Printing 3D Protein Models

 

Under the guidance of biochemist Shahir Rizk, students in CHEM-C 486 Biological Chemistry Laboratory ended the Fall semester printing 3D models of the proteins they had been working with in this capstone course for the biochemistry major.  Rizk obtained an internal MALT (Materials for Active Learning Techniques) grant to help promote visual literacy in this project to better appreciate the three-dimensional nature of biological molecules.  Students were able to hold in their hands models of protein and substrate to experience how they interact, move, and change their structures to promote biological processes.  To create the models, students first prepared digital code for their molecules with the help of  the molecular visualization software PyMol.  They then used the code to program our own IU South Bend 3D printing facility to print the models in clear resin. The students were very excited to see the results of their work. 

Biochemistry Major Khai Pham Presents at ACS Meeting

Last month biochemistry student Khai Pham presented a poster at the 51st Midwest Regional Meeting of the American Chemical Society.  Her poster was titled A Novel Benchtop Time-of-Flight GC-MS System for High Throughput Qualitative and Quantitative Analysis of Drugs of Abuse in Human Urine and is now on display on the walls of Northside Hall.  Clicking on the title will take to you a larger version of the poster that is readable.  This poster details work done by Pham and colleagues at Leco Corporation this past summer where she completed an internship.  She collaborated with Adjunct Professor David Alonso who works at Leco full time, but generously teaches organic chemistry laboratories for us in the evenings.  Leco is an international company with its world headquarters not so far away in Saint Joseph, Michigan.  They produce many types of analytical equipment and develop testing procedures for these devices.

Presenting at this regional conference is a step-up for Pham who last year tied for best presentation in the Natural Science Division of our campus's Undergraduate Research Conference describing research she helped conduct during the prior summer at the Eck Institute for Global Health of the University of Notre Dame. With two summer research experiences and two conference posters under her belt, Pham is rounding out her resume very nicely.

Chemistry Picnic on Campus next Monday

 

Chemistry and biochemistry majors unite!  Join us at our fall celebration pinic to meet classmates, alumni, and professors. Model your lab coats and show us your tie-dyed apparel. Get to know your fellow majors and network for opportunities (research, tutoring, scholarships, and internships). Eat pizza and play corn hole.  Bring your appetite and any questions you might have about our program.

When?     Monday, September 19, 5:00 PM
Where?   Riverside Pavilion (across the street from Northside)

Be there, or be cyclobutane!

RCMed Review Fellowship Winner Returns

In the Spring, biochemistry major  Alexandra Hochstetler won the RCMed Review Fellowship and chose to research this past Summer at the South Bend campus of the IU School of Medicine  with Professor of Pediatrics, Dr. Margaret Schwarz. Hochstetler spent the summer studying the role of the protein EMAP-II in lung development at the molecular and the cellular levels. A particular project investigated the development of mice which lacked the genes that code for EMAP-II. Hochstetler describes her experience as "awesome" because she got to do "new things everyday". It must have indeed been awesome as Hochstetler will continue to work with Dr. Schwarz during the school year.

Hochstetler is grateful for this opportunity which allowed her to further develop her critical thinking and trouble shooting skills. She also learned to see how the work of individual research teams fits within the big picture of scientific discovery. Hochstetler plans to take a year "off" after college to carry out some more laboratory research, then go to medical school, and finally work in medical research.

Our campus will be accepting applications for next year's RCMed Review Fellowship in the Spring semester. If you are interested in this fellowship or other research opportunities, please contact your favorite biology, chemistry, or biochemistry professor for details.

Biology Chemistry Club Welcomes Students

The Biology Chemistry Club welcomed new students this week by helping them make “slime” and blowing off steam launching film cans into the air with Alkaseltzer and water. They also displayed several examples from the biological world with molecular models. The club has plans for science outreach, tie-dyeing lab coats, tours of local industries, guest speakers from academia and industry, informational panels from medical school admissions, and, of course, the traditional end of year geek party. For more information about the club you can check them out on Facebook and their university site.

Summer Research in the Anderson Lab

Niles High School student Madeline Stanton and biochemistry major Victor Gutierrez-Schultz have been working with Professor Gretchen Anderson this summer to correct a mutation in the enzyme, arsenite oxidase. The two genes for the enzyme (one gene for each subunit) were cloned into E. coli by previous IU South Bend students, but along the way, a mutation was introduced in the smaller subunit. Victor analyzed the sequencing data from last year (thanks to 2016 biochemistry graduate Jared LaRue), found the mutation, and used genetic engineering to fix the mutation back to its native nucleotide. Both Madeline and Victor then worked together to confirm that the mutation was indeed fixed, and are now sequencing the two genes to determine if any further mutations were introduced during the fix.

Summer Research in the Muna Lab

David Aupperle is making the transition between his freshman and sophomore year as a chemistry major - and he isn't taking the easy road.  He is spending most of his summer in Professor Muna's laboratory learning and applying electrochemistry.  David's project is to develop a stable palladium modified electrode that offers long term stability and efficiency in catalyzing the electro-oxidation of steroid hormones. The ultimate goal is to employ this electrode for electrochemical detection of steroid hormones in water. 

David is the first student to be awarded the new Carolyn & Lawrence Garber Summer Research Scholarship which provides support for full-time research for one lucky student in the department.  David plans to attend graduate school to receive a Ph.D. in chemistry.  With interests in education, he is uncertain whether to pursue a career in industry or academics - but he has plenty of time to decide.

Summer Research in the Rizk Lab

Biochemistry Professor Shahir Rizk has three students working with him on three separate projects. The first is Pierre-Emmanuel N'Guetta [left photo], an international student from Ivory Coast majoring in biology.  He is continuing a research project that began in the Fall semester with the CHEM-C 486 (biochemistry laboratory) students designing a biosensor for glyphosate, the active ingredient in the herbicide RoundUp . Pierre plans to pursue a career in the medical field.

Next up are Michele Costantino (left) and Riley Bigelow (right) shown in the second photo.  Both students are biochemistry majors funded by SMART grants (student-mentor academic research team).  Michele is working on engineering reversible self-assembly of biological molecules with applications in the design of new nano materials and biosensors. She hopes to continue doing research at the graduate level.

Riley is working on engineering new proteins that can modulate the activity of enzymes with the hope of rescuing a dysfunctional enzyme that is caused by genetic mutations associated with inherited severe combined immune deficiency (SCID). This is a deadly disease with very few treatment options. She will also be investigating whether this technology can be applied to other genetic disorders.

Shahir Presents Work at Protein Symposium

Biochemistry professor Shahir Rizk travelled to Baltimore, Maryland last week to attend the 30th Annual Symposium of the Protein Society.  This is a yearly gathering for protein scientists spanning many disciplines including protein folding, structure, characterization and engineering. It also features the latest technologies and cutting-edge tools for researchers. Rizk presented his poster titled Controlling protein structure and function using engineered allosteric effectors which describes work based on collaborations with Rizk's colleagues from the University of Chicago, Notre Dame and Indiana University School of Medicine.  Rizk has only been at IU South Bend for a year, but has already built a bustling research program with three undergraduate students hard at work this summer.

Internships at IU South Bend

The IU South Bend Foundations magazine for alumni and friends of the university feature two students from our department in an article about internships for their spring/summer 2016 issue.  The photographs above are taken from the Foundations magazine - online issues may be found here: Foundations magazine.  Internships, and also undergraduate research, are valuable opportunities that help students learn more about their subject and get an idea of what working full time in their field might be like. Such experiences also look very impressive on resumes and applications to graduate or medical school.

 

Carrington Boyd is a senior chemistry major who received internship credit for her work at The Indiana Whiskey Company.  She was introduced to the occasional distillation in the sophomore organic chemistry lecture and lab, but now deals with the process daily. Carrington is quoted in the article as saying "I put into practice the concepts I learned in the classroom to make enough whiskey to meet the demands of our customers." 

Krista Schilling interned at Lebermuth Company during the summer after her junior year. Lebermuth extracts and purifies naturally occurring fragrances, flavors, and essential oils.  Krista remarked "I learned what it really means to be a scientist.  Instead of using some of these instruments once, I was able to use them every day.  My summer internship at Lebermuth taught me what it means to work as a scientist, all day, every day.  I loved it."  Krista graduated with a B.S. Biochemistry degree just this past May.

Summer STEP Program

This summer our department offered one of three classes as part of the campus's STEP program (Summer Teen Enrichment Program).  STEP offers students who are entering one of the four years of high school exposure to an area of college study with a focus on hands-on experience.  Adjunct Professor Pat Boettcher took a group of these students through a one-week adventure in forensics science in five three-hour lab based sessions.  Boettcher is pictured here holding a piece of thin-layer chromatography paper in a developing jar used to separate the different components in certain over-the-counter medicines according to their solubility in a solvent.  Classroom data - in the form of unitless retardation factor - appears behind him on the blackboard.

Alumnus Spotlight - Kasey Clear

IU South Bend graduate Kasey Clear (Chemistry, 2011) was awarded his Ph.D. in Chemistry from the University of Notre Dame for his dissertation Molecular Probes for Biomembrane Recognition.  During his five-year journey through graduate school, Kasey published research in Bioconjugate Chemistry, Chemical Communications, Journal of Materials Chemistry, Analyst, and even co-wrote the book chapter Synthetic Receptors for Polar Lipids in the book titled Synthetic Receptors for Biomolecules edited by his thesis advisor.  He somehow still managed time for activities other than coursework and research. Here he is pictured helping out with the "You be the Chemist" Challenge - a nationwide contest for students in grades 5 to 8. 

 

This fall Kasey is heading to Murray State University in Kentucky to start his professional career as an organic chemistry professor.  The department offers undergraduate and masters degrees.   He was attracted to Murray State in part by its well-equipped research laboratories where he plans to continue research - but Kasey also says that his positive experiences as an undergraduate at IU South Bend influenced his decision to take a position at Murray State, a regional public university like ours.  We are all very proud of you, Kasey.  Congratulations! And good luck! 

Graduate Letty Black Publishes Research

Almost two months after graduation, Letty Black has received a late graduation present: becoming a published author.  Her computational work with Professor Marmorino was just published in the Journal of Mathematical Chemistry in an 'Online First' format before being assigned to a particular volume of the print journal.  Letty worked with Marmorino during the summer of 2015 between her junior and senior years.  Their research generalized an old formula (scalar version) that computes lower bounds to the expectation values of positive operators to a matrix method, hence the title: Lower bounds to the ground-state expectation value of non-negative operators.  Essentially this means that they improved on a method to calculate HALF of an error bar (just the LOWER bound) to properties such as the average distance (always positive) of an atom's electron(s) from the nucleus. Such a distance varies with the state of the atom - for example the 1s state of the hydrogen atom keeps the electron close to the nucleus but a 4d state of the hydrogen atom keeps the electron much further on average.  Only for the hydrogen atom are these distances known exactly; for all other atoms we have only estimates from theory.  Congratulations to Letty on her publication!

Awards and Graduates 2016

Our department is blessed with many clever, industrious, and friendly students that make our jobs so enjoyable.  Most of them were able to attend the graduation ceremony and are eager to start the next phase in their life - whether work, medical school, or graduate school.  Many of the students pictured above in cap and gown are award winners, but each year the department also honors excellent students that have yet to graduate. After graduation, many students were able to gather with faculty, family, and friends for a relaxing evening of food, conversation, and games.  Congratulations to all these students for their hard work and success!

Freshman Chemistry Achievement Award

   Madison Kozlowski
Undergraduate Award in Analytical Chemistry
   Christopher Warkentin
Undergraduate Award in Organic Chemistry
   Rebecca Shembarger
Student Excellence Award in Biochemistry
   Krista Schilling
Student Excellence Award in Chemistry
   Mackenzie Redman
Joseph H. Ross Seminar Award

   Mackenzie Redman

Zeider Excellence in Biochemistry Scholarship
   Michael Rauschenbach
George V. Nazaroff Scholarhip

   Hannah MacLoed
   Christopher Warkentin

Fun in Organic Chemistry Lab

Students in Organic Chemistry lab finished off the semester by making polymers, including nylon 66 and polyvinyl alcohol gel. Student Ashley Dawson demonstrates the delights of synthetic polymers as she shows off her "slime" (polyvinyl alcohol gel).

This is the second year of the return of organic chemist Professor Doug McMillen to the lecture hall after many years of absence due to administrative duties. This year we also welcomed biochemist Professor Gretchen Anderson to the laboratory section. Our adjunct professors are a vital part of our department and serve our department and students wonderfully, but it is good to also have representation from the full-time research faculty in this sophomore chemistry sequence that caters to biology majors as well as chemistry and biochemistry majors.

Professor Rizk Receives Community Honor

Photo by Bluekrishna Photography

Biochemistry professor Shahir Rizk was recognized this afternoon at the Gillespie Conference Center by the Michiana Forty Under 40 program for his contribution and accomplishments in both the workplace and community.  One might claim that IU South Bend is where "it all" started for him: while much of the world was worrying about possible Y2K problems in 2000, Rizk was focused on graduating from IU South Bend with a B.S. in Biology and applying to graduate school.  But a more honest assessment must be that Rizk is one of those rare alumni who give back more than they have received.

Rizk chose to attend Duke Univeristy and obtained a Ph.D. in Biochemistry in 2006 for his thesis on rational design of biosensors and multi-sensor arrays.  Rizk then worked as a National Institutes of Health postdoctoral fellow at the University of Chicago in the field of antibody engineering and drug delivery for brain cancer research.  In 2012 he returned to the state of Indiana as a Research Assistant Professor at the University of Notre Dame where he engineered antibodies to study the pathogens that cause malaria and Ebola. He also served as Director of External Programs at the Boler-Parseghian Center for Rare and Neglected Diseases where he worked to connect rare disease patients within the community with healthcare professionals and researchers through outreach programs. There he remained until last fall semester when he joined our department and set up a research lab with undergraduate students just as easily and quickly as he delivered successful lecture and laboratory courses.  His scientific enthusiasm and interest in students makes them, in turn, interested in and enthusiastic for biochemistry.

As a musician and a published poet, Rizk has a deep interest in promoting the arts and art education in the Michiana area and proves himself as a Renaissance man of sorts. He is founding member and president of Ulreia, Inc, a local non-profit organization that has organized and supported several local productions in visual, musical, theatrical and literary arts.  Rizk is currently leading an initiative to showcase the integration of different forms of art with elements of science, technology, engineering and mathematics.  He can often be found at Langlab South Bend, a venue partner for Ultreia, Inc.

We are thrilled that Rizk was chosen this year to be among the forty young professionals honored in the Michiana area, but we are more thrilled that he has chosen to work with us at IU South Bend in the Department of Chemistry and Biochemistry.  We hope that this award is icing on the cake of a wonderful academic year.  Congratulations!

Upcoming Online Course in Nanotechnology

This spring Professor Marmorino (top right) completed an 8-week course in distance education to prepare him for the development of our department's first online course: Nanotechnology.  We decided to go with the broader course nanotechnology rather than nanochemistry for many reasons, two of which are that (1) the field is so interdisciplinary that is hard to stick to just chemistry, and (2) this will be the only "nano" course at our campus so we wanted to give it a wider appeal.  The course will be offered this fall as a general education course (Natural World, N390) that simultaneously serves as a chemistry elective. Below is a tentative description of the course - tentative because Marmorino will spend the summer hashing out the details of topic spread and depth along with the method of delivery and evaluation.

 

Nanotechnology is the application of the science of small – small particles, but also small features on macroscopic objects. The size scale is so small that the atom must be constantly considered and the properties of bulk matter no longer apply. The course begins by developing an appreciation of the small scale and the implications this has on the variability of the properties of matter once thought to be constant for a given substance regardless of size. Students learn about naturally occurring nanoparticles and their impact in the natural word, but also consider the anthropogenic production of materials and the probing of their properties (mainly through various types of microscopy). Applications of nanomaterials to different disciplines are investigated with a focus on how the peculiar behavior of matter on the nanoscale allows technological advance. Selected topics may include air pollution, clouds, dust, DNA, proteins, micelles, drug delivery, buckyballs, nanotubes, surface tension, diffraction, scaling laws, quantum dots, wave-particle duality, compact discs, paint, and even Himalayan salt lamps.

Professor Anderson Wins Teaching Award

 

Our department is proud to announce that Professor Anderson was recently awarded a Trustee's Teaching Award for her sustained and consistent teaching excellence.  Especially impressive is that she was able to keep up her level of excellence while serving as department chair - a role which might have diverted the focus of lesser faculty.  Although we are proud, we are certainly not surprised; all the chemistry and biochemistry faculty recognize Anderson as a leader in education. If this one award does not convince you, then one need only consider the many other awards she was won for teaching and advising - and the many awards students have won to research with her as their mentor.  Congratulations Professor Anderson!

2016 Undergraduate Research Conference

 

Last Friday several students presented their work at our campus's annual Undergraduate Research Conference.  Biochemistry major, Khai Pham (top left), tied with another student for best presentation in the Natural Science Division with her poster presentation Comparison [of] Growth Rates in Cultured Malaria Parasites which described research she performed with colleagues at the Eck Institute for Global Health of the University of Notre Dame last summer. Chemistry major Chris Warkentin (top right) presented his summer research under a SMART grant with our analytical chemistry Professor Grace Muna entitled Preparation of Ni-Pd Modified Glassy Carbon Electrodes and their Characterization by Cyclic Voltammetry and won an honorable mention.  From last fall's biochemistry capstone laboratory course were biochemistry majors Krista Schilling (bottom left) and Andrea Vrydaghs (bottom right) presenting Developing a Biosensor for Glyphosate, the Active Ingredient in RoundUp which highlighted the results from a group of seven students under the guidance of biochemistry Professor Shahir Rizk.

 

Thanks go to Professors Grace Muna and Shahir Rizk as faculty organizers and also biochemistry major Riley Bigelow for their help to make the conference possible and run smoothly. And naturally we must thank the students presenters for their dedication to perform research as undergraduates and their courage to showcase their work to the students, faculty, and general public who attended the conference.

Student Photographs to Appear in Academic Bulletin

Look for these students from the Department of Chemistry and Biochemistry in the new edition of the IU South Bend Academic Bulletin.  Some of our students were chosen for this special photo shoot and we are pleased to have them advertise our programs and the university.

Judging at Local Science Fairs

 

The spring semester at IU South Bend offers a particular way for faculty and students to reach out to the community: science fairs.  This year the chemistry department was involved in three ways.  First Professor Doug McMillen let a Marian High School student work on a small project associated with McMillen's main research. The student explored the oxidation of alcohols with iodine and received an early introduction to FT-IR and NMR spectroscopy used to analyze the reaction products during their purification. Next, Professor Bill Feighery and biochemistry major Janae Lee helped judge the science fair projects of 6th and 8th grade students at St. Anthony de Padua School.  Janae Lee (left foreground) is shown in the picture above listening to a student's presentation with a fellow judge. Finally Professor Grace Muna served as judge at the Northern Indiana Regional Science and Engineering Fair held at Notre Dame's Stepan Center where each year the best projects of the local schools are displayed and judged at a higher level. While judging can sometimes be stressful and tedious when many projects must be viewed in a limited time, there is a great pleasure that comes from seeing children talk about science. 

Guest Speakers in Senior Seminar

Our senior chemistry and biochemistry majors are once again preparing their formal capstone seminars. By choosing topics related to their future jobs, students use the senior seminar to provide closure of undergraduate work and also launch their careers.  Several guest speakers were invited to give tips on preparing student talks and review papers.

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Two weeks ago,  Dr. Betty Lise Anderson (Professor of Electrical Engineering at The Ohio State University) provided invaluable information via her seminar, “Terrific Technical Talks” and fielded questions such as  “What happens if you run out of time before your last slide?” Her answer: “That means you didn’t practice your talk. Cut to the last slide." Anderson has been a guest speaker in this course for several years  - and many students have benefited from her advice.
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This week, two alumni of the biochemistry program gave tips from the students' perspective: Calvin Streeter (Biochemistry, 2011) is in his second year of medical school at the Marian University College of Osteopathic Medicine in Indianapolis, while Geoffrey Taghon (Biochemistry, 2015) won a research award last spring that led him to be coauthor of a biochemical research article published just last month (click here for the full story). Both students are previous winners of the Joseph H. Ross Seminar Prize awarded to the best seminar each year. Their take away lesson: start preparing early, use your coach, and practice your talk.

 

Calvin Streeter, is pictured above with Professor Gretchen Anderson, who has been teaching the seminar course for the past several years and has made plans to expand the course to allow it to satisfy general education requirements in the future. With 16 students in senior seminar (record breaking!), there will be a wide variety of topics, ranging from nanochemistry to medicinal chemistry to environmental chemistry. 

Student Publishes Resarch on Ebola Virus

Last spring biochemistry major Geoffrey Taghon was awarded the campus' first RC MedReview Fellowship which enabled him to research last summer with  Dr. Robert Stahelin (of the Harper Cancer Research Institute) at the University of Notre Dame. Our department just received word that their work on the Ebola virus was published in the January issue of Nature's Scientific Reports. Taghon and his colleagues investigated one of the proteins produced by the virus; specifically they explored its binding to the cell membrane and its organization into a hexamer.  Taghon graduated last fall and is now in the process of applying to graduate school. Previously he had planned to attend medical school, but he enjoyed his summer research so much that he has decided to become a different type of doctor by earning a Ph.D.  This illustrates one of the many advantages of an undergraduate research experience: a glimpse into the career of a research scientist. His picture above was taken in the hallway at IU South Bend where research posters of other students are seen in the background.  Congratulations, Geoffrey, we are all very proud of you!

Chemistry Student Showcased to Alumni

 

Last spring, chemistry major Chris Warkentin applied for the Barry M. Goldwater Scholarship and Excellence in Education Program.  He did not win the award, but did receive an honorable mention for his achievements.  This is a first for our campus.  Later that semester he received a SMART grant to research with chemistry professor Grace Muna over the summer.  Now a year later, Chris plans to apply for the Goldwater Scholarship again.  Armed with more research, more awards, and more education, his chances are good and we hope for the best.  The full story about Chris' scholarship effort and research were highlighted in the 2015 Fall/Winter issue of alumni-reaching Foundations magazine, which is also the source of the picture above (unfortunately the current issue is not yet online - please click here for a temporary link). 

Carolyn & Lawrence Garber Summer Research Scholarship

Emeritus Professor Larry Garber and his wife Carolyn have generously established funding for students interested in summer research.  Garber was the inorganic chemist for many years before he was called to serve in administration (vice chancellor and dean were some of his titles).  He was a prominent voice in the department and is now making an impact even in retirement.  Because many IU South Bend students must juggle course work with part-time jobs to pay for school, research is often not an option. The summer research scholarship provided by the Garbers will change this.  The photograph above was taken from  the Fall/Winter 2015 issue of IU South Bend's Foundations publication where you can find more information about the Garbers and their scholarship (the previous issue, and perhaps soon, this one, can be found online  - please click here for a temporary link).  This scholarship is just one of several recent examples of the community giving back to IU South Bend: in 2015 RC MedReview Fellowship was established and in 2012  the Brian A. Zeider Excellence in Biochemistry Scholarship was first offered. Thank you very much, Larry and Carolyn, for the generous opportunity you have provided for our students.