The Binghamton Biochemistry Club Proudly Presents:

Biochemical Literature Reviews | Student Opinions

Volume 1, Number 0001| Spring 2012

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Table of Contents

Cover Art

- Lance Kong -

Letter from Vice President and Publications Coordinator

- Michael Chung -

- Stefano Quarta -

Biochemical Literature Reviews

Protein G, Protein A and Protein A-Derived Peptides

Inhibit the Agitation Induced Aggregation of IgG

- Michael Paollilo -

Memory in Mice

- Andrew Cohen -

Student Opinions

Dr. Anna Tan-Wilson: Binghamton’s Biochemistry Legend

- Michael Chung -

Making the Most of Your Undergraduate Years at

Binghamton University

- Nicele Arana -

The Bound Nature of Competitiveness in Human Behavior

- Prometheus Blank -

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Letter from President Elect: Dear Students of Binghamton University, The release of our first issue of Titin marks a new chapter in Binghamton Biochemistry Club’s his-tory. Binghamton Biochemistry Club was once called Biochemistry Advisory Board when it provided advis-ing to Biochemistry students and students interested in taking Biochemistry courses. The name change reflects the evolution of the club from just providing advices to now contributing Magazine and Newsletter, holding academic tournaments, holding forums and reaching out to other science related organizations. As the President Elect of Binghamton Biochemistry Club, I am proud and honored to have served in a year that provided so many positive changes. The tremendous progress and resilience of our organization give testament to the character of the members who compose our organization. In the future, I am confident that the Binghamton Biochemistry Club will carry its powerful momentum to produce even greater impact on students of diverse disciplines and backgrounds. Sincerely, Michael Chung President Elect

Letter from Publications Coordinator: Dear Students of Binghamton University, The Binghamton Biochemistry Club would like to thank countless individuals but would like to thank the Biochemistry Students the most for the publication of this magazine. Thank you to New Moghul’s Fine Indian Cuisine and Tappas and to Moe’s Southwest Grill for spon-soring us. Kamalika Mukherjee for her ongoing support as the Biochemistry Undergraduate Advisor. Thank you to all contributors to the magazine: Michael Paolilo, Andrew Cohen, and Nicele Arana for writing and to Betty Chu and Jenny Tse for editing. A special thank you to Michael Chung, our club’s President Elect, for bringing the idea of ‘Titin’ to life and to Lance Kong, our Treasurer, for an awesome front cover and for managing the funds for the magazine A special thank you to Dr. Bane and all professors, staff and graduate students supplying Binghamton’s Biochemistry students with never-ending support on the admin-istrative and academic level. On behalf of the Biochemistry Club, I hope you enjoy our very first magazine which contains content on Scientific Articles, Faculty Interview and Student Opinion. An electronic copy of our magazine is available with free registration through issuu.org. The Biochemistry Club Publications team aims to provide the most beneficial and diverse information for our readers to maximize the reading horizons. If there is anything you would like to read more on or if you have any ideas for future publications, please email me at squarta1@binghamton.edu. I will be eager to hear from you. Sincerely, Stefano Quarta Publications Coordinator

Letters from President Elect and

Publications Coordinator

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Protein G, Protein A and Protein A-Derived Peptides Inhibit the Agitation Induced Aggregation of IgG Review by Michael Paollilo In recent years, interest in antibodies as drugs has grown substantially. There are more than thirty antibody drugs approved by the FDA and many more in development. An antibody is a protein produced by B-cells for immune response. It consists of four units, two heavy and two light chains. It is shaped like the letter “Y” and the top portion of the “Y” is where binding to a particular epitope occurs. However, some issues arise when attempting to design antibodies for medicinal purposes. Perhaps the most threatening of these problems is aggregation. Aggregation is the process in which multiple antibodies cluster together, resulting in the formation of a large collection of inactive antibodies. The body must then find a way to eliminate this aggregate, which can otherwise result in serious side effects. A study, con-ducted at Purdue University, focused on the aggregation of the specific antibody, IgG. IgG stands for Immu-noglobulin G and is involved in the secondary immune response. Two mechanisms of aggregation were determined: aggregation resulting from the denaturation of proteins, termed conformational instability, and aggregation resulting from protein-protein interactions, termed colloidal instability. Researchers then measured the ability of protein A and protein G to prevent aggregation of human IgG. It was hypothesized that both would improve the conformational stability and thus reduce the formation of ag-gregates. The study was conducted using UV-spectroscopy, SDS-PAGE, High Performance Size Exclusion Chromatography (HP-SEC), Dynamic Light Scattering (DLS), and Fluorescence Spectroscopy. Due to length constraints, only the method of SDS-PAGE will be discussed. SDS-PAGE stands for sodium dodecyl sulfate polyacrylamide gel electrophoresis. In this study, SDS-PAGE was used to qualitatively detect large aggregates. Picture A was done under non-reducing conditions, meaning that the disulfide bonds were kept intact, while B was done under reducing conditions. The gel suggested that aggregates had formed. How-ever, when a sample containing IgG and protein A was run down the gel, results indicated the lack of ag-gregate formation. The same was true of protein G with IgG.

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Biochemical Literature Reviews

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The conclusion of the study was that both protein A and protein G helped to prevent the formation of IgG aggregation. Researchers stated that the results suggest that IgG aggregation involves a consensus bind-ing site. Protein A seemed to interact with the binding site, which thus prevented aggregation. Compared to protein A, protein G was less effective in preventing aggregation. This study is a great step forward in better understanding the mechanism by which aggregation of antibodies occurs. With this knowledge, further re-search can be conducted to design antibody drugs that circumvent problems such as aggregation, which would otherwise prevent the development of antibodies as drugs. Citation: Jun Zhang and Elizabeth M. Topp. Protein G, Protein A and Protein A-Derived Peptides Inhibit the Agitation Induced Aggregation of IgG. Molecular Pharmaceutics 2012 9 (3), 622-628

Memory in Mice Review by Andrew Cohen

The brain’s mechanism of memory storage is still not well understood. However, MIT researchers have shed light on this once dim area. The work, published in the journal Nature, gives scientists a way of un-derstanding how memories are stored and maintained in the brain. When one learns something, a very specific neural circuit fires off. With the proper techniques, this circuit can be cleverly tagged for later testing and manipulation. MIT scientists subjected mice to fear conditioning. When frightened, the mice entered a state characterized as “freezing behavior.” The exact hippocampal neural pathway that activated was tagged with a protein called “channelrhodopsin-2.” This is an optically activated protein (activated by light) that is similar to the G protein mechanism responsible for vision. After the fear-inducing stimuli had worn off, the researchers optically reactivated the channelrhodopsin-2. The mice exhibited the same “freezing behavior” as induced by the original stimuli. This time, however, targeting and activating a specific neural pathway in the brain induced the behavior. In mice that weren’t subjected to the initial fear inducing stimuli, the optical trigger had no effect.

Biochemical Literature Reviews

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In the words of the researchers, “Together, our findings indicate that activating a sparse but specific en-semble of hippocampal neurons that contribute to a memory engram is sufficient for the recall of that mem-ory.” The significance of these findings is obvious; however abstract it may be, the brain does have a for-mula; and at that, one that we are beginning to resolve. Citation: Liu, Xu, Steve Ramirez, Petti T. Pang, Corey B. Puryear, Arvind Govindarajan, Susumu Tonegawa, and Karl Deisseroth. Optogenetic Stimulation of a Hippocampal Engram Activates Fear Memory Recall. Na-ture (2012). Nature. Web. 22 Mar. 2012. <http://http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature11028.html>

Biochemical Literature Reviews

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Dr. Anna Tan-Wilson: Binghamton’s Biochemistry Legend By Michael Chung

For Biology and Chemistry majors, it is a course to be avoided at all costs. For Biochemistry majors, it is an inevitable course taken for graduation. This course that some believe to be the hardest on campus is Biology/Biochemistry 302, or simply Biochemistry. Contrary to popular belief, this lecture style class is not taught by a grumpy professor, a tyrant or a supervillain. The lectures are led by someone soft-spoken, kind, and always willing to help: Doctor Anna Tan-Wilson. After speaking to her in person, it became very clear to me that the tremendous myths conceived regarding the course and its professor can be dispelled once we understand her research and teaching philosophy. Doctor Anna Tan-Wilson completed her undergraduate degree at the University of Philippines, her Masters at the University College in London, her PhD at the University of Buffalo and her Post-Doc at Purdue University. She joined Binghamton University in 1976, initially teaching Advanced Biochemistry. After realizing the difficulty of obtaining grants, Doctor Tan-Wilson joined her research with her husband’s, Doctor Karl Wilson. Since then, she has worked on countless projects on plant enzymes and proteins, with each reflecting new discoveries. She currently receives her research grants from the NSF and the USDA to pursue her research interests, including the study of soybean serine protease and the usage of cDNA to monitor gene expression of the enzyme. Serine protease, which functions in the early stages of germina-tion, cleaves peptides at regions containing specific acidic amino acid residues. Study of the cleavage sites may also be valuable in attempting to cleave peptides in other legumes with the same acidic amino acid residues. In the future, Doctor Tan-Wilson will further the bounds of her research by working with profes-sors from other disciplines. For the Howard Hughes Medical Institute program, she will collaborate with Dr. Rozners of the Chemistry Department to utilize peptide nucleic acids (PNAs) to easily target her plant pro-tease. She will also work with Dr. Madden to improve computer program software for mass spectrometry. In addition to working with other Binghamton professors, Dr. Anna Tan-Wilson recruits undergraduate and graduate students for her research. When I asked about the types of students she is interested in, she stated that she

picks based on their ability to think analytically and their tenacity to carry out the procedures. She believes that culti-

vating the analytical mind trumps monotonous robotic memorization. This research philosophy of the importance of

critical thinking is translated into Biochemistry 302, as well. She shared that the difficulty of Biochemistry arises

from its combination of the biology component of memorization with the components of application from chemistry

and physics. Most students are adept at either memorizing or applying, but have a difficult time doing both; however,

it is possible to cultivate the skills with time. I realized at that moment that this is crucial to becoming a successful

scientist—a realization Doctor Anna Tan-Wilson desires from us all. These two qualities define a scientist and failure

to exercise both of them encourages the false myths spread about Biochemistry.

Doctor Anna Tan-Wilson ended the interview by stressing the promise of biochemistry and biology, as they

Dr. Tan-Wilson with undergraduate alumnus Adam Hill

(Photograph courtesy of www2.binghamton.edu)

Student Opinions

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are such promising fields with an abundance of new disciplines innovated every decade. For example, bio-informatics did not exist long ago but is now a thriving field. She encourages us all to fulfill our potentials as we are more than capable of not only working in these various disciplines, but to also formulate our own.

Advice on making the most of your undergraduate years at Bing-hamton University By Nicele Arana There are still a variety of lessons I am learning on a daily basis as the days to graduation count down. Looking back at my four years here as a Biochemistry major at Binghamton University, I’d like to think that I made a substantial effort to spend my time here wisely. Indeed, a few important lessons were learned along the way. As a peer advisor, I do my best to convey some of these messages to my peers during ad-vising sessions. Don't be afraid to go out of your comfort zone. It’s natural for most to stick to doing what they do best. However, having the willingness to go out and do something you usually don't allows you the opportunity to find new interests and skills you may originally not have realized. Not many people have this quality because it does involve taking some risks-- this in-cludes enrolling in a challenging class that you find interesting or even switching majors halfway through your undergraduate years to follow your calling and do something you truly enjoy. Find yourself a mentor, and speak with them frequently. Having a mentor is important at every stage of your life and your undergraduate years are no exception. The hardest step is probably finding a mentor you are compatible with and one that can actually help you. No one likes a person of authority who simply puts you down but they also don’t like a mentor who agrees with everything they say. The ideal mentor is one who can listen to your accomplishments as well as your failures and help you develop new perspectives from what you confide in them. You'll find that a good men-tor is someone who can teach you to think outside of that box in which you might unknowingly keep your-self locked up in, and enables you to see the bigger picture. Don't just do things for your resume. You've probably heard this line before, but it doesn’t hurt to hear it again. Students who want to be the most competitive applicants are especially concerned with building up their resumes, and for good reason. But the wrong way to go about it is, for example, to join as many clubs as possible as a superficial mem-ber—this includes being an e-board member yet not fulfilling your role. It might seem like a good idea be-cause your resume can increase by another two lines, but in the long-run it will most likely have repercus-sions against yourself and the club. Committing yourself to any task is a huge responsibility, and there are no short-cuts to fulfilling these responsibilities. The best resumes are about quality, not quantity. You might have only joined one club but with significant contribution, your time commitment, dedication, and strong work ethic will be evident during interviews.

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Student Opinions

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The only competition that really matters is with yourself. It's easy to get caught up in numbers, especially when keeping up your GPA is essential for competitive graduate schools and jobs. This thought makes sense because you can deduced your relative academic standing. However, the downside is that there are those who adapt to the idea that they must "do better than 98% of the class" (if you're on the higher end) and those on the lower end can lose faith in themselves because so many others are doing better. Adapting either of these thought process is detrimental to your future. In the first case, taking on condescending characteristics will not work in your favor because un-healthy competition in the workplace will result in less effective output in your part or the affiliated company, lab, or other organizations. In the second case, being too negative will keep you from reaching your full po-tential. The best kind of attitude to adapt is one which you simply compete with yourself. Rather than think-ing, “I have to do better than this person”, aim to do better than your last test score, or increasing your GPA from a low point you had in a previous year, all while setting a higher goal for yourself each time.

The Bound Nature of Competitiveness in Human Behavior By Prometheus Blank In my opinion competitiveness is a mindset which all humans use. It is a powerful tool which can be used both constructively and destructively. It can help people push to achieve their goals or it can subject them to resist coordination with others. Especially prevalent in the academic setting, where the critique of intelli-gence is supported, the competitive attitude among students can sometimes lead to absurd behavior (e.g. outright arguing against the professor or sabotage between students). Is there any way to supersede com-petitive attitudes to fulfill what we really care about? Human beings are by nature competitive. Our existence as humans is the product of billions of years of natural selection/competition; our birth is the product of competition between hundreds of millions of sperm. For this reason, I do not think there could be anyone who is not competitive. Whether an individual occu-pies an alpha or beta role, everyone has a competition in which they invest towards, their own niche. Some people are outwardly competitive, working towards accurately projecting themselves in front of others to share their ideas, while others work anti-competitively, towards passing over differences to yield opportunity from situations. Overall, competitiveness is unavoidable due to its imperative usefulness for survival which ultimately habituates the development of skills and working knowledge in today’s society. In humans, competition also modulates a process of distinction, giving them the ability to discern which methods and ideas to invest in. Human investment stretches across varieties of interests: knowledge, afflu-ence, athletics, imagination, social capability, etc. Therefore human competition and interest share a posi-tive feedback cycle. For example, a person proficient with the English language will probably find it more interesting than working with numbers because they are relatively better at the subject, and thus will prac-tice the English language more often which makes them better. This positive feedback cycle is why care should be taken when time is invested.

Similarly, entertainment is a competitive practice as well. Entertainment distracts us from exploring our natural talents and investing time towards developing a substantial skill set. I think the distracting invest-ment in internet media, video games and gossip is catalyzed from the feeling of an inner gap, from a lack of feeling in control. It is because humans are better at being entertained than most other things that entertain

Student Opinions

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ment fills this gap for us, fooling us in believing an illusion that we are in control. Although the illusion may be useful, I feel many students should move forward from the habitual indulgence in entertainment. After all, what one does is what one teaches the self. Competition can be tough on the self-esteem, but there is a difference between investing in relaxation, stimulation and entertainment. All this ranting has a point: What are you investing in? What do you want to what to do with your time at

college? By considering how you are naturally competitive and by taking notice of what you are investing

your efforts in, it may help simplify complicated decisions. With an understanding of competitiveness, we

Binghamton Biochemistry Club Tee Shirts

$15

If interested in purchasing, please contact Michael Chung ’12-’13 President of the Biochemistry Club by email: mchung5@binghamton.edu

Design by: Helen Pozdniakova and the Binghamton Student Design Agency

Student Opinions

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Club Photo

Back Row: Luke Pettinato, Betty Chu, Lance Kong, Stefano Quarta, Michael Chung, Morgan Zhao, Jenny Tse Middle Row: Katie Cherny, Stephanie Mejia First Row: Kurnvir Singh, Karen Fu, Nicele Arana, Mogana Jayakumar Missing from Photo: Dan Sha Li, Travis Lageman

2011-2012 Executive Board President: Stephanie Mejia Vice President: Michael Chung Secretary: Katie Cherny Treasurer: Lance Kong Publications Coordinator: Stefano Quarta Newsletter Coordinator: Mayesha Quasem Advisor Coordinators : Nicele Arana and Mogana Jayakumar

2012-2013 Executive Board President: Michael Chung Vice President: Lance Kong Secretary: Morgan Zhao Treasurer: Luke Pettinato Historian: Karen Fu Publications Coordinator: Stefano Quarta Magazine Coordinator: Jenny Tse Newsletter Coordinator: Betty Chu Advisor Coordinators: Dan Sha Li and Kurnvir Singh