Saturday, July 7, 2018

Summer research with Muna

Professor Grace Muna is the analytical chemist of the department. She shares with Professor Rizk the uncanny ability to keep her lab occupied year-round with undergraduate research students, which is a very difficult task because coursework typically pulls students away during the fall and spring semesters. This summer she has three students working with her on projects combining electrochemistry and nanochemistry.

Stacey Jean-Baptiste (pictured middle) is a biology major and LSAMP scholar. She is working on developing a sensitive method to detect homocysteine in biological samples by electrodepositing gold nanoparticles onto a glassy  carbon electrode to modify its surface. Gold nanoparticles are expected to catalyze the oxidation of homocysteine. Thiol-containing amino acids, such as homocysteine, play crucial roles in key physiological processes; homocysteine levels have been linked to a number of health disorders such as Alzheimer’s, Parkinson’s, and cardiovascular diseases. Therefore, developing a sensitive method to measure homocysteine in biological samples such as urine is important for prevention and treatment of these diseases.

Another biology major, Joel Green, (pictured left) came on board just three weeks ago. He stopped by to chat with Stacey and he took so long that Dr. Muna thought she should put him to work. She asked him whether he would be interested in research and he was up to it. Joel is working on the same project with Stacey, however, he's modifying gold (not glassy carbon) electrodes with gold nanoparticles and testing their performance on the catalytic oxidation of homocysteine and cysteine. This allows the group to do a comparison study to see which modified electrode outperforms the other in terms of selectivity, sensitivity and stability.

Chemistry major Joseph Williamson (pictured right) was continuing the ongoing work of developing a portable method to detect lead in water. He was testing whether bismuth nanoparticles on glassy carbon electrodes can be stabilized by a nafion polymer (based on Teflon) to enhance their long term stability. Joseph recently moved back to his home state, and will be continuing his education at University of Arkansas in the fall.

Thursday, June 28, 2018

Summer research with Rizk

The biochemistry lab of Professor Shahir Rizk (pictured second from the right) is rarely quiet during the academic year – and it is even busier this summer with three undergraduate research students. Biology major Pierre-Emmanuel N'Guetta (pictured far right) is continuing work on a project to develop a biosensor for glyphosate, the main ingredient in the herbicide RoundUp. He began the project last year with the help of a SMART grant, and now he has a protein-based fluorescent biosensor that can detect micromolar amounts of the pollutant. He is currently trying to use this biosensor to test for glyphosate in soil samples.

Biochemistry major Winnie Ihano (pictured far left) is funded by the LSAMP program. Her goal is to express and purify mutants of the human enzyme adenosine deaminase. This enzyme is important in the degradation of the nucleotide adenosine. Individuals with mutations in this enzyme suffer from Severe Combined Immune Deficiency (SCID), a fatal disease that leaves its victims susceptible to all kinds of infections. Winnie is generating recombinant forms of these mutants found in SCID patients and trying to isolate them in order to characterize them in the lab.

Biology major Chris Stewart (pictured second from the left) is also working on adenosine deaminase. His work, funded by a SMART grant, is concerned with engineering antibody fragments that can bind to the active form of the enzyme. By recognizing the active form of the enzyme, we hope that these antibody fragments can be used to convert the less active mutants found in SCID patients into active enzymes with the hopes of reversing the effect of the disease (at least in the test-tube).

In addition to his research with these three students, Rizk has been busy with other projects. He attended the first Regional Cottrell Scholar meeting in April at the University of Illinois, Urbana-Champagne, at the invitation of St. Mary’s chemist Dr. Kathryn Haas, a recent Cottrell Scholar who had previously taught at IU South Bend for a year before teaching at St. Mary’s College. The Cottrell foundation supports chemistry, physics, and astronomy professors who are developing innovative research and teaching programs at their institutions through their Cottrell Scholars Program. The meeting included former Cottrell scholars and members of their research groups as well as hopeful future Cottrell Scholars (such as Rizk).The meeting included presentations and roundtable discussions on research and teaching methods. Rizk had the chance to present a poster on his research in protein engineering and his teaching strategies that use discussion sections to introduce STEM majors to current events in science policy and new research developments through assigned readings and guest lectures by practicing scientists from academia and industry. Rizk was invited to submit a full application for the Cottrell Scholar program in July and we wish him success in this endeavor. 

Saturday, June 9, 2018

Summer research with Marmorino

No goggles for these students. Chemistry majors Conor McGee and Christian Moreno are spending the summer working on quantum mechanical problems with Professor Matt Marmorino. Their work is a combination of theory and computation - not a single chemical will be harmed in their research. Instead they'll be making good use of Mathematica to run number-crunching programs that they are very busy writing.

McGee is funded by the Carolyn & Lawrence Garber Summer Research Scholarship which is awarded each summer to just one chemistry or biochemistry major. He is testing (on the hydrogen atom) some old, but underutilized, techniques to calculate bounds to the energy and position moments for atoms and molecules. These techniques require information that is typically not available for traditional trial wave functions, but Conor is introducing an adjustable defect into the wave functions that, while reducing the quality of the wave function, allows for atypical information about the system to be calculated and utilized. If the approach works well on the hydrogen atom, then it should also work on more complex atoms and molecules too.

Moreno's work  is supported by one of several Louis Stokes Alliances for Minority Participation  (LSAMP) grants provided to STEM students at IU South Bend. He is testing simple quantum mechanical models to duplicate the known trends (such as atomic radius, ionization energy, and ground-state electron configuration) in the periodic table. The hydrogenic model, which ignores electron-electron repulsion is too simple to reproduce the trends; but the commonly-used Hartree-Fock method, which incorporates repulsion, is too complex for the beginning science student to fully appreciate and lacks a [rigorous] simple orbital interpretation.  Moreno is testing a model based on first-order perturbation theory that partly mimics the hydrogen model in simplicity, but incorporates at least some of the repulsion to reproduce the periodic trends. He's hoping that he doesn't need to deal with the repulsion in its full glory, because that is quite a task.

Tuesday, May 22, 2018

Outreach to Discovery Midde School

Last Friday, Professor Grace Muna went to Discovery Middle School in Granger to advertise science to the children. She was accompanied by some of her past and present research students Stacey Jean-Baptiste, Keon Jones, and Joseph Williamson. Muna and her team let the children perform several mini experiments, but one of their favorites was the production of worms using "worm goo" and "worm activator" available from Steve Spangler Science. The worm goo is an aqueous  solution of sodium alginate (a carbohydrate polymer found in seaweed) and the activator is just aqueous calcium chloride (used in pickles). The calcium displaces the sodium and with its greater charge (2+ not 1+) is able to bind strands of polymer together so that they lengthen and thicken to produce a precipitate of sorts that looks like gooey worms! 

Friday, May 4, 2018

Awards and Graduates 2018

While it is just the end of another year for many students, it is the end of journey for others. Whether they are off to graduate school, medical school, industry, or a gap-year of relaxation and soul-searching, our chemistry and biochemistry graduates are preparing to embark on a new adventure outside of IU South Bend - and most likely outside of South Bend itself. While we certainly congratulate all our graduates for their success, we would like to highlight those graduates - and their non-graduating classmates - who earned special recognition this year by winning awards and scholarships. Last night was an enjoyable time as Professor Gretchen Anderson (as Chair) announced our department's prize winners at the Honors Convocation of the College of Liberal Arts and Sciences.  Each student then each received a certificate acknowledging their achievement on stage from Professor Bill Feighery (as Associate Dean).

Freshman Chemistry Achievement Award
  Audrey Doue
ACS Undergraduate Analytical Chemistry Award
  Abigail Praklet
Student Excellence Award in Biochemistry
  Michele Costantino
  Khai Pham
Joseph H. Ross Seminar Award
  Khai Pham
Zeider Excellence in Biochemistry Scholarship
  Caitlin Schulz
George V. Nazaroff Scholarship
  Sandy Ho
  Conor McGee
Carolyn & Lawrence Garber Summer Research Scholarship
  Conor McGee
RC Med Review Research Fellowship
  Sandy Ho

Sunday, April 22, 2018

Professor Rizk receives teaching award

Assistant Professor Shahir Rizk was hired in 2015 to help with our expanding biochemistry chemistry. His sharp research skills and natural charisma quickly attracted a team of student researchers that seems to work non-stop. But if there was any doubt that his teaching abilities were are as sharp as his research skills, they've been put to rest because last week it was announced that Rizk was awarded a Trustee's Teaching award for, what else, excellence in teaching. While Shahir is well-known in the department for teaching junior-senior level biochemistry lecture and laboratory, he also teaches students in their first semester (freshman general chemistry discussion) and their last semester (chemistry senior seminar). Congratulations, Rizk!

Wednesday, April 18, 2018

2018 IU South Bend Undergraduate Research Conference

Last Friday, students from all over the campus gathered at Weikamp in the morning and early afternoon to present research and creative works from the past year. As usual, our department was well-represented; this year our students contributed two talks and three posters. Pictured above-left is biochemistry major Maggie Fink with her mother on her right arm, while pictured above-right we have fellow biochemistry major Michele Costantino. Further down we see biology major Keon Jones shown with Associate Vice Chancellor (former organic chemistry professor) Doug McMillen. Keon presented his poster earlier this month at MoLSMAP in Missouri (click here for abstract). Jones and Costantino tied for the best poster presentation from the crowd of science and non-science posters.

And finally we find chemistry majors David Aupperle and Abigail Praklet - who both gave talks - pictured with biochemistry professor Shahir Rizk (who moderated the science session). They also traveled out of state in early April to present their work, but they went to NCUR in Oklahoma (click here for abstracts). Praklet's efforts won her the award for best talk in the science session which was an excellent way to cap her summer-fall-spring research adventure with Muna.

But all of our student researchers - whether they presented at the conference or not - deserve acknowledgement for their research efforts and have gained a valuable experience that other students may have yet to claim.  If you are interested in research, please don't hesitate to ask about it. You can get the student point of view from fellow classmates - or visit one of your favorite professors to see what is happening outside of class.

Self Assembly of Novel Proteins Using Maltose Binding Protein and Engineered fABs
Maggie Fink, Professor Shahir Rizk

Many proteins undergo a large conformational change upon binding to a ligand. This conformational shift can expose protein surfaces previously shielded in the unbound state. A class of proteins that exhibits this conformational change is the bacterial periplasmic binding proteins. Each member of this family of proteins binds to a specific ligand, resulting in a shift from an open (unbound) to a closed (bound) conformation. Maltose binding protein undergoes this conformational change in response to maltose binding and transitions from an open to a closed form. To characterize the thermodynamics of these transitions and lock MBP into specific conformations, synthetic antibodies were designed to bind to MBP and screened in different maltose conditions to target both open and closed conformations. Three of these antibodies were isolated, one of which was found to bind to the open form of MBP endosterically (7O) and the other two, D1 and A1, bind to the closed form allosterically and peristerically. The aim of my project has been to construct a novel protein fusion where MBP and one of antibodies identified in the previous research are fused together. In this way the engineering proteins will potentially self-assemble into a nanostructure in the presence or absence of maltose, depending on the specificity of the antibody to the conformation of MBP. Once each of the three fusion proteins have been successfully cloned, expressed and purified, testing will be carried out to determine if a higher order complex can form in response to ligand addition or removal as a trigger.

The Effects of Metal Cofactors on Adenosine Deaminase Activity
Michele Costantino, Maggie Fink, Sandy Ho, Professor Shahir Rizk

Adenosine deaminase (ADA) is a zinc-dependent enzyme that converts adenosine to inosine as part of the purine degradation pathway. In humans, mutations in ADA are associated with severe combined immunodeficiency (SCID), an often fatal syndrome, due to accumulation of adenosine. This leads to B- and T-cell death, compromising the ability of the patient to fight infections. Previous work has shown that enzymatic activity depends on zinc concentration; however, at greater than 1:1 ratio, Zn can act as a negative allosteric effector of ADA activity. Other divalent cations — such as Co2+, Cu2+, Mn2+, and Cd2+ — can act as competitive or non-competitive inhibitors of the purified human enzyme. Additional studies indicate that Hg2+ inhibits crude ADA extracts from zebrafish at high concentrations. To characterize human ADA, kinetic studies with purified enzyme were conducted using direct colorimetric assays. Under optimal conditions, the rate of reaction was used to determine the KM and kcat of the uninhibited enzyme. The KM and kcat values were also obtained in the presence of coformycin, a known competitive inhibitor. The activity of ADA was measured in the presence of various divalent cations and Hg2+ was found to have the most profound negative effect on ADA activity. The inhibition of ADA by Hg2+ was found to be concentration dependent. This is the first study where the effect of Hg2+ on purified human enzyme was determined.