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The Spin

Chair’s Column
Alumni: Save the Date
Student News
Alumni News
Student and Alumni Awards
Staff and Administrator News
Post-Doc Updates
Faculty News
Faculty Research Updates
Recent Faculty Publications

University of San Diego

Department of Chemistry
and Biochemistry

5998 Alcala Park
San Diego, CA 92110-2492
(619) 260-7512

www.sandiego.edu/cas/chemistry/

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Chemistry & Biochemistry

Chair’s Column

Debbie Tahmassebi
Artwork by Shannen Cravens '11

Like all others, this has been an exciting and eventful year. The students, staff and faculty in the department remain busy and continue to excel on many fronts. It is my great pleasure to share some of the department news from the past year.

In this issue, you will hear news from the department students, staff and faculty. Additionally, we love keeping up with our alumni and sharing some of their stories as well. For the first time this summer, the department will be hosting a multi-purpose alumni event on July 23rd. The department has changed dramatically since many of our alumni last visited and it'll be very exciting for everybody to reconnect.

In recent years, undergraduate research activity has grown tremendously in the department. Now, all majors graduate with at least a one-semester experience. The research experience helps to prepare students for when they graduate and attend graduate school in chemistry or biochemistry, enter a graduate health-professional program, join the local industry workforce or for whatever else they choose to do. In this edition of The Spin, you'll read about the research activities of faculty and students over the past year as well as student and alumni awards that have stemmed from these research experiences. The stories below represent just a sampling of the interesting and impressive work coming out of the department. Enjoy!

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Debbie Tahmassebi

debbiet@sandiego.edu

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Alumni: Save the Date

Saturday, July 23rd, 2011 – please join us for our very first Alumni Celebration/ Summer Undergraduate Research Fundraiser.  Come back to campus - catch up with friends over appetizers and drinks, meet the current faculty, tour the Shiley Center for Science and Technology, and learn the latest department news and the exciting research going on with undergraduates.  All alumni are invited to join us.  You will be hearing more soon and check the department website for information!

Student News

Chem Club

Chem Club

Chem Expo – L to R:  Shannen Cravens, Shimmy Gabbara, Jessica Tran, Dr. Christopher Daley, Sabrina Phillips, Molly McCluskey, and Phillip Guichet

This year, the USD Chem Club became an informational source to students, facilitated science club collaborations, and increased our presence in the community. We started off the year with a whirlwind of activities to celebrate National Chemistry Week, which included performing exciting demonstrations at ChemExpo, lab coat tie-dye, chips and guacamole, liquid nitrogen ice cream, a Halloween costume party, and the start of our new Careers in Chemistry seminar series. Thus far, Chem Club has invited a forensic scientist, a slew of professors with interests in art, NMR, and environmental chemistry, and we have hosted a biotech company career fair. Our biggest event to date was our Science & Tech Holiday Party where we collaborated with the Biology Club and Marine Science Club to host a cookie and ornament decorating social in the atrium. We had over 100 people attend! In honor of the International Year of Chemistry, Chem Club will be focused on its outreach activities in Linda Vista during 2011. During summer 2010, President Shannen Cravens wrote an ACS Community Interactions Grant and was awarded $300 to start a new outreach program. Phillip Guichet, the Chem Club Community Service Coordinator, has launched the new project, “The Traveling Scientists.” Students travel to local elementary/middle schools and host a lesson and hands-on experiment to promote science education for the underprivileged youth around USD.

Strawberry research

Traveling Scientists at Bayside – Kids had fun extracting DNA from strawberries

We kicked off the outreach initiative on March 2nd with a DNA extraction activity at the Bayside Kids After-School Program. On March 5th, USD hosted Expanding Your Horizons, a conference that aims to promote female interest in the pursuit of careers in the sciences. The members of the USD Chem Club took an active role in planning and hosting two of the workshops held at this event. The semester is far from over and Chem Club plans to continue staying active by running a coffee filter chromatography booth at the San Diego Science Festival (organized by Vice-President Alyssa Navapanich), working with our ACS Local Section to run an Earth Day booth, and collaborating with the Biology Club to celebrate National DNA Day on campus in April. We plan to finish off the semester with our first on-campus spring formal called “The Bucky Ball”, co-hosted by a number of science and pre-health organizations. You can now keep up-to-date on all of our activities at the new USD Chem Club website: http://sites.sandiego.edu/chemclub/

Research from Start to Finish – April Stanley ‘11

ResearchApril has been engaged in research since the first day she set foot in the department the summer prior to her freshman year. When she graduates this spring, April will have had experience in two different labs at USD as well as an internship in industry.  The strong connections that the Department has with our alumni and with local industry were important to her – read our recent interview.

How did you get involved with Pharmatek?  What got you interested in working there?

I participated in the PURE research program during the summer before my freshman year.  At the end of my sophomore year Dr. Tahmassebi had a reunion lunch with everyone else that had participated in the program, and I met a senior who, at the time was an intern at Pharmatek.  I had been doing research throughout the second semester of my freshman year and during the summer and fall of my sophomore year, but I didn’t feel a real passion about the research I was doing, but I knew I liked working in the lab, so I decided to try something new and my professors suggested an internship.  The student I had lunch with said she enjoyed working at Pharmatek, so a few months later I put in an application.  I came out of the Pharmatek interview feeling very excited, hoping they would hire me.  The atmosphere at the company was very positive and everyone that interviewed me seemed engaged and interested in the work they did, and were excited to share their experiences with me.

Can you describe a typical day at work?

The typical day for a Pharmatek intern is fairly busy.  I do everything from washing glassware to helping out in the initial stages of developing a formulation, to GMP testing of formulations in production, to stability testing once the formulation has been optimized.  We follow test methods, protocols and standard operating procedures for all of the tests that we do, and everything is recorded in a professional notebook.  Working in the lab is nice especially when everyone is working on something because we can all talk to each other and everyone is willing to answer any questions I ever have.

What do you enjoy most about working at Pharmatek?

The work that Pharmatek does is really interesting because you can see the development of a drug from an active pharmaceutical ingredient to an actual dosed tablet, capsule, or solution.  And it’s really great because the interns can be involved in almost every step of the process.  There are a number of experiments that we do on a regular basis (dissolution and water content testing of capsules or tablets), but I’ve also gotten exposure to a number of different types of technologies such as differential scanning calorimetry, thermogravimetric analysis, and lyophilization (freeze-drying).  Pharmatek also has capabilities of working with high-potent drugs, many of which are prototypes for cancer treatments.  I really like that you can get as involved in a project as you want to.  If you show interest in something, people will teach you about it and let you try new things.  I also like the fast-paced nature of the work that we do because I feel like there is constantly something new going on.  It’s also really cool to be able to look at the list of ingredients in my Tylenol and Motrin and know why each component is necessary for the drug to work effectively.

What advice do you have for current USD student considering finding similar internship possibilities?

I would say that students seeking internships should be willing to take a chance.  I remember accepting the offer at Pharmatek my sophomore year feeling like it was the biggest decision of my life.  While it is a big step to take on a job, you might end up really liking it like I did.  And if things don’t work out at your first internship, don’t be afraid to try another one.  I did research in two completely different labs on campus before I realized I wanted to try something outside of academia.  While I value the research experience I gained in the labs at USD, I knew that academic research wasn’t the only thing I could do with my major, and I wanted to find out what else I could do to see if I might like it better.  I questioned and struggled with my major for a while, but I shopped around a lot throughout my college experience and think that the freedom and opportunity to try out different things is one of the great things about being a college student.

Do you work with any current/former USD students at Pharmatek? Who?  What do they do?

There are actually a number of USD Alum and current students working at Pharmatek both as full-time chemists and interns.  Tim Murphy (’06), a USD alum is a full time Chemist II, and two other alumni- Jessi Cryder (’10) and Amelia Pedneault (’10) are both Chemist I’s.  Myself, Alyssa Navapanich (’11), Stephanie Wood (’11), and the newest addition to the team, Urszula Milewicz (’12) are all interns at Pharmatek.

What are your plans after graduating?

Ideally I would like to stay at Pharmatek.  I have really enjoyed the past two years and feel like I have gotten to learn a lot, but I know there is so much more to learn and grow in with the company.  If not at Pharmatek, I would like to pursue some sort of career in industry for the next year or two while I save up money and figure out if or what I would like to study in graduate school.

Can you think of a particular class and/or experience that had a big impact on your academic career?

All of the classes I have taken have been challenging, but I always enjoyed my labs more than anything.  I like the hands-on experience you get in lab.  I really enjoyed my analytical and instrumental labs because of the practicality of the experiments we did.  The projects we tackled in those classes connected the chemistry that I read about in textbooks to things I encountered in everyday life such as determining the actual amount of Vitamin C in orange juice, or the amount of a certain drug in store-brand vs. generic medicines.  The freedom that we are given with the instruments in the labs we take at USD is so valuable because there are too many people at the larger universities for them to be able to run their own tests.

Any other thoughts you want to share?

One other positive aspect about my internship was that I was able to use the research I did on one of the projects (once approved by the department) for the Chem 396W class research requirement.  I had to keep the names of the drugs we used confidential, but it was an interesting way for me to get to know more about the technologies and techniques we used to develop the formulation, as well as work on my scientific writing and presentation skills.  Both my supervisor and the professors were helpful throughout the process.

Bridges to Doctoral Institutions

In the Bridges to Doctoral Institutions, USD students work closely with faculty, post-doc and graduate student mentors in order to learn about and prepare themselves for graduate school.  The goal of this program is to increase the number of women successfully earning their Ph.D.’s in Chemistry and Biochemistry. 

In our first summer of this program supported by the Luce Foundation, Hadley Krizner ’10 and Caitlin Stevens ’10 were awarded funding to spend the summer engaged in research at a research-intensive university in order to prepare them for graduate school.  Hadley spent her summer at UCSD in Dr. Mark Thiemens’ lab.  She is currently a first year graduate student at UCLA.  Caitlin spent her summer working with Dr. Heather Maynard at UCLA.  Caitlin is also currently a first year graduate student at UCLA.  We wish them both much success in their graduate work and future careers.

In Summer 2010, current senior Shannen Cravens worked with Dr. Gabriele Varani at the University of Washington.  Her project entailed determining the solution structure of miR-21 and miR-18.  Shannen had a great summer and is spending this spring traveling the country assessing her many wonderful options and trying to determine which graduate school to attend. 

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Alumni News

The Joint USD-Scripps Training (JUST) for future faculty program offers fellowships to post-doctoral students to complete research at The Scripps Research Institute (TSRI) and mentored teaching at USD. The goal of the program is to prepare JUST Fellows for careers that involve teaching and research with undergraduate students. The progress of our two current fellows is below. We wish both Dr. Koudelka and Dr. Bumpus good luck as they start their careers as Assistant Professors this summer. Congratulations to both of them.

Alumni Biotech Map

Map

Click to view larger

Many of our alumni work in the local biotech/pharmaceutical industry after graduation.  We figured it would be fun to put a map together to illustrate the impact that our graduates have had in numerous companies.  Thanks much to alumni Stephanie Kishbaugh ’09 for her fabulous work on the map below.  If you work at a local company that is not represented in the map, please e-mail and let us know (Desiree Harpe e-mail:  dharpe@sandiego.edu).  This map is and will remain a “work in progress” and will be updated as often as possible. 

 

 

 

Alumni Highlight - Dr. Megan Boysen '02

Megan BoysenDr. Boysen earned her B.A. in Biochemistry with minors in Business Administration and Biology.  While an undergraduate, she worked as a laboratory assistant at The Salk Institute for Biological Studies and then worked as a Research Assistant at The Scripps Research Institute for a year prior to starting medical school.  She graduated from USD in 2002 earning the Outstanding Senior Award in the department. Dr. Boysen then completed her medical degree, graduating in the top 10% of her class and with distinction in research, at UC Irvine.  From 2007-2010, she was a resident at UCI in emergency medicine.   During that time, she was the American Academy of Emergency Medicine (AAEM) resident section national president and was chief resident.  After that, she spent a year on an Academic and Administrative Fellowship in the Division of Emergency Medicine at Stanford University Hospital.  She is starting a new position as an Assistant Professor and the Associate Residency Director for the Department of Emergency Medicine at UCI and also working on her Master’s in Health Professions Education (MHPE) through the University of Illinois, Chicago. 

How did you get your initial research position at the Salk Institute?  

Being lucky enough to live in San Diego for college gave me a number of institutes to choose from for research and job opportunities.  I worked at the Salk Institute during college and at the Scripps Research Institute (TSRI) the year between college and medical school.  Their respective websites have job opportunities for students as a "laboratory assistant" or a "research assistant." I applied, got the job, and was lucky enough to get matched up with a mentor who involved me in their research in addition to my duties of making lab agar plates and solutions.  From these jobs, I was able to get a couple of publications and conference abstracts before medical school.  USD faculty members also offer lots of opportunities for students for research.

With a strong background in research and clear continued interest, why did you decide to pursue an MD rather than a PhD?

I always enjoyed research, but, for me, it was a means of building a foundation for a career in medicine.  My goal was always to be involved in patient care.  During college, I also was a volunteer at UCSD hospital in the pediatric ward and post-anesthesia care unit. From these experiences, I knew that I wanted to translate the basic science into clinical care.  

How/why did you decide to study emergency medicine?  How does that mesh with your research interests?

I always wanted to be the type of physician who could take care anybody -- regardless of illness or ability to pay.  In emergency medicine, we're able to see any patient who walks through the doors. This is what drew me to the field.  Plus, we have the added bonus of doing shift work.  I'm never on call; which is nice for my personal life.  During medical school, I became involved in emergency medicine research, specifically looking at the use of ultrasound in pediatric trauma.  Although this research was different than the research I was doing as an undergraduate, the same basic principles of research applied (statistical analysis, constructing effective studies, etc).  I think it's important for an undergraduate to obtain a foundation in research.  Regardless of the subject, it's important to know research’s basic principles.

What is the purpose of pursuing a Master's in Health Professions Education (MHPE)?

The MHPE Master's in Education is geared toward people in the health professions (dentistry, medicine, nursing, etc).  My position as an Associate Residency Director requires me to be able to teach residents and medical students about emergency medicine.  I’m using this degree to further my research abilities in medical education and to be a better teacher for my residents and medical students.

What hints do you have for current pre-med students at USD?

The process of applying to medical school is a little bit tricky.  It's much easier to get into medical school with an excellent GPA than with a mediocre GPA.  The hard thing about this is that it makes you decide on a career when you’re only a freshman in college!  So, if you’re considering going to medical school, make sure you really focus on your grades before you do anything else.  If you’re having trouble, meet with your advisors regularly to identify the problem before it’s too late.

If your early grades in college suffered a bit, you may consider doing a post-bach program.  This is a program offered by many medical schools.  It allows you to take medical school classes to strengthen your academic foundation and to prove to medical schools that you can “cut it.”

Once you feel comfortable with your time management, then I would recommend volunteering at a hospital, getting involved in research, or getting involved in some other volunteer experience/on-campus activity.  Take your involvements seriously, and do them well.  Medical schools would rather have you do a few things well, than many things second-rate. 

Make sure you are ENJOYING this time, though.  When else are you going to be able to live in San Diego and have awesome chemistry professors?

What activities/experiences at USD best prepared you for medical school?

I learned how to study (and made sure I enjoyed doing it)! The best way you can be prepared for medical school is to manage your time effectively and study effectively.  Also, try to get some sort of experience in the hospital so you can make sure medicine is the right career for you.

You were awarded a BP Foundation full-tuition scholarship for medical school.   On what basis was the award made?  Did you complete medical school with no debt?

There is a wonderful scholarship foundation called Santa Barbara Foundation.  I was eligible for scholarships from them because I grew up in Santa Barbara County.  They granted me the BP scholarship on the basis of academic merit.  While I do have some school loans, they're significantly reduced from what they could have been.  The average medical student graduates with $150,000 to $200,000 worth of debt!

In your new position as Associate Residency Director at UCI, will that be a completely administrative position or will you also be practicing medicine?  How did you decide to head in this particular direction?

Part of my position will be administrative (overseeing residents, helping select medical students for our residency programs, working with other departments within the hospital), but the majority of my position will be clinical.  In other words, the majority of the time I will be working shifts in the emergency department with residents to take care of patients.

 As an emergency physician, one can get a job in the “community” or in “academics.”  I’m choosing a career in academics because I enjoy working with residents, being involved in their education, and conducting clinical research in an academic setting.

What are your interests outside of medicine?  What do you do in your spare time?

I LOVE to get up to the mountains, lake, or river with my fiancée. Sometimes it’s a little hard to find time to get away, so I enjoy the little things like eating non-hospital food, spending time with my family and friends, and wedding planning.

Any others information/pearls of wisdom you think would be interesting/valuable to current students?

I’m so thankful to my education at USD! I was so lucky not to be just another student in a large lecture hall.  I felt so prepared for medical school.  While I was learning about chemistry and biology, USD developed me as a person and developed my faith.   

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Student and Alumni Awards

2011 Student Leadership Award Shannen Cravens '11

Shannen Cravens was awarded the 2011 Student Leadership Award from the American Chemical Society's (ACS) Committee on Education Task Force on Undergraduate Programming. The program recognizes emerging leaders and helps them prepare for leadership opportunities at volunteer organizations and in their professional career. Her award is based on contributions she made to the ACS through her role as a chemistry club officer. Shannen enjoyed an all-expenses paid trip to Fort Worth, Texas, over Intersession to attend the 2011 ACS Leadership Institute, where she participated in a development course titled "Engaging and Motivating Volunteers."

Hayes Scholarships Alyssa Navapanich '11 and Michael Harlander-Locke '12

June 2003 marked the grand opening of the Donald P. Shiley Center for Science and Technology and the retirement of Alice B. Hayes, Ph.D., as president of the university.  As part of the opening of the Shiley Center, a scholarship fund in honor of Hayes was established in support of sophomore and junior level students who display merit (a minimum cumulative GPA of 3.25) and who are majoring in Biology, Chemistry, Biochemistry, Marine Science, Environmental Studies, or Physics.  Alyssa received an award in 2010 and Michael in 2011.

2010 Iota Sigma Pi Scholarship Shannen Cravens '11

Shannen Cravens was awarded a $2,000 Iota Sigma Pi Gladys Anderson Emerson Scholarship. The award is given annually for Excellence in Chemistry.  Shannen was one of two students awarded this prestigious national scholarship.

2010 Noyce Award Alyssa Navapanich '11

The USD Noyce Scholars Program, funded by the National Science Foundation, is a collaborative project between the University of San Diego’s College of Arts and Sciences and School of Leadership and Education Sciences (SOLES) as well as San Diego County school districts.   The goal of the program is to produce much-needed highly-qualified secondary science and mathematics teachers for California schools. With funding from the Noyce award, Alyssa will be completing her Master’s in Teaching Education next year at SOLES and plans to teach high school Chemistry – lucky students!

2010 Alcala Award Ryan Brennan '10

Ryan was recognized at the 2010 Commencement as a recipient of the Alcala Award.  The award is given out to a graduate who has excelled in scholastic achievement, leadership in academic and extracurricular activities and service to the university community.  Ryan completed a degree in Biochemistry, was the President and founder of the USD Dental Club, chief photography editor of The Vista, a pre-dental peer advisor and ambassador, the historian for Mortar Board, a member of the National Society of Collegiate Scholars, a member of USD’s Ambassador’s Club, a member of intervarsity surf club and a senior resident assistant.  Additionally, he was involved in undergraduate research with Dr. Bob Dutnall.  Ryan is currently a first-year dental student at UCLA.

Graduate Fellowship Ashley Corrigan '09

Ashley Corrigan was awarded an Office of Science Graduate Fellowship from the Department of Energy to support her research at The Scripps Institution of Oceanography.  Ashley is working with  Professor Lynn Russell in the Atmospheric Aerosol Group.  This very prestigious Fellowship was awarded to fewer than 5 % of applicants.

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Staff and Administrator News

We are so lucky to have such dedicated and excellent staff and administrators in the department.  There are a tremendous number of students taking chemistry and biochemistry classes.  Preparing for those classes and keeping our instruments up-to-date and working are critical jobs.  Sharon Ferguson, Jessica Kramer and Danny Rillera coordinate with the Directors to prep all of the labs, supervise work-study students and much more.  Dr. Hélène Citeau facilitates the purchase of new instruments, maintains our current holdings and helps faculty develop new instrument grant proposals.  Some details of their work are described below.

Lab Curriculum Updates

During the last year in Biochemistry and Biophysical Chemistry, some new labs were developed and some older ones were optimized. Sharon facilitated the development of techniques for purifying proteins from raw materials, such as Lysozyme from egg whites and Lactate Dehydrogenase from Chicken meat.  She also prepared the peptides and phospholipids for student identification using mass spectrometry and NMR. An increase in the number of students interested in taking general chemistry necessitated the addition of four new sections of 151L and 152L during the fall and spring semesters this year. The department recently purchased a new atomic absorption spectrophotometer just in time for 151L students to use for the determination of zinc in Vitamin water, which helped Jess keep the labs running smoothly.  Danny has kept busy ordering chemicals for organic and upper division labs as well as ordering the cryogens, feeding the NMR magnets, and providing safety training to research students.

News from the Scientific Instrument Front

Undergraduate Chemistry & Biochemistry students are the main users of our department’s Scientific Instruments Facilities, which contain over $2 million in state-of-the-art equipment. Most scientific instruments held by our department were purchased in 2003, with a few being from the previous century. As a consequence, one of the challenges of our department is to keep its pool of scientific instruments functional and up to date. To assist in this task, the Chemistry & Biochemistry department is staffed with a dedicated Scientific Instrument Specialist, who can support research and teaching activities by providing advice, training, technical assistance and access to advanced scientific equipment. 

Among the latests acquisitions purchased through a combination of Department, University and faculty research funding are a new atomic flame absorption spectrometer, heavily used by general chemistry, analytical chemistry, and instrumental analysis classes. Another new acquisition is the gel permeation chromatograph, to characterize polymers based on their size. The department also recently purchased a suite of state-of-the-art thermal analysis instruments including a differential scanning calorimeter and a thermal gravimetric analyzer.

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Post-Doc Updates

Supported by external funding, faculty in the Department recently started incorporating post-doctoral fellows into their research with undergraduate students.  At USD,  post-docs have the opportunity to prepare for a career at a Primarily Undergraduate Institution (PUI) by teaching our students in the classroom and working with them in teaching and research labs.  Our students benefit from their recent experiences in graduate school and their enthusiasm about undergraduate education.  Over the past few years, we have hosted two excellent post-doctoral fellows in the department.  We are excited for both of them as they prepare to begin their careers as Assistant Professors this fall.  Congratulations to both Dr. Lelia Hawkins (Harvey Mudd) and Dr. Andrew Korich (Grand Valley State) – we will miss you!

Dr. Lelia Hawkins

Even after a few weeks as a new postdoc at USD, I knew I made the right choice. The faculty here went out of their way to welcome me, to give me advice on applying for jobs and grants, and to offer encouraging words during the days leading up to my first classes. My summer was spent preparing lectures and mentoring undergraduate researchers in the De Haan lab. Neither of these would have been possible as a postdoc at a large university. When jobs became available in August, I began receiving mail from Dr. De Haan, Dr. Tahmassebi, and many others in the department who were eager to help me make the transition to tenure-track faculty member. Although my teaching experience was limited to only a fraction of a semester at the point of submitting applications, I was able to prepare an application tailored to meet the needs of a chemistry department at a small, undergraduate college. Most notably, my research proposal was geared toward projects that could be successful with undergraduate students while generating interest among the atmospheric chemistry community. Finally, the faculty at USD had many professional connections to other top-notch chemistry departments, giving me an extra, more personal advantage when speaking with potential employers. I have no doubt that my experiences at USD gave me the necessary skills for attaining a faculty position, and I am excited to put those skills to work in the coming years.

Dr. Andrew Korich

When I came to USD in 2009 to work with Professor Iovine, I had one goal: to find a faculty position at a primarily undergraduate institution (PUI).  Like many, if not all postdocs, my position centered on research, but unlike the “traditional” postdoc, I had the ability to mentor and teach undergraduates.  While working alongside Prof. Iovine, I quickly became aware of the joys and challenges that come with running an undergraduate research group.  I became acutely aware of the dedication required by faculty to develop projects, train undergraduate researchers, and navigate student schedules. I also saw the “light-bulb” moments that make undergraduate research so exciting and rewarding.  

My position at USD allowed me to develop a greater understanding and to gain first-hand experience of the delicate balancing act between research and teaching.  The entire faculty at USD provided a support network as I taught Organic Chemistry for the first time.  They offered their own lecture notes and provided valuable feedback on exams and quizzes. More importantly, however, the faculty allowed me to grow as an educator. 

This past fall, as I was going through the application process for faculty positions, I developed a deeper appreciation for the help and support that Prof. Iovine and the entire faculty at USD had given me.  As a result, I felt confident during interviews, to answering questions on how to balance research objectives with teaching loads, what my teaching style is, and what type of educator I aim to be.   Although I am extremely excited about my upcoming move to Michigan, I am sad to be leaving the Iovine group, the department, and USD.

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Faculty News

The Intersection of Science and Art

Science and ArtAdjunct faculty member Dr. Mary O’Reilly has just finished illustrating a collection of chemistry poetry written by former graduate school classmate Dr. Mala Radhakrishnan, an Assistant Professor in the Chemistry Department at Wellesley College. Dr. Radhakrishnan began writing humorous chemistry poems for her high school chemistry students before she entered graduate school. Since then, she has completed an entire collection of poems, now compiled in the book “Atomic Romances, Molecular Dances”, which encompasses general, organic, inorganic, physical, and biological chemistry. In addition to teaching chemistry, Dr. O’Reilly is a freelance science illustrator, so when a mutual friend got them together for this project, it was an ideal collaboration. Dr. O’Reilly chose a poem to illustrate from each of the fourteen chapters, and designed the cover and layout for the book. The poems were written to be an educational resource, conveying chemical concepts accurately. However, unlike the real world, the atoms endure such struggles as making friends, finding love, and pursuing their dreams. “Atomic Romances, Molecular Dances” will be available from Lulu.com and Amazon.com this spring. More of Dr. O’Reilly’s illustrations can be found at www.oreillyscienceart.com.

TV Star In Our Midst

Dr. Lauren Benz went on the set of our local NBC San Diego news team on Dec. 9th, 2010 during the burning of a house in Escondido which was found to contain large quantities of self-made explosives.   She provided expert commentary related to the explosive material, HMTD, found in the home.  Currently, the safest way to remove a high density of sensitive explosives such as HMTD is to employ a controlled burn.  This method was used on the home in Escondido in order to prevent risk of accidental detonation of any material left in the home.   To check out a video of her during the live broadcast, go to: http://www.nbcsandiego.com/news/local-beat/Raw_Video__Bomb_House_Burns_San_Diego-111616899.html

Outreach Activities with local Catholic high school

Catholic High School

Dr. David De Haan working with two students from Mater Dei High School

The ALSAM foundation continues to support an innovative educational project between the University of San Diego and Mater Dei Catholic High School.  Mater Dei Catholic High School, located in Chula Vista CA, maintains a Science Academy program for students interested in a more intense scientific experience.  USD was funded by the ALSAM foundation to support Mater Dei’s Science Academy program and help shape the curricular direction of the program.  Several faculty members from the Chemistry and Biochemistry Department have contributed to the program by delivering hands-on workshops to Mater Dei Science Academy students.  In addition to academic year workshops, Mater Dei students also have the opportunity to conduct summer research in the labs of USD science faculty.  The program, facilitated by Dr. Iovine, continues in 2011 and we are grateful to the ALSAM foundation for supporting such an important program.

National Leadership in Undergraduate Research

Along with two colleagues and the Council on Undergraduate Research, Dr. Mitch Malachowski was awarded a $1,000,000 grant from the National Science Foundation to help improve the quality of undergraduate science, technology, engineering and mathematics (STEM) education.  This grant is a follow-up to a very successful $500,000 NSF grant that was used to assist 90 different universities who wanted to imbed more undergraduate research on their campuses.  The new grant focuses on entire state university systems and private and public consortia.  Over the course of the next three years, Dr. Malachowski and his colleagues will offer 12 weekend workshops for up to 100 universities.  After a highly competitive selection process, the California State University System, the University of Wisconsin State System and the Council on Public Liberal Arts Colleges (COPLAC) are the first of six awardees that have been chosen to participate. 

All of the awardees will work to build and enhance a culture that supports undergraduate research at the institutional and system/consortium level. The workshops will assist participants in articulating goals for institutionalizing undergraduate research, as well as developing strategies to achieve these goals on each campus.  As Dr. Mitch Malachowski said in their recent press release, “undergraduate research is one of the most powerful educational experiences students can have. It helps move them from studying a subject to becoming an active participant. This grant will allow us to display to institutions the wonders of undergraduate research and strategies – and to overcome the challenges. Our goal is to support campuses that are committed to achieving more active forms of learning.”  During the workshop participants will also be developing an integrated approach for initiating and sustaining faculty-student collaborative or mentored undergraduate research across the system/ consortium.

Ephraim P. Smith, Executive Vice Chancellor and Chief Academic Officer, California State University notes the large scale impact the participation of the CSU team members will have on the system, “as the largest public baccalaureate degree-granting system in the country, CSU is committed to educating more students to enter careers in the Science, Technology, Engineering, and Mathematics (STEM) fields.  We know that undergraduate research is a proven strategy to increase student retention, graduation, and success, and can be particularly effective for groups underrepresented in STEM.  That makes our selection for the prestigious CUR workshop opportunity an exciting development for us.” 

Rebecca Martin, Senior Vice President for Academic Affairs at University of Wisconsin System has expressed how excited the team from Wisconsin is to get started and stated “this workshop is an excellent opportunity to further the work that we are doing across the University of Wisconsin System to institutionalize undergraduate research.  There is a steadfast commitment on the part of the UW System leadership to facilitate and sustain undergraduate research for two very intentional reasons:  it is a high impact practice for achieving excellence in education and a high impact practice to revitalize regional and state economies.” 

William Spellman, Director of the Council of Public Liberal Arts Colleges acknowledges the considerable impact the workshop will have on COPLAC, “the Workshop Program will allow over ninety faculty members at twenty-three member campuses of the Council of Public Liberal Arts Colleges to strengthen collaborative efforts in the high-impact practice of undergraduate research. This workshop will have a long-term impact on the public liberal arts sector across the U.S.”

Dr. Malachowski already has coordinated over 40 weekend workshops for CUR so he is well equipped to lead this effort.  He will coordinate putting together the curriculum for the workshops, will design the weekend activities, will deliver the lectures and will work with the system offices to coordinate the follow-up activities.  He has published broadly in the area of undergraduate research and is invited to many campuses to deliver talks/workshops on the value of these activities.  

Book Club

If you are looking for a good book to read…

Book ClubThis past fall, Ms. Debbie Finocchio organized a community of students, faculty, and staff from the Dept. of Chemistry and Biochemistry to get together to discuss, “In Defense of Food: An Eater’s Manifesto,” by Michael Pollan.  This book takes a look at the fascinating evolution of the American diet and the idea of “nutritionism”– our culture’s focus on basing our diet on nutrition labels rather than on whole foods.   Pollan encourages readers to “Eat food. Mostly plants. Not too much.”  This book club was inspired by the success of a previous book club held last year, also organized by Mrs. Finocchio, in which “Napoleon’s Buttons: 17 Molecules That Changed History,” by Penny Le Couteur & Jay Burreson was read and discussed.   These evening discussions took place in the comfortable faculty reading room in the Shiley Center for Science and Technology, giving students and faculty the opportunity to relax a bit together around wonderfully themed dinners featuring particular spice molecules and “real food” with minimal added components (like fillers and preservatives) and minimal packaging waste.

Book ClubThis semester, Dr. Lauren Benz has organized a book group to read and discuss “Why So Slow?” by Virginia Valian. This book addresses the effect of gender schemas on the professional advancement of women and men, presenting research on the topic from a range of perspectives.  The book presents interesting findings from biological studies, as well as eye-opening observational and experimental data.  Finally, potential remedies are discussed.

Students have been very excited and engaged in these clubs as noted by comments we have received including the one below:

Jennifer Fleischmann ‘11:  I cannot express my appreciation for the In Defense of Food book club this semester. The book itself was wonderful and engaging. I constantly looked forward to our meetings. We were able to discuss the book and related topics in a way that was relevant to all attendees. We were also able to bond over meals which reflected the themes which were raised in the book. The meetings provided a wonderful forum for students, faculty, and staff to mingle in a casual environment outside of the classroom. 

All of these events were made possible by USD EFSI grants (Enhanced Faculty-Student Interaction).

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Faculty Research Updates

Benz Group

Benz Group

L to R:  Aliza Cruz, Dr. Lauren Benz, Aileen Park, Tran Le and Karen Cesafsky

The Benz lab is now up and running and in full swing!  Current group members include Karen Cesafsky (’11), Tran Le (’13), Aileen Park (’14), Aliza Cruz (’11), and Di Pham (’11).

Karen, Tran and Aileen have been busy at work exploring the use of magnetic levitation to investigate solid phase reaction kinetics.  They have made significant progress in demonstrating the feasibility of this technique for monitoring reaction rates as a function of temperature.  Their work will be presented at this year’s Creative Collaborations in April, as well as at the American Chemical Society’s National meeting in March.

Aliza and Di are using thermal desorption to explore the chemistry between benzenethiol and a titanium dioxide surface.  Benzenethiol is a representative compound for the heteroatom structures present in petroleum.  The existence of heteroatoms (non-hydrogen, non-carbon atoms) is problematic when burning petroleum as it leads to the formation of harmful pollutants such as nitric and sulfuric acid.  We are interested in understanding the chemistry of this system in order to gain a broader understanding of defect-driven reactions on reduced titanium dioxide surfaces.  We recently were awarded an ACS Petroleum Research Grant for this work which enabled us to purchase an X-ray photoelectron spectrometer.

Bolender Group

The past year has been very productive in the Bolender Lab.  Ashley Cobb (Biochem ’10) and Denise Do (Biochem ’10) graduated in May 2010, and spent part of the summer finishing their projects on blue crabs and white clams from Magdalena Bay.  During my sabbatical in the 2011-12 academic year, these projects, along with several others will be written up for publication.  Shane Smith (Bio ’12) continued his work on heavy metals in blue crabs from Magdalena Bay, and this will become his Honors Thesis in Spring 2012.

Alana Calise (Chem ’11) has been analyzing samples collected in Mbarara, Uganda.  I did not take a group to Uganda this past January.  My collaborator, Dr. Anita Hunter, left USD to take the Dean’s position in the Nursing School at Dominican College, so we are in the process of reevaluating the direction of the scientific work. 

The nanocrystal side of my lab has taken a step in a direction that will hopefully lead to marketable materials.  Erica Hewitt (Chem ’09), Taylor Caldwell (Biochem ’11) and Scott Belding (Chem ’11) have been able to determine the chemical parameters that determine the size distribution of the various nanocrystalline materials. We currently have three different materials that we are working with, and all have excellent potential to applied in the biomedical field.  I will be spending the majority of my sabbatical working on this project to bring it to fruition.

Daley Group

Another year and a new batch of eager students joined the Daley Group!  Last Spring we said goodbye to Jessica Cryder, Kyle Cordova, and Grant Ferrell, as they all graduated, leaving Lauren Bernier as the only member who remained from spring ’10.  However, the group grew again with the additions of Jessica Rodriguez, Daniel Huh, and Eric Czer during the summer ’10 and the return of Amber Vitalo in fall ’10.  As of spring ’11, we have added another four members to the fold: Emily Prieto, Daniel McCourt, Hillary Hawkins, and Kimmi Cordova, bringing our total to 9 current members (wow!). We have a very full lab and hopefully it will lead to a fun and productive year.

Daley Group

L to R: Row 1 - Lauren Bernier, Jessica Rodriguez, Kimmi Cordova, and Emily Prieto. Row 2 – Dr. Daley, Daniel Huh, Danielle McCourt, Eric Czer, and Hillary Hawkins. Amber Vitalo was unavailable for the picture.

On the research front, we published our first major paper (Dalton Transactions 2010, 39(44), 10671) on the preparation of complexes that contain our designed chiral ligands bound to zinc.  This project has succeeded largely thanks to the tremendous efforts of Jessica Cryder and her crystal growing abilities! We also published work on a series of platinum complexes that Kyle Cordova and Ryan Haywood (’09) contributed to (Inorganica Chimica Acta 2011, 368, 74) and we have submitted another paper on the synthesis and characterization of our nitrile hydratase synthetic analogue (our first paper on this project), to Lauren Schopp (’09), Amber Vitalo, and April Stanley made significant contributions to.    

While we did not go to an ACS meeting this past year, the Daley Group plans to have a good representation at the summer meeting in Colorado (August 2011).  At the meeting, our plan is to have several of the current group members present their work at a poster session.  Look to next year’s SPIN for a report on our mile high fun. You can follow the group’s progress (including each individual research member) on the Daley Group Webpage at http://home.sandiego.edu/~cjdaley/.  On that note, if you are a Daley Group Alum, please contact Dr. Daley with updates so that we can keep your page up to date with all your latest and greatest exploits!

De Haan Group

The De Haan group has been developing new analytical methods this year in order to study the formation of light-absorbing materials by atmospheric reactions in clouds and aerosol. Postdoc Lelia Hawkins has transformed the particle chamber into a system that can measure the time-dependent interaction of particles with water vapor, which Molly Baril is now using for experiments with aldehydes, amines, and ammonia salts. Kevin Forey and Tseday Siyoum are working to measure reaction rates of aldehydes with protein side chains, while Kristin Sullivan measured reaction rates of aldehydes with amino acids. Dr. Hawkins, Alec Rynaski, and Michelle Powelson presented posters of their research on March 3 at a local atmospheric chemistry conference at UC Irvine. Finally, Don Millar is working on a joint project with the department of anthropology to measure the chemical residues of chocolate on 700-year-old pottery artifacts.

De Haan

The De Haan group enjoys a hazy afternoon on the balcony of the Shiley Center for Science & Technology.  L to R:  Dr. Lelia Hawkins, Kevin Forey, Don Millar, Dr. David De Haan, Michelle Powelson, Kristin Sullivan, Molly Baril.  Not pictured:  Tseday Siyoum, Alec Rynaski

Over the past summer, Isabel Stonehouse, a student from Mater Dei high school, worked with Jake Turley to explore the reactions of hydroxyacetone and glycerol with amine and aldehyde compounds in clouds and aerosol.  Alec Rynaski looked into the formation of light-absorbing compounds in the glyoxal + SO2 reaction system.  Stephanie Wood and Julia Kononenko measured the ability of aerosol formed from methylamine + aldehyde mixtures to evaporate. Tseday, Jake, Stephanie, and Julia are all scheduled to graduate this year! 

Julia, Jake, Ashley Corrigan (’09), Grant Ferrell (’10), and Kyle Cordova (’10) were co-authors on publications from the De Haan group this year.  The first was a paper summarizing our work on the atmospheric reactions of methylglyoxal:  D. O. De Haan, L. N. Hawkins, J. A. Kononenko,* J. J. Turley,* A. L. Corrigan,* M. A. Tolbert, J. L. Jimenez, “Formation of nitrogen-containing oligomers by methylglyoxal and amines in simulated evaporating cloud droplets.”  Environ. Sci. Technol. 45 (3) 984-991(2011)

The second was a paper from summer work in Margaret Tolbert’s group at CU Boulder on the chemistry of Mars:  R. V. Gough, J. J. Turley,* G. R. Ferrell,* K. E. Cordova,* S. E. Wood,* D. O. De Haan, C. P. McKay, O. B. Toon, M. A. Tolbert, “Can rapid loss, high variability of Martian methane be explained by surface H2O2?”  Planet. Space Sci. 59 (2-3) 238-246 (2011).

Dutnall Group

My research group focuses on how DNA is packaged in cells and how this regulates cellular processes such as gene expression. Our paper describing improved methods for making histone proteins in bacteria was published in Protein Expression and Purification in May (Anderson, M., Huh, J.H., Ngo, T., Ing, A., Hernandez, G., Pang, J., Perkins, J. and Dutnall, R.N. Co-expression as a convenient method for the production and purification of histones in bacteria. (2010) Protein Expr. Purif. 72: 194-204. doi:10.1016/j.pep.2010.03.013) and was presented as a poster at the annual meetings of the American Society of Biochemistry and Molecular Biology and The Protein Society in April and August. I also recently presented a seminar on this work at the CHI PepTalk Symposium in San Diego. There has been a lot of interest in this work from other researchers as it provides a more convenient way to make raw materials to study chromatin structure and function.

Dutnall
L to R:  Michael Bagley, Shimmy Gabbara, Ali Bigeh and Elyssa Pickle

My lab has grown to four students. Ryan Brennan (Biochemistry 2010) graduated and was recipient of the USD Alcala Award in recognition of his achievements as a student at USD and we wish him well as he pursues his graduate studies at the UCLA School of Dentistry. Continuing members Elyssa Pickle and Allison Bigeh have now been joined by Michael Bagley and Shimmyram Gabbara. Michael and Shimmy joined as pre-freshman in summer ’10, supported by the USD PURE program, and are currently working on developing further improvements and extensions to our histone production methods. Elyssa and Allison are working on the Hat1 histone acetyltransferase complex, an enzyme complex that consists of five proteins (Hat1, Hat2, Hif1 and two histones called H3 and H4), and that chemically modifies histones and helps package DNA. They are working on the Hif1 protein and have made excellent progress towards understanding how this protein interacts with histones. Elyssa will leave the lab when she graduates in May but will continue to pursue her research interests this summer at an external research institution as part of the Bridges to Doctoral Institutions program. We have also overcome major technical challenges to be able to make the Hat2 protein, a key component of the complex that helps to tie all the pieces together. So we are now able to make all the components of the Hat1 complex and our studies are currently focused on assembling and characterizing 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. You can read more about my research and follow more news at my lab website: http://home.sandiego.edu/~rdutnall/

Dwyer Group

My research group continues to explore structure and recognition in DNA duplexes containing non-natural nucleobase mimics.  In 2010 we had one paper published on this project led by the efforts of Shannen Cravens (’11) with strong contributions from Alyssa Navapanich (’11) we determined that the DNA binding drug actinomycin D indeed recognizes (and binds tightly to) a sequence containing a non-natural nucleobase, however the orientation of the drug is 180° opposite of the orientation in the duplex containing the natural bases.  See “NMR Solution Structure of a DNA-Actinomycin D Complex Containing a Non-Hydrogen Bonding Pair in the Binding Site”, Cravens, S.L,*; Navapanich, A.C.*; Geierstanger, B. H.; Tahmassebi, D.  C.; Dwyer, T. J., J. Am. Chem. Soc., 132, 17588-17598 (2010) for all the details.  Alyssa also completed work on the NMR solution structure of a novel DNA duplex containing a non-natural guanine mimic (that we call “H”) and Hannah Sadler (’12) has been working to predict by computational methods the stable conformations in the “H” containing duplexes.  Our collaborative work with Floyd Romesberg at the Scripps Research Institute exploring structure and function in a DNA duplex containing an optimized non-natural base pair was also published in 2010: Malyshev; D. A., Pfaff, D. A.*; Ippoliti, S. I.*; Hwang, G. T.; Dwyer, T. J.; Romesberg, F. E.; Chemistry – A European Journal, 16(42),12650–12659 (2010).  We’ve begun a new project to use NMR relaxation measurements to study dynamics in small molecules of biological relevance in collaboration with Leigh Plesniak.  Brogen Atkinson (’13) is working on the small cyclic ionophore nonactin as a model system and making great progress.  Finally, my wonderful co-author Charlie Grisham (University of Virginia) and I have produced many new chapters of content for the General Chemistry e-text under development with W.H. Freeman. 

Iovine Group

The Iovine research group traveled to San Francisco in the spring of 2010 to attend the ACS national meeting.  Two research veterans, Chris Hincke and Caitlin Stevens, presented a poster inside the ACS Division of Polymer Division.  Abe Ichinoe and Amanda Walker also attended the meeting and continued their research during the summer of 2010.  Kristiana Lehn worked across disciplinary boundaries spanning both the Iovine lab and the Bird lab (USD Biology).  Lastly, Ramez Nasry conducted research during the summer of 2010 and continues to pursue research in the spring semester.

Iovine Group

L to R:  Andrew Fleming, Dr. Andrew Korich, Jeff O’Brien, Dr. Peter Iovine, Austin Apramian, Michael Higgins and Amanda Walker (not pictured:  Abe Ichinoe, Kristiana Lehn and Ramez Nasry)

Our group continues to develop expertise in the area of polymeric materials including new collaborative projects focusing on antimicrobial materials and starch-based biomaterials.  Christopher Hincke and Caitlin Stevens graduated in the spring 2010.  Chris is currently attending the University of Washington where he has joined the Totah lab.  Chris is pursuing a Ph.D. in medicinal chemistry focusing on the role of bisphosphonates in osteonecrosis.  Caitlin Stevens has moved on to UCLA where she is pursuing a Ph.D. in organic and materials chemistry.  Caitlin splits her time between the Yaghi and Rubin research groups.  Best of luck to both Chris and Caitlin!

Michael Higgins, Austin Apramian, Jeff O’Brien, and Andrew Fleming all joined the group in the spring of 2011.  We greatly expanded our research capabilities by acquiring a differential scanning calorimeter (DSC) and a thermogravimetric analyzer (TGA).  Several of our projects are mature enough to yield meaningful results so we are looking forward to an exciting year in the lab.

Dr. Andrew Korich, the first postdoctoral fellow in the Iovine lab, will begin his academic career in the fall 2011 at Grand Valley State University.  Grand Valley is a primarily undergraduate institution located in Grand Rapids Michigan.  Andrew will be greatly missed but he will carry forward the traditions of the USD Chemistry and Biochemistry Department as he begins his independent academic career.  Best of luck Andrew!

Kua Group

The Kua research group has made progress in several fronts. Work by Hadley Krizner ('10) on understanding the reaction of glyoxal and amines to form imidazoles is currently in press and will appear in the Journal of Physical Chemistry A shortly. Lorenzo Bautista ('11) has made good progress in parameterizing the torsion angles for boroxines for use in a reactive force field after completing the quantum chemical calculations of the torsional barriers. Lorenzo also completed a study on the Jahn-Teller distortion of copper amine complexes and a manuscript is currently being written. Christopher Lee ('12) has been running molecular dynamics simulations on titanium-benzene clusters to observe the dynamics of self-assembly. Dr. Kua is currently on sabbatical and is learning about the chemistry of the origin of life. He spent the Fall visiting the lab of Dr. Ulrich Muller at UCSD learning about ribozymes. This winter quarter, Dr. Kua is visiting the lab of Dr. Jeffrey Bada at the Scripps Institute of Oceanography and is learning about geochemistry and prebiotic syntheses.

Malachowski Group

Our research has moved into making organic molecules called dipyrromethenes that can bind to metal ions.  These beautiful compounds are related to the naturally occurring porphyrins found in compounds such as hemoglobin and chlorophylls.  Not only do they bind to metals, but they make the most beautiful, intensely colored compounds imaginable. We are particularly fond of the orange ruthenium complexes, the green copper complexes and the red iron complexes. My students (Michelle Grau, Taylor Hepp, Jordan Thomas and Lindsay Row) made some impressive progress this year, as we have been able to make a large series of new metal complexes. With the help of Arnie Rheingold at UCSD, we have solved the structures of ten new compounds and are in the process of writing up many of these new results.  We still have a backlog of results that need to be published so my 2010-2011 sabbatical year is being taken up trying to get manuscripts out the door.

We did publish one paper this year detailing our results from the dipyrromethene project. This publication was: Mitchell R. Malachowski, Michelle F. Grau, Jordan M. Thomas, Arnold L. Rheingold, Curtis E. Moore, “Heterometallic Complexes Derived from Ruthenocene-functionalized  Dipyrromethenes,” Inorganica Chimica Acta, 364, 132-137, 2010.  This paper has many examples of the crystal structures of metal complexes formed from our ligands.

I also have continued to pursue my work on the impact of undergraduate research on students and student learning and have published a series of articles and chapters in books on this topic during 2010. I have run workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities. This work has accelerated as I (along with three colleagues from other institutions) have received a $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.  Our first workshops for these state systems (Wisconsin and California) will be in 2011.

Matulef Group

The Matulef lab has had a busy year continuing our studies on a family of chloride-transport proteins called CLC proteins.  Last spring, Jennifer Wooley (’10) and Sabrina Phillips (’12) finished setting up a lipid bilayer rig, an apparatus that allows us to measure the activity of chloride-transport proteins while precisely controlling the voltage across the membrane and the solutions on both sides of the membrane.  This paved the way for Sabrina to spend last summer and fall characterizing the mechanism of a novel inhibitor of the E. coli CLC homolog (called CLC-ec1).  Sabrina found that this small molecule (called OADS) inhibited CLC-ec1 reversibly and has the highest affinity of any CLC inhibitor yet known!  We were excited to present her work as a poster with the Maduke and Du Bois labs at the Protein Society Meeting in San Diego last August.

Mutalef
L to R:  Sabrina Phillips and Luis Rodriguez

Luis Rodriguez (’11) joined our team last summer to test whether we could find any better inhibitors of CLC-ec1.  We chose to test the effects of a variety of natural products from scorpion, sponges, and myxobacteria that were donated to us by Dr. Nael McCarty and Dr. Phil Crews.  The rationale was that some of the most potent ion channel inhibitors known came from natural products, and a particular toxin from scorpion was previously found to inhibit the mammalian homolog CLC-2.  Luis became an expert at protein purification, reconstitutions, and chloride flux assays, and he concluded that none of the natural products he tested affected the function of CLC-ec1.  Luis is now characterizing the function of a novel bacterial CLC homolog called CLC-b.  While inhibited by OADS similar to CLC-ec1, CLC-b has a much lower activity than CLC-ec1.  Luis is learning molecular biology in order to use a chimera approach to understand functional differences between CLC-ec1 and CLC-b.  We look forward to more exciting results to report next year!

Mills Group

The Mills group has been working to understand the role of metals in proteins. This year, we evaluated the effect of replacing copper with cobalt in the copper amine oxidase from pea seedlings (PSAO). With cobalt in the active site, the enzyme is much less active than with copper. This result suggests that cobalt changes the mechanism of the enzyme. We presented our results at the Protein Society meeting in August and submitted the results for publication. Kaitlyn Dang and Jennifer Nguyen had worked on this project until they graduated last May. Dayn Sommer and Eunah Choi are now working on this project. Michelle Dominguez and Jourdain Artz have been characterizing the metal binding properties of two Ferric Uptake Regulators (Fur). Michelle was able to measure the affinity of cobalt for the Fur proteins from Shewanella oneidensis and Pseudomonas aeruginosa. She presented her results at the Protein Society meeting in August. Since Michelle graduated in May, Megumi Sugawara has picked up this project. She has cloned the gene for a closely related protein – the Zinc Uptake Regulator (Zur) and will compare the metal affinities for this protein with Fur. Megumi will graduate this May.

Tahmassebi Group

Tahmassebi

L to R:  Urszula Milewicz, Dr. Debbie Tahmassebi, Raymond Sullivan and Michael Hughes

This past year has been great.  Michael Hughes continued work from alum Michelle Grau and was able to complete the synthesis of a novel mimic of the natural C DNA nucleoside.  Michelle is now in her first year of pharmacy school at UCSD.  Michael got some help from alum Kristy Clarke.  Kristy, who is currently a high school chemistry teacher at Dana Hills H.S. in Orange County, received a fellowship from the American Chemical Society to support her work this past summer.   This synthesis will be scaled up so that the mimic can be incorporated into DNA and its impact on DNA structure and interaction with DNA binding drugs can be studied in collaboration with the Dwyer group.

Also new over the summer was Raymond Sullivan.  Raymond was a PURE student and is currently completing his freshman year.  He worked to complete a scale-up synthesis of a fluorescent dideoxynucleoside, tCdd.  The original synthesis was completed and published by alum Will Porterfield.  Will is currently teaching English and Chemistry on an island called Pohnpei in the middle of the Pacific.  With help from a collaborator, tCdd has now been successfully incorporated into DNA.  Raymond will return to the lab this summer to study the properties of the dideoxynucleoside in the context of duplex DNA.  Another student will study the duplex structure by NMR.

This spring, Urszula Milewicz is continuing work from Katie Scott and Suzanne Nelson to develop an undergraduate laboratory to measure ascorbic acid concentration using stopped-flow fluorescence.  This project originated with a group of students in Chemistry 421 and should be completed and prepared for publication by Urszula. 

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Recent Faculty Publications - *undergraduate co-authors

  • Haubrich, Jan; Quiller, Ryan G.; Benz, Lauren; Liu, Zhi; Friend, Cynthia M. “In Situ Ambient Pressure Studies of the Chemistry of NO2 and Water on Rutile TiO2(110) “Langmuir (2010), 26(4), 2445-2451. 
  • Malyshev, Denis A.; Pfaff, Danielle A.*; Ippoliti, Shannon I.*; Hwang, Gil Tae; Dwyer, Tammy J.; Romesberg, Floyd E. “Solution Structure, Mechanism of Replication, and Optimization of an Unnatural Base Pair.” Chemistry--A European Journal (2010), 16(42), 12650-12659, S12650/1-S12650/28. 
  • Kahn, James*; Dutnall, Robert N.; Matulef, Kimberly; Plesniak, Leigh A. “Measurement of kon without a rapid-mixing device. ”Biochemistry and Molecular Biology Education (2010), 38(4), 238-241. 
  • Anderson, Megan; Huh, Joon H.; Ngo, Thien; Lee, Alice; Hernandez, Genaro; Pang, Joy; Perkins, Jennifer; Dutnall, Robert N. “Co-expression as a convenient method for the production and purification of core histones in bacteria.”  Protein Expression & Purification (2010), 72(2), 194-204. 
  • Malachowski, Mitchell R.; Grau, Michelle F.*; Thomas, Jordan M.*; Rheingold, Arnold L.; Moore, Curtis E.   “Heterometallic complexes derived from ruthenocene-functionalized dipyrromethenes.”  Inorganica Chimica Acta (2010), 364(1), 132-137. 
  • Korich, Andrew L.; Iovine, Peter M. “Boroxine Chemistry and Applications:  A Perspective” Dalton Trans., 2010, 39, 1423-1431.
  • Korich, Andrew L.; Walker, Amanda; Stevens, Caitlin; Hincke, Christopher.; Iovine, Peter M.  “Synthesis, Characterization, and Star Polymer Formation of Boronic Acid End-Functionalized Polycaprolactone”   J. Polym. Sci. Part A:  Polym. Chem. 2010, 48 (24), 5767-5774.
  • Malachowski,  Mitchell R. “Is CUR Helping Diminish the Importance of Teaching at Predominately Undergraduate Institutions?” Council on Undergraduate Research Quarterly, 31, 32-36, 2010.
  • J. L. Axson, K. Takahashi, D. O. De Haan and V. Vaida, “Gas-Phase Water Mediated Equilibrium Study Between Methylglyoxal and its Geminal Diol.”  Proc. Nat. Acad. Sci. 107 (15) 6687-6692 (2010), doi: 10.1073/pnas.0912121107
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