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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 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 […]MORE

Frozen Proteins & Fun in Friartown

Posted by: on July 1, 2015   |Comments (0)|Undergraduate Research

Hello everyone!

jurassic worldIs summer treating everyone well? I hope so! Max and I are having a good time, and I’m learning a lot in the lab. Did you know that you can’t freeze proteins?  It denatures them, and then they’re essentially useless. I learned that one the hard way. Always store your proteins in the fridge, NOT the freezer.

Something else I’ve learned from my summer in Friartown is how much you can do in the city! After the research day, the nerds come out and play because it’s a lot better than sitting around on campus. Don’t get me wrong, I love campus, but your options for fun in the sun are limited when there’s no one around. There isn’t even a line at the Dunkin Donuts in the Slavin Center. That’s when you know it’s empty.

The city certainly isn’t empty. There are a plethora of activities in Providence to keep anyone occupied. My friends and I went to the premiere of Jurassic World in IMAX at the Providence Place Mall. It was awesome. Who wouldn’t want to see Chris Pratt riding a motorcycle alongside velociraptors coming at you? The mall is about a 5-10 minute bus ride from campus on the good ol’ RIPTA 55, and public transportation is free to all PC students as long as you show a student ID! Not only is there a movie theater, but there are three floors worth of great stores and restaurants. There’s even a Dave n’ Busters if you want to get your game on.

A little further away (but still within RIPTA distance) is Thayer Street, which is practically on the Brown University campus. It has a lot of cute shops and unique restaurants along with some crowd pleasers. I mean, there’s a Froyo World and a Chipotle. Chipotle has become at least a once-a-week event for me. The only reason that I haven’t ballooned is that the PC gym is open during the summer.

andreasOne Saturday, we went to Thayer Street for brunch and ended up at Andreas, a cute Greek place that actually serves really good breakfast food. Who knew? I couldn’t decide between a classic Greek meal and chocolate chip pancakes, so I had a gyro with home fries. Both were delicious.

You might be wondering who I’m talking about when I say that “we” did something. When I’m talking about things I’m doing in the lab, I’m usually talking about Max. However, Max can’t come on adventures with me no matter how much he enjoys Greek food–being a machine and all. When I say “we,” I’m talking about the other students here for research in different labs. I’ve decided to introduce you to them and their research to give you a taste of everything going on in our science building, Albertus Magnus (Al Mag), this summer. Also I kind of want to prove to you that I have friends other than a scientific instrument. Let’s get started!

Today, I’m going to introduce you to Dr. Brett Pellock’s lab and some of the research students who work there. Most of his research students are funded by the Research in Undergraduate Institutions (RUI) grant that Dr. Pellock received from the National Science Foundation (NSF) Division of Integrative Organismal Systems (IOS). Their job is to research the metal-reducing bacterium Shewanella oneidensis.

bio groupBiologists. They always have the strangest names for things. Anyway, what I mean by ‘metal-reducing bacterium’ is that S. oneidensis can take certain metal elements outside of the cytoplasm and change the charge, or oxidation sate, of those metals. Changing or reducing oxidation states in certain elements is actually how batteries are powered (any begrudging AP chemistry student will tell you), so the hope is that one day metal-reducing bacterium could be used as an alternate power source! How cool is that?!

The Pellock lab is also working with Hfq, a protein that interacts with the bacterium. After years of research, the lab created a mutant strain of the bacterium without Hfq. As it turns out, the removal of Hfq leads to a gene that they have nicknamed ‘catastrophic death’ that results in slower growth, slower reduction, and – you guessed it – catastrophic death of the bacterium. Whoops.

After that, the lab focused on the death phenotype. Why does that happen? How can it be fixed? The lab discovered that plating the bacterium on blood agar reverses the catastrophic death and that the mutant death lacked a biomolecule known as HEME a. The lab is hard at work with this information, also looking at how stress may affect the mutant S. oneidensis and trying to figure out what exactly causes the bacterial doom so that it can be prevented.

Now we can meet the team! First up is Matt Cupelo ’17, or “Coops” a biology major with a talent for cooking and a passion for everything super. Then there’s Dan McGrath ’17, another biology major who researches during the weeks and saves lives on the weekends lifeguarding in Worchester, MA. Emma Hodges ’17 is a biology major thinking about going into nursing. She loves the team’s “Friday Lunch Adventures” and has a sever nap addiction. Ally Luongo ’18 is a rising sophomore in the biology department that can often be found at the gym jamming to Luke Bryan. Another member of the Class of 2018, Ryan Silva is another biology major (surprise there) training to get his EMT (Emergency Medical Technician) certification this summer.

And that’s the team! Dr. Pellock is one lucky scientist. They’re all hard workers, and there’s certainly no lack of fun, either. There’s always music blasting in the lab, and I may or may not have seen a few of them take part in a light saber duel the other day.

Earlier in the week, the group took a two day trip to Harvard University to take part in the 21st Annual Boston Bacterial Meeting (BBM) 2015. The BBM brings together researchers working with bacteria in academic or industrial settings from the Boston area. The PC students submitted their poster presentation to the contest that BBM hosts every year. With over 500 scientists present, competition was fierce, and the results are still pending on their final score. Either way, it’s always fun to go on adventures under the pretense of science. Good job, guys! You all looked great!

That’s all I have to say for now. I hope you’re getting plenty of pool time! I can’t say that I’ve spent enough time near the water. I’m too busy drowning in lipids. I think I’ll leave you with that train wreck of a joke, and you’ll hear from me, Max, and everyone else in Al Mag again soon!

Peace and Blessings,

– Bri and Max

Hello everyone! Is summer treating everyone well? I hope so! Max and I are having a good time, and I’m learning a lot in the lab. Did you know that you can’t freeze proteins?  It denatures them, and then they’re essentially useless. I learned that one the hard way. Always store your proteins in the […]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 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 […]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 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 […]MORE

Wordsworth Day Five: ‘Never Felt More Privileged’

Posted by: on June 3, 2015   |Comments (0)|Undergraduate Research

day5bannerMaymester in England

KonnorOn our last day in Grasmere, students quickly finished up their online exhibition, linking the writings of William and Dorothy Wordsworth and images of their manuscripts with photographs and drawings of the places they describe.  Their intention was to assemble something that the Trust would find useful for its outreach program to seniors with memory loss.  Then came the test: how would it be received?  They had an exacting audience: Jeff Cowton, Curator of the Wordworth Trust, and Gillian Dow, head of research at Chawton House Library, the center of Jane Austen studies.  I was impressed with the clarity of their presentation, and the sophistication of the project—and so were Cowton and Dow.  It was a triumph.

Triumphs deserve rewards, so Jeff brought out some of the Trust’s greatest treasures for us to hold and admire.  The earliest complete manuscripts of The Prelude, Wordsworth’s autobiographical epic, a beautiful Lake District watercolor by J.M.W. Turner,  a first edition of Lyrical Ballads which we passed around while reading Coleridge’s “Rime of the Ancient Mariner,” and, for Konner Jebb, a first edition of Mary Shelley’s Frankenstein, and a recitation of the moment of the monster’s creation.

stonesAfter lunch and souvenirs at the sheep shop, we headed north to Keswick for our last excursion.  First stop: Castlerigg Stone Circle, a Stonehenge in miniature, ringed by Skiddaw, Blencathra, and Helvellyn, three towering Lake District mountains.  Next, Jeff drove us through the village of Keswick and, ever so gingerly, along a narrow road around Derwentwater.  Try doing hairpins in a minibus!  We stopped at Brandelhow Woods for dramatic views of the mountains and the lake.  The poet Gray called Derwentwater “the Vale of Elysium,” and we could all see why.

The day ended with rest in the Dove Cottage gardens and another meal in Wordsworth’s home: salads and cold meat pies, and plenty of laughter and memories.  It was a fitting end to a perfect week.

Sometimes, teaching is simply sharing a gift.  30 years ago, I was given the gift of Wordsworth’s lakes by the late Stephen Parrish of Cornell.  Last week, I was able to pass that gift on to eight PC students—John Connolly, Branan Durbin, Kris Gianquitti, Konnor Jebb, Abby Johnston, Patricia Krupinski, Brendan Murphy, and Nick Tavares.  I have never felt more privileged.

–Dr. Bruce Graver

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Maymester in England On our last day in Grasmere, students quickly finished up their online exhibition, linking the writings of William and Dorothy Wordsworth and images of their manuscripts with photographs and drawings of the places they describe.  Their intention was to assemble something that the Trust would find useful for its outreach program to […]MORE