Chemistry Newsletter 2016

Chair’s Column

Greetings from USD Department of Chemistry and Biochemistry! 

There is never a dull moment in our department!  The past year has seen quite a bit of change, brought us new faces and department members, we lost two very important people in our lives, and department members continue to achieve and give us reasons to celebrate.  As you will read about in this newsletter, we welcomed three new members to our department team in the last year (Executive Assistant Kristen Stout, Purchasing and Budget Coordinator Megan Kyle, and Lab Technician Conner Houghtby) who have each contributed enormously to keeping the department functioning at a high level.  Our dear friend and former colleague Donald Peterson passed away suddenly in fall 2015. We honor Don’s life and contributions to USD in this newsletter.  Debbie Tahmassebi has moved on in her career and is now Dean of the College of Arts and Sciences at Santa Clara University – we miss her and wish her all good things.  Lastly, in people news, the department completed a successful faculty search in fall 2015 and we will welcome Dr. Anthony Bell to USD in fall 2016.  Dr. Bell is a biochemist who comes to us as an experienced teacher with an established research program in which he studies the HMGB1 (high mobility group B1) protein linked to lupus, sepsis and cancer.  His group uses peptide nucleic acids to design novel 4-way DNA junction ligands against HMGB1.

Notable achievements by department faculty in the past year have been:

  1. Jessica Bell and colleagues studying structure-function relationships in the PIP2 regulation of potassium channels landed the cover of an issue of Journal of Biological Chemistry.
  2. Lauren Benz earned the Undergraduate Research Mentor Award at USD.
  3. Jim Bolender was selected as the College of Arts and Sciences Knapp Chair for 2015-2016.
  4. Tim Clark was awarded a Research Opportunities in Europe for NSF Career grant recipients.  Tim will spend fall 2016 in Madrid, Spain working with a collaborator.
  5. David De Haan had his NSF-RUI grant renewed for 3 years.
  6. Lauren Benz, Tim Clark, and Peter Iovine were all named Cottrell Scholars by Research Corporation in recognition of the quality and innovation of their research programs.

We appreciate hearing from you and keeping in touch – remember to 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”).


Warmest Regards,

Tammy J. Dwyer

Update on Summer Alumni Reunion and Fundraiser

We are moving the 2016 Alumni reunion event to summer 2017 to make an even better program. This year (summer 2016) we will hold an online/silent auction (as well as accept donations) in support Chemistry and Biochemistry Undergraduate Research. Up for bid will be two stained glass windows (a protein ribbon diagram and a caduceus on a USD blue background) and various chemistry/biochemistry themed items.  We thank you for your continued support of the department and look forward to seeing you in summer 2017.

Don Peterson Remembrance (1931-2015): Joined USD in 1964

Don PetersonEmeritus faculty member and former chair of the Chemistry Department, Donald Peterson passed away on Friday, October 30th, 2015.

In 1964 Donald Peterson joined the chemistry faculty at the University of San Diego. He served as the chair of the Department of Physical Sciences and Mathematics before chairing the Chemistry Department for 25 years. During his time at USD, Donald also served twice as the Acting Dean of the College of Arts and Sciences. He retired from USD in 1996, having published more than 20 scientific papers and technical reports during his career.

During his time as USD, Donald taught and worked with several of the current faculty members, including, Dr. Tammy Dwyer, Dr. Mitch Malachowski and Debbie Finocchio. As Debbie Finocchio remembers, “Don Peterson was one of my absolute favorite teachers at USD. He taught me first semester P Chem, and to this day, I appreciate his ability to clearly convey the essential concepts in that course, to whittle it down to its essence. He was also a pioneer in our department by offering the first “computers in chemistry” course, which I also took – this was way back in the mid-80’s. After returning to USD as an employee, I always enjoyed conversations with Don – I am grateful for the many wisdoms he imparted on me”.

Renate Valois was Executive Assistant in the department for 38 years before she retired in 2007. She knew Don better than anyone, and recalls: "I met Don Peterson at the beginning of February 1970, a few days after I started working at USD. At that time I really did not get to know him well since he soon was off to Hawaii on a one-year sabbatical. Upon his return we had more and more contacts and shortly later he became Chair of the Chemistry Department. At this time, he became very ill, too ill to teach for several months. Because of the seriousness of his illness, I offered to transcribe his lecture notes and tests each evening over my home telephone. The following morning I would give these materials to the appropriate faculty members who had taken over his classes. We became very close during this time and developed a strong friendship that persisted throughout his remaining time at USD and into his retirement years. Don made a significant impact on my life. When I arrived at USD I was very insecure but through his encouragement, trust and guidance I was able to develop confidence in myself both as a person and a professional. Don was not the traditional stereotypical "boss". He was always thoughtful, down-to-earth, and thoroughly genuine human being who always treated me with courtesy and respect. His ultimate gift to me was his friendship."

Donald Peterson was the first person that Dr. Malachowski met when he arrived in San Diego when he arrived for his job interview in 1984. “He (Don) was so kind and accommodating that I instantly knew that I wanted to come to USD. I had flown in from Pennsylvania where I was teaching and when he drove me up to campus and we arrived at the West entrance, I commented on how it must be pretty difficult to get up that hill in the snow. He looked at me with his wry smile and said, ‘You’re not in Pennsylvania anymore’; let me describe some of the differences to you.” And that was the start of a wonderful relationship as he shepherded me through many challenges in my first years at USD and I can certainly say that he greatly enhanced my life in ways that have carried me to the present day.”

Donald retired in 1996 and spent his retirement traveling, cooking, bike riding and enjoying the richness of life. He will be missed by all who knew and worked with him; Dr. Malachowski puts it best when he states that “I remain confident that what he helped develop in our department all those years has carried on to this day and will take us into the future.”

Congratulations to Post-Docs Kathryn McGarry and Arijit Sengupta

katie mcgarryKatie, what made you decide on the University of San Diego for a postdoctoral position?

The postdoctoral position at USD appealed to me because I believed it would best prepare me for my chosen career. Ever since I was an undergraduate student, I have wanted to be a college professor. Towards that end, I intended to pursue a postdoc position after graduate school, and as I was finishing my studies I learned about the position here at USD. The opportunity to focus on research with undergraduate students and gain experience teaching chemistry courses appeared (and proved) to be a worthwhile experience!

What is your best memory from being a postdoctoral fellow at USD?

It is really hard to choose just one memory! I have really enjoyed all of my interactions with the students, in class and in the research laboratory, and the faculty members in chemistry department have been incredibly welcoming and supportive throughout my time here. Particularly memorable are the times in the research laboratory when a student has experienced a “learning moment” where something might have gone wrong but they have learned how to avoid that pitfall the next time! I have also really enjoyed running into students from classes I’ve taught a semester or year ago and learning about what they are doing now. I had this happen with a student from the very first organic chemistry laboratory I taught here and I found out she is now doing organic chemistry research for a faculty member here at USD!

In which areas do you feel you’ve made the most progress?

Two areas I have improved considerably are my skills in teaching a lecture course and learning how to balance my time between teaching and research (although that is still a work in progress). I feel significantly more prepared for my new position than I would have when I started here. I believe that my postdoctoral position at USD has greatly prepared me for the expectations and daily routine of an assistant professor.

What are you most looking forward to upon starting your new position at the University of Wisconsin – Stevens Point?

I am greatly looking forward to moving back to the Midwest to work with some great people and do what I love doing – teaching undergraduate students chemistry both in the classroom and in the laboratory! I am also excited about beginning my own research program in which I will mentor students in developing new synthetic methods to access molecules with useful technologic or biological properties. Getting to see students discover their own excitement for chemistry and develop as scientists is one of the most rewarding aspects of being a professor. I am overjoyed that I get to begin this journey at the University of Wisconsin – Stevens Point.

arijit senguptaArijit, what was your initial draw to the University of San Diego for a postdoctoral position?

As an academic professional I always want to grow my teaching and research experience hand-in-hand. In 2014 I started looking for a unique postdoc position, which would combine research and teaching. University of San Diego was providing such opportunity that would help me to grow both aspects of my portfolio (research and teaching). So when I read about this position in ACS Poly career section I was thrilled and applied for the job immediately.

What experiences stood out to you as a postdoctoral fellow at USD?

As a graduate student I have had worked with undergraduates on independent projects and also did undergraduate laboratory teaching. However, this postdoc position at USD in Prof Iovine’s group, gave me the opportunity to design undergrad research projects, which helped me thoroughly understand the value of undergraduate research. I have mentored 3-4 students during my stay in USD in their research activities. I also taught organic chemistry lecture course for the first time and I was super excited about that. This is the quality of experience I was hoping to achieve from USD. I think my academic portfolio has become much better and stronger with all these experiences.

In which areas do you feel you’ve grown?

Other than teaching and research, one of the most important areas where I feel stronger now is lab management involving undergraduate students.

What comes next for you with your new position at Bradley in Illinois?

As an assistant professor at Bradley University I’ll be involved in intense undergraduate teaching (General Chemistry, Organic Chemistry) and research with undergraduate students.

Instrument Update


The year 2015 has been fertile in instruments acquisitions. Among the most significant acquisitions made by the USD Chemistry & Biochemistry Department this year are: a Flash Purification Chromatography System by Interchim, inc; and two modern instruments by BioRad: a Fraction Purification Liquid Chromatography instrument, and a Gel Documentation System.

flash chromatographThe Flash Chromatography Instrument with combined UV & ELSD detection will allow quick separation of components in a sample based on their UV or ELSD signal. It has been put to work immediately by our new Teaching Lab CHEM422 and will be used by the Schellinger, Clark, and Daley research groups in the near future. CHEM422 Teaching labs students will have an opportunity to use this instrument to collect different fractions from the samples they've synthesized, each with distinctive UV or ELSD characteristics. This is a state-of-the-art instrument and USD serves as a pilot facility for InterChim as one of the first academic institution in southern California hosting their PuriFlash instrument.

gel documentation

The robust, compact, and easy to use new BioRad Gel Document System replaces an obsolete similar system. The Gel Doc EZ system is a compact and automated Gel Imaging instrument designed to yield publication-quality images. Our Biochemistry Research students and our Biochemistry Teaching labs students will be able to analyze their gels with the push of a button. The system also allows for stain-free gel imaging, using Bio-Rad stain-free gels: these "green" gels provide equal or better sensitivity than traditional staining methods and eliminate organic waste disposal. This instrument will support research activities for the Provost and Bell research groups.

fplcLast but not least, our department has acquired a modern FPLC instrument by BioRad: NGC Medium-Pressure Chromatography system with multi-wavelengths UV-Vis detector and a BioFraction Collector. This state-of-the-art instrument is designed for the all-purpose purification of biomolecules and simultaneous detection of proteins, peptides, nucleic acids, and other chromogenic molecules. The system is ideal for small-scale preparative purifications and can also be used for analytical HPLC separations. Biochemistry and BioPhysics Teaching labs students will get a true hands-on experience with this amazing instrument. Our student researchers in the Bell and Provost groups will use it abundantly.
Our department will continue its efforts to ensure that our students have access to modern scientific instrumentation in a safe environment, thus preparing them well for their future careers.

BRIDGES Program Update

The Bridges Program continues to seek out and support USD’s outstanding women chemistry and biochemistry majors intent on pursuing a graduate degree following graduation. The program allows students to spend one summer (typically following their Junior year) in a research group in an area of interest at a Ph.D.-granting institution. Students have used the opportunity to spend time at schools across the country, including Boston College, University of California, Berkeley, and University of Washington. Past Bridges participants are now pursuing graduate work at Johns Hopkins, Stanford, University of Georgia, and Vanderbilt.

NSF REU Program at USD

NSF REU Grant (Climate Change Across The Various Scales of System Organization) is a collaborative grant whose creation was led by Debbie Tahmassebi with contribution from several departments including Biology, Engineering, Math and Environmental and Ocean Sciences. Drs. Clark, De Haan and Provost participate in the program. This is a three-year award to fund summer research for USD and external students including a special focus on veterans and community college transfer students. Ten weeks of each summer, students will be engaged in a collaborator interdisciplinary research with USD faculty to learn about the factors that lead to and impact climate change and conduct climate change-related research projects.

New Faculty and Staff Introductions

Conner Lincoln Houghtby

conner houghtbyConner is a Laboratory Technician working in both the Physics and Chemistry departments. His responsibilities include setting up labs, maintaining equipment, and ordering supplies. With wide-ranging interests, Conner enjoys moving freely between physics and biophysics and chemistry and biochemistry. Previously, Conner worked as a science and mathematics tutor and a high school substitute teacher. In college, he assisted in research on using self-assembling lipid-DNA complexes as novel vectors for gene delivery. In his spare time, Conner volunteers as an editor and administrator for Free the Marquee, a San Diego non-profit magazine and cultural collective.

Conner is most interested in developing scientific literacy among the general population. While widespread understanding of scientific applications to current technology and environmental issues is certainly important in our rapidly advancing society, he is a firm believer in fostering an appreciation for the beauty and depth apparent in the world when viewed through the lens of modern natural philosophy.

Kristen Stout

kristen stoutKristen joined the department in July 2015 as the Executive Assistant, and helps to facilitate the day-to-day running of the department. She graduated in 2005 from San Francisco State University and worked in the Bay Area before moving back to San Diego in 2008. Previous experience includes work in academia at San Francisco State University, the legal industry in both the Bay Area and San Diego and the biotech industry here in San Diego.

Megan Kyle

megan kyleMegan Kyle joined the department in July 2015 as Chemistry Purchaser and Budget Coordinator. She receives and organizes all purchasing requests made by faculty and oversees the department budget. As a former USD student and current USD volunteer for Alumni Relations, Megan is passionate about the University and is enjoying her new role in the Chemistry department. In her free time, Megan plays beach volleyball, kickball and is an avid reader.

Alumni Profiles

Julio de Unamuno (Biochemistry 2007)

Please tell us what you have been up to (personally and professionally) since you graduated from USD?

julio deunamunoAfter graduating from USD's first batch of Biochemistry majors in 2007, I spent the next two years pushing modeling and simulation software to help scientists fail experiments fast in silico and save time and money for only the most promising work at the bench. With the country still deep in the Great Recession, I was tapped to head business development for several scientific equipment manufacturers trying to crack into the unscathed life sciences market. Over the next five years, that role exposed me to the many sales, regulatory, and manufacturing hurdles the BioTech and Medical Device & Diagnostics industries face.

Around this time, my wife and I sprouted our third little munchkin and bought our home in Eastlake, where we currently reside. In 2014, I received my Executive MBA from UCSD Rady School of Management. During the program, I quit my comfy job at a Fortune 200 company to put my unique insights taking a drug from lab to market to the test by launching my own startup, LabFellows.

What is your current career position and what do you enjoy most about it?

Today, I’m co-founder and CEO of LabFellows. For BioTech startups who can’t find affordable, shared lab space and equipment, our Digital Research Platform does it all in a few clicks.

I was inspired after noticing how difficult it was for BioTech startups to thrive due to limited funding and the high capital costs of spinning up one’s own lab, and yet these same assets went underutilized every day in universities and small industrial labs that had them.

What I truly enjoy most day-to-day is sharing tribal knowledge with fellow entrepreneur scientists we help - especially those transitioning straight out of academia. Whether it’s exchanging tips on investor fundraising, sales negotiation tactics, or how to attract early employees, I enjoy it all. I’m proud to say we work with a few Torero spinouts too!

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

Running a startup with investors and employees is not an opportunity to “be your own boss” –if you’re looking for that, go into Sales. As CEO in a startup, my greatest challenge is making sure there’s always plenty of money in the bank and communicating a clear vision for the company.

Realizing this as the true role of a startup CEO has produced the most rewarding aspect of leading LabFellows: Funding and cultivating a team developing some very cool Tech that’s helping startups discover and develop more cures, faster.

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

USD gave me access to research resources that allowed me to pursue what I call my “mini-PhD”, even as my wife and I raised our first daughter and son between our sophomore and senior years.

With support from the Department, USD funded my four straight years of wet lab research outside class through grants, scholarships, and Pre-Undergraduate Research Education (PURE) and McNair Scholar programs. Opportunities ranged from designing new antibiotics to investigating genetic mutations correlated with autistic spectrum disorder. A project on the Hunter Killer Peptide, a potential anti-cancer therapeutic, even led to me co-authoring publication in a peer-reviewed scientific journal - as an undergraduate!

These rich experiences provided me the confidence, strong technical grounding, and network of help I’ve relied on my entire career for building and leading high performing, cross-functional teams in science and technology driven companies.

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

Aside from swapping baby carriers with my wife between classes on campus, get-togethers with fellow summer research students at USD for bagel & coffee breakfasts or kayaking La Jolla Cove were always special times. We’d hang up our pipettes for a few hours and enjoy sharing the highs and lows of our research’s progress. Those candid and open dialogues did a lot to foster relationships that have served me well over the years. Science is tough, and the best teams win. Never lose alone.

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

In life I’ve found there are only two types of decisions: those with irreversible consequences, and then the reversible ones. Spend the bulk of your time around irreversible decisions, and just make quick, educated guesses around reversible ones and get on with things.

Getting your bachelor’s degree was a major, irreversible decision. Figuring out what you want to do with it –your career– is a fun and reversible experience. Don’t overthink it. Go out and just take action, you’ll know the right career when it finds you. Everyone has a career plan, until they start one.

Vince DeTuri (Chemistry 1994)

Please tell us what you have been up to (personally and professionally) since you graduated from USD?

vincent deturiSince graduating from USD in 1994 I have continued in Chemistry and I am now teaching and doing research with undergraduates at Ithaca College. I earned my PhD in Chemical Physics from the University of Nevada at Reno in 1999. Reno was a great place for me, their chemical-physics faculty are excellent, the cost of living was reasonable, and the weather was not too much of a shock from San Diego. From Reno I started a teaching postdoc at Ithaca College which turned into a tenure track position in Chemistry. I’ve taught across the curriculum from general education courses for non-science majors to both semesters of physical chemistry and advanced electives in Instrumental Analysis and Computational Chemistry. I was drawn to Ithaca College because of the strong culture of promoting undergraduate research in chemistry. I have an active research group working on computational chemistry projects, which is very different than the multi-step organic synthesis project I did as an undergraduate.

While at college I met my wife, Molly, and we have been happily married for the past 20 years. Molly is also a chemist and works at Ithaca College. We have two boys, 12 and 10, and live on a small patch of land, 10 acres, with horses and chickens.

What motivated you to pursue a PhD? What was your graduate school experience like? And what advice can you offer current students with similar aspirations?

My motivation to pursue a PhD was a strong desire to just learn more chemistry, physics, and math and continue doing research. I learned a lot in my chemistry courses at USD, but I had the best learning experiences doing undergraduate research with Pat Traylor during the summer and during the academic year. The unknown of how a reaction would work or figuring out the best way to purify a compound or using an instrument to identify what I made had the biggest impact on me as a chemist. Getting a chance to present my research at the National ACS meeting was also a great experience.

The undergraduate research at USD prepared me for graduate school and I felt confident getting into a laboratory and jumping into a research project. I had a great time in graduate school. My best advice to succeed in graduate school is to be self-motivated and be ready to learn by making lots of mistakes. For many (~90%) students the second year of graduate school is the toughest time. This is where students often question why they are in graduate school, question if they want to continue, and question their ability to succeed. A great way to get through this rough patch is to contact your undergraduate mentors for support and keep your eye on your goals. Graduate school is tough, research is hard (or someone else would have already published the answers!), and a PhD is a long road; but if you can get over the second year activation barrier it is all downhill after that.

Ashley Parks (Chemistry 2004)

Please tell us what you have been up to (personally and professionally) since you graduated from USD?

ashley parks 1After graduating from USD in 2008 I started working on my PhD at the University of South Carolina, but moved to Duke University in 2009. I graduated in 2013 with a PhD in Environment and a Toxicology Certificate. From there I moved to Rhode Island for a postdoctoral fellowship at the U.S. Environmental Protection Agency (U.S. EPA), where I am now. In November 2015, Ryan Haywood (another USD chemistry graduate) and I were married in a ceremony officiated by Dr. Jim Bolender. This summer we will be making our way back to California after my postdoc position ends and Ryan graduates from the University of Rhode Island with a Masters in Secondary Education and Chemistry Teaching Certificate. Aside from research and teaching, Ryan and I enjoy going on backpacking trips, SCUBA diving, cooking/baking, and spending time with our dog, Roxy.

What motivated you to pursue a PhD? What was your graduate school experience like? And what advice can you offer current students with similar aspirations?

During my sophomore year at USD I joined Dr. Jim Bolender’s research group, where I worked on the Baja project for 2.5 years. It was through that experience that I really found my love for research. I enjoyed the challenges and excitement of the work, and realized I wanted to continue working on novel scientific problems after graduating. I applied to graduate school and decided to move across the country to join the Department of Chemistry and Biochemistry at the University of South Carolina in Columbia, SC. It was there that I entered the world of nanotechnology, from the perspective of an environmental chemist and toxicologist. After the first year, my PhD advisor, Dr. Lee Ferguson, moved to Duke University. Since I was invested in my research, I applied to the Nicholas School of the Environment at Duke to continue working with Lee. It was there that I really learned how to plan and manage research projects of my own. To help fund my graduate work, I applied for and received two U.S. EPA student service contracts, which allowed me to work at the U.S. EPA laboratory in Narragansett, RI during the summer months. During those summers I performed most of my toxicology and bioaccumulation studies, and shipped my samples back to Duke to analyze during the school year. I also spent about 2-3 months back in South Carolina in my third year doing a bioaccumulation study with carbon-14 labeled nanomaterials. Lee would joke about how I was his traveling grad student.

To say that I had a unique graduate school experience would be an understatement, but I am really thankful for it. It taught me to be more flexible and open-minded, both with my time and perception of what graduate school “should” look like. When I applied to schools I focused only on chemistry departments with environmental chemistry projects, but I would urge anyone interested in that field to consider environmental programs like the one at Duke, as well as civil and environmental engineering programs. My graduate lab and office were housed in the engineering department and I learned so much from working with those faculty and students. One other piece of advice: choose a project you love because the day will come (probably more than once) where you will want to call it quits. Loving your project will make it much easier to stay and push through the moments where you feel like you can’t stand it anymore.

What is your current career position and what do you enjoy most about it?

I am currently in my final three months as a Postdoctoral Research Associate funded through the National Research Council Fellowship Program. My position is at the Atlantic Ecology Division of the U.S. EPA in Narragansett, RI (yes, the same place I worked during the summers of my PhD). The research I proposed for this position was still in the nanotechnology realm but I shifted my focus from the environmental fate and effects of carbon nanotubes to copper nanoparticles used in pressure-treated lumber. I really enjoy getting to work on projects that provide important and necessary information for risk assessment and future regulations to help minimize any negative impacts on our environment. In July I will be starting my new position as a Scientist at the Southern California Coastal Water Research Project (SCCWRP) in Costa Mesa, CA.

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

One word comes to mind: comprehensive. First, the liberal arts education USD provides allowed me to have the breadth of knowledge necessary for cross-discipline collaborations. Second, the chemistry curriculum in particular provided me with the exposure to each major field of chemistry to better understand how they contribute to my specific research projects. I also have to credit the amazing instrumental analysis course for my ability to approach almost any new instrument and learn how to use it. The extensive experience I got through laboratory courses and independent research was critical to my success as a graduate student and allowed me to jump into the details of my research much more quickly than if I had to learn those skills at the start of graduate school.

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

ashley parks 2I have so many fond memories of USD. I was a member of several organizations including Chemistry Club and Kappa Kappa Gamma, and I served as an orientation team leader/preceptorial advisor as well as a Resident Assistant. My experiences in undergraduate research are certainly a highlight. I made countless trips to Bahia Magdalena, Baja California Sur with the Bolender and Boudrias research groups as well as one trip each to Jamaica and Uganda. The friendships forged during those long car or plane rides and even longer field days are everlasting. I also believe there were at least two times I beat Bolender during our Texas Hold ’em poker tournaments, although he’ll probably deny it.

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

Try to get as much laboratory experience as you can and make sure you learn different techniques and instruments. This will also allow you to determine if laboratory science is the path you want to pursue. I also suggest you take a variety of classes in related disciplines. Environmental chemistry overlaps with so many other fields such as oceanography, geochemistry, biology, toxicology, engineering, environmental policy, etc. Having a better understanding of the overlapping fields can make a huge difference in making sense of your own data.

Faculty Research Group Updates

Jessica Bell Research Group

The Bell laboratory was founded at USD in August 2014. The lab focuses on host:pathogen interactions and the subsequent innate immune signaling pathways that block pathogen from infecting the host. Our current work examines the signaling pathway that is initiated by double stranded RNA, a key pathogen associated molecular pattern associated with viral infections. Toll-like receptor 3 initiates the cell’s response choosing one of three fates, apoptosis (die rather than replicate a virus!), inflammatory response (produce signals that cause fever and recruitment of additional immune cells – better known as swelling), and the interferon response (as the name suggests, “interferes” with viral replication). Our lab has discovered a molecule associated with the last pathway. This molecule, Suppressor of IKKepsilon (SIKE), redirects the interferon pathway to an, as yet, undefined response. We have shown that SIKE interacts with the cell’s cytoskeleton and may play a role in cytoskeletal rearrangement associated with an immune response, such as immune cell migration to the site of infection or phagocytosis of an infected cell. The lab received an R21 from the National Institute of Allergy and Infectious Diseases to examine this relationship.

The lab: At any given time we are 4-10 members strong. Over the last two years, we have presented our findings at the annual Experimental Biology (EB) meeting (2015 and 2016) and the American Society for Cell Biology annual meeting (2015). Jilan Knoblauch competed in the Undergraduate Poster competition in Boston, MA as part of EB2015 and Emerald Dohleman presented at the ASCB 2015 meeting and will present at the EB2016 meeting in April. All members of the lab will participate in Creative Collaborations 2016 at USD. This past summer, we welcomed Ms. Louise Zhou a high school teacher from Las Vegas, NV as part of our research team. She subcloned a new construct, wit3.0, into bacterial expression systems and tested expression. We hope to continue our research collaboration this summer! Erica Skerven, a Pre-Undergraduate Research Experience (PURE) student, spent several weeks learning the joys of enzyme kinetics using malate dehydrogenase (MDH) as her model system – she will also be presenting at CC2016. Finally, we were also happy to have Bell lab East led by Mr. Dr. Bell from the University of Richmond, Richmond, VA, join us for 4 weeks in July to collaborate on SIKE and MDH studies. For academic year 2015, Mr. Dr. Bell is on sabbatical at USD as a Visiting Distinguished Professor of Chemistry & Biochemistry and the 2015-16 Knapp Chair of the Liberal Arts. His 12 USD research students added to our group make for a boisterous and full lab space!

Accomplishments: In spring 2015, Emerald Dohleman was awarded the Hayes Scholarship. Jilan Knoblauch and Sean Fahey were award summer 2015 Summer Undergraduate Research Experience fellowships. Jilan Knoblauch graduated with her biochemistry degree in December 2015 – our first Bell lab USD alum! Congratulations, Jil! This spring, the Bell lab will celebrate the graduation of Emerald Dohleman, Sean Fahey, Chanelle Ankeney, and Hannah Steele.

jessica bell labIn the picture (L to R), back row: Nicholas DiChristofano, Emerald Dohleman, Frank Slykas, Jilan Knoblauch, Chanelle Ankeney, Flowreen Shikwana; middle row (and horizontal): Sean Fahey; front row: Halie Sonnenschein, Mariam Dawood, Jessica Bell, Hannah Steele.

Lauren Benz Research Group

The Benz lab had a productive and exciting 2015! The highlight of the year was the group’s attendance at the National American Chemical Society meeting in Denver, where Amber Mosier, Hanna Larson and Bette Webster presented their work on the adsorption of methanol, and reactions over nanoporous thin films. We also managed to squeeze in an outing before the meeting to visit the beautiful “Garden of the Gods” in nearby Colorado Springs, where we hiked around in the park as a big, happy departmental group! Other milestones included several graduations, a publication, and other successes: Amber graduated and began graduate school in chemistry at UCSD, Hanna graduated and started working towards a Masters in Global Health at UCSF, and Bette started graduate school at Stanford in pursuit of a Ph.D. in Biochemistry. Bette also was awarded a prestigious NSF graduate research fellowship. Dr. Fangyuan Tian began her independent career as an Assistant Professor at Cal. State Long Beach in the fall. Congratulations all around! We welcomed Mia Ivos, Emily Pitsch, and Alexi Odegard to the group, and welcomed Kendall Kehr back from her studies abroad in the UK. Dr. Benz also spent the fall semester on sabbatical in the Cohen lab at UCSD working on a joint review article in the metal organic framework field, and began building connections between the fundamental surface science work of the Benz lab and the Cohen lab’s expertise in MOF mixed matrix membranes for applications in liquid separations. It was another great year!

lauren benz labIn the picture (L to R): Elizabeth Webster (’15), Hanna Larson (’15), Alyssa Rodriguez (’15) and Amber Mosier (’15). The snow-capped mountain in the background is beautiful Pike’s Peak.

Tim Clark Research Group

The past year in the Clark research group has been very successful. Three papers have been published, including a review on α-hydroxyboronate esters. We have also made a great deal of progress on ongoing projects, which should lead to additional publications in the coming years. Two students are graduating this year and both are currently deciding which school to attend for their Ph.D. Dr. Kathryn McGarry, post-doc in the lab recently secured a faculty position at the University of Wisconsin-Stevens Point for fall 2016. This past summer (2015) the Clark lab was very full again. During that summer there were 6 undergraduate students, a high school teacher, a high school student, and a post-doctoral research associate. The result of all this activity was a lively and exuberant environment for undergraduate research. Two new students have joined the group to replace the graduating seniors, welcome Stephen Hyland and Alexis Ogtong. Dr. Clark has been awarded a supplemental grant from the National Science Foundation for a collaborative project with Dr. Mariola Tortosa in Madrid, Spain. Dr. Clark and his family will spend six months abroad starting in July.

tim clark lab

Some specific recent accomplishments by Clark research group members:

  • Justin Marcum was awarded USD SURE (Summer Undergraduate Research Experience) fellowship during the summer of 2015.
  • Carl Ferber was awarded a American Chemical Society Division of Organic Chemistry Summer Undergraduate Research Fellowship for the summer of 2015.
  • Taylor Thane was awarded Beckman Foundation fellowship to support her research for the summers of 2015 and 2016.
  • Justin Marcum and Carl Ferber have been accepted to a number of graduate programs and are currently visiting them to decide where to accept.
  • Lillian Hale (undergraduate and technician), David Emmerson (high school teacher), Emma Ling (high school student), Andrew Roering (post-doc), and Marissa Ringgold (undergraduate) are co-authors on a manuscript published in Organic Chemistry Frontiers (2015, 2 661-664).
  • Katie McGarry (post-doc) and Ali Duenas (undergraduate) are co-authors on a manuscript published in the Journal of Organic Chemistry (2015, 80, 7193–7204).
  • Dr. Kathryn McGarry, post-doc in the Clark group has accepted a tenure-track faculty position at the University of Wisconsin-Stevens Point…Congratulations Katie!
  • Carl Ferber, Shawn Wright, and Kathryn McGarry gave poster presentations at the Fall 2015 ACS National Meeting in Boston, MA.
  • Effie Albitz, Justin Marcum, Carl Ferber, Clay Oliver, David Emmerson and Kathryn McGarry will give poster presentations at the Spring ACS National Meeting in San Diego, CA.

Christopher Daley Research Group

The 2015 Daley Group consisted of Kristina Zivkovic (Junior Biochem), Alexa Villasenor (Junior Chem), Dominic Pultz (Junior Biochem), and Lilia Baldauf (Freshman Chem) during the academic year with an incoming freshman, Raquel Markham (PURE program) and two Mater Dei High School students, Franco Faucher (ACS SEED program) and Carlos Alcocer) joining the group for summer research. To start 2016, Kristina, Alexa, Lilia, and Raquel have signed on with newcomer Wesley Chow joining the fray. Below is a recap of the Daley Group’s efforts since the last Spin.

On the research front, we have made strides on the latest generation of the NHase ligand analogue, containing a serine backbone. Previously it has been prepared on a larger scale but in a racemized form, thanks to the efforts of Raquel, we believe we may have found a new synthetic pathway that will maintain the enantiopurity of the compound. This work should be completed this academic year; hopefully culminating in an x-ray structure of the cobalt complex. In other (older) news, the work of alumni Grant Ferrell, Eric Czer, and Daniel Huh on diamidato-bis(phosphine) ruthenium complexes should finally be published this spring. Our biggest success has come from the breakthrough with our enantioselective catalysis project! Yes, I know we have made the claim before with this project but this time it has made it to completion so we are sure of it. Thanks to the hard work of past group members, most notably Jessica Cryder, Lauren Bernier, Raymond Sullivan, and Kayleen Fulton, we had methods to prepare our chiral ligands in-situ as Cd-complexes and we had preliminary successes using a solid phase thiol column to decoordinate the ligand with minimal decomposition. While that work did not pan out, this past summer Kristina optimized a new protocol that is repeatable and yields the desired ligands in high yields with minimal decomposition. The drawback – we use thiols …. lots and lots of thiols! So much that Kristina can now definitively distinguish the smell of our thiols from those from a gas leak. For once, I am happy we have a project that stinks in the literal fashion, not just the figurative one. We anticipate submitting the work by the end of the semester, hopefully with our first enantioselective catalysis study.

The Daley Group will attend a conference in the far off exotic location of “downtown” with Kristina and Alexa presenting their work at the 251st ACS National Meeting in San Diego (March 2016). Pictures and updates from this conference will be found on our webpage.

As always, you can follow the Daley Group progress on our webpage at, and/or Dr. Daley on Facebook or Twitter. 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! 

David De Haan Research Group

david dehaan labResearch on sunlit cloud chemistry in the De Haan group went on in two places during summer 2015. At USD, postdoc Melanie Zauscher managed the day-to-day with undergraduates Alexia De Loera, Natalie Jimenez, and Praveen Wickremasinghe (l to r in the picture). Dr. De Haan checked in via a daily Skype session from the cloud chamber at the University of Paris East - Creteil, where he was organizing and conducting experiments on the same chemical systems as the group at USD. The Paris experiments involved scientists from University of Eastern Finland, University of Genoa (Italy), UPEC (France), and Harvey Mudd College (Claremont, CA). At the end of the summer, Melanie Zauscher went off to start her new position as a grants program officer at the California Air Resources Board in Sacramento! In September Tobin Gramyk joined the undergraduate research group, followed in January 2016 by Benn Joyce, Shanel HIll, Jin Xiang Low, and Alyssa Andretta.

Tammy Dwyer Research Group

In 2014-2015 I enjoyed a wonderful sabbatical, returning to the department in August 2015. During my sabbatical, I worked with my co-author Dr. Charles Grisham (University of Virginia) to developing our digital first edition of a yearlong General Chemistry course textbook and online learning environment. The goal of this project is to deliver course content (eText, homework system, learning resources, etc.) using an Internet browser based interface. We collaborated with an educational technologist at the University of Virginia who has written an interface (called QMedia) to deliver video content for educational purposes. We adapted his interface to serve the needs of our project and we created a fully functional demo version of an entire chapter’s worth of material including videos and animations, eText, homework and assessment, molecular structure drawing and viewing tools, periodic table, calculator and solved problems. At this point, we are working with our editors and publisher to further build-out the interface to include additional functionality. As of this writing, I have five research students working in my lab (three first-year and two third-year) on various project related to NMR structural studies of 1) novel DNA duplexes containing non-natural base pairs and 2) a four-way DNA junction in anticipation of a potential collaboration with Dr. Anthony Bell who will join the department as Assistant Professor in fall 2016!

Jeremy Kua Research Group

In 2015, the Kua group, in collaboration with the De Haan group published a study on the co-oligomerization of formaldehyde and ammonia.Alyssa Rodriguez ('15) did the bulk of the work, both computational and experimental. She is headed to Vanderbilt this fall to join the Ph.D. program in interdisciplinary bimolecular sciences. Lily Marucci ('13), a math major, was also a contributor to this project, and she is enjoying her third year in dental school. Russ Adwan (graduated Dec '15, and applying to medical school) made good progress extending the free energy map of formaldehyde oligomerization work to acidic and basic conditions. Dr. Kua presented some of those results at the recent San Diego ACS meeting in March. Previous work had only examined the reaction under neutral conditions.

Vanessa Vargas ('16) joined the group last summer and is working on a massive project - devising a group additivity scheme to quickly generate solution free energies of polar organic molecules in water. The project is still in its early stages but Dr. Kua was able to share preliminary data at the Boston ACS national meeting in Aug 2015. Kyra Thrush ('18) also joined the group last summer, and made fantastic progress on calculating a free energy map for the reactions of HCN, NH3 and H2O in aqueous solution. This included studying the trimerization of HCN, formamidic acid and formamide into 6-membered rings. A manuscript with Kyra as a co-author was recently submitted to the Journal of Physical Chemistry and we hope to see it in print soon. Both Vanessa and Kyra presented posters at the San Diego ACS meeting in March.

Lauren Sweet ('17) recently joined the group and is studying an interesting reaction, ester-mediated amide bond formation, based on recently published experimental work from the NSF/NASA Center for Chemical Evolution. Lia Hebert ('18), a math major, has volunteered to do some analysis on reaction networks using MATLAB. On the hardware front, Dr. Kua has collaborated with the I.T. department to build a new modular blade server that might be the start of a high-performance computing core facility at USD. Tests are being run on the cluster now, and while there are kinks to be worked out, things are looking good. So we have more computational power now!

Mitch Malachowski Research Group

Dr. Malachowski’s work on synthesizing new dipyrromethenes ligands and binding them to metal ions continues to move forward and his students have prepared large numbers of new, interesting compounds. The metal complexes of the dipyrromethenes are beautiful as they are brightly colored and highly crystalline with the challenge in our lab being the need to grow single crystals for X-ray analysis. His students are becoming incredibly proficient at purifying and crystallizing the metal complexes. Daniel Reitzler has spent uncounted numbers of hours in the lab over the past two semesters growing crystals and has made impressive progress over that time.

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 China, Texas, New Jersey, Washington, DC, and Colorado to give presentations. A good deal of this time was taken up running workshops describing the wonders and challenges of undergraduate research to faculty and administrators at many other universities. This work has been extremely rewarding as he now has been able to work with over 500 schools and 2,500 faculty and administrators and has raised the undergraduate research and USD flag to all of these participants. Along with three colleagues at other institutions, he recently submitted a $2,000,000 grant to the NSF to further this project.

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 2015. His most recent work appeared in the Jossey-Bass series on New Directions for Higher Education where he co-edited a volume entitled, “Enhancing and Expanding Undergraduate Research: A Systems Approach.”

Dr. Malachowski also taught a class in our Florence study abroad program on the “Chemistry of the Renaissance” where he probed atoms and molecules and structure and bonding with non-science majors. Along with more traditional chemical topics, they studied the history and philosophy of chemistry/science by probing the evolution of chemical thought from Aristotle through alchemy to modern chemistry. The students particularly enjoyed the trips in Florence to the Galileo museum, the Uffizi gallery, the Leonardo da Vinci museum and a very bizarre anatomy museum with many strange body parts.

Joe Provost Research Group

jos provost labThe Provost lab has graduated its second class of students, joining the workforce, graduate and medical school. We miss you each. This summer was a busy time with two high school students and a lab filled with five research students. We continue to work on processes involved in lung cancer invasion and metastasis focusing on NHE. This past January we were happy to publish a nice paper on phosphorylation of the sodium hydrogen exchanger and are very close to another on how the protein is regulated by protein-protein interactions. We welcome Shane Davis (freshmen), Emily Pritsch (sophomore) and Rubin Schleiger (Senior) to the lab with returning Thomas Polveroni-Edwards, Chelsea Marshal, Wayne Taylor Cottle, Daniela Silva, Chyna Grey, Dan Hastle and dropped in by UFO is Colton Gregori (he was busy playing Torrero Football). They did a great job doing research between parties at the Provost house and hours hanging out waiting for the IFO to come back. Several students presented last year at the ASBMB meeting in Boston. Wayne Taylor Cottle and Lea Kiefer were honored with membership into the ASBMB Honor Society and Jevaughn Davis and Danelia Silva were awarded a price for their presentation in a cancer poster session where they even won a cash prize! We look forward to seeing what this year at the ASBMB meeting brings! This year Provost will serve as a committee member on the ACS and the ASBMB. He will be presenting a few times at the both meetings this year making a very busy summer.

Joan Schellinger Research Group

joan schellinger labWow… the Schellinger lab is already in its second year and the group keeps growing. Our first lab alumnus, Francisco Hidalgo ‘15, graduated last Spring semester and is now geared up for graduate school. The Schellinger lab’s first summer at USD had been fun and productive. Ella Giles ’16 was awarded with the SURE scholarship and led the project on the microwave-assisted RAFT polymerization of peptide-based polymers. Francisco continued his summer research at USD and worked on thiol-responsive starch-peptide conjugates. Two student volunteers, Alisson Magsumbol ’16 and Olnita Martini ’18, also joined the lab last summer. Our group attended and presented at several undergraduate research conferences: 2015 Creative Collaborations at USD, 2015 ACS Southern California Undergraduate Research Conference in Chemistry and Biochemistry and 2015 UCSD Summer Research Conference. The group (with student volunteers Danny Arias ’16, Ella Giles ’16, Alisson Magsumbol ’16, ) was also co-organized the second annual symposium for SD PolyGrid, a local network that promotes collaborations in polymer and material science. We are looking forward to the coming years as we welcome new students, progress in our research work and engage in more activities. Current Schellinger group members are: Danny Arias ’16, Ella Giles ’16, Alisson Magsumbol ’16, Micaella Jorge ’17, Praveen Wickremasinghe ’17, Callie Cuff ’18 and Olnita Martini ’18.

Faculty Publications 2015

(Undergraduate students indicated by *, post-docs #)

Tang, Q.-Y., Larry, T., Hendra, K., Yamamoto, E., Bell, J., Cui, M., Logothetis, D. E., and Boland, L. M. “Mutations in nature conferred a high affinity PIP2 binding site in vertebrate inwardly rectifying potassium channels.” J. Biol. Chem. 290,16517-16529 (2015).

Tian, F.; Mosier, A.M*; Park, A*; Webster, E.R.*; Cerro, A.M.*; Shine, R.S.* and Benz, L. “In Situ Measurement of CO2 and H2O Adsorption by ZIF-8 Films” J. Phys. Chem. C., 119, 15248, (2015).

Benz, M.; Benz, L.; Patel, S.V. “High Temperature Mass Detection Using a Carbon Nanotube Bilayer Modified Quartz Crystal Microbalance as a GC Detector” Analytical Chemistry, 87(5), 2779, (2015).

McGarry, K. A.; Duenas, A. A.*; Clark, T. B. “Selective Formation of ortho-
Aminobenzylamines by the Copper-Catalyzed Amination of Benzylamine Boronate Esters” J. Org. Chem., 80, 7193–7204 (2015).

Hale, L. V. A.; Emmerson, D. G.; Ling, E. F.; Roering, A. J.; *Ringgold, M. A.; Clark, T. B. “An ortho-Directed C–H Borylation/Suzuki Coupling Sequence in the Formation of Biphenylbenzylic Amines” Org. Chem. Frontiers., 2, 661–664 (2015).

Hale, L. V. A.; McGarry, K. A.; Ringgold, M. A.*; Clark, T. B. “Role of Hemilabile
Diamine Ligands in the Amine-Directed C–H Borylation of Arenes” Organometallics, 34, 51–55 (2015).

Wang, G.; Guino-o, M.A.; Glueck, D.S.; Golen, J.A.; Daley, C. J. A.; Rheingold, A.L. “Synthesis of a phosphapyracene via metal-mediated cyclization: structural and reactivity effects of acenaphthene precursors,” Dalton Trans., 44(21), 9943-995 (2015).

Kua, J.; Rodriguez, A.A.*; Marucci, L.; Galloway, M.M.#; De Haan, D.O. “Free energy map for the co-oligomerization of formaldehyde and ammonia,” J. Phys. Chem. A 119 (10) 2122-2131 (2015).

Naleway, Steven E.; Yu, Christopher F.; Porter, Michael M.; Sengupta, Arijit#; Iovine, Peter M.; Meyers, Marc A.; McKittrick, Joanna. “Bioinspired Composites from Freeze Casting with Clathrate Hydrates” Materials & Design, 71, 62-67 (2015).

Tan, J.-K. Y.; Choi, J. L.; Wei, H.; Schellinger, J. G.; Pun, S. H., “Reducible, dibromomaleimide-linked polymers for gene delivery.” Biomater. Sci., 3, 112-120 (2015).

Faculty Research Grant and Funding Awards 2015

Tim Clark was awarded an ACS-PRF grant ($70,000) for his work on “Phosphine-Directed C-H Borylation of Arenes: Facile Access to Ambiphilic Phosphine Boronate Esters”.

Tim Clark was awarded a Research Opportunity for NSF-CAREER Awardees to pursue a research collaboration in Madrid, Spain in fall 2016.

David De Haan was awarded an EMSL Access Grant, Environmental Molecular Sciences Laboratory ($18,233) to study “Atmospheric Brown Carbon Production: Cloud Chamber Experiments on Methylglyoxal, Methylamine, and Ammonium Sulfate Seed Particles in the Presence of Sunlight and Oxidants”.

David De Haan was awarded an NSF-RUI grant ($366,635) to investigate “Brown carbon aerosol production in polluted environments: the effects of oxidants, SO2, and sunlight on aqueous-phase aldehyde reactivity”.

Peter Iovine was awarded an NSF-REU Collaborative Proposal with Colby College, Northern Kentucky University, Trinity University, University of Richmond and Grand Valley State University ($32000).

Department of Chemistry and Biochemistry
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