only bring empathy to work in order to protect their own mental health. He also added “There will be some deaths but everyone does that.” Hence, you have to accept the fact that you did all you could do and that it was that person’s time. Moreover, Dr.Perfect referred to the AIDS epidemic in the 80’s and know one understood what or how to address AIDS at the time. Consequently, there were several deaths that took place because of this lack of information. What also bothered him was not just that he couldn’t help these vicitms at the time but that these victims were were forced to die alone while disowned from the families because of their sexuality (AIDS epidemic affected gay men predominantly). He advised me to prepare and not worry about how I was to obtain a medical degree but discern whether or not I had a gift for it.

Overall, this is a man who can say he influenced the future in a positive manner. He helped buid a field of molecular mycology, help construct antifungals, made friends globally, developed a productive lab that publishes regularly, as well as  taught and trained 60-70 students. What I admired most was how he used his position to bridge a connection between medincine and scientific research thus shortening the  intellecutal divide between PhD’s and MD’s. He expands his medical degree from simply seeing patients to research and teaching. He was also able put his kids through school and see them develop to influence the world, too. Lastly, he hopes that I develop an excitement in discovery and truly experience what it is like to be in a research project this summer.

My first week in the Perfect Lab

My core expectation for the summer is to gain a general perspective of how research is conducted. In addition, I would like to at least be exposed to some of the basic experiments and techniques used in molecular biology and possibly master these skills by the end of July. I’m currently working with members of Dr. John D. Perfect’s lab. In general, the lab focuses on various strains of Cryptoccocal neoformans but has several projects taking place simultaneaously. However, the project I’m working on pertains to a transcription factor, BZP4, in C. neoformans  that may be associated with the expression of melanin, which is affects a fungu’s extent of virulence.

Over this past week, I feel that the lab has and will exceed my expectations for the summer. On day 1, I was being trained to perform gel electrophoresis and patch plates with transformed E.coli. By the end of last week I had been taught to innoculate fungi, perform PCR, precipitate DNA from PCR, clone DNA, conduct biolistic transformation and prepare media for plates. My mentor, Dr. Jennifer Tenor, has taken the time to sit down with me to not only fully explain the project but the general construction of a research project. Such projects start with a question, individual research and then a plan of activities to answer the question. The Perfect lab is very organized and, in my opinion, a “perfect” example of a lab that efficiently contributes to science and medicine.

More importantly, I’ve learned how the social atmosphere affects the efficiency of a lab. Each person in the lab has a relationship and there is a general positive energy in the lab everyday. The lab is welcoming and people are almost always willing to help. Moreover, everyone has a technical/intellectual strength that they bring to the lab and that helps forces the project further. My hope now is that I’ll be able to develop such a strength from this summer and be able to carry it into the future.

 

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