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The power of seminars…

The seminars are an enjoyable opportunity to learn how other scientists became who they are. I was especially fascinated by the differences that emerged; some knew what they wanted to do from kindergarten while others experienced a wild transformation at a later stage of their college education. I might fall in the first category but I really don’t know, maybe I’m yet to experience my college transformation.

The group of speakers brought different dimensions to the whole seminar experience – a collaboration I found impressing. One such a dimension was the interlocking of seemingly different fields to explain a given phenomenon. A professor of biology and evolution anthropology, Susan Alberts gave us a glimpse of the work she does with baboons in Kenya. She studies mainly the effects of social environment on Darwinian fitness in these animals. I thought her work was an intersection of a sense of adventure and the love for science.

The other strong aspect of her work was the importance of team-work. She elaborated on how most of the data she used in the lab was collected by locals. The collaboration with locals is interesting in that it can be very useful to get other people thinking differently about the animals they previously viewed as merely creeping creatures. It is also important for the creation of more scientists interested in studying the primates from the African continent.

It was amazing to experience many fields of science from the perspective of experts. I certainly would love to have more of such seminars in the future.

Considering Research Environments and Science Policy

Dr. Charlie Gersbach’s seminar was one of the most interesting talks presented during the BSURF program. What really struck me about his path to where he is now was his consideration between the environments of working in industry versus academia. He described how academia provides flexibility to study what you wish, but at the cost of spending a lot of time applying for funding. On the other hand, industry can provide funding, but for projects that are often more repetitive or lacking stimulation. It made me realize that applying what is discovered in research to the real world requires an adaptation from the mindset that was performing research, to a focus on optimization. I am considering studying biotechnology and, if I go down that path, that choice is going to be critical. Even now, there is no clear answer and I think I will need more experience in both environments for an effective consideration.

His talk also brought up the state of public policy when it comes to genetic engineering and gene editing. I was surprised to hear that editing the DNA of food does not make it a GMO. Instead, ‘foreign DNA’ must be introduced. It demonstrated that, regardless about how one feels about GMOs, there is a gap between public policy and science that needs to be resolved. This requires people trained in the sciences and who have the ability to communicate effectively to those who implement policy.

A Passion for Baboons

One of the reasons I applied for this fellowship program, besides my interest in biology, was to discover what I wanted to do with my life. I wanted to know if biomedical research was for me. With the help the culmination of my summer experiences, including the very insightful faculty seminars, I am now able to confidently say I believe I am following the right path for me. As each faculty member stood before us throughout the summer, I would look at all of them and say to myself this is what I want to do. A common theme a found throughout all of the speakers was a sense of passion. I could feel how every speaker radiated a certain passion for the work they are doing. And I believe this is a goal to admire and strive for: to have passion with what you do in life.

One speaker that I could feel had such a unique and admirable sense of passion was a speaker from our first week here this summer: Dr. Susan Alberts, professor of Biology and Evolutionary Anthropology. Let me start by saying I am usually more interested in cell and molecular bio topics rather than ecology or animal behavior fieldwork, yet I found myself enraptured by Dr. Alberts’ discussion on baboon social affiliation and its effects on animal fitness. First off, I found it amazing how Dr. Alberts spent countless hours in the field in Kenya dedicated to her work. Also, who knew the baboons could have such intricate social relationships. What’s more than that, the social relationships of these baboons could possibly translate into relatable outcomes observed in humans. Perhaps I found her lecture more interesting because this type of research was so different that what I am used to. Perhaps it was because baboons are pretty amazing creatures. But I also think a large aspect of her talk that captured my attention was her apparent passion for her work. Listening to her that morning, I hoped that one day I could feel the same about the work I was doing because for me there is nothing more inspiring than having passion in what you do like Dr. Alberts.

Faculty Talks: Dr. Raphael Valdivia

We have all once experienced a fork in the road. I have always heard that the difference between those who are successful and those who are not is how much one is willing to overcome certain obstacles. Dr. Raphael Valdivia truly drove this message home as he emphasized the importance of never giving up in the midst of adversity, allowing creativity and passion to guide you, and always giving back to society. Not only did those words resonate with me, but I was able to relate to his story regarding his upbringing. Dr. Valdivia was born in Lima, Peru and his father always stressed the importance of receiving an education. Because of this, he was motivated to find any way possible to leave his native country and pursue higher education in the United States. After attending UWC USA for the remainder of his high school career, Dr. Valdivia attended Cornell University where he had wonderful mentors who shaped his career as a future scientist. Here at Duke, I have been able to find advisors who have encouraged me in the same manner so I was able to understand when he said “find someone who’s career you admire.”

Although Dr. Valdivia did not have a successful first round of attempting to apply to graduate school, his determination and persistence as well as knowledge of what his true passion is kept him going. After getting accepted to Stanford University, Dr. Valdivia was able to work on a project dealing with bacteria for his doctorate degree. It was, again, because of a very involved mentor, that he was able to successfully enter the field of science with full force. After a while, Dr. Valdivia came to work at Duke University where he now studies Chlamydia, a pathogen that is now associated with sexually transmitted infections. His research focuses on the pathogenicity of Chlamydia and how a cell is unable to perform apoptosis or cell death when infected with Chlamydia. I found the videos of this process to be very interesting and informative.

Dr. Valdivia spoke on the importance of hard work, serendipity, and service to society. I was inspired by his willingness to continue mentoring others as he realized the impact his mentors had on him. Currently, Dr. Valdivia is a Vice Dean and he helps counsel students as well as faculty on effective learning methods. He also works closely with legislature in improving the way lawmakers view discovery science research in hopes of increasing the number of grants that are given out to scientists. Overall, every faculty talk has truly taught me a lot. I have been inspired by female scientists such as Dr. Williams and her work on neuroplasticity and aerobic exercise and I am privileged to have been granted such an opportunity.

Faculty Seminars – Dr. Raphael Valdivia

Throughout the entirety of our program, we’ve had the privilege of getting to hear several speakers from the Duke faculty describe  their lives and their experiences in research.  I’ve really enjoyed receiving insight from each faculty member in regards to their life before research and what events or decisions lead them into the world of research. A common theme I noticed was many of the faculty credited excellent mentors with leading them to where they are today; I find that extremely encouraging, in that Duke is an environment full of amazing mentors.

In particular, one faculty member whose research caught my attention Dr. Raphael Valdivia. Dr. Valdivia studies the pathogen Chlamydia trachomatis, which can cause sexually transmitted infections. I’ve always been interested in the study of pathogens, so I immediately found Dr. Valdivia’s work fascinating. I really enjoyed his use of videos describing how the pathogen thrives within membrane-bound compartments in cells (I had never heard of bacterial pathogens doing this!). I also found it very interesting how he described social stigma related to his work (due to the nature of transmission of the pathogen). Overall I found his research extremely exciting, and am very curious to learn more about it.

Faculty Seminars

I really enjoyed listening to the different faculty members that came in to speak to us this summer. Not only was it interesting to hear about the research that they all have done / currently do, but it was cool to see how each of them got into science and the many pathways they’ve taken to get to where they are today.

As a biomedical engineer, I personally found Dr. Charlie Gersbach’s talk to be very interesting. I’ve always had a narrow mind about what biomedical engineering really meant, but I realized throughout the talk that genome editing through the usage of CRISPR and other technologies could also fit the term “engineering”, just maybe not in the way we are really accustomed to. In fact, it also makes me appreciate the fact that Duke’s Biomedical Engineering Department does range from research fields such as genetic engineering to brain machine interface development, as it accurately represents and showcases the many applications of the major. Gersbach’s research itself is fascinating as well, as the future of the work being done in this field can have massive potential to treat genetic diseases.

I also learned a lot from Gersbach’s path to where he is now. I am still very unsure about what I want to be doing exactly in the future, but it’s nice to see that many people have the time to explore both industrial and academic fields before settling on something they enjoy doing. I’m excited to see where my experience in research early on takes me, and I’m glad to have had the opportunity to listen to all these professors this summer!

 

Picking (faculty) favorites

This summer, one of the most rewarding parts of B-SURF was getting to hear from multiple members of Duke faculty about how they got involved in research and then specifically the research that they currently do. It is certainly endearing to know that you can have absolutely no idea what path you want to take in life, but still end up somewhere great. I also enjoyed the fact that we got to hear from people researching such diverse topics. Some of the biology was evolutionary and some micro. Some of the research implications dealt with the human brain and some with the colon. And some didn’t deal with humans at all. The one thing that was consistent among all the seminars is that each and every one of our speakers was extremely passionate about their contribution to the scientific community and that passion is what I enjoyed the most.

My favorite seminar this summer was Dr. Susan Alberts’. Her work on social determinants of health, ironically a class I planned on taking this spring, was so fascinating to me for a variety of reasons, the obvious being that I am intrigued by evolutionary biology/anthropology and the ways that are still very similar to some of our pretty close primate relatives, but also because I am interested in socioeconomic levels in the US and how it affects a person’s life. I found it fascinating that Dr. Alberts’ discussed not only the importance of socialness and social status in humans but also in baboons. The findings of her work also seemed to draw so many parallels between humans and baboons socially. For example, higher social status tends to correlate to higher access to resources and thus a lower mortality and higher fitness. While higher resource access doesn’t necessarily mean higher fitness in humans, it does usually equate to a lower mortality. I found the best part of her work was its’ interdisciplinary nature as it dealt with psychology and sociology, in addition to the obvious biology and evolutionary anthropology.

I am looking forward to the last two faculty seminars this week and learning more about some of the amazing research being done here at Duke.

Dr. Brian Coggins—Radioastronomy meets Medicine

The series of seminars I have had the privilege of partaking in this summer have been very interesting and enlightening. The science was exciting and the presenters offered thought provoking ideas and concepts. It was very interesting to see people from different fields and explore areas of science I never would have sought out on my own.


One of my favorite things about this summer was having the opportunity to hear about people’s career pathways. One of the seminars that I found very interesting was by Dr. Brian Coggins who works in the department of biochemistry at Duke. The science was interesting, but one of the things I liked the most about what he said was that curiosity drove his career path. It was inspiring to hear a story of someone who was not entirely sure about their scientific path going in, but was shaped by their experiences during education. I also found it odd that I really enjoyed seeing the connections between different scientific fields. He connected physics, chemistry, and biology in ways that made all of the fields seem interesting and less divided. It was cool to see the scientific fields presented together, instead of in categories from which you can only like one and must hate the rest.


I think my favorite quote from his talk was the following:

“There’s more to life than science.”

Choices

These past few weeks, I’ve truly enjoyed hearing all of the faculty seminars. I love learning about their research and how they had different backgrounds and paths yet all ended up here at Duke. In terms of research, it probably comes as no surprise that I really enjoyed Dr. Williams’ talk on aerobic fitness and neurogenesis because I love neuroscience, and I’m probably going to major in it. I actually took Neuro101 with her as my professor, and it was interesting learning about the research she does. Normally, when you think of exercise, you think of your muscles getting stronger, from your arms and legs to your core. However, normally people don’t think about exercise affecting their brain. Dr. Williams’ research shows that exercise/aerobic capacity does in fact affect the brain. A higher aerobic capacity and more exercise leads to increased neuron proliferation or survival in different parts of the brain. Now I’m starting to regret all those times this summer I’ve debated whether to go to the gym or stay in and watch Netflix and chosen Netflix.

Beyond my choices this summer on whether or not to exercise, there’s also many choices that I’ll face in the future in regards to my career path. There isn’t one particular talk that stood out to me regarding their career path, but that’s only because they have all shown me how diverse the path can be and how it can change. From being the director of the Duke Lemur Center to working in industry or academia to receiving dual degrees, everyone eventually ended up doing what they love. Of course, the road there isn’t easy and takes a lot of hard work, but I’m ready to put in that hard work and hopefully, end up doing what I love too.

Faculty Seminar Reflection: Dr. Raphael Valdivia

Every week this summer, we had the opportunity to listen to esteemed Duke scientists share about their current research as well as their career paths. Not only was it fascinating to learn about the diverse projects they’ve dedicated their careers to, but it was very intimate to learn about their personal journeys that have made them the successful scientists they are today. It was comforting to hear their stories and to learn that a lot of them did not follow a linear path to become a scientist. Instead, many of them took non-traditional paths that allowed them to explore many different avenues and discover many valuable experiences.

Though I enjoyed listening to all the faculty seminars, Dr. Raphael Valdivia’s talk caught my attention the most. Dr. Valdivia’s lab studies the pathogen chlamydia, a bacteria that is responsible for infecting thousands of men and women with sexually transmitted diseases as well as causing infectious blindness in humans. His work mainly involves identifying the mechanisms of how chlamydia mediates reprogramming of host cells and investigating how they occur. One of the mechanisms he observed is how chlamydia infections prevent cells from undergoing apoptosis, or cell death. I thought it was interesting how chlamydia uses this mechanism to proliferate in cells.

However, what really drew my attention was how personal he was with sharing his story. Dr. Valdivia grew up in Lima, Peru. He obtained his undergraduate education at Cornell University, attended Stanford for his Ph.D. and Berkeley for his post-doc. It wasn’t an easy road for him, however. After not being able to get into grad school right after college, it was his amount of determination to get in after his gap year that really inspired me. He was also faced with many tough decisions, such as having to decide to work in a lab where he values intellectual stimulation and being outdoors where he loves the adrenaline rush of climbing mountains. His gap year helped him decide that his true calling was with science and discovery. He really emphasized how important hard work is. If you’re willing to put in the work that it takes, you can go far. Ultimately, it was this amount of determination and authentic passion he has for his work that I enjoyed hearing the most.

Biology and Engineering

Hearing about the research and life stores of various Duke faculty members was really enlightening; every speaker took a different path in science, yet all seemed to truly love where they ended up in their research. While some knew from a young age that they wanted to pursue research, it was reassuring to learn about the large number who had to explore a range of possibilities before arriving at their current profession.

One speaker I really enjoyed listening to was Dr. Charles Gersbach. As a biomedical engineering major, I found his story about making the decision between research and industry extremely relatable. Also, the way in which his research combines genomic research and engineering (two fields that really interest me) is fascinating, and the possibilities of using genome editing for gene therapy opens up a number of possibilities nearly unimaginable to me. DNA used to be considered this unchangeable aspect of our selves, and for a long time there was nothing that could be done about life-threatening mutations, even if it was a simple base change. CRISPR-mediated genome editing is truly thinking outside of the box by manipulating a bacterial mechanism in order to potentially treat diseases (such as muscular dystrophy), whose causes are locked within our own genome.

To me, Dr. Gersbach’s research really exemplifies the unique interdisciplinary type of research that occurs at Duke. I first heard about his research while doing an AP Biology project in high school, and I think that was the first time I was really taken aback by how far science has come and the possibilities that are awoken by research. Someday, I hope that I can also find a way to combine my interests in genetics and engineering in a way that not only contributes to scientific knowledge, but also makes me look forward to continuing my work every day.

Reflecting on Dr. Gersbach’s Talk

The morning seminars have all been absolutely amazing. It’s great to hear about how all the speakers got to where they are, and most importantly, the science that they are doing. From fruit flies to lemurs, from evolution to medicine, it has never occurred to me that there are so many distinct yet interrelated branches under the huge umbrella of biological science, and every single one of them deserves being delved into.

As someone who is extremely fascinated by genes, I found Dr. Charles Gersbach’s talk on his life path and his research particularly fascinating. Dr. Gersbach focuses on cellular and molecular engineering. Specifically, one of the major aspects of his research is using genome editing technology to correct mutations that cause genetic diseases. For example, he and colleagues have successfully corrected dystrophin mutations in vivo in mouse models with CRISPR/Ca9 system, and this technology can potentially be translated to bedside, curing Duchenne Muscular Dystrophy in human patients. I found gene/cell therapy very promising because it can get deep down to the fundamental level of genetic diseases and correct the mistakes at that level. In contrast, most of the therapies currently are only able to ameliorate the symptoms at the surface level rather than actually cure the disease. There is a fundamental difference between drugs targeting bad proteins produced by bad genes, and drugs that directly target and fix those bad genes. I believe that once the gene editing technology becomes mature enough, it will have wide-ranging effects on healthcare.

Also from Dr. Gersbach’s talk, I learned that being a biomedical engineer does not mean dealing with brain signals / machines all the time, as how biomedical engineers are stereotypically pictured. Editing genomes and regenerating tissues are also part of problem-solving, therefore also part of engineering. The use of the CRIPR/Cas9 system for genome modification is an excellent example. The technology is adapted from bacterial adaptive immune system, and therefore part of basic science. On the other hand, it is utilized to solve problems on actual human patients, and therefore part of engineering. Dr. Gersbach’s research is really at the intersection between basic science and engineering, and for me personally, working at the interface between these two would be a very enjoyable and rewarding experience.

Of course, Dr. Gersbach’s life path is very inspiring too. Started off as a chemical engineer, he didn’t follow the majority and went into chemical industry. Instead, he tried to figure out what he wanted and followed it. This let me know that, as an aspiring scientist, there are really thousands of different roads ahead. No matter it’s the main street or it’s the road less taken, it’s important to always find my passion and follow my heart, alway do things I truly enjoy. As the program is almost coming to conclusion, I want to thank all the faculty members who shared about their life paths and research with us. All the seminars so far have been really fun and inspiring, and I can’t wait to hear about the life and research of the last two scientists next week!

Week 7: Genetic Engineering and Gene Therapy with Dr. Charles Gersbach

For the past 7 weeks, I’ve thoroughly enjoyed all of the faculty seminars, which have given me both breadth and depth of knowledge in the many disciplines within biological science. I came into Duke last year with a focused interest in cell/molecular biology and genetics and apathy towards other biological areas of study such as evolutionary anthropology and ecology, but after spending a year taking biology courses and attending these faculty seminars, I’ve begun to really appreciate the diversity of biology and the worth each individual discipline contributes to science and society as a whole. I’ve also really appreciated being able to hear everybody describe their path to becoming a scientist and all of the hurdles and choices they had to make; some were more straightforward than others, but ultimately, many speakers placed an emphasis on striving to do what you enjoy, regardless of all the trials and tribulations you might encounter.

I could say plenty of good things about every seminar, but I’ll be choosing to focus on Dr. Charles Gersbach’s seminar specifically for this blog post. His talk fascinated me for a variety of reasons: for one, my dad is an engineer, so I grew up thinking that I knew a good amount about how engineers think and the type of work they did. However, he’s a structural engineer, dealing with massive amounts of steel and concrete, which is the polar opposite of Dr. Gersbach’s work with genetic engineering on the molecular level in biological systems. Being able to hear Dr. Gersbach detail a completely different type of engineering, as well as his perspective on what constitutes as engineering as the scientific community becomes increasingly interdisciplinary.

In addition to that, Dr. Gersbach’s work on gene therapy and gene editing immediately intrigued me, since I’ve been avidly interested in the topic since high school after first learning about the concept for a research paper. For a period of time, I had even considered going into his line of work as a career path before orienting myself more towards cell/molecular biology and/or clinical medicine. Regardless, I’m still deeply interested in both the technical aspects of how gene therapy is done and the potential ethical and social implications that genome editing in humans generates, should it become more precise and possibly even marketable in the future. I’m especially excited to see how geneticists will utilize the CRISPR/Cas9 system, which has immense potential, to both improve gene modification as well as discover new things about biological systems and the organisms they reside in.

I was also surprised to find out that the label “GMO” specifically indicates the insertion of genes into cells, so it doesn’t include precise modification of sequences such as changing a base from one type to another. Some of my friends are fervently anti-GMO, but I’m sure they’d be surprised to learn that plenty of foods we eat are actually genetically modified, although in a different way from the ones actually labelled as GMO.

I’m a bit sad that next week will be the end to all of these faculty seminars, but I’m still looking forward to them nonetheless. Thanks to all of the faculty who have taken time out of their day to share with us their individual paths to science and their research!

 

How did we come to exist?

Throughout the past seven weeks, we have had the opportunity to hear from many faculty members about the fascinating research they are doing on campus.  The work I found to be the most interesting was that of Dr. Mohammed Noor.  Evolution was something that I grew up simply believing to be true, but I never really gave thought to how it occurred, beyond natural selection (or genetic engineering, in this day in age). I recently listened to a podcast on which an evolutionary biochemist spoke about a current theory of how eukaryotes evolved from prokaryotes.  The very simplified version of that story is that one prokaryote swallowed up another, then the inner cell developed into the mitochondria and this source of energy allowed to cell to evolve beyond the reaches of prokaryotic cells and thus eukaryotes were born. Essentially, all eukaryotic species developed from that one, singular event. This singular event took over a billion years to occur.  This theory blew my mind and made evolution a much more intriguing topic to me.  It seems unlikely that such a diverse array of species developed from that single event, but on the other hand it makes sense that such an improbable event would occur only once ever.

Anyway, I only bring up that podcast because it is what sparked my interest in evolutionary biology, the field in which Dr. Noor works. His research questions focus on the more recent evolutionary events, specifically the genetic evolution that allows new species to develop and persist.  However, I learned that defining a species is a very difficult process because there are often many subtle differences in populations that are debated as to whether qualify organisms to be a new species.  Interestingly, there are barrier traits that exist between gene pools, to deter species from interbreeding.  These barrier traits could cause sterile offspring or an absence of attraction.  Dr. Noor’s specific questions focus on the genetic changes that produce barrier traits and how the barrier traits are driven, in order to drive speciation.  I am very glad that I had the opportunity to hear Dr. Noor speak about his research and I look forward to taking his class next spring!

“There is Always a Path,” Science Outreach, and Chlamydia

This title suggests a blog post that’s all over the place, right? Well, I wanted to talk about all three aspects covered in one faculty seminar this summer so hold on to your hats. Whee!

I’ve truly enjoyed all of the faculty speakers this summer; it was great to hear about their individual paths to Duke, and to learn about their research and how they got interested in their specific fields. I ultimately decided to choose Dr. Raphael Valdivia to talk about, though Dr. Kontos, Dr. Williams, and Dr. Gersbach were all close runners-up (for very different reasons!).

Dr. Valdivia’s talk resonated with me for multiple reasons. Most importantly, Dr. Valdivia was adamant that if you are willing to put in the effort and seize available opportunities, you can achieve anything you are striving for. As he said, “There is always a path.” As someone whose mantra has been “hard work always pays off” ever since I practiced a beam routine for a gymnastics meet 30+ times and placed first for it eight years ago, hearing a researcher at Duke speak similarly about getting where he is today was encouraging. He also offered some unique advice, such as being open to new experiences as a scientist and not becoming comfortable with just working in the lab day in and day out, and reading papers outside your area of expertise for new ideas.

Another topic Dr. Valdivia touched on was scientific outreach efforts, and the importance of educating the public on scientific matters. This is also something I’m very interested in, because there is so much misinformation out in the vast and shifting oceans of the World Wide Web. As an avid reader of food blogs, I’ve seen a lot of blogs promoting various lifestyles for optimal health, which is great. . . until they spread false or poorly researched information, influencing their sometimes huge following of readers into believing things like, oh, cooking honey makes it toxic (http://www.thehealthyhomeeconomist.com/is-cooking-honey-unhealthy/).

Here’s a paragraph that’s a particular gem in case you were too lazy to click the link:*

“In addition, Ayurvedic dietary principles warn that consuming honey that has been cooked, baked or added to hot liquids contributes to ill health over time. The reason is because honey that is cooked becomes like glue. The molecules then tend to adhere to mucous membranes in the digestive tract producing toxins, called ama. The literal meaning of ama is undigested food or toxins stuck within the digestive tract. It is considered to be the root cause of most ill health in Ayurveda with heated honey one of the most difficult forms to detoxify.”

All right. Okay. Someone has clearly never learned the basics of human digestion, yet is acting like an expert and causing this information to be circulated. And the author’s readers thank her for sharing this IMPORTANT information, never again to expose honey to any form of heat before consuming it for fear of coating their GI tract with honey glue.

Sigh.

Science outreach is incredibly important to preventing misinformation like this being spread, and it’s something I hope to try getting more involved in beyond posting comments attempting to refute information on blogs.

I went off on a tangent there, but I’ll get back to Dr. Valdivia now to wrap up because what he studies is also cool: chlamydia infections. Chlamydia bacteria can infect a cell and prevent it from undergoing apoptosis in response to this rude intruder. Thus, when the cell divides, it splits into two cells with the chlamydia bacteria. Then those divide, and so on, resulting in scores of cells infected with the freeloading bacteria. Dr Valdivia’s lab studies how the bacteria take over and prevent cell death from occurring, and he showed us a few videos of cells dividing and spreading the chlamydia. Microbiology is just the coolest!

Thanks for sharing your science, words of wisdom, and path to success, Dr. Valdivia!

*Just for fun, here is another one of my favorite misinformation/pseudoscience posts by a food blogger who clearly never took a science class:

http://www.freezepage.com/1415667665TBMRBWICKU

This is a hilarious post for multiple reasons, not least of which she’s bashing airplanes for not having the air in the cabin be 100% pure oxygen (omg there’s nitrogen being pumped in too! *Gasp,* it’s a conspiracy)

Work in Progress

My time in the Perfect lab has been highly rewarding. I have had some setbacks but none of them was enough to upset my work. Firstly, the important part of my experiments involves mapping the whereabouts of an incision that was made during the production of my tps1 mutants. All the gDNA has been extracted and is ready to go for sequencing. After the sequencing, I will work with a bioinformatics team to interpret the meaning of the results and point exactly where the mutation occurred. This is a crucial part of my project. Potentially most of the mutants will have an incision in the same position or very close by. If so, the project will change course to focus on understanding more about the loci involved and establish its relationship with the compensation mechanism for the trehalose pathway.

Unfortunately, l do not expect the sequencing to be complete before the end of the BSURF 8 weeks. This might force me to present partial or no results at the poster session. However, I do not think this is a failure; it’s just work in progress. I do have other results that are fascinating although they were cannot compensate for the sequencing results.

Zeno’s Plasmids

Going into the program, I certainly expected experiments to completely fail. I expected them to return completely unexpected results. I expected them to be unidentifiably wrong in some way. But what I did not expect is for the experiments to tease me with how close they were to what I wanted.
For much of the summer, my major goal has been to confirm the identity of several plasmids. In order to do so, the plasmids need to first be isolated from bacteria and resuspended in solution. Then restriction enzymes are used to cut up the DNA into single strands that can be visualized on gels in order to see if the expected bands appear.
The first step of isolating the DNA started off well enough. I was able to produce a solution of at least 0.1 micrograms of DNA per microliter. The problem was that two of the plasmids just wouldn’t surpass this threshold. One only reached 0.09 micrograms per microliter, while the other only reached 0.07 micrograms per microliter. I attempted each at least three times, and each time, it was so close, but so far. It was not a complete failure, but just not enough success to warrant using the solution in future experiments.
Also, when using the restriction enzymes to confirm the identity of the plasmids, it seemed as if only a fraction of each run would work, even though there doesn’t seem to be a reason one would work, while another wouldn’t. I started with ten plasmids. Two were confirmed during the first run. Four on the next run. Two during the third attempt. Only one was confirmed during the fourth attempt. The final confirmation required streaking, culturing, purifying, and digesting all over again in. It reminded me of Zeno’s dichotomy paradox that only allowed a weary runner to travel half the whole distance, then half of the fraction remaining, and so on, never reaching the finishing line.
Despite taking much longer than anticipated to confirm the plasmids, there was a great amount of satisfaction after accomplishing something that took that much patience. Additionally, it was much faster to see the application of the labor as two of the plasmids were transfected into HEK 293 cells and shown to express in vibrant reds and greens.
What I have definitely learned through this experience is that the best accomplishments cannot occur suddenly or without trial. Being able to do something immediately, without effort or thought just breeds complacency with the result. The best joys of research have been at the end of periods of exacerbation.
While I am quite confident that my project will produce results within the next week and a half, I am hesitant to admit so since it might jinx the effort. Just as I have learned to trust but verify results, I have also learned to hope for a good outcome, but be prepared for an unexpected result.

It’s been a long time coming: The joys and woes of research

 

World without malaria

Well, it turns out this is not an easy task. Everyday is not sunny, but everyday is certainly a small adventure in itself. Looking back, I was very naïve about the process of scientific research. I had always heard that scientists experience failure and they learn from it, that is what makes a good scientist. It all sounds very pleasant and ideal, until I was the one experiencing the failure. At the moment, it does not feel as though I am learning from it. Whenever I have finished expressing the PK9 and UBC13 and I am well on my way in the purification process, my heart drops every time I see a truncation of the protein in a Western Blot. This usually means two things: we need to start over which means preparing 4 more liters of media, incubating overnight, inducing with IPTG, batch binding overnight, etc. Though tedious, I have repeated this process so many times that I now do not even think twice when I see that we do not have enough protein to begin an assay with.

Recently, however, we had a small breakthrough in our experiments due to changing various conditions in our buffers, IPTG, as well as incubation conditions. A few weeks ago, I would never think I could celebrate at the sight of just a few more microliters of protein. (And by this I mean microliters of protein when diluted). I have also found it very difficult to make certain choices such as whether to use a protease and cleave the protein in order to get rid of any non-specific protein. However, this has sometimes resulted in losing more protein than intended. On the other hand, not cleaving could mean ending up with unpurified protein which would bring us back to the same point. This checks and balances system is quite frustrating.

In the next two weeks, I hope to be able to finally purify enough protein to be able to begin an ATPase assay where I would be able to determine whether the phosphorylation of UBC13 is being affected (by measuring the amount of ATP being converted to ADP). I am extremely hopeful that I will be able to get some results in time for the poster session. This summer has been quite a rollercoaster and although I am sad to see it come to a close, I am excited to continue my project in the Derbyshire lab during the Fall semester.