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.

Wednesday, April 11, 2018

Students give research talks in Oklahoma

From April 4 to April 7, chemistry majors David Aupperle and Abigail Praklet attended the National Conference for Undergraduate Research (NCUR) at the University of Oklahoma in Oklahoma City. Both students gave oral presentations describing their research with analytical professor Grace Muna. The fact that each of their efforts spanned more than one semester or summer of work is a testament to their dedication and love of chemistry. Aupperle and Praklet had a wonderful time at the conference (travel was supported by a SMART travel grant) and we are proud to have them represent our department and university. The titles of their talks and abstracts are given below.

Electrochemical Detection of Estrogenic Compounds Using Palladium Nanoparticle Modified Electrodes
David Aupperle, Professor Grace Muna  

Chemical pollution in water is one of the major environmental problems in today’s world. Polluted water poses a threat to the aquatic organisms and human health. The pollutants such as estrogenic phenolic compounds (EPCs) need to be monitored constantly to control their impact on the environment and the ecosystem. These EPCs can be found in fresh water from waste treatment facility effluents as well as agricultural runoffs. Although the concentrations these compounds are typically low in the ng/L range, they have been found to feminize male fish and disrupt human endocrine function. Electrochemical detection provides an alternative to other analytical methods because it has attractive attributes such as high sensitivity, less expensive instrumentation, ease of sample preparation and field deployable. This work utilized the unique properties of electrodes modified with metal nanoparticles. The nanoparticles circumvent the electrode fouling seen on bare electrodes during the electro-oxidation of phenolic compounds. In the present work, glassy carbon and gold electrodes were modified with palladium nanoparticles to catalyze the electro-oxidation of EPCs. The modified electrodes exhibited good catalytic properties, good response precision and stability. For example, 50 consecutive measurements for 100 mcM estriol solution using palladium modified gold electrode gave a %RSD of 5.3%, indicating good reproducibility and response stability exhibited by the modified electrode. Future directions will be to couple the modified electrode to flow injection analysis and high-performance liquid chromatography. Results from the analytical performance of palladium modified glassy carbon and gold electrodes towards the catalytic oxidation of EPCs will be presented.

Developing a Sensitive Stripping Voltammetric Method to Detect Lead in Water and Soil
Abigail Praklet, Keon Jones, Joseph Williamson, Professor Grace Muna 

Lead is one of the most toxic heavy metal in the environment. Its presence is due to human activities notably, lead in gasoline, lead-based paint, lead-containing pesticides, lead in ammunition and sinkers, and incinerator ash or water from lead pipes. Lead poisoning can cause a number of adverse human health effects, but it is particularly detrimental to the neurological development of growing children. Therefore, frequent testing and precise monitoring of Pb in soil and water is important to assess and control lead contamination. We hereby report on developing a stripping voltammetric method using glassy carbon electrodes modified with bismuth nanoparticles (GC-BiNPs) to detect lead in drinking water and soil. Voltammetric stripping measurements have historically utilized mercury in the forms of hanging mercury drop and mercury film electrode to measure heavy metal ions. This is mainly because clean surfaces can be easily be regenerated with a new mercury drop. However, because of mercury toxicity and risks associated with its disposal its use as an electrode material for stripping measurements is severely restricted. We’re utilizing the unique properties of bismuth such as its ability to form alloys with different metals, to develop a sensitive method to detect lead. Preliminary results show that using GC-BiNPs we can detect low levels of lead down to one part per billion in water. The research findings on the stripping voltammetric method development will be presented.

Monday, April 9, 2018

Student presents research poster in Missouri

Biology major, Keon Jones, travelled to Missouri a couple weeks ago to attend the two-day (March 23 & 24) MoLSAMP (Missouri Louis Stokes Alliance for Minority Participation) Undergraduate Research Symposium. His poster describes research done last summer with chemistry student Abigail Praklet under the guidance of Professor Grace Muna. Harnessing the power of electrochemistry to develop methods to analyze the components and concentrations of solutions is standard practice and led to the development of pH meters long ago. But Jones' project takes a relatively new twist by incorporating nanoparticles of bismuth into the electrodes of the detection unit to increase sensitivity to lead. Jones' poster and presentation were well received at the symposium and we are proud to have him represent both the biology and chemistry departments, as well as the entire campus. Jones plans to continue researching this summer, but this time under an REU at another university studying molecular biology as his attention turns toward life after IU South Bend using his upcoming biology major. The abstract for his poster is given below.

A Sensitive Electrochemical Method to Determine Lead in Water and Soil
Keon Jones, Abigail Praklet, Professor Grace Muna

Lead is one of the most toxic heavy metal in the environment. Its presence is due to human activities such as the use of leaded gasoline before it was banned and lead in paint in older homes. Lead poisoning can cause a number of adverse human health effects but it’s particularly detrimental to the neurological development of growing children. Therefore, frequent testing and precise monitoring of Pb in the soil and water is important to assess and control lead contamination. We hereby report on developing a sensitive electrochemical method by using glassy carbon electrodes modified with bismuth nanoparticles (GC-BiNPs) to detect lead in drinking water and soil. Preliminary results show that with GC-BiNPs can detect low levels of lead down to 1 parts per billion in water. The developed method will be employed to detect lead in drinking water and soil. Preliminary results on the electrochemical method development will be presented.