Duke University | Howard Hughes Undergraduate Program

Research has its ups and downs. Just like pretty much everything else in life. Unfortunately unlike life, research can have a slightly higher failure rate. This is one of the downsides of research. In addition to the anguish and frustration that a failed experiment causes, it also means that you have to repeat the experiment. This is probably my least favourite part of research mainly because it is so inefficient. I really don’t like it when I do a PCR that takes like 2 hours to set up and then another 5 to run and then when I run the gel I find out that I lost a whole day cause the bands are too weak. Another part of research which isn’t always pleasant is analysis. I usually like to do analysis, but when it comes to fixing sequences it can get monotonous really fast. Thankfully when all the sequences are fixed I can analyze them statistically which is a lot more funner than is sounds(thanks to Gotwals and my stats teacher). You can generally make the statistics fit specifically to your needs mainly because it “statistical analysis” is so vast.

This brings me to the better part of research. For me I prefer to proceed the science with math just because I am more comfortable with it. Another part that I enjoy is work at the bench. Doing the PCRs and gels can be fun. Just so long as you don’t daydream and mix together 4 primers in a single tube when you are only supposed to do one (I did this once and sadly for me all of the sample had run out once I realized I did it incorrectly). I should say that the most satisfying part of research is when you get a successful experiment the first time it was run. The efficiency and rewarding feeling that you get is great. It also means that you made some headway in your project. After I get back a good sequence which I don’t have to spend time fixing I feel awesome..until I see the next sequence with a bunch of “N”s. The nice thing about this work is that you do learn to deal with the frustration and learn a lot about perseverance which is irreplaceable in this field.

Anyways research can be good or bad. It just depends on the way you look at it.
 

Life in the lab is constantly changing. It is really a great experience that allows me to explore different concepts in the lab. A typical day for me though is, after the morning meeting or seminar, to come to my lab and maybe run a PCR, cleaning or sequencing prep to run in a gel later. While I am waiting for the experiment to finish, I usually do microscopy and clean (via washing) zygospores. This process is probably my least favourite as it is very grueling and takes a lot of concentration (especially when you are doing it for 6 hours!). Using forceps and needles I have to first pick out zygospores from a petri dish (hoping I don’t crush them) and then use the needles and water to wash away and other fungus (such as conidia or mycelium). I have to wash them multiple times to assure that when I plate them only the zygospores can germinate and nothing else will contaminate them. After they are clean I go to the hood and plate the zygospores. This process is harder than the microscopy in that you can hardly see the spores (because I don’t have a microscope!). Before plating them I have to do one quick wash where I just transfer the zygospores through autoclaved water. After that I can plate them (usually 3-4 to a plate) and mark them. After this is my favourite part of this process. Parafilming!!! Idk why I like this part so much. This might just be because I have finished the whole process, or because parafilm is so awesome to play around with!

The end result of plating the zygospores and parafilm!

In-between steps of plating the spores I usually run other experiments such as PCR cleaning or cloning depending on how the gel turned out. Some times when I get the sequences back I get to analyze them and see how it fits in with the whole big picture and evaluate where we need to run more PCR’s and find places in the loci that we need a better sequence. So as you can see my day is usually pretty filled with stuff to do. This usually keeps it from getting boring, and also gives me a great chance to learn about research.
 

The second week of the Howard Hughes Program I really got to know my mentor, Andrii Gryganskyi, better.

 Not only did I find out that his awesome accent comes from Ukraine, but I also learned about many other thing that influenced his decisions in life that arrived him in his current position, a postdoc in the mycology field. He also now has a family with two young children. The story of how he arrived to this point shows his determination and perseverance.

(ukraine flag and symbol)

Ever since he was a child he was always into plants and biology. He was fascinated with plants and fungi since he was a child. However when it came time to choose what path he wanted to take in life he was restricted by the few professions that were acceptable in Ukraine at that time. He seemed like he would probably be a hunter – that is a far stretch from what he is now! After graduating high school he went to Kyiv State University in Ukraine. This was no small accomplishment as he was the first person to attend a university in his family. It was during his college schooling that he took a mycology class and found out what he wanted to do in his career.

During his professional career Andrii enjoyed what he does immensely. His favourite topic of mycology is the phylogeny and evolution of fungus. He also enjoys the cultivation of mushrooms, which encompasses a lot of his field work! Some of the thing that he finds harder is the molecular biology part of his job. Since he started on this topic later than most people now coming into this field, and since it is now such a big part of mycology, he finds it a little more challenging and gets frustrated when it is not successful. However, he said it is a fundamental topic for most mycologist and biologists. He also said that in addition to molecular biology a good understanding of bioinformatics and computational knowledge can be a big help.

When I asked Andrii to sum up what he did he told me that he is “trying to build a natural system of part of the fungal kingdom by using molecular data.” What he enjoys most from his job is the constant challenge to discover something new that can make a difference in his field. I also asked Andrii whether he ever thought of an alternate career. He said that he would have liked to pursue biological medicine, such as neuroscience, or genomic research focusing on human diseases such as HIV (which actually have had cases where because of the immunodeficiency allows a fungus that usually don’t grow on human to proliferate on them particularly their tongue). Speaking of the immune system, I asked Andrii what the most dangerous part of the job is, and he said its not something big like exposure to radiation which causes him harm, but little things like fungal cultures, which can expose him to dangerous fungus and since the since the immune system is not 100% safe-proof chemicals that he works with can also be hazardous if not handled properly.

So basically Andrii has had a very interesting life and enjoys what he does thoroughly. Sorry to say I don’t have more any pictures with Andrii wearing cool t-shirt to put up, but if any come up ill be sure to!
 

Hey everyone. My name is William Colquhoun. I currently am a rising senior (class of 2010!!!) at Orange High School in Hillsborough. I enjoy playing sports namely soccer, football and wrestling. I also enjoy working in the science field. What is especially interesting to me is medical biology such as chemistry and pharmacology. A few years ago I was lucky to take part in a summer program called Launching into education about Pharmacology. I learned heaps of things about medical science and research from basic pipeting techniques to completing a full research project (in which pipeting was essential). This year I am fortunate to get the opportunity to explore in the environmental biology area. My mentor, Andrii Gryganskyi is a postdoc in the Vilgalys fungi lab at Duke.

MY Mentor! Dr Gryganskyi

My first day in the lab, I got to complete a Polymerase Chain Reaction (PCR) lab. In this lab we are trying to amplify DNA so that we can compare the length of the fragments – via gel electrophoresis - as well as choose samples which will be good to clone and clean so that we can eventually send them in for sequencing.

My PCR Bench

PCR is a process that basically takes the DNA that you put in (a small amount) and amplifies it via thermal cycling to and replicates it using and replicates it using other material (dNTP’s). After this you can use the PCR product to run a gel to tell you which fragments show promise for sequencing. We take those fragments and clean and clone them so then they are finally ready to be sequenced.

A lot of prep is necessary to do PCR labs. One thing is identifying strains of the fungus that you want to test. The strain that we are using is called Rhizopus Orzyae. Different species of this are found so we have to filter them out for the ones that fit our purpose. The species that we are looking for produce zygospores. This indicates that they do not follow the normal fungi asexual reproduction habits. Hence, they mate and produce offspring, called zygospores. We use a microscope to look for zygospores in different strains of Rhizopus Orzyae.

As I found out it is actually very hard to separate the zygosphores from sporangia as they are almost identical except for some details such as a tail and a fuzzy display.

This week I learned more about fungus and mycology that I expected I ever would. It was an awesome surprise and I’m excited to see what comes next!!