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Department of

Chemistry and Biochemistry

Chemistry Newsletter 2013

Chair’s Column

Greetings from the Department of Chemistry and Biochemistry! While Debbie Tahmassebi has been on a well-deserved sabbatical during 2012-2013, I have served as Interim Chair and have the pleasure of sharing some of the fantastic news and happenings in the department in the last year. As you’ll read inside, we had a busy and productive 2012 in which we said goodbye to some old friends and welcomed new ones. I am pleased and proud to report that USD Chemistry and Biochemistry students and faculty are gaining local and national recognition for their quality, talents and achievements. Here is a summary of the outstanding accomplishments:

Dr. Dwyer - Artwortk by Shannen Cravens '11

Artwork by Shannen Cravens '11

Student Awards and Achievement

Student (Graduation Year) Award/Fellowship/Scholarship

Michelle Mezher (Chemistry ‘12)
Aileen Park (Biochemistry ‘13)

Outstanding Research Poster (Division of Colloid and Surface Chemistry at the March 2012 national ACS conference in San Diego)

Courtney Chow (Biochemistry, ‘13)

Alice B. Hayes Science Scholarship (2012-2013)

Danielle McCourt (Biochemistry, ‘12)
Amanda Walker (Chemistry ‘12)
James Walston (Biochemistry ‘12)

Phi Beta Kappa

Michael Bagley (Biochemistry ‘14)

USD Chemistry & Biochemistry Alumni Research Fellowship (Summer 2012)

Randall Clendenen (Biochemistry ‘14)
Wendy Guan (Biochemistry ‘14)
Jeff O’Brien (Biochemistry ‘13)

Jean Dreyfus Boissevain Research Fellowship (Summer 2012)

Faculty Awards and Achievements

Faculty Member Award

Jim Bolender

2012 Mens et Spiritus Award for Honors Professor of the Year (USD)

David De Haan

2012 Outstanding Undergraduate Research Mentor (USD)

Tammy Dwyer

2012-2013 University Professor Award (USD)

Tammy Dwyer

2012 Iota Sigma Pi Centennial Award for Excellence in Undergraduate Teaching

Mitch Malachowski

2012 Patrick F. Drinan Award for Distinguished Service (USD)

Steve Mills

2012 Order of Omega Faculty of the Year Award (USD)

Debbie Tahmassebi

2012-2013 American Council on Education Fellowship

Lastly, we remain committed to building our alumni network using social media sites. Please stay in touch, share your latest news, and let us know what you are up to via Facebook and LinkedIn! If you are looking for employment or are in a position to hire or advertise for a position, we hope you will share these opportunities with your fellow alumni.

Find us on Facebook (University of San Diego Chemistry and Biochemistry) and LinkedIn (send a request to join the group “University of San Diego Chemistry and Biochemistry”).

As always, thank you for your support of USD Chemistry and Biochemistry!

- Tammy Dwyer


Alumni Highlight Back TO TOP

Alumni_MarkRussell10 years later: Dr. Mark Russell, Class Valedictorian, College of Arts and Sciences, 2003

Dr. Mark Russell earned his medical degree from the University of California School of Medicine, Irvine (UCI SOM) that was followed by an internship in internal medicine at the University of Colorado Health Sciences and a residency in emergency medicine at Harbor-UCLA Medical Center. While a medical student Mark earned the Robert Earle and Grace Bell awards for the top grade in his pharmacology and molecular biology courses. While at UCI SOM, he was selected as a member of Alpha Omega Alpha Honors Society for academic excellence and leadership and he was elected by his peers to the Gold Humanism Honors Society for demonstrating humanism in medicine. Mark is now an Emergency Physician at St. Johns Medical Center in Oxnard, CA and Pleasant Valley Hospital in Camarillo, CA.

As an undergraduate, along with a major in Chemistry with an emphasis in Biochemistry (prior to our biochemistry major), you completed minors in both business administration and theology. How has that well-rounded education impacted your professional career?

USD is very unique in that one can receive a very strong education in science and also a very well rounded liberal arts education. I have since realized that this is quite rare from a university education and has proved invaluable in my career. First, my science background at USD was outstanding. But, I also had interests in theology and business. I did not have to abandon those to pursue a major in Chemistry. I use some of my education in theology and business nearly everyday as an emergency physician. First, there is not a day that goes by that someone does not die or nearly die in the emergency department. Understanding a patient’s religious background helps in their care as well as comforting the family. This is part of the art of medicine. My theology background definitely peaked my interest in this area and has helped me be a better physician. Second, medicine is definitely a business. If one does not understand some basic principles of business, accounting, and finance, they will be swallowed up by a very money-driven healthcare system. This is an unfortunate reality, but one my education has prepared me for.

What was the best part of being named Valedictorian of your graduating class at USD? What parts of your valedictory address still make you smile?

Becoming Valedictorian was quite a surprise for me. I tried to do the best I could at the time and was very blessed to receive this distinction. There were quite of few things that I remember from that time. It was great to represent the Chemistry department and the sciences and I believe this award had almost always gone to someone studying liberal arts prior to 2003. Additionally, I had gotten into quite a bit of trouble in high school and was told I probably would not go to college, or at least not succeed if I did attend. It was pretty cool to receive this award in that context. Finally, it was nice to thank my family for their large part in my education and for sticking by me in the rough times. My dad is a pretty tough dude and I had never seen him cry. He cried during the speech and that was pretty powerful.

When did you decide to pursue a career in emergency medicine? Why that area of medicine?

I decided during my last year of medical school to pursue a career in emergency medicine. There are a number of reasons I chose this field of medicine. First, as an emergency physician you are on the front lines. You are usually the first in the healthcare system to see the patient and that usually means when they are the sickest. As an ER doctor, I stabilize and diagnose. The stabilization part is usually an adrenaline rush, full of lots of procedures and stress, like on television. I like that aspect of emergency medicine. The diagnostic part is very cerebral, trying to figure out why a patient is sick so that I can better help them. This part, the problem solving, is very logical, and scientific. You kind of get the best of both worlds. Additionally, I chose a career in emergency medicine because I have a family and this specialty is very conducive to family life as it is shift work. I am never on call. I work about 16 shifts per month and am usually off on the other days. This is quite rare in medicine.

In 2010, you volunteered as part of the Haiti Earthquake Disaster Relief. What was your role and what made you decide to get involved?

I volunteered in the disaster relief effort during my first year of residency in emergency medicine. I had wanted to go right after it happened, but was too busy with my residency schedule until March of 2010. My wife and I went together along with some doctors and nurses and security personnel. Our church sponsored the group. We all knew there was still great need and just wanted to help. We treated relatively minor conditions while we were there. In hindsight, I think just bringing food and clean water would have been more helpful. The people of Haiti are really quite amazing. It was very life changing to see such happy people in spite of their tragedy.

What are some of your best memories from your time at USD?

I spent a lot of time studying while at USD. The Animal House picture of college was definitely not mine. I remember the beauty of the campus overlying the Pacific Ocean. I really enjoyed studying in the libraries and their nostalgic feel. I meditated a lot in the church on campus. The thrill of learning I had during that time I will never forget. It sounds pretty weird I know, but those were my fondest memories. My time at USD was one of tremendous academic and spiritual growth, maybe not as much social growth as college usually is for people. I loved living in San Diego and surfing there. It is really quite a unique place.

What aspects of your USD education were most important to your success in medical school?

There are many, but I will boil it down to two. First, my professors at USD, largely Dr. Tahmassebi, taught me how to problem solve and not memorize. This style of learning is unique to USD because of the small class sizes and great professors. Though this seems minor, it was probably the single greatest principle I have ever received in my education. There are too many facts in our modern world to just memorize. One must learn the underlying mechanisms, theories, physiology etc. and how to apply them. This is the modern world and USD was well ahead of its time. Learning this early in life has been a great help. Understand the “why” and not the “what.” Second, USD taught me to love learning and to teach myself. It is a cliché, of course, to say that you will never stop learning, but it is quite true. The learning just starts in college. It is definitely life long, so you better learn to love it. These two principles have made my life enjoyable and easy. Medical school was actually quite easy compared to my USD science courses. I was way ahead of my peers (who went to Yale, Harvard, UC Berkeley, etc.) when I started medical school. USD provides an outstanding background. Take advantage of it.

You were clearly very focused on academics while at USD.  What were some of the ways you spend your leisure/extracurricular time?

In college I largely just studied, surfed, and worked. I was quite an introvert, though I did not have much time to be social then. Thankfully, I married a wonderful girl and now have a family. I live in Ventura, CA. I spend most of my free time with my wife and daughter. I also surf and ski when I can.

Transitions Back to top

Professor Emerita Patricia Shaffer, RSCJ Retires to Oakwood in Atherton, CA

Sister_ShafferSister_Shaffer_2012After 54 years of dedicated service, teaching and research at USD, Sister Pat Shaffer will formally “retire” and move to Oakwood, the RSCJ retirement community in Atherton CA on June 2, 2013. Sister Pat promises to return often for visits, especially to our biennial alumni gatherings! We asked Sister Pat to comment on her inspirations in science, her proud moments and other fond memories of USD.

Who or what inspired you to become a Chemist?

My science professors at the San Francisco College for Women (now the University of San Francisco), Stanford University and SDSU/UCSD. I entered the Society of the Sacred Heart before I graduated from college. Two and a half years later I returned to San Francisco and, while teaching at our RSCJ high school, I took just enough classes to graduate with my B.A. in Natural Science. It was our nuns on the faculty who inspired me to study science. At Stanford University, Dr. Eric Hutchinson, who later became Assistant to the President at Stanford, was the person who advised and helped me complete my Masters degree in physical chemistry. At SDSU/UCSD (Joint Doctoral Program), Dr. Mitchel T. Abbott, my advisor, helped me become the first woman to complete this program.

Which research are you most proud of in your career?

I am most proud to have been able to clone and sequence from Aspergillus nidulans, the specific gene for L-asparaginase (AhrA) and to express it. It could be used as part of the treatment for childhood acute lymphoblastic leukemia, but another person came up with this enzyme from another source before my laboratory group completed the research.

Can you share some of your fondest memories at USD?

As a nun (a religious who made a vow of obedience) I was sent here to assist Sr. Agnes Schmit, RSCJ, who was the Chairperson of the Dept. of Chemistry at the College for Women. I was also the Resident Assistant for the women’s dormitory rooms in Camino Hall. What I loved most over these years were the relationships with Faculty with whom I collaborated and with students with whom I have worked in the classroom or in my research laboratories. We have published papers and given presentations at science meetings. We have established deep relationships and look forward to Alumni Reunions.

Do you have a message for young people?

Value your time in classrooms or in research laboratories and the relationships you have built with faculty and classmates. It is good to retain these relationships over your lifetime.

Bidding Farewell to Dr. Steve Mills

Dr. MillsAfter 7 years at USD, Dr. Mills is leaving USD to take a new position at Xavier University in Cincinnati. While at USD, the Mills group made good progress toward understanding the role of metal in the copper amine oxidase (CAO) family of enzymes. We replaced the native copper in the enzyme from pea seedlings with cobalt and showed that the enzyme does not work well with this metal. Our results support other studies examining the mechanism of these enzymes. Our work continues with CAO homologs from E. coli, yeast and cow. We will continue our studies at Xavier. I have enjoyed working with many students at USD, both in my research lab and in my courses. If any of you are in Cincinnati, drop by. I’m taking my M&M jar with me.


Department Back to topNews

New Senior Faculty Member: Dr. Joe Provost will join the department as a Professor of Chemistry and Biochemistry in August 2013

Dr. ProvostDr. Provost comes to us from Minnesota State University, Moorhead with extensive experience in teaching, research and leadership in biochemistry. Dr. Provost earned his undergraduate degree in chemistry with a minor in biology from Bimidji State University, his Ph.D. in biochemistry and molecular biology from the University of North Dakota and was a Howard Hughes Postdoctoral Fellow at Vanderbilt University in the Department of Molecular Physiology. Dr. Provost is a very creative teacher who designed the biochemistry and biotechnology majors at MSU, Moorhead and recently designed and taught a Science of Cooking course for non-majors. Approximately $2.5 million in external funding has helped Dr. Provost support a strong undergraduate research program focused on membrane transport proteins and their biochemical role in cell motility with a current focus on non-small cell lung cancer.

National Science Foundation CAREER AwardsBack to top

Career Awards

Assistant Professors Lauren Benz and Tim Clark Win National Science Foundation Awards

Dr. Benz Dr. ClarkThe NSF Faculty Early Career Development (CAREER) Program offers the Foundation’s most prestigious awards in support of junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research. Awardees are expected to build a firm foundation for a lifetime of leadership in integrating education and research. In 2012, two faculty members in the Department of Chemistry and Biochemistry have been recipients of these awards. In July 2012 Dr. Tim Clark was awarded a 5-year grant for “Substrate-Directed C-H Borylation Reactions”. Then, in December 2012 Dr. Lauren Benz was awarded a 5-year grant for “Fundamental Investigation of Supported Materials: ZIFs and Nanoclusters”.

Dr. Clark’s research interests lie in the use of metal catalysts to mediate organic reactions. The work of his laboratory could lead to the design, synthesis and understanding of complex organic molecules with applications in the pharmaceutical and materials industries. The research objectives of his CAREER project are to address fundamental questions in organometallic chemistry leading to the development of ligand-directed borylation catalysts. Additionally, Dr. Clark’s $400,000 grant will allow him involve high school students in his research. He will engage teens with outreach activities, and study the most effective ways to encourage them to pursue careers in the sciences.

Dr. Benz’ research interests involve developing nanoporous hybrid frameworks and other supported materials that act essentially like sponges with an excellent capacity for storing gases such as carbon dioxide, thereby retarding its action as a greenhouse gas. The CAREER project will enable Dr. Benz to explore the properties and reactivity of these materials to establish important connections between material composition and gas binding. Dr. Benz’ $450,000 grant includes an integration of her research in materials chemistry into the undergraduate curriculum and a portion of the award will be used to form a network of women in the science, technology, engineering and mathematics (STEM) fields in San Diego to provide support for women transitioning to academic positions.

Faculty NewsBack to top

Chemistry Study Abroad Courses for Non-Science Majors in London and Italy

The Chemistry of SportMitch Malachowski

During the summer of 2012, Dr. Malachowski taught a “Chemistry of Sport” class as part of the London, England summer program for USD students. This class satisfied the physical science core requirement for non-science students. The summer Olympics were held in London that summer so the course was loosely connected to the summer games. Students probed issues such as structure, bonding and chemical reactions and then considered the impact of chemistry from a scientific, political, philosophical and consumer viewpoint with an aim at probing the impact of chemistry on society. Sports were used as the primary way of studying the chemistry. Topics related to sport such as synthetic materials used in tennis rackets, golf clubs, soccer balls; artificial limbs and the use of performance enhancing drugs such as steroids and human growth hormone were probed from a chemical perspective.Students also studied the ways in which sports drinks and supplements work in the body and considered ways that athletes try to maximize performance.

Various trips were part of the discovery process in the course. A trip to the 2012 Wimbledon tennis tournament provided an opportunity to see Andy Roddick and Maria Sharapova play; the group also saw a cricket match and a soccer match; students saw the play “Chariots of Fire” and visited numerous science museums. Day trips to Oxford and Cambridge (to see where the electron was discovered) and a visit to Westminster Abbey to see the tombs of Newton and Darwin added a flair that was hard to beat. The students’ favorite trip was to a medical operating museum where they were able to recreate surgical procedures such as amputations done without anesthetics. Happily, all the students returned with their bodies intact! Plans are in the works to teach this course again in the summer of 2014.

The Science of Food and CookingPeter Iovine

Food has always been a rallying point for my family–something that brings us together each and every day. Like many other Italian American families, my grandparents were a huge influence on our family culture. Grandma was the executive chef but there were many other sous chefs helping here and there. Although the food was not high end, it was always homemade and delicious.

I never considered a career in the culinary arts yet I was always passionate about food and cooking. When the opportunity presented itself to teach a food-related class in Florence, Italy during the January 2013 term, I jumped on it. The class was titled “The Science of Food and Cooking”. The course was part of a University-wide program called “Sophomore Year Experience” during which sophomores choose from several sites around the world and take just one class at the site. In addition to the course requirements, the program features embedded cultural activities that prompt the students to think more deeply about their new surroundings and their study abroad experience.

The “Chemistry of Food and Cooking” was great fun. My 23 students arrived with diverse interests (including some with culinary school experience) but left the course, hopefully, with a deeper appreciation of the science underlying both food and cooking. What are the critical components of an emulsion? How does crystallization relate to the tempering of chocolate? We came together each day to make, taste, and talk about food while simultaneously engaging a large chunk of traditional chemistry curriculum. I am very excited to teach this course again. Moreover, I am especially excited to welcome a new colleague Professor Joe Provost in fall 2013. Dr. Provost is not only a top-notch teacher scholar but also someone who is nationally recognized as a leader in kitchen chemistry.

If you would like to read more about our experience, please check out our “Chemistry of Food and Cooking” blog: http://www.peteriovine/blog


InstrumentsBack to top

Update on Instrumentation in the Department
Dr. Helene Citeau, Director of Scientific Instruments

InstrumentThe USD Chemistry & Biochemistry Department continues its efforts to provide students with state-of-the-art scientific instrumentation in a safe environment. We have improved our instrument usage and education efforts including online calendars and on-going training sessions. We have acquired several modern instruments this past year and phased out several obsolete ones.

The department’s old HP 5890/ 5970 GC/MS instrument has finally, after 25 years of remarkable service, been replaced by a 2012 Bruker GC/MS instrument– a Premium Scion model complete with autosampler, PTV injector and quadrupole mass spectrometer. This modern GC/MS has a novel EDR detection system and can easily analyze complex mixtures that contain both trace residues as well as compounds of high abundance in the same run. We have purchased optional hardware for SPME injections (solid-phase micro-extraction) on this GC/MS instrument, a technique that was not available to our department users until now.

InstrumentOur old (circa 1998) Shimadzu UV-Vis spectrophotometer has been replaced, after 25 years of sometimes frustrating service, by a 2012 Cary UV-Vis instrument, a UV brand recognized for its accuracy & robustness among UV-Vis manufacturers.

This replacement is aligned with our strategic needs to phase out aging instruments from disparate brands with modern ones from reputable manufacturers, thus ensuring a smooth and easy operation for all department users. We pay particular attention to the hardware robustness and software ease of use. Four new Cary instruments have been purchased over the past four years to meet this goal. These new instruments expand the range of experiments we can do in both teaching and research. As an example, for the first time, we were able to measure diffuse reflectance on thin films in our new instrument.

InstrumentWith safety foremost in our minds, we also replaced our 1986 Parr Hydrogenator with a 2011 model from the same vendor, complete with an explosion-proof motor – a valuable feature since this equipment handles high pressure of hydrogen gas at high temperatures.Instrument

We also were able to replace our 30-year old atomic absorption spectrometer with a modern 2012 Varian/Agilent instrument, complete with several safety interlocks to prevent issues with the acetylene / air flame.

Finally, over the past five years our department has developed strong ties with major instrument manufacturers, who now offer in-house training and technical seminars, open to faculty & students alike, several times during the year.

Student News Back to top

Inaugural 2012 Alumni Summer Research Fellowship

Michael BagleyMichael Bagley (Biochemistry, ’14) was selected as the first recipient of the department’s Alumni Summer Research Fellowship for 2012. The award provided a $4,000 stipend funded by the generous support of our fantastic alumni who wish to give back to USD and contribute to the success of a fellow (future) alum. Michael was also a PURE (Pre-Undergraduate Research Experience) who started his research career at USD in the summer prior to taking classes at USD in fall 2010.

Can you describe the research you are working on with Dr. Dutnall.

In the Dutnall lab, we are studying various chromatin assembly factors, specifically histones and their chaperone proteins. I'm in the process of purifying and characterizing one of the chaperone proteins, Histone acetyltransferase Interacting Factor 1 (Hif1). First, I express the protein in E. coli cells then lyse the cells to extract the protein. Following this, I purify Hif1 via column chromatography. With the purified protein, I can then crystallize it to determine its structure by subjecting it to x-ray analysis. I will also be determining the binding properties of Hif1 by performing gel shifts and cross-linking studies using my protein along with the other proteins, histones H3 and H4 and Hat1 that the other students in my lab are purifying.

What does receiving this award mean to you?

It's a great honor to receive this award. Having also been a SURE and PURE student, it is encouraging to know that multiple people not only show interest in my research but also support the progression of my project. I am very grateful to receive funding from this award because it has been my goal to publish the results of my work before I graduate and this award has helped make that dream more of a reality. I hope that my current and future successes can be linked to this award and in return, give it even more prestige.

What is your inspiration for the research you do?

As soon as I decided to pursue science, I knew that I wanted to cure diseases but I had no idea how it was done. After taking a few science courses in high school, it became more clear as to how these cures come about. I particularly liked the genetic aspect and I determined that I would like to focus on regulating genetic expression and fixing damaged genes. When interviewing for the PURE program, I asked each of the five professors interviewing me to share the research they were doing in their labs. All were interesting but I was most intrigued by Dr. Dutnall's project since I had always wanted to work with genetic expression. Being fairly new to science, I barely knew any of the words he was saying but the words "genes, expression, and proteins" really stood out. Once he was done speaking I shared what little knowledge I had on the subject, which I guess was enough for me to be selected to do research in his lab.

2013 Alumni Summer Research Fellowship Awards

Alex_HellerOne of the distinguishing features of USD Chemistry and Biochemistry is the capacity to offer significant research experiences to our undergraduates. Alumni from our department have given back generously to support research by current undergraduates.  The Alumni Summer Research Fellowship recipients for 2013 are Alexandra Heller (Biochemistry ’15) and Alyssa Rodriguez (Biochemistry ’15). Alex will spend summer 2013 in the laboratory of Dr. Tim Clark studying the asymmetric copper-catalyzed diboration of aldehydes by using chiral anheterocyclic carbenes. During summer 2013 Alyssa will work with Dr. David De Haan to study the formation of hexamethylenetetramine (HMTA), contributing to the presence of brown carbon in the Earth’s atmosphere.

Alyssa RodriguezThank you to alumni and friends of the department who gave generous donations to the Alumni Summer Research Fellowship fund, whether you were able to attend the June 2013 reunion or not. We sincerely appreciate your contributions! We intend to hold the alumni reunion and fundraiser biennially and our next event will be in summer 2014.

Our ability to offer the Alumni Summer Research Fellowship each year depends on the generous support of our terrific alumni and friends of the department. It makes us enormously proud to know that our alumni “give back” and wish to provide exceptional opportunities for summer research experiences to current and future students. In this ongoing effort, we are presently fundraising to support one or more students for summer 2014. If you are able to make a contribution to help fund a summer research fellowship in the department, please click on the following link and make your donation now. We are so proud and grateful for your support!

Donate now!

BRIDGES Program Update

The Bridges Program continued going strong in year 4. This past year we sent 2 students for summer research experiences at larger, graduate-degree granting institutions. Taylor Lasof (’14) worked in Dr. Denise Galloway’s group at the Fred Hutch Cancer Research Institute, performing experiments which explored the biochemistry of HPV and its link to middle-aged women. Sabrina Phillips (’12) worked for atmospheric chemist Geoff Smith at the University of Georgia, and is currently completing her first year in graduate school (in the same group). We look forward to hearing about both of your bright futures!

Alumni News Back to top

Dr. BaileyDr. Denise (Dunn) Bailey graduated with a degree in Chemistry (Biochemistry emphasis) from USD in 2001. She received Departmental Honors in Chemistry upon graduation. While at USD, supported by a Presidential Scholarship, she also completed minors in Biology and Spanish. Denise then went on to complete her Ph.D. in Organic Chemistry from the University of California, Irvine in the Chemical Biology Program. Denise is currently an Assistant Professor of Chemistry at Santiago Canyon College in Orange, CA. Prior to this position, she taught at San Bernardino Valley College, Mt. San Antonio College, Irvine Valley College, Cypress College, Concordia University and Orange County High School of the Arts.

What made you decide to pursue a PhD in organic chemistry? What was your experience at UC Irvine like for graduate school?

Graduate school just seemed like the next step for me. I knew that if I got a lab position straight out of undergraduate school, that is all I would ever be, a lab technician. If I ever wanted to plan my own research I would have to go to graduate school. I also felt I had a lot more to learn about the field of chemistry. It seemed the more I read the literature and the more I learned (especially in upper division classes like physical chemistry), the more I was aware that I did not know but the very “surface” of the knowledge about chemical reactivity.

Biochemistry and Organic Chemistry were my favorite chemistry courses. With a minor in Biology (I actually was a biology major until my junior year of college – Organic Chemistry is what switched me), I have always been fascinated by how chemistry works in biological systems. I searched for doctorate programs that had opportunities to work with the biological applications of chemistry. UC Irvine’s graduate program was top 10 in Organic Chemistry and they were launching a new “program” with an emphasis in Chemical Biology. They accepted a cohort of about 20 students and we started our graduate class work during the summer, before most other graduate students started in September. My class work was that of a typical Organic Chemistry doctorate with electives in chemical biology. I joined an Organic Chemistry research group, but got to work on a project where I was synthesizing organic molecules as substrates for biological systems. It was a great experience! Don’t get me wrong, it was tough, very tough, but an amazing experience.

What aspects of graduate school did you feel most prepared for? Least prepared?

Going into the Chemical Biology program, the professors assumed the students were not as well prepared for the rigorous Organic program; this is the real reason we started in the summer so they could “prep” us and we could “catch up” to the level of the regular Organic Chemistry graduate students. I let this thought, that I wasn’t as well prepared as other students, creep into my head. Once we were in the classes with ALL of the chemistry graduate students, I realized this was not the case; I was just as competent in my class work as students from all over the country, including schools with larger chemistry programs (having taken my classes in the basement of Camino Hall and earning a B.A. in Chemistry). I was extremely well prepared. I did have research experience at USD with Professor Gegner, which focused on the internalization rate of the CD14 receptor in CHO cells. My lab experience consisted mostly of biological assays. This did end up helping me later in my graduate career as I was able to run my own biological testing of the compounds I synthesized, but I did not have any synthetic experience outside of lab work for my classes at USD. That is an area in which I was lacking, but was able to quickly catch up in.

At USD, along with a major in chemistry, you completed minors in biology and spanish. Have either or both of those minors impacted your professional career?

I find that being able to relate chemistry to biology and use real life examples helps me make chemical concepts more relevant to my students. Spanish always comes in handy working in Southern California. When I was working in San Bernardino the majority of my students were of Hispanic decent and many were not native English speakers. Being able to communicate with my students in their native language and understanding their customs allows me to have a more personal interaction with them.

After graduate school, you started out as a substitute teacher for high school chemistry. Since then, you have moved through several adjunct faculty positions at community colleges and are now an Assistant Professor at Santiago Canyon College, a community college in Orange, CA. What made you decide to move from high school teaching to a community college? What are the advantages/disadvantages of teaching in each of those environments?

I defended my thesis in late August. Most colleges had fully staffed their classes by then. I had taken and passed the CBEST (California Basic Education Skills Test) while at USD and thus decided to get my emergency teaching credential to be a substitute teacher at the high school level until the next college semester started. I ended up finding a posting for a long-term substitute for a chemistry teacher out on maternity leave. It was at a charter high school for students gifted in the arts. It consisted of a full teaching load with all of the responsibilities of a regular teacher including making lesson plans, grading, and having parent-teacher conferences. I never went for my full “clear” teaching credential and am therefore not licensed to teach high school permanently. But I knew after that experience that I wanted to move up to college-level teaching. I like having students that have at least an interest in chemistry and actually chose to take the class. And to be completely honest, I like not having to deal with parents. Although I chose not to stay at the high school level, that teaching job really helped shape my teaching. I had to learn to be more creative and hands-on with my presentation of chemistry in order to excite and grab the interest of the art students; I carry this into the classroom even today. I also knew that I wanted to work in the community colleges, rather than a four-year university, in order to have more interaction with my students and really focus on my teaching style and helping students, while not having to focus on my own research.

What are some of your best memories from your time at USD?

I was a true science nerd in disguise while at USD. I had the full load of science classes and spent my days in the basement of Camino Hall, yet I was also in a sorority. I remember hanging out in a computer/study room down the hall from the professors’ offices where we would all do our homework and analyze our data for our lab reports; it was great camaraderie. It was an amazing dynamic, having my professors be so accessible. When I had a question, I went and interacted with them directly during their office hours. At a Cal State or UC school I would have been talking to a TA, instead of going straight to the source. I also have great memories of liquid nitrogen ice cream parties out on the lawn with the Chem Club/ACS student affiliate.

Have you remained connected to the department since you graduated from USD? If yes, how?

I have not remained in very good contact with the department since my graduation. Facebook has allowed me to reconnect and follow the current happenings. I still haven’t even seen the inside of the new science building (it was a parking lot when I was there!)

Have you remained connected to fellow chemistry majors from USD? If yes, who? What are they up to these days?

Tim Clark (I believe you know him J) and I went to grad school at UCI at the same time, but were in different areas of research and did not cross paths often. The other 7 (I believe) chemistry graduates from 2001 are all over the country last I knew.

How did you spend your time outside of the classroom at USD?

I lived in the dorms on campus for my first two years at USD, but being from Orange County I travelled home at least once a month. I lived with sorority sisters the other 2 years. I worked part-time for public safety and actually drove the tram around campus during my sophomore and junior years. I also played intramural soccer and volunteered at a local elementary school. I spent a summer being a camp counselor in Pennsylvania and another summer with USD abroad in Guadalajara. Of course I loved spending time down in PB as well ;).

What advice do you have for current students considering a career in chemistry?

I think current chemistry majors/graduates should know that there is a lot out there that you can do with your degree; and it’s okay if you don’t know exactly what you want to do and/or you change your mind over time. Even once I changed my major to Chemistry, I thought for sure I would work in big pharma. Then as I got more into biochemistry, a biotech company seemed likely. Either of which would include being inside a lab all day. As the market took a dump and industry was not hiring, I started considering my personal interests. My first job offer out of graduate school was actually to be a wine analytical chemist up in Napa, CA. My life was changing and I was focusing more on family life, which is why I did not end up taking that amazing job opportunity. That is when my path led me to teaching; it had always been part of my life, but it was never my ultimate goal. Being a teaching assistant in graduate school helped me find my true calling and I could not be happier with my professional career and family life now. It’s not always a straight path; it may have bumps and turns, but you will end up where you are meant to be. Don’t pigeon hole yourself into a specific profession. Chemists are needed in a wide variety of industries, not just pharmaceuticals.

What are your present and/or future goals?

I got married a year after graduating from USD and we just celebrated our 10-year wedding anniversary this past summer. This past year I welcomed my third child. We have 2 boys, Owen (4) and Logan (2), in addition to our little girl, Samantha (7 months). Next year I will become department chair of the Chemistry Department at Santiago Canyon College. Life is crazy busy, but I wouldn’t have it any other way.

Kristy ClarkeKristy Clarke ‘02 - Supported by a GAANN Fellowship, Kristy completed a M.S. in Chemistry at UCSD after graduating from USD with a degree in Chemistry (Biochemistry emphasis). She earned her teaching credential from Concordia University and has been teaching AP chemistry, chemistry and biotechnology at Dana Hills High School since 2005. Kristy also served as the assistant coach for the varsity softball team at Dana Hills from 2005-2007. Recently, she developed the syllabus and curriculum for a new course called Biotechnology, which has been adopted by her entire school district. At USD, Kristy was a member of the women’s softball team and involved year-round in undergraduate research.

In what ways have you remained connected to the department since you graduated?

Since graduation I have gone back and done research in different labs during four summers. For two summers I worked with Drs. Tahmassebi and Dwyer performing computational calculations from 2D NMR data to determine the solution structure of a DNA duplex containing non-natural base pairs. It was a lot of fun to be able to learn a whole new field in bioorganic chemistry. In a third summer I worked in Dr. Iovine’s lab synthesizing boron-based linker molecules and during a fourth summer I worked again with Dr. Tahmassebi to synthesize additional non-natural nucleobase analogs for future NMR studies.

What are some of your favorite memories from USD?

I have several fond memories of USD both in the Chemistry department and on the softball field. I remember the late nights cramming for different physical chemistry tests with some of my fellow softball teammates. I didn’t know physical chemistry could be fun, but when you add lack of sleep, caffeine and the stress of potentially failing, it turned out to be quite a good time. I also remember giving my senior seminar. I was so stressed out about it, but Dr. Tahmassebi kept reassuring me that I would do fine. During my presentation, I had the Chemistry department faculty on one side and the softball coaches and team on the other. It was a clash of both my worlds. I was scared to death of the professors’ questions, especially Dr. Traylor’s, but I survived. Afterwards I felt such a sense of accomplishment. It showed me just how far I had come in my four years at USD.

How did your USD education shape your professional life?

USD has had a direct impact on my teaching. I was fortunate to have some great teachers in my Chemistry classes. I have been able to reflect about the teaching styles of the different professors and implement them into my own classroom. I have also been able to take my research experience from USD and share how certain concepts taught in a high school chemistry class are applied in the real world.

What made you decide to become a high school chemistry teacher?

When I was in graduate school I had to TA for several quarters. As I interacted with those students I noticed that most of them already had their mind made up about studying chemistry. They either loved it or hated it, mostly the second. I wanted to be their first experience in chemistry and hopefully help them gain an appreciation for chemistry regardless if they wanted to choose that as a major.

You earned a master’s degree in Chemistry from UCSD. How has the degree impacted your career as a teacher?

I spent three years doing research in a bioorganic chemistry lab at UCSD, and they have proven instrumental in my teaching. It was during those three years that I continued to develop my skills as a scientist. In the lab, I worked in both the organic chemistry and biochemistry sides of the projects. As a result of my research experience, I have developed a Biotechnology class in which students are introduced to basic protocols of biochemistry laboratory.

You were a student athlete at USD. How did your time on the softball field impact your experience at USD? How has it impacted your professional life?What advice do you have for current student athletes?

I loved playing softball for USD and representing the school. I spent more time on the softball field than any other place during my four years. I made some amazing friends that I still keep in contact with. I was extremely fortunate to play Division 1 softball and major in Chemistry.  It was definitely a challenge to be able to balance such intense activities, but both my coaches and my chemistry professors were supportive. I would encourage current student athletes to be disciplined in both their sport and their major. I will never forget the feeling I had after my final softball game – softball was my life for over 10 years and now it was over. Luckily I had a degree in a field that I loved and my life wasn’t over, it just took a different direction. Playing a Division 1 sport has impacted my teaching career. I try to talk to my current students about the balance of a student athlete and how to balance the demands of both.

Describe your experience as an undergraduate research student and then your role in research post-graduation.

I worked for Dr. Tahmassebi for a couple of summers and winter breaks during my time at USD. I loved my research experience at USD and it probably had the biggest impact on me as a chemistry major. I would recommend that every chemistry major spend time working in a lab. It is where you actually get a taste of what chemistry is all about. It provided me the opportunity to learn to think like a scientist and not just solve problems out of textbook. While teaching high school, I was lucky to be able to go back to USD during the summers and work in a variety of labs. This was such a good opportunity for me to get back into the lab and carrying out original research. It allowed me to continue to learn even though I was teaching basic chemistry. It also allowed me a great chance to work one on one with undergraduate students who were working in the lab for the first time. I was able to help show them the lab techniques and help them analyze their data. I got to do what I love, teaching, but in a different environment.

Dr. JohnsonDr. Tyler Johnson ‘03 graduated from Loma Linda University’s Dental Anesthesiology program following his dental degree there. He graduated ranked first in his class from his dental anesthesia residency program. Tyler moved back to San Diego and opened San Diego Dental Anesthesia, his own office which partners with dentists across San Diego to provide in-office anesthesia.

How did you spend your extracurricular time at USD?

As a student at USD, I spent a lot of my time as a guide for the Outdoor Adventures program on campus. If you haven’t heard of the program, consider leaving the science building and venturing over to the UC. They have something for everyone. You can sign up for anything from a One-Hour Star Gazing class to a One-Week Kayaking trip in Mexico. Awesome!!!

What made you decide to pursue dental school? What advice do you have for current students considering a career in dentistry?

Lifestyle. As a dentist you don’t work the long hours of a physician. You have time for your family and friends, which in the end are all that matters. If you’re considering dentistry, make sure you like people. As scientists, we tend to be introverted. If you go into dentistry and you don’t like interacting with people, you won’t be happy.

What made you decide to open your own business, San Diego Dental Anesthesia, after graduation?

Being a general dentist was great! But as hard as we try as dentists, it is always the case that at some point during treatment, someone will feel pain. That was not acceptable for me. I decided to go back to school and train to be an anesthesiologist so that I would no longer have any patients feel pain during treatment. San Diego Dental Anesthesia is the ultimate result of that promise.

What have been some of the greatest challenges and greatest rewards associated with owning your own business?

Owning your own business is great because that means you are the boss. Only problem with that is you are the boss. Being a dentist puts you into many roles. You act as a radiologist, as an anesthesiologist, as a surgeon, and ultimately as a business owner. You must be able to wear many different hats throughout the day.  When the end of the week rolls around, your staff and their families count on you for their paychecks.

What aspects of your education and experiences at USD have been most important to your academic and professional successes?

USD is an amazing school academically. But for me, the academics were not the most important aspect of my education.  There is a sense of openness in the people that I have yet to see anywhere else. The faculty, students, staff, and clergy all work together to encourage creativity, making the school a truly excellent learning environment. Seeing this openness has helped me to encourage this same type of creativity in others, and it has become the most important aspect of what I learned at USD.

Did your time at USD prepare you appropriately for dental school? How?

As much as I love being a dentist, the dental school training was tough.  The Chemistry department prepared me by giving me a strong foundation on how to think about, and approach problems. Also, the study habits I developed in college transferred straight into dental school on day one. Chemistry relates to everything. Now as a dental anesthesiologist, I see real time biological chemistry on a daily basis. I am grateful that USD provided the education I needed for a seamless transition to dental school.

What are some of your best memories from your time at USD?

Long nights in C16. When Chemistry was in the old Camino building, we had a study room in the basement of the building called Camino 16. It was a space for students to gather, collaborate, and study together. Teachers would pop in and out while we studied for exams and we could always ask them questions. All the students that did research had a key to C16 so we would go back at night and study in that room when the library closed or when we needed a group study room. At the time I don’t recall it being so great, but now looking back, I have fond memories of those long nights.

Dr. KentDr. Kyle Kent ‘06 completed his medical degree at Oregon Health Sciences University (OHSU) after graduating Phi Beta Kappa from USD with a degree in Chemistry (Biochemistry emphasis) at USD. He is currently completing the Internal Medicine Residency Training Program at OHSU and will be Chief Resident next year. While a student at USD, Kyle was the President of the USD Young Democrats and a chemistry department tutor. At OHSU, he traveled to Ecuador with Interhealth South America to provide free medical care while living with a host family and learning and practicing Spanish.

In the summer of 2007, you traveled to Ecuador with a group called Interhealth South America. What did you bring home from that experience?

It was a much needed adventure. Portland is my comfort zone so learning to salsa dance in Quito, playing soccer and nervously practicing Spanish in a mountain town called Otavalo, and trying not to die in the rainforest were certainly new experiences and challenges for me. My Ecuador host family was composed of an honest hardworking father, a devoted loving mother, two energetic and bright teenagers, and an adorable golden retriever. Despite the differences in culture, hemisphere, and language there were more commonalities with my Portland family than differences. The rest of the group was composed of medical students from all over the U.S. so it was fun to learn how similar our medical school experiences had been and to feel an instant bond because of our shared paths.

The last thing I took away was my desire to provide direct patient care rather than dedicate my life toward larger public health goals. In the rainforests of Ecuador a group of students had developed a simple but effective water purifying system out of two plastic buckets and a special filtering material. We trekked through the jungle and delivered these water purifiers to schools in each nearby village. There were communities all around Ecuador without clean water and the related diseases took a great toll on the people. Bringing clean water to communities did more for their health than all the medicines we could have administered. This was a great lesson in public health but I didn’t find the work as fulfilling as I expected. I still felt that helping one person in need at a time utilized more of my talents and was more fulfilling than larger scale efforts that could help many people I’d never have the privilege of meeting. Fortunately there are a lot of people who feel about clean water and mosquito nets how I feel about a lifetime of small encounters with people in a clinic or hospital so we can address different needs.

Congratulations on being named Chief Resident at OHSU for 2013-2014. What are you looking forward to most about that role?

Teaching and giving back to the residency program. I went into Internal Medicine because of mentors who taught me the wonders of interpreting heart murmurs, the joys of solving puzzles, and the challenges of explaining complex concepts to patients and students in understandable ways. I see next year as a chance to further develop all of the skills that will serve me well as a doctor and teacher.  It should be noted that I give full credit to my time as a tutor in the Chemistry department at USD for whatever teaching skills I possess. The challenge of explaining organic chemistry to people prepared me for explaining the complexities of the heart and kidneys.

In terms of giving back to the program, here’s what I wrote in my Chief Resident application: “I love my life. I see my parents once a week, courted my wife during Intern year, and pulled off a proposal during CCU (a notoriously challenging cardiac ICU rotation). I play soccer most Thursdays and get to laugh and cry with incredible colleagues whom I consider close friends. I spend my days as well as many nights helping people when illness tries to steal their livelihood. I am tired yet wonderfully fulfilled. This has all been possible for me at OHSU and as a Chief Resident I will do my best to see that our program continues to grow and provides such a home for generations to come.”

How did you meet your wife?

I was a 4th year medical student rotating through the Dermatology department and she was working there while applying to medical school. I was getting something out of my locker in the break area and she was filling up her water bottle when she introduced herself. Hallelujah! We spent a few minutes talking about growing up in Portland, playing soccer, and why she should go to OHSU for medical school instead of elsewhere. She had a shy smile, adorable freckles, and the most beautiful big brown eyes I’d ever seen. I didn’t think it would be appropriate to ask her out at work, but luckily we ran into each other a few months later and finally went on our first date.

What are some of your favorite memories from your time at USD?

I miss the sun and the ridiculously nice science building. My freshman year we took science classes in a basement and then all of a sudden we had smart boards and a garden with double-helix shrubbery! I loved taking liberal arts classes (International Relations, Judaism, History of Music, Philosophy) and feeling like an “intellectual.” I was a crusader for the USD Young Democrats and learned a lot about fighting for what I believe in and how to keep going after losing elections (thank you John Kerry and Donna Frye). Lastly, I cherish the laughs and great times shared with remarkable friends and mentors.

When did you decide to go to medical school and why? What do you hope to do following your residency?

In high school I had a sense that I wanted to go to medical school but I realized it was in part because I was a straight A student and felt an unspoken pressure to pursue a profession such as medicine or law. It wasn’t until I spent a summer shadowing doctors and doing research that I had the chance to see what medicine was really all about. I saw in my own family how much health played into happiness and I admired the compassion and commitment of the doctors I shadowed. They were invited into the sacred spaces in which people and their families were completely vulnerable and in need.  Inside those spaces there were celebrations and there were tragedies. I wanted to be able to help guide people through these challenging times and if possible help them get on with enjoying their lives.

After my year as one of the Chief Residents I hope to find a job as an academic hospitalist. This means I will be caring for sick adults in the hospital, at times on my own and at times supervising residents and medical students. There will be time to build and keep my own skills sharp and a lot of time to teach the next generation of physicians.

In what ways did your time at USD best prepare you for medical school?

Medical school applicants now get a lot of credit for being “different” so if you are a Theater major for example who has also taken science classes you can pitch yourself as well rounded or unique. At USD I felt like the liberal arts classes opened my mind and provided me with a nice well rounded knowledge base of the human condition and ways to relate to people. That said, the best decision I made was to become a Chemistry major. I entered college thinking all pre-med students should be Biology majors but I was assigned to Dr. Tahmassebi as my initial advisor who convinced me otherwise. She nicely made the case that in Biology, no offense to Biology majors, there is a lot of memorization and in Chemistry there is a lot of complex reasoning. She said if I became a Chemistry major I would learn how to solve problems even when I didn’t have the answer memorized and that would help me in medicine. Boy was she right! Doctors typically make diagnoses in one of two ways. The first is instant pattern recognition. For example, if a person comes in coughing up rust colored phlegm with fever, low oxygen saturation, and crackly sounding lungs they have pneumonia. The second is deductive reasoning. This method involves framing the key elements of a patient’s story, building a framework of potential diagnoses, and creating a plan to check things off the list until the answer is reached. The first method is easy, intellectually pleasing, and anybody who has paid attention in medical school and residency should be able to come up with the answer. The second method is much more intellectually taxing, frustrating, humbling, and separates great diagnosticians from the mean. I am working every day and will spend a lifetime developing the latter method of clinical reasoning but I truly believe my training as a chemist has given me an advantage.

What advice do you have to current students planning to attend medical school?

First, become Chemistry majors. Second, truly stop and think about what it will be like to survive medical training because most people will not tell you about or minimize the unglamorous side. First you spend two years studying more than you’ve ever thought possible and you’re no longer the smart kid in the class because your classmates are all geniuses who somehow still have time to run non-profits and knit blankets for the homeless. You get to see patients on occasion to help remind you of why you wanted to go into medical school in the first place but not nearly as much as you’ll crave. You spend the third year rotating through every specialty to see which one fits best. You get up early, work long hours, are the lowest on the totem pole, have no control of your schedule, and while you’re racking up debt for the privilege of doing this during the peak of your youth your friends will be making money and have evenings and weekends off. Then you decide which field you want to go into, apply to residency programs, travel around the country checking out your options, make a rank list of your top choices, and the contents of an envelope tell you where you will live the next several years of your life. In residency you start to make enough money to pay the bills but work even more than you did in medical school. By the time you’re finished you are older, wiser, and hopefully you’ve put enough effort into maintaining your relationships that you have a life outside of the hospital. This is the unglamorous side of medical training. With that said it is still the best job in the world.  I get to listen, advise, debate, guide, learn new things every day, feel at times like I’m a master diagnostician and at others be brutally humbled by the mysteries of life and the human body. I can’t see myself doing anything else that would be as challenging and fulfilling. If you spend time with doctors to see firsthand what day to day life is like, acknowledge the unglamorous aspects of medical training, and you can’t see yourself doing anything else…then you should apply.

How did you spend your extracurricular time at USD? Have you found time for extracurricular activities while a medical student and resident? If yes, how do you spend your time and why?

In college I played intramural and pick up soccer, golfed in Coronado and at Torrey Pines, ran on the beach, ate amazing Mexican food, laughed a lot with my friends, tutored in the Chemistry department, attended Sunday Mass at Founders Chapel, campaigned for any respectable Democrat running for office, delivered meals to homebound folks with AIDS, did Chemistry and Biology basic science research, and served on the Academic Integrity Hearings Council.

In medical school and residency I have continued to play soccer. I play indoor most of the year and outdoor during the spring/summer session. This keeps me in shape, allows me to relieve stress, fuels my competitive drive, and is a piece of my pre-doctor self I swore I would not abandon. I play golf with my family and friends when I can though certainly a lot less than before medical school. I also make time for karaoke! I always loved music and singing but was too shy to sing in front of other people. Then one night I finally sang with my friends. It was an incredible rush, I was hooked, and now I try to go at least once every few months. I’ve also done research in the realm of curriculum development to help improve resident skills when discussing resuscitation preferences with patients or facilitating patient transitions from hospital to home.

My biggest extracurricular project was courting, proposing to, and marrying my brilliant and beautiful wife Cate. We have made a wonderful life together enjoying our city, our families, our rescue dog Lulu, and our shared passion for medicine.

Faculty Research Programs Back to top

Benz Group

The Benz group continues to explore the interactions of organosulfur compounds with surfaces, and is making good headway on the investigation of nanoporous hybrid films. Work on the first project was accepted for publication in Langmuir last year thanks to the hard work of four of our undergraduate group members: Aileen Park, Jenelle Corey, Victoria Park, and Michelle Mezher. Thanks to the group’s hard work on both projects we recently received an NSF CAREER award for the support of our work on supported hybrid materials which will provide 10 students with summer stipends over the course of the next 5 years, and will allow for some important equipment upgrades to make the next step of this work possible.

Benz GroupWe are looking forward to welcoming our first postdoctoral scholar to the group this summer! The Benz group has welcomed a number of new group members since the last report: Miranda Stratton (’13), Elizabeth Webster (’15), Andrew Cerro (’14), and Brian Benedicks (’14). Some group Alumni news: Michelle Mezher (’12) graduated and has gone on to start the Ph.D. program in chemistry in the Heske lab at UNLV. Karen Cesafsy (’12) also recently received word that she’s been accepted to several Ph.D. programs in chemistry, and will soon decide where to go. Tran Le (’13) will be headed to pharmacy school following a successful series of interviews. Jenelle Corey is currently in the “Teach for America” program in Connecticut. And last but not least, Miranda Stratton received word that she has been accepted to a number of excellent graduate programs in biology. Congratulations to all of you!! We are looking forward to another great year, and the upcoming American Chemical Society meeting in New Orleans!

Harbor Cruise with the Summer Scholars: Summer 2012: From left to right: Dr. Benz, Brian Benedicks, Bette Webster, and Miranda Statton.

Bolender Group

Where to begin?  In January 2012, I went to Uganda with my colleague, Dr. Anita Hunter of Dominican University of California, to restart our project that assists the Holy Innocents Children’s Hospital with their water issues. I was able to take two students – Heidi Hirsh (MARS, ’12) and Em Cullen (MARS, ’12) – with me on this trip. In many ways, I thought it was my last trip to Mbarara because there were no truly interesting scientific questions that were coming up. However, Dr. Beth O’Shea suggested that I take a field test kit for arsenic with us on this trip. Every water sample we tested had arsenic in it at levels that are at least three times the World Health Organization limit for drinking water. This includes bottled and tap water. The worst was nearly 60 times that limit.

Fast forward to July 2012. I went to Kimana, Kenya with my colleague Dr. Rich Malatesta to assist The School for Field Studies site with a water quality assessment. Their water sources are much more pristine, many of them being springs fed by the snowmelt from Mt. Kilimanjaro. Again, arsenic at similar concentrations in nearly 95% of the samples we collected. Both reports submitted to our colleagues in Uganda and Kenya have been forwarded to the highest levels of their water ministries.

The scientific question has been defined. We – Dr. Bethany O’Shea (MARS/ENVI) and Prof. Keith Macdonald (Bio) - are currently in the process of writing and submitting a major research proposal to fund our work that will take us through Uganda, Kenya, and Tanzania assessing arsenic and other heavy metals concentrations and providing our public health colleagues starting points to assess the impacts of arsenic on the local communities.

Description: Macintosh HD:Users:bolender:Desktop:facebook kenya:IMG_1371.JPGIn January 2013, I took three students back to Uganda for continued work on the water issues. These students are Erin Hong (Biochem ’13), Sarah Leitheiser (ENVI ’13), and Olivia Igoe (Visual Arts ’13). They took part in confirming our arsenic results from 2012 and worked with our nursing colleagues on several of the community assessments. Other work continues in my lab, and I have just taken on four new students – Adan Cortez (Biochem ’15), Allison Ferrer (Biochem ’15), Nessa Seangmany (Biochem ’15), and Sarah Baker (Biochem ’15). They are either working on the arsenic related project or the nano crystal project which is still part of my research life. It is going to be an exciting year!

Dr. Bolender and our guide Sipaya overlooking one of our sampling sites in Amboseli National Park in Kenya.

Clark Group

Clark Research GroupThe Clark research lab has grown significantly during the second year at USD. There are now seven undergraduate students (Marissa Ringgold–’14, Peter Cannamela–’14, Randall Clendenen–’14, Weiye Guan–’14, Timothy Ramseyer–’14, Nicholas Huynh–’15, and Alexi Duenas–‘15), a part-time lab technician (Kristina Crawford), and a postdoctoral research associate (Andrew Roering–Ph.D.) in the research lab. Over the summer (2012) six continuing undergraduates and one PURE (Pre Undergraduate Research Experience) student worked in Dr. Clark’s research group.

Recent Accomplishments by Clark research group members:

  • Randall Clendenen and Weiye Guan received a Dreyfus Undergraduate Research Fellowship to support their research during the summer of 2012.
  • Peter Cannamela received a USD SURE (Summer Undergraduate Research Experience) summer research fellowship to support his research during the summer of 2012.
  • Kyle Proctor was chosen as a USD PURE summer research student and worked in the Clark research group for the summer of 2012.
  • Weiye Guan received a USD SURE (Summer Undergraduate Research Experience) summer research fellowship to support his research during the summer of 2013.
  • Dr. Clark and Dr. Andrew Roering gave oral presentations at the Spring 2012 ACS National Meeting in San Diego.
  • Marissa Ringgold, Peter Cannamela, Lillian Hale, and Casey Medina gave poster presentations at the Spring 2012 ACS National Meeting in San Diego.
  • Marissa Ringgold (undergraduate) and Andrew Roering (post-doc) are co-authors on a recent publication in Organic Letters.
  • Dr. Clark was awarded an NSF early CAREER award for research on “Substrate-directed C–H borylation reactions.”

The Clark group is planning to attend the National Organic Symposium in Seattle, WA and students will be giving four posters about their research progress.

Daley Group

The 2012 Daley Group consisted of the old guard; Lauren Bernier, Daniel Huh, and Jessica Rodriguez as well as the new troop; Alexandra (Alex) Heller, Madelegne (Maddie) Gerling, Raymond Sullivan, and Kayleen Fulton. During the 2012-2013 academic year our group has held to 4-6 research students but that number will shrink to zero in the upcoming 2013-2014 academic year. Before we get to what is happening next year, below is a recap of the Daley Group’s efforts since the last Spin.

On the research front, we have continued our work on the latest generation NHase ligand analogue, preparing it on a larger scale and making its coordination complexes with cobalt and iron. We are currently trying to get an X-ray crystal structure of the cobalt complex to complete a nice story that we hope to publish in 2013. In other news, Daniel Huh’s diamidato-bis(phosphine) metal complex studies have yielding very interesting results and we are in the process of preparing stubborn reduced Ni and oxidized Ru complexes that will complete two stories for anticipated publications in 2013. We have also had great breakthroughs with our enantioselective catalysis project! Thanks to the hard work of past group members, most notably Jessica Cryder, we were able to prepare our chiral ligands in-situ as Cd-complexes but we have always had difficulties isolating the ligands themselves for use in catalysis. In the fall of 2012, Kayleen Fulton worked on this challenge as part of her Chem 396W work and together we figured out a way to use a solid phase thiol column to decoordinate the ligand with minimal decomposition. This work is currently being refined by Kayleen and Ray Sullivan and we hope to do out first enantioselective catalysis reaction before the end of this semester!

The Daley Group did not go present at an ACS meeting in 2012 but several members will be presenting their work at the 245th ACS National Meeting to be held in New Orleans, Louisiana (April 2013). Pictures and updates from this conference will be found on our webpage on our return!

Finally, next year the Dr. Daley will be on sabbatical and so the lab will be empty of undergraduates for the first time. For much of the year, Dr. Daley will be working at UCSD in the X-ray crystallography laboratories of Professor Arnold Rheingold learning and mastering X-ray crystallography. However, you may think you see Dr. Daley constantly in his lab at USD completing some older research and beginning to develop new projects for fall 2014 and on. While you may think it is his physical form – it is not, so do not be offended if it keeps its head down and just works, ignoring you and everyone else. Oh and the music you think you hear from the Daley lab during that time, that is also just your imagination. In alumnus news; in the fall of 2012, Jessica Rodriguez and Eric Czer started their new careers in medical school and Lauren Bernier landed a nice job with Glanbia Nutritionals (NA), Inc.

As always, you can follow the Daley Group progress on our webpage at If you are a Daley Group alumnus, please contact Dr. Daley with updates so that we can keep your page up to date with all your latest and greatest exploits!


The De Haan group continues to look for reactions between compounds found in clouds and aerosol, looking for the fastest and “brownest” reactions possible in the atmosphere, funded by a grant from the National Science Foundation. In most fields of chemistry, brown products are what get thrown in the waste bottle, but in our group brown products get carefully analyzed. We want to find out more about what they are, why they form, and if they can form in the atmosphere, where they would absorb light and affect the climate.

Ryan Sueme has been studying the reaction of glyoxal and sulfur dioxide, both present in clouds, which react under the right conditions to produce a red benzoquinone and several other yellow and brown products.

Nazin Sedehi, Kat Millage, and high school intern Jonathan Bartolomucci have been characterizing the ability of aldehydes to evaporate from water droplets containing ammonium sulfate, a salt commonly present in clouds and aerosol.

Kat also did a detailed study of the 10 different forms that glycolaldehyde can take in aqueous solutions, gathering lab data in parallel with computations being done by Dr. Kua. She is completing her Honors thesis on these topics.

Michelle Powelson has mastered the differential scanning calorimeter and is using it to look for evidence of solid-like organic material formed by aldehyde – amine reactions.

Brenna Espelien is conducing linked UV-Vis and mass spectroscopic studies to indentify brown molecules produced in a variety of atmospheric aldehyde reactions.

Over the summer, Alyssa Rodriguez was a joint member of the De Haan and Kua groups, and did a combined computational/lab study of formaldehyde plus ammonium sulfate reactions.

Nazin Sedehi and Kevin Forey have continued electrospray mass spectrometry studies of aldehyde – protein reactions.

Created with GIMP on a MacFinally, Lauren Klein has continued the analysis of ancient pottery for cacao residue, a joint project with the anthropology department started by Don Millar. She has already found cacao residues on two vessels from USD’s May Collection and is improving her detection limits.

In December, Brenna, Michelle, Kat, Nazin, and Alyssa travelled with Dr. Galloway and Dr. De Haan to San Francisco to present their research at the annual fall meeting of the American Geophysical Union.

The De Haan group summer 2012 research crew. Back row: Dr. Melissa Galloway (postdoctoral researcher), Nazin Sedehi, Kat Millage, Ryan Sueme. Front row: Dr. De Haan, Michelle Powelson, Brenna Espelien, Alyssa Rodriguez.

Dutnall Group

My research lab studies the Hat1 acetyltransferase complex. This complex is involved in depositing histone proteins onto DNA to help package the enormous amount of genetic material inside the cell nucleus. It is also involved in regulating gene expression and DNA repair. The Hat1 complex consists of at least five proteins (Hat1, Hat2, Hif1 and two histones called H3 and H4). The Hat1 protein chemically modifies histones while Hat2 and Hif1 are histone binding proteins. Our overall goal is to assemble and characterize the entire complex so that we can understand the molecular mechanisms by which it modifies histones and how it contributes to regulating gene expression and DNA repair.

Our current work is focused on the Hif1 protein. Hif1 binds histones and can deposit them onto DNA and we are trying to understand the molecular basis for these activities. We can make the protein in bacteria and show that it binds histones. We know that the protein is a dimer (two identical copies of the protein stably associate) and we have mapped the region of the protein necessary for dimer formation. Students Michael Bagley and Stephen Szabo are working on mapping the region of the Hif1 protein required for histone binding and determining what structural features of histones H3 and H4 are important for this interaction. Michael is also trying to crystallize the Hif1 protein so that we can determine the structure of the protein via X-ray crystallography, using our X-ray diffraction system. Michael and Steve will present their work at the ASBMB national meeting in Boston this April.

Section of an Electron In a separate project, I have been working with student Lani May Centeno to determine the structure the serine protease enzyme trypsin via X-ray crystallography. This project involves exploring the operational capabilities of our new X-ray diffraction system to develop optimal procedures for using this instrument in teaching and research. Lani developed protocols for obtaining high quality crystals and has solved the structure of the complex at very high resolution using software packages that are highly amenable to teaching the theory and implementation of X-ray diffraction in an undergraduate setting. These have been used in a special topics course that I am teaching this semester. Lani will present her work at the ASBMB national meeting in Boston this April.

I have also been working with students from USD Traveling Scientists to bring hands-on learning activities to middle school students at a local charter school, the San Diego Global Vision Academy. This project is funded by a grant from the ASBMB HOPES project. I will be co-presenting our work with teachers from SDGVA at a workshop at the ASBMB national meeting in Boston this April. You can read more about my research and follow more news at my lab website:
Image Caption: Section of an electron density map (blue grid) of the trypsin structure showing details of a tryptophan amino acid side chain clearly delineated in the high resolution (1.3 Å) structure.

Dwyer Group

chemical structureDr. Dwyer’s group continues to study the structural implications of incorporating non-natural, non-hydrogen bonding nucleoside analogs into DNA duplexes. In 2012, we pushed forward on two projects: 1) In our ongoing collaboration with Floyd Romesberg at the Scripps Research Institute in which we are determining the solution structures (by NMR) of DNA duplexes containing a single 5SICS:NaM pair (see structure, right) and more recently a DNA duplex containing two 5SICS:NaM pairs side-by-side.

Our preliminary results on the duplex containing a single 5SICS:NaM pair was published in June 2012 (Nature Chemical Biology, 8, 612–614 (2012). Two students (Eric Arnold, Biochemistry ’14 and Joseph Avila, Biochemistry ’14) are working diligently on these structures currently. 2) In our investigation of the solution structures of hairpin DNA sequences containing the thymine analog difluorotoluene. We are particularly interested in sequences containing the T4 loop and understanding whether difluorotoluene stacks similar to thymine in the context of a loop. One student (Joel Feldman, Biology ’14) is working on this project currently.

Lastly, Dr. Dwyer is still involved in the digital-first General Chemistry e-book project along with my co-author Charles Grisham of the University of Virginia. Particularly rewarding for me in addition to working with Charlie is the opportunity to work with my former colleague Leigh Plesniak (who is writing end of chapter problems for us) and Mary O’Reilly (a current colleague in the department who is a talented scientific artist/illustrator and developing animations for us!)

Iovine Group

The Iovine lab continues to keep one foot in the small molecule synthesis world and one foot in the polymeric materials world. Our research is constantly evolving and hopefully moving toward a more interdisciplinary focus. Summer 2012 was extremely active with a great bunch of students working in the lab. The 2012 summer scholars include: Jeff O’Brien, Gabriel Short, Alex Skribin, Jerry Sorriano, and Drew Ilijevski. Seniors Jeff O’Brien and Gabriel Short traveled to Philadelphia in August 2012 to present their research at the ACS national meeting.  Their poster was well received and also selected for Sci-Mix. Both Jeff and Gabriel are still making decisions about graduate programs but hopefully the recruiting weekends will help crystallize their choices. Best of luck to both students!

Iovine GroupAs I look forward to 2013 I am excited about where our group is headed. Our polymer-based research has matured considerably and we are moving those projects in exciting directions. One other bit of exciting news is that Dr. Lisa Ryno will join the group as a post-doctoral scholar. Lisa obtained her Ph.D. from the Scripps Research Institute and will teach biochemistry in our Department during the fall 2013 semester. Welcome Lisa.

As always, I am eager to hear from Iovine group alumni; so many of you are doing great things. Please email or call!

Jeff O’Brien (left) and Gabriel Short (right) present their research at the ACS National meeting in Philadelphia in August 2012.

Malachowski Group

Dr. Malachowski’s work on synthesizing new dipyrromethenes ligands and binding them to metal ions continues to expand and his students have prepared large numbers of new, interesting compounds. The copper cobalt complexes of the dipyrromethenes are beautiful as they are brightly colored and highly crystalline. His students are becoming incredibly proficient at purifying and crystallizing metal complexes. We were able to solve the structures of quite a few new complexes this year and we have hundreds of crystallizations going on at all times in the lab. There are now four students working in the laboratory this semester. David Peters has been with us for over a year and is working on the most challenging compounds as their size and symmetry make them very difficult to solubilize and purify. Michael Perkins is making Schiff base complexes related to compounds he made last fall to see how their properties compare. Taryn Parsons and DeLora Faaborg are the newest members of the group and have made amazing progress in expanding our inventory of new dipyrromethene ligands and complexes. All four of the students are planning to present their work at USD’s Research Day Celebration this April, 2013.

Dr. Malachowski continues to travel extensively to conferences, gives talks on various campuses and offers workshops to campuses interested in doing more undergraduate research. Since last spring, he has traveled to Texas, New Jersey, Washington, Pennsylvania, Ohio, New York, Virginia, North Carolina, Oklahoma, Indiana, Idaho, Wisconsin, Nevada, Florida and New Orleans giving presentations. A good deal of this time was taken up by running workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities. This work continues to accelerate as he received a $175,000 supplement to his $1,000,000 grant from the National Science Foundation to work with state systems of higher education that are interested in doing more undergraduate research. This work has been extremely rewarding as he has been able to work with over 400 schools and 2,000 faculty and administrators and has raised the undergraduate research and USD flag to all of these participants.

Dr. Malachowski also has continued to pursue his work on the impact of undergraduate research on students and student learning and published a series of articles and chapters in books on this topic during 2012-2013. His most recent work appeared in the Carnegie Academy for the Scholarship of Teaching and Learning book series. In these articles, he argues strongly for the need for research that focuses on contributing to our disciplines along with having a positive impact on students and student learning.

Tahmassebi Group

Dr. TahmassebiDebbie Tahmassebi is on Sabbatical for academic year ’12-’13. She is spending this year as an ACE Fellow (American Council on Education). As a Fellow, she is working in the President David Burcham’s Office at Loyola Marymount University and visiting a variety of US and international institutions learning about current issues and leadership challenges in higher education.

Prior to the start of her Fellowship, she presented her research results at the Fluorescent Building Blocks and Biomolecules Conference in Gothenberg, Sweden (lots of water in Gothenberg pictured on left). Additionally, she visited Ramon Llull University/IQS in Barcelona, Spain and helped to coordinate a new study abroad opportunity there for chemistry, biochemistry and engineering students from USD.

Recent Faculty Publications - *undergraduate co-authors Back to top

Recent Publications from the Department

“Living in Parallel Universes: The Great Faculty Divide between Product-Oriented and Process-Oriented Scholarship”,Malachowski, M. R.,in Faculty Support and Undergraduate Research: Innovations in Faculty Role Definition, Workload and Reward, Carnegie Academy for the Scholarship of Teaching and Learning, 2012.

“A Fundamental Investigation of the Interaction of Petroleum-Relevant Organosulfur Compounds with TiO2(110)”, Benz, Lauren; Park, Aileen; Corey, Jenelle R.; Mezher, Michelle P.; Park, Victoria, Langmuir, 28, 10209, (2012).

“Iridium-Catalyzed, Substrate-Directed C–H Borylation Reactions of Benzylic Amines”, Roering, A.J.; Hale, L.V.; Squier, P.A.; Ringgold, M.A.; Wiederspan, E.R.; Clark, T.B. Organic Letters, 14, 3558-3561, (2012).

“KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry”,Betz, K.; Malyshev, D.A.; Lavergne, T.; Welte, W.; Diederichs, K.; Dwyer, T.J.; Ordoukhanian, P.; Romesberg, F.E.; Marx, A., Nature Chemical Biology, 8, 612–614, (2012).

“Employing Magnetic Levitation To Monitor Reaction Kinetics and Measure Activation Energy”,Benz, Lauren; Cesafsky, Karen E.; Le, Tran; Park, Aileen; Malicky, David, Journal of Chemical Education, 89(6), 776-779, (2012).

“Heterogeneous Glyoxal Oxidation: A Potential Source of Secondary Organic Aerosol”,Connelly, Brandon M; De Haan David O.; Tolbert Margaret A., The Journal of Physical Chemistry. A (2012) DOI:10.1021/jp211502e.

“Optical Properties of the Products of α-Dicarbonyl and Amine Reactions in Simulated Cloud Droplets”,Zarzana, Kyle J.; De Haan, David O.; Freedman, Miriam A.; Hasenkopf, Christa A.; Tolbert, Margaret A., Environmental Science & Technology (2012), 46(9), 4845-4851.

“Chemical modification of organosolv lignin using boronic acid-containing reagents",Korich, Andrew L.; Fleming, Andrew B.; Walker, Amanda R.; Wang, Jifu; Tang, Chuanbing; Iovine, Peter M., Polymer 53(1), 87-93, (2012).

“Cobalt substitution supports an inner-sphere electron transfer mechanism for oxygen reduction in pea seedling amine oxidase”,Mills, Stephen A.; Brown, Doreen E.; Dang, Kaitlyn; Sommer, Dayn; Bitsimis, Alexandra; Nguyen, Jennifer; Dooley, David M., Journal of Biological Inorganic Chemistry (2012), 17(4), 507-515.

“Thermodynamics and kinetics of imidazole formation from glyoxal and methylamine: a computational study”, J. Kua, H. E. Krizner, D. O. De Haan, J. Phys. Chem. A 115(9) 1667-1675, (2011).

“Formation of nitrogen-containing oligomers by methylglyoxal and amines in simulated evaporating cloud droplets”, D. O. De Haan, L. N. Hawkins, J. A. Kononenko, J. J. Turley, A. L. Corrigan, M. A. Tolbert, J. L. Jimenez, Environ. Sci. Technol. 45(3) 984-991, (2011).