Summer Research Leads to Boston

Summer Research Leads to Boston

Posted by: on July 1, 2015   |Comments (0)|Walsh Fellows

satyamHi – I’m Satyam Khanal from Kathmandu, Nepal, and I am a senior biochemistry major doing research this summer as a Walsh Summer Research Fellow in the lab of Dr. Seann Mulcahy. I will be blogging this summer about my experiences in (and out of) lab.

On Thursday, June 18th this past week, as I was getting ready to continue my research in Hickey Hall, Dr. Mulcahy, our PI, announced that we had the opportunity to go and see the 15th Annual BU- Center for Molecular Discovery (BU-CMD) Symposium on the next day. We were immediately interested at the opportunity of going up to Boston to attend the event. From my own past experience, symposiums, seminars, poster sessions, etc. are excellent ways to gain more knowledge on the current research conducted by other groups and to learn more about application of chemistry in other, overlapping fields–especially medicine. So, I was naturally excited when I met my research team at the train station on Friday morning. We took the commuter rail up to Boston and got off at Back Bay Station. It was a 20-minute walk from the train station to the Life Science and Engineering Building of Boston University. While we walked, Seann showed us around, and we passed by the Public Library, which was also close to the finish line of the Boston Marathon. Seann also showed us the direction of the close-by Fenway Park, home turf of the Boston Red Sox. To amuse myself, I counted all the Dunkin’ Donuts and Starbucks coffee shops that I could see (by the end of the day, DD won 5-3).

After we reached our destination, we grabbed a quick breakfast provided by BU-CMD and then the symposium started off with opening remarks by the Director of BU-CMD Professor John A. Porco. He explained that BU-CMD focused mainly on discovering novel, small molecule chemicals designed to be used as medicinal probes. The seminar presentations that followed Dr. Porco’s introduction were on the same track. The first seminar given by Dr. Paul Hergenrother from University of Illinois at Urbana-Champaign was titled “Traversing the Valley of Death to Anticancer Drug Discovery.” During the presentation, he explained how difficult it is for organic molecules made in the synthesis lab to actually make it through to the drug industry. It was captivating for our group, especially because we also synthesize organic molecules in lab for research–it was good to see the application of research similar to ours in the real world. Dr. Alanna Schepartz from Yale University gave the second talk–“How EFGR encodes and decodes chemical information”. She explained how an extracellular messenger molecule communicates with complex proteins that are embedded in the cell membrane and how this process affects signal transmission inside the cell. I was glad that I had already taken biochemistry in the past year. I understood most of what was going on and I found the talk especially fascinating. After the seminar ended, we had a very good lunch break (the coconut macaroons were delicious) and then we decided to leave since it would take us a good amount of time to get back to PC. Thus we headed back, discussing all we had seen, taking in the beauty of Boston in the middle of summer and looking forward to doing something noteworthy in lab ourselves.

Satyam

Hi – I’m Satyam Khanal from Kathmandu, Nepal, and I am a senior biochemistry major doing research this summer as... MORE

Walsh Fellow: My summer with science and ‘Max’

Posted by: on June 18, 2015   |Comments (0)|Walsh Fellows

brianna1Hi everyone,

Welcome to my new summer blog! I’m thrilled that you’ve decided to check it out. My name is Brianna Abbott. My hometown is Wrentham, MA, and I’m a rising junior just down the road at Providence College. After realizing that I should actually start preparing for a future after graduation, I decided to spend my summer in Friartown doing research in the Department of Chemistry and Biochemistry. Because I’m an English: creative writing and chemistry double major, I was approached and asked to blog about my research experience, and I was more than happy to oblige.

And if you’re wondering what I’m planning on doing with an English and chemistry double major, because most people do, the answer is that I have absolutely no idea. Maybe I’ll get paid to professionally write chemistry research blogs. A girl can dream.

I’m one of the six students funded by the Walsh Student Research Fellowship, a fellowship created by Robert H. Walsh ’39 and ‘66Hon. to allow for more student research on campus in the fields of chemistry, biochemistry, and biology. Thanks, Robert! Though there are dozens of other researchers on campus, this summer I’m the only student researching under Dr. John Breen, who specializes in analytical and physical chemistry. He was my professor for General Chemistry during my freshman year, and I’m taking his Analytical Chemistry I class in the fall. Though it may seem as if I’m just out to get extra brownie points for my class (which isn’t completely wrong), it is a bonus to be able to foster close personal relationships with your professors in the research lab as well as in the lecture room.

Dr. Breen and I are doing a few different experiments this summer, all of them involving lipids. For the first part of my research, I’m replicating research conducted by Emily Mohn ’10 and Jung-Min Lee ’10 in 2009–repetition and reproducibility are important to any successful scientist! They’re even important to the unsuccessful scientists, too. Anyway, the project they started and that I am reproducing is the observation and study of the interactions of Cytochrome c with D_PG containing vesicles.

When I first heard that mouthful of an experiment, I could barely pronounce half of those words, let alone understand them–so I’m going to take a second to explain what’s going on. D_PG vesicles are sacs made from lipid membranes that carry substances throughout the cell. They are formed from lipids of various chain lengths ranging from eight to 18 carbons. Cytochrome c is a protein that lives in the inner membrane of the mitochondria and interacts with that same lipid membrane. It has been suggested that Cytochrome c binds to the lipid membrane and causes the lipids to move from their usual, parallel conformation to an extended conformation with one tail of the lipid rotated at a 180° angle, or antiperplanar. This conformation would reduce the strain of the tightly packed lipids, like someone shouting ‘SHARK’ in a crowded pool and causing half of the people to leave the water, giving those in the water more space. This formation of lipids in the membrane could possibly be the standard position during protein-lipid interactions and could enable vesicle fusion.

fluormaxI set out studying the interactions between these vesicles and Cytochrome c with my friend, the FluoroMax-3. The FluoroMax-3, or Max for short, is an instrument that measures the fluorescence of liquid solutions. A fluorescent label was added to the lipids, and those lipids were then turned into vesicles through a process known as extrusion. Max then took the vesicles and gave me a number based on the amount of fluorescence he observed. If Cytochrome c binds to the vesicles, it blocks the fluorescence, and the number Max calculates decreases. Through this process, I can determine how chain length and amount of Cytochrome c added affect the binding of Cytochrome c to the vesicles! There are all sorts of mini experiments I can–and will–do based off of this general concept, and I’m sure I’ll share all of them with you before the summer sun sets and no longer … fluoresces (I know it’s a terrible joke, but I couldn’t help myself).

I’ve been researching for about three weeks, and now we’re really getting into the meat of the experimenting. During the meat, however, Max does a lot of the time-consuming work, meaning that I have some time to update my lab notebook, study papers that Dr. Breen gives me, read the entirety of Game of Thrones, and, of course, blog! You’ll be hearing from me and Max soon as our productive summer in Friartown gets under way.

I hope you’re as excited as I am (you’re probably not)

– Bri

Hi everyone, Welcome to my new summer blog! I’m thrilled that you’ve decided to check it out. My name is... MORE

Summer of fun: When research becomes play

Posted by: on June 18, 2015   |Comments (0)|Undergraduate Research

kt1Hey Friends!

It’s week three here at Kid Think, and we are getting settled in the lab! There are three research assistants working here for 10 weeks this summer. Emma is a rising senior psychology student with a business minor. Mikaila is a double psychology and history major. And lastly, Jamie is a psychology major and business minor. We enjoy studying psychology and all hope to continue our studies in psychology after we graduate from Providence College.

During the 10 weeks, we will be running two studies. The first study is titled “Factors Influencing Children’s Causal Learning” and tests children three to five years of age. This study examines whether or not children can learn through pretend play. Children are presented with a pretend machine and are given the chance to apply the information they learn from that pretend machine to real life afterward. The second study is funded through a program at URI. This study, Comprehension of Pretense, or the “Toddler Study,” as we call it, is made up of games for 18-24 months old–testing their understanding of pretend play and their self-control.  The kids are all so cute to work with, and we love having them come in for appointments!

On Thursday mornings we go to the Providence Children’s Museum and run their “Mind Lab.” From 10:00 a.m. to 12:30 p.m. we walk around the museum and invite families into the lab. If children are eligible to participate in our studies, we play the games with them and, afterward, they get to pick out a prize! We love going to the museum to see a new set of children every week! We also enjoy playing with the toys there just like the kids.

We are looking forward to a summer filled with play!

Over and out,

The Kid Think Team

Hey Friends! It’s week three here at Kid Think, and we are getting settled in the lab! There are three... MORE

Stevens and Satisfaction: The end

Posted by: on May 21, 2015   |Comments (0)|Undergraduate Research

Wallace-StevensThe goal of my research project was to learn more about the life of modern American poet, Wallace Stevens, and to decide whether or not his conversion to Roman Catholicism on his deathbed should be considered authentic.

In addition, I hoped to determine if there are any signs of a conversion could be seen in Stevens’ poetry. I read biographies of Stevens, as well as interviews, criticisms, and his own poetic collections for my preliminary research. Then, I wrote on a weekly basis about my thoughts and discoveries. My Honors Independent Research Project turned out to be 43 pages or 16,000 words—just about thesis length (but who’s counting?). I focused on four of his poems—Anecdote of Men by the Thousands, Sunday Morning, Notes Toward a Supreme Fiction, and Of Mere Being—as well as accounts about his final days. I believe that I wrote a convincing paper about why Wallace Stevens’ conversion to Catholicism at the end of his life should be viewed as genuine, and also about the indicators of his affinity for religion that I noted throughout his poetic career.

I plan on continuing to research this project. I felt crunched for time at the end of the semester, and I wish that I could have devoted more time to polishing this paper. But, I still have more reading and thinking to do, and I also plan to write more about this topic. It is close to my heart, and I want to develop my argument to the best of my ability.

Although I found this assignment to be very challenging at times, in hindsight, this is one of my favorite academic experiences as a student at Providence College. I am proud of myself for finishing this project, and I am satisfied with the end result. I couldn’t have asked for a better advisor than Dr. Hogan. He was knowledgeable, flexible, and he always provided me with the encouragement that I needed. I could not have turned out a finished product of this caliber without him. I found it very helpful to meet with him on a weekly basis and to bounce my ideas off of him because they often turned into even better thoughts. This honors independent research project/thesis helped me to grow as a person and in my faith. I found personal inspiration in the life-story and the poetry of Wallace Stevens, and I believe that to complete an essay of this length and depth allowed me to become more organized, self-disciplined, and efficient. I would absolutely recommend conducting research to other students who consider themselves to be up to the task.

The goal of my research project was to learn more about the life of modern American poet, Wallace Stevens, and... MORE

A better scientist because of opportunity

Posted by: on May 20, 2015   |Comments (0)|Undergraduate Research

rogersOn April 18th, Matthew Sanborn ’15 and I attended the annual Eastern Colleges Science Conference (ECSC) at Niagara University. The day before, we had taken the long drive to the city of Niagara Falls so we could see the falls. ECSC is a relatively small conference, typically hosting representatives from about 20-30 universities. All of the students in attendance are undergraduates, who give oral platform presentations or poster presentations. It’s a great conference because it’s interesting to see what other undergraduates are doing as research. Also, both the platform presentations and poster presentations are judged as part of a competition. As always, it was fun to meet undergraduates from other schools.

I gave a platform presentation at this conference titled “Characterization of Yeast Bax Inhibitor, bxi1, Function in Cell Death, the Unfolded Protein Response, and Calcium Signaling in Saccharomyces cerevisiae.” The presentation was centered on research done over a number of years by many students. Specifically, our work suggests that the yeast Bax Inhibitor gene has functions both in programmed cell death and the unfolded protein response in yeast. Both programmed cell death and the unfolded protein response are ancient molecular pathways found in organisms from yeast to humans, so learning more about how these processes work is fascinating basic research.

sanborn1I have given a few poster presentations before, but this was my first time ever giving an oral presentation. I was nervous, but I found that I really enjoyed giving my talk. I learned later in the night that I had won an award for the best poster presentation in my group of talks, which I was very happy to receive. The conference was a nice way to round off my senior year in the lab. I’m sad to be leaving PC and the lab soon, but I will always remember what I have learned here. I think that my research in Father Austriaco’s lab has helped me become more competent as a scientist — both in my way of thinking and in my skills at the bench. I hope that many others will have the opportunity for a great undergraduate research experience, just as I have had.

On April 18th, Matthew Sanborn ’15 and I attended the annual Eastern Colleges Science Conference (ECSC) at Niagara University. The... MORE