Hanging Up the Lab Coat

I am very sad to announce that my internship came to an end last week.

I have learned so much about the different techniques I was using as well as the different careers and the workplace environment in a lab such as CIHR.

My favorite part of my internship is what most people hate most about research… when things go wrong. I have really enjoyed all the problem solving that I have done this summer. I have spent countless hours researching online, speaking with coworkers, and designing and executing experiments to figure out what was going on with my project.

I have (almost) successfully finished making the vector that will be used to insert the sgRNA into the final parent vector. This is something that a previous researcher really struggled to do. I was able to do it, however there are small mutations in the sequence that I am still trying to research whether they will have deleterious consequences or whether I need to go back and redo everything I did this summer. It wouldn’t be too difficult to do this as I know the process that works and the techniques that are used.

I also was able to catch multiple mistakes that were made by the original researcher who was working on this project. I have ordered new DNA primers to fix these problems so that someone is able to take over the project in the future.

It has been such a pleasure interning at CIHR and writing this blog. I can’t thank my supervisor and the Center enough for their support. Of course none of this would have been possible without the help of Dickinson’s Career Center through their internship grant program. Without the support, I would not have been able to afford having this wonderful internship!

Thank you to all for following my adventure!

A Typical Day at the CIHR

I know before I started my internship that I wanted to know what to expect daily in terms of what I’d be doing so I hope this helps future interns.

8:45 – I drive 45 minutes to Providence, RI each day. I have the great fortune of being a recipient of an internship grant through Dickinson that made this commute possible. As this internship was unpaid, I would’ve had to pay for the gas had it not been for the internship grant. Check out the Career Center’s Internship Grant here!

9:30 – I arrive at work wearing pants and close-toed shoes carrying my laptop and personal notebook. A number of things can happen following my arrival; it could be any of the following:

  • Remove samples from the incubator from the experiment I started the day before. This happened about once a week.
  • Review my laboratory notebook to find out what I need to do next or to add any notes that were missing from the day before
  • Write out a plan in my personal notebook of the experiment I would be doing. I would typically run the procedure by my supervisor before starting.
  • Work on researching my project or troubleshooting (my favorite part!)
  • Prepare a presentation

12 – Around this time almost everyone in the lab gets together and eats lunch in the lunch room. I brought my lunch everyday and left a large container of yogurt in the fridge. This was one of my favorite times at my internship because this is when I was able to learn about the careers and experiences of the different researchers that got them to where they are now.

At least once a week there would be a “journal club” during which someone(s) presented on their research. The people who presented ranged from me to the head of the CIHR. I really enjoyed these because I learned what other people were doing which gave me a better idea of who I was interested in shadowing during my free time.

12:45 – After lunch I typically would be done with my morning project and I would move on to something new which again could be any of the following:

  • Complete the morning’s experiment or receive the results
  • Meet with my supervisor to go over the general state of the project and the plan moving forward
  • Send things to be sequenced
  • Learn new techniques!!!
  • Shadow a researcher
  • Record in my lab notebook
  • Conduct a new experiment

I almost never left my internship at the same time. Depending on whether I was done with my afternoon experiment, whether I could do anything without assistance, and how much I understood about my project all determined how late I stayed. Because it is the summer, many of the researchers arrive and leave early (like 6am-2pm). However, hours really depend on what you are working on. For example, two researchers were performing ELISAs so they would have to come to lab every 7 hours in order to get them done in time.

It is always a pleasure to go to the Center as there is almost always someone there or something to do.

CRISPR Cas9

Recently I gave a presentation on the CRISPR system at CIHR. The system is the main tool that I am using in my research project and I have spent much of my free time at my internship working to understand it.

CRISPR, or clustered regularly interspaced short palindromic repeats, has multiple different uses. It can be used to knock out, activate, or repress specific genes or to purify a specific region of DNA. I am using CRISPR to make very specific, small changes in the DNA that encodes the protein I am studying. I am making these changes to see their affects on the parasite’s ability to leave the red blood cell.

There are two main components of CRISPR, a CRISPR-associated endonuclease and a guide RNA (gRNA). In my project, I am using Cas9 for the CRISPR-associated endonuclease. An endonuclease is a protein that is able to cut DNA. The gRNA is a  sequence of RNA that has a Cas9 binding domain (so that it is able to bind to Cas9) and a guide sequence. The guide sequence matches the DNA sequence where you want to make the cut.

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Notice in this picture that the gRNA has the “scaffold” which is the Cas9 binding domain and the “spacer” which is the guide sequence. The Cas9 protein is shown in green.

As shown in the above diagram, the gRNA and the Cas9 protein join together and look on the DNA for the place where the gRNA’s guide sequence matches the DNA (shown in black). When the sequences match, the Cas9 makes a cut in the DNA.

In my project, there is going to a piece of DNA that is going to be able to be inserted into the cut. This piece of DNA will contain the small, specific change that I am studying.

The CRISPR system is a recent discovery in the field and the exploration of its use is just getting started. It has the potential to greatly expand current research because for the first time, we have an accurate way to make small, specific changes in DNA. I look forward to seeing how other researchers use the CRISPR system in the coming years.

My project…

I am still working to understand the project I am working on as it is multifaceted and was left incomplete by a previous researcher at the CIHR. However, I am going to do my best to give you a brief overview of the project. I hope to go into further detail about the scientific methods in future posts.

In my last post, I explained that a critical part of the parasite’s life cycle is escaping the red blood cell to infect more red blood cells. My research is based on this need to escape and the idea that if we can prevent this, we may be able to create a novel vaccine for Malaria.

Researchers at the CIHR recently discovered a protein, PfSEA-1, that is necessary for the parasite to escape the red blood cell. The parasite’s escape is closely regulated by phosphorylation (the addition of a phosphate group to a molecule). My research is based on changing the phosphorylation of the PfSEA-1 protein to see if it will affect the parasite’s ability to escape the red blood cell.

In order to test whether phosphorylation of the protein is significant, four of the places on the protein where phosphorylation occurs will be changed (either to a mimic or a lack of a phosphorylation site). Finally, I will watch to see what affect these changes in the protein’s phosphorylation have on the maturation and/or escape of the parasite.

Malaria: Everything you need to know about it for my project

We have all heard of Malaria but even I knew little about it until my “Infectious Diseases and Immune Defense” course at Dickinson. Hundreds of millions of people are infected with the disease each year according to the WHO. Malaria is the greatest single-agent killer of children on the planet with over 1 million children killed each year.

Malaria is a disease caused by a certain parasite that is spread by mosquitos. The parasite travels through a person’s body using our body’s red blood cells. A critical part of the parasite’s life cycle is escaping the red blood cell to infect more red blood cells.

malaria

Above is a cartoon of a red blood cell (maroon) full of parasites (blue) that has been lysed by the parasites so that they can escape and infect healthy red blood cells (red).

My research is based on the fact that the parasite needs to escape the red blood cell and that if we are able to prevent this, we may be able to create a novel vaccine for Malaria.

Learning…

One of the biggest lessons I have learned while at my internship is the value of working through new information rather than being taught it. Instead of sitting down with me for my first week and explaining to me the project that I would be taking over, my supervisor encouraged me to read through the lab notebook and thesis written by the researcher whose project I was taking over.

I took my time reading through the material and looking up and taking notes on anything I didn’t understand. At the end of the day, I sat down with my supervisor and went through my list of questions and took notes as she explained some of the ideas or suggested how I could find the answer to my question.

At first this approach was very frustrating as often as students we are explicitly told what information we need to know. Reading through the thesis and notebook, I wasn’t sure what was important and what I should be learning from them. My supervisor’s strategy forced me out of my comfort zone and I believe it resulted in me having a much stronger understanding of my project.

An ‘Egg Shell’ent Discovery…

One morning before my internship, I was on Facebook and saw that a friend had posted an article about a high school science project, but I was in too much of a rush to open the link.

Later that day, I was working in the lab when one of the researchers asked if anyone had seen the article about the science project. Suddenly, the whole lab was talking about the article I had seen earlier that morning on Facebook.

The article was about a high school in Japan that discovered a way to hatch a chicken egg without its shell. This had never been done before and would allow people to watch the development of a fertilized egg up until the day the chicken hatches. Their work was credible and significant enough that they were able to publish their protocol in a scientific journal.

If you are interested in learning more, check out the journal article at the following link:

https://www.jstage.jst.go.jp/article/jpsa/51/3/51_0130043/_pdf

We watched the following video which shows the process:

We all agreed that it was amazing that you could actually watch the development instead of just studying it from a textbook and that it was all because of a group of high school students.

My supervisor mentioned that we may have to give it a try ourselves sometime this summer so keep your eye out for an update on that.

How I got my internship…

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In January 2016, I reached out to a family friend and mentioned that I was looking for an internship for the coming summer and asked if she knew of anyone working in biology that may be able to help me. She got back to me within a week with the name and email address of my current supervisor who I’m going to call ‘C’.

I looked C up on LinkedIn and found that she worked at the Center for International Health Research (CIHR). After doing a bit of research about CIHR, I sent C and email introducing myself, explaining my interest in a summer research opportunity, and attached my resume (which I got a lot of help on from the Career Center).

C requested that we speak over Skype so we could discuss the projects going on at CIHR and what we are both looking for in terms of an internship. It was during that Skype conversation, that she offered me the internship.

Through later email conversations, we discussed me completing the Research Experience Notation requirements and she agreed to support me throughout it.