Blog Challenge #5

 Part 1
On Friday July, 26 Duquesne held its 16^th annual Undergraduate Research Symposium. This is a day were all undergraduates and Project SEED students get a chance to present their work that they did over the summer to friends, family, and students. The day started off with a continental breakfast, which was really nice. Then everyone moved to the auditorium for the welcome and keynote address, which was given by Dr. Karl Johnson. He talked about using Carbon Nano- tubes as a filter to clean arsenic filled water in third world countries. Next, some of the undergraduates gave 15 minute presentations about their projects. One of the presenters was my co- mentor Andrew Adams and his presentation was great. To hear him talk about everything that we did over the course of this year and last year was amazing to me. Another presenter was Kelly’s mentor . I thought she did a fantastic job. The last presenter talked about pain receptors in the brain, which was very interesting. Then there was a picnic lunch, which was very nice. I did not have to present the first hour, so I got to walk around and look at other undergraduates’ projects, but that time was shortly lived. The only people that talked to me about my project were my sisters, Andrew, Dr. Partha Basu, and James Claybourne. I mainly talked to James because he used to work in the same lab as me, so he had many questions to ask about the project so far. I also talked to him about his senior thesis because he is going to be running the same experiments that we ran. All in all I thought the symposium was great, especially compared to the one last year. I just wish I had the chance to talk to more people about my project.

Questions

1. Did you participate in any internships in high school?
2. What made you choose your career?
3. What made you choose Duquesne over any other college
4. What made you interested in science?
5. Was there ever a time when you thought about changing your career?
6. How is college?

Blog Challenge #4

Yesterday was the first ever Project SEED celebration day. It was a gathering of current Project SEED members, mentors, alumni of the Project SEED program, faculty members, and donors. This also marks the first time that I ever presented to a large group of people with high stature, so I was very nervous. That being said I think I did okay. If given the chance to present again I would explain my procedures and data more clearly. Also, I would have talked to more people individually during lunch.

 I did get a chance to talk to Tim McFadden, Kathy Fleming, Lauren from Bayer, a woman that networked, and the dean. Getting the chance to talk to Tim McFadden was great, because he did the same thing as me in SEED. I mainly talked to him about college. He told me that it is really fun, but you have to be able to balance yourself out between studying and everything else. He also told me about some of his friends that majored in nuclear engineering, which I thought was intriguing. Kathy Fleming actually came to me and said that her favorite part of my presentation was that I said "Although this isn't the best representation of a gel it was still a great learning experience". She said it was because in life sometimes things don't work out, but you still have to manage. Lauren, the lady that took our pictures, was wondering how I got to Duquesne everyday and if I thought transportation would be a reason not to do SEED. I told her I took the bus everyday and it shouldn't be an issue because Dr. Aitken would help them. The woman that networked told me about networking and how important it is. She also told me to be calm and relax before I presented. The dean was curious about how long our experiments took, which I told him each one takes a few days and we are currently working on a methyl viologen assay. He was amazed at the work that we all do. 

All in all the event was a great learning experience. I learned how great geology is and how to network. I learned that I need to be more confident in my abilities and less nervous. I got to hear from the alumni how the Project SEED program affected them. I learned truly how everyone cares about us and wants to see us succeed, which could just be seen in Larry's presentation.

Abstract

The Investigation of periplasmic nitrate reductase

Thornton, Charles; Adams, Andrew K.; Thomas, John; Basu, Partha

Department of Chemistry and Biochemistry;  The Project SEED Program; Duquesne University

Abstract:

The molybdoenzyme, periplasmic nitrate reductase (NapA), plays an important role in the vitality of the pathogenic bacterium, Campylobacter jejuni. C. jejuni is a microaerophilic bacterium that grows anaerobically by utilizing nitrate as an electron acceptor. Infection by C. jejuni is one of the most common causes of gastroenteritis in the United States. NapA cloned from C. jejuni has successfully been overexpressed in E. coli. Produced protein has also been successfully isolated and purified for further studies using a reduced methyl viologen assay. Other techniques, such as Immobilized Metal Affinity Chromatography (IMAC) and Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE), have been used to further study this enzyme. IMAC was performed to retain the protein in a column that contained immobilized nickel ions for the purification of the polyhistidine tag. SDS-PAGE was done to see if NapA was present in the protein sample.

Blog Challenge #2 Pictures

For our second blog challenge we had to take pictures of the other Project SEED members engaged in their work. We were also assigned partners to interview and my partner was Deion Grant. Deion is 17 years old and is going into his senior year at Pittsburgh Science and Technology Academy. He is interested in engineering because he likes to build and create things. He wants to attend the University of Pittsburgh for further studies because they have a really good engineering program. This year he is working with Vitamin D receptors to measure the effects of different substrates. He is going to do this by replacing each substrate with Alanine, which is known as Alanine scanning. Alanine scanning is usually done experimentally. He is trying to reproduce those results from the experiments through computor simulation.




Kelly Pesta cleaning her beaker with DI water.




Emily Janicki working on the SEM.




Deion Grant replacing his Vitamin D receptor with his substrate.



Melissa Fowkes comparing bond distances on the C6H4O2 molecule.




Cheyenne Simmons adding 1M HCL to her crystal mixture.












 



















 







 



Blog Challenge #1

Ever since I was a child I have been interested in science. What first interested me about science was stars. I used to look up at the stars with such amazement until I figured out that they were just massive balls of helium and hydrogen. As I grew up I became interested in the inventions and theories of Einstein, which spiked my interest in nuclear engineering. In 1905, as part of his Special Theory of Relativity, he made the intriguing point that large amounts of energy can be released from small amounts of matter. This theory eventually lead to the development of the atom bomb. I then started to do more and more research on nuclear engineering. The colleges that I would like to attend are the University of Pittsburgh, Penn State University, and the University of Tennessee.

University of Pittsburgh, Main Campus, located in Pittsburgh, Pennsylvania, is the first college that I ever considered to go to for nuclear engineering. For admission, you must have your high school transcript and admissions test scores(SAT/ACT). Half of the students that are admitted have an SAT math score of 590 and reading score of 570. For the Nuclear Engineering Undergraduate Program, students can chose to major in Engineering Science with a concentration in Nuclear Energy. For a certificate in nuclear engineering it is required that students take three units of ENGR 1700: Introduction to Nuclear Engineering, ENGR 1701: Fundamentals of Nuclear Reactors, and ENGR 1702: Nuclear Plant Technology. This will also give the students a background in nuclear engineering. Pitt offers a variety of internships and fellowship programs, which is why I really want to go there.

Penn State University, Main Campus, located in State College, Pennsylvania,  offers a very immersive nuclear engineering program. For admission, you must have your high school transcript, GPA, and admissions test scores. Half the students that are admitted have an SAT math score of 570 and a reading score of 530. It is also required that you have three units (years) in math, science, English, and social studies. Their nuclear engineering program is ranked eighth in the nation. As a nuclear engineer at Penn State you have the chance to participate in the Toshiba-Westinghouse Fellowship Program, which allows you to work on your own research project with a Penn State nuclear engineering faculty member.

University of Tennessee is a college that I would be honored to attend. I actually had a chance to speak with a representative of the university that talked to me about their nuclear engineering program. For admission you must have your high school transcript, GPA, and admission test scores. Half the students that are admitted have a SAT math score of 530 and a reading score of 510. To get into the nuclear engineering program it is required that you have a minimum grade point average of 3.0- 4.0 or a 3.0 during your senior year of undergraduate study. Students must also submit an application for admission to the Graduate School. Once selected, students may elect a traditional nuclear engineering program focusing on fission energy or a radiological engineering concentration, which prepares students for careers in the radiation safety field. Students without a Bachelor of Science degree must take the 433 and 470 course for graduate credit.

 These colleges present the best programs for me if I do decide to go for nuclear engineering. They each offer a number of different scholarships for students. Both Pitt and Penn State are fairly close to where I live. If I do decide to go to the University of Tennessee I will have family members there that will support me. I believe I have what it takes to make it in to anyone of these colleges because of my work ethic and strive for success.

The Beginning

Hello everyone! I cannot even explain how excited I am to be back at SEED and continue to work with everyone I did last year! Last year my project was on learning molecular biological and biochemical techniques in investigating periplasmic nitrate reductase A. I mainly learned about PCR, gel electrophoresis, and how to grow bacteria. This year is a continuation of that project, except I will actually be able to handle the protein. I have mainly been reviewing  the progress that they made over the year. This is exciting to me because I get to read Sammy's thesis, which has pictures of the gels that I helped him with! Today we are actually going to lysate cells! I also learned about a new technique called IMAC, which allows proteins with an affintity for metal ions to be retained in a column containing immobilized metal ions for the purification of histidine containing proteins. I believe this allows us to get rid of the polyhistidine-tag. So far this year everything is going well. Hopefully it continues to go this well.

Symposium

The symposium went well. At first I was very nervous because I do not like to speak in front of large groups, but as the symposium progressed I became less nervous. The symposium is an event that I will cherish for the rest of my life.

Abstract

Learning Molecular Biological and Biochemical Techniques in Investigating Periplasmic Nitrate Reductase

Thornton, Charles; Adams, Andrew; Nassif, Samih; Basu, Partha

Department of Chemistry and Biochemistry, Department of Biological Sciences, Duquesne University, Pittsburgh, PA, USA

Molybdenum containing enzyme, periplasmic nitrate reductase (Nap), plays an important role in the vitality of pathogenic bacterium, Campylobacter jejuni. The catalytic subunit, NapA, is being cloned and overexpressed in E. coli. There are many techniques such as cell culture, DNA extraction, purification and cloning that are involved in the proper overexpression of this important protein. To this end, I have been learning these techniques, and how they apply to the overall goals of this project. In this presentation, I present my experience with the experiments and results. 

Blog Challenge #2

1. What type of cosmetic benefits will there be if we are able to mutate the NapA?
2. How are we going to get rid of the insertion loops from the NapA inside C. jejuni?
3. Why are we focused on the reaction of the molybdenum enzymes if we mainly care about the NapA?
4. Are we able to use a zwitterionic detergent as a way to stabilize the NapA?
5. Why do we mainly care about the Histidine Amino Acid above all the other ones?
6. How does the Bradford machine work?
7. Why is it necessary for us to use pure Ethanol when we are straining the bacteria on the Agar plates when we are just gonna mix it with water anyways?
8. What does the R. spaeroides have to do with our project?
9. Will I get the chance to use the Mass Spectrometer or see an example of a sample that comes out successful?
10. What is the next step after we are able to mutate the NapA inside the C. jejuni?

Blog Challenge #1

  Our focus for this year is on reactions of molybdenum enzymes and proteins in organisms. The protein we are most interested in is paraplasmic nitrate reductase A in C. jejuni, which is one of the most common causes of human gastroenteritis in the world.  One of the things that we do is grow bacteria.We grow bacteria by making plates.  We had to first make up the Agar and mix it.The reason we use Agar is because the bacteria loves it. Then we had to put it in the Autoclave for a half an hour. When it was done we took it out and waited till it cooled down enough to handle, then we began to pour the plates. When I was pouring the plates for the first time I had to work as close to the Bunsen Burner as I could so there was a less of a chance for unknown substances to contaminate and ruin them. I also had to move very fast so the Agar didn't coagulate. I was excited when I was done, because Andrew told me that I made 17 plates. After that we streaked the plates with old bacteria, which will allow us to organize how it should grow, and put them in the Incubator at 37 degrees Celsius. We put them in at 37 degrees Celsius because that is the temperature that they are most active in. The next day we took them out of the Incubator and started to seal them with para film. We seal them to cut off all of the oxygen. After sealing them we put them in the fridge at 4 degrees Celsius.   

Project SEED blog

So far Project SEED has been fun and very interesting. The first day was very challenging for me because I didn't really understand what I was doing, but after my mentors explained everything to me I sort of got the hang of it. That day I received a "Crash course" in Molecular Biology from Sammy and Andrew so I could have a better understanding of everything that we are doing. Today Andrew and I created a Tris buffer, Sucrose buffer, and a Sodium Chloride buffer. It was pretty easy doing these things, because all we really had to do was measure and mix each substance. We also had our very first group meeting which was very interesting and frightening. I also got to meet Dr.Basu who, if I may say, is a very kind and intelligent man. The only challenge I have, as of right now, is reading and understanding all of the packets I received.