College of Science

Faculty Research Projects:

Dr. Preston Aldrich, Professor, Biological Sciences:
paldrich@ben.edu

Dr. Jim Fackenthal, Associate Professor, Biological Sciences:
jfackenthal@ben.edu
 

• mRNA splice variants in BRCA2, a breast cancer tumor suppressor gene
  Background. Mutations in the BRCA2 gene are one of the two major genetic risk factors for familial Breast Ovarian Cancer Syndrome (HBOC). Individuals with strong family histories of breast and/or ovarian cancer are counseled to seek genetic testing for BRCA2 and other genes, but often DNA sequence analysis can be ambiguous because of DNA sequence variants of uncertain clinical significance (VUSs). To provide the best possible genetic counseling, it is important to characterize the potential pathogenic nature of these variants.
  
  One way that a DNA sequence variant could disrupt the function of the gene is by causing disruption of an mRNA splicing site. Analysis of such mutations is complicated by the large number of splice variants associated with wild type genes that appear with varying frequencies and abundances. The splice variants could give rise to alternate protein products, play regulatory roles as non-coding RNAs, or simply reflect splicing errors. Thorough understanding of all splice variant functions is critical to understanding both developmental and tumor suppressor functions of BRCA2. To begin this analysis, we will determine which splice variants are conserved between species and which are transported to the cytoplasm where translation is possible.

Research could be in-person or remote at Benedictine University.

View Dr. Fackenthal's home page

Dr. Ian Hall, Assistant Professor, Biological Sciences:
ihall@ben.edu

• Research in the Hall lab focuses on integrative physiology in amphibians. Students working in the Hall lab will utilize a variety of experimental techniques- including electrophysiology, behavioral monitoring and quantification- as well as amphibian care and handling. There are multiple projects in progress and under development. Students working in the lab are likely to get involved in most, if not all of them.
  • Project 1: Endocrine regulation of osmoregulation – Fresh water organisms face two major osmotic problems – they take on water and they lose salt. To deal with these problems, amphibians will osmoregulate with their skin. These processes are regulated by the endocrine system. Students interested in this project will measure ion movements through skin and how it changes under different conditions, in particular the presence of the hormone prolactin.
  • Project 2: The role of olfaction in sexual reproduction – In amphibians, vocal communication has been widely studied as a means to communicate sexual receptivity and locate a mate. Anecdotal evidence suggests that olfactory cues are also important in the species we study in the lab, but this has never been formally quantified. Students interested in this project will monitor and quantify behavior. If results are positive, there are opportunities for collaborations with Chemistry to isolate and identify important olfactory cues that can be identified behaviorally and electrophysiologically as potential pheromones.
  • Project 3: Amphibians in the changing world – Amphibians are often seen as indicator species for the effects of ecological change. For example, pesticides and other endocrine disrupting chemicals influence amphibian development and behavior. In addition to those ecological challenges, global climate change is already having serious deleterious impacts on animal populations around the world. Students interested in these concepts will develop hypotheses and examine the effects of water composition and temperature on a variety of physiological and behavioral variables.

Research will be in-person only at Benedictine University.

Dr. Leigh Anne Harden, Assistant Professor, Biological Sciences:
lharden@ben.edu
 

• The Harden Lab conducts integrative ecological research on reptiles and amphibians. Our lab’s central research questions revolve around of how these organisms function and interact with their increasingly modified environment, by studying them on a physiological, behavioral, and spatial/temporal level. This research is primarily field based; however, we utilize a number of computer-based and laboratory-based techniques (e.g. biochemical assays of animal tissues, microscope slide preparation and analysis, stable isotope analysis). All research has applications for conservation and management.
  
  Research projects for summer will involve intensive outdoor fieldwork 4-6 days/week of trapping turtles in local wetlands to investigate their species diversity, population structure and demography. Students will have the ability to develop their own side projects of interest within this larger project. Much of this fieldwork may be done in hot, muggy, and buggy conditions, so a hardiness in this kind of weather is a must. Attention to detail is important for high quality science. Curiosity and an ability to troubleshoot will contribute substance as well as enjoyment to our shared work experience!
  
  Research will be in-person only at Benedictine University.
  View Dr. Harden's home page

Dr. Casey Larsen, Assistant Professor, Chemistry:
clarsen@ben.edu

Transition metal-catalyzed isomerization of alkenes, which involves the atom economical migration of carbon-carbon double bonds. The challenges to be met include: positional and stereochemical selectivity, substrate generality, and simplicity of catalyst use. Alkene isomerization is an important process in the chemical industry that contributes to many applications, including the SHOP process, DuPont’s adiponitrile process, Takasago synthesis of (-)-menthol, and for the synthesis of fragrances, to name a few.

Students will learn techniques in organic synthesis to synthesize parts of the catalyst and organic substrates for catalysis; organometallic synthesism to make the catalyst; and molecule characterization to analyze the synthesized compounds and products made during catalysis. Students will not only perform chemistry in open air, but will be exposed to air free techniques (Schlenk techniques and glove box).

• Project 1: Synthesis of Royal Jelly Royal Jelly is a natural product synthesized by worker bees as a form of nutrition for the queen bee in a colony, where this compound has been reported to have pharmacological properties. The current synthetic route requires 6 steps for its completion. We are seeking a more economical approach to its synthesis.
• Project 2: Synthesis of Pheromones Pheromones are signaling molecules naturally synthesized by organisms as a social cue to impact social behaviors. Harnessing unique reactivity using the alkene isomerization catalyst has the potential to lead to a class of Lepidopteran pheromones.
• Project 3: Construction of a Catalytically Active Metal Organic Framework (MOF) Metal Organic Frameworks (MOFs for short) are a subclass of polymeric compounds. Organic scaffolds are linked together with structural metals to form 3-dimensional structures that have pores for molecules, solvent or substrates, to move in and out of the structure. With the right organic scaffold linker, we have the potential of making a new class of catalysts using organometallic synthesis.

Research will be in-person only at Benedictine University.

Dr. Annie Lin, Assistant Professor, Nutrition:
alin@ben.edu

The ENACT (Electronic Nutrition Approaches for Cancer-related Topics) Research Group focuses on using technology-assisted strategies to promote healthy lifestyle (diet, physical activity) behaviors for cancer prevention and symptom management. Students who join the group will learn how human interaction with technology can be used to promote shared patient care. We currently have several ongoing projects that will be conducted over the summer. Students will have the opportunity to participate in most of these studies, depending on remaining research hours per week. All research projects can be performed remotely during COVID-19.

• Project 1: Testing a Colorectal Cancer Nutrition App. For this project, we will be testing the feasibility, usability, and preliminary efficacy of a mobile nutrition app to promote healthy lifestyle behaviors among cancer survivors. Students will be asked to help assist with the trial and data collection.
• Project 2: Detecting Food Triggers for Gastrointestinal (GI) Symptoms. With collaborators from Northwestern University and Indiana University Bloomington, we will be using novel technological approaches to detect potential food triggers for GI symptoms. Students will be asked to help assist with study recruitment, management, and data collection.
• Project 3: Evaluating the Reliability of Nutrient Data from a Weight Loss mHealth App Intervention. We are investigating the reliability of food items and nutrient items that are reported in a mHealth app that has been used in weight loss interventions. Students will be asked to assist with data management and manuscript preparation.

Dr. Robert McCarthy, Associate Professor, Biological Sciences:
rmccarthy@ben.edu

• Research in the McCarthy Lab is focused on hominin skull anatomy and brain/body evolution. Summer 2021 research will focus on different approaches to reconstructing body size and shape in Homo erectus and other early hominin species. Students can expect to (1) collect measurements on specimens available at the Lisle campus or Field Museum of Natural History (if COVID19 pandemic restrictions are lifted); (2) identify, download, and archive data using Microsoft Excel; (3) manipulate images using Adobe Photoshop/Illustrator, tpsDig, 3DSlicer, MorphoDig, and other visualization software; (4) undertake statistical analysis in R; and (5) prepare a manuscript in coordination with Dr. McCarthy. Research can be conducted in-person (face-to-face) or virtually over Zoom. Prior experience with Adobe Illustrator and R is desirable but not required.
  View Dr. McCarthy's summer research page

Dr. Lindsey Mao, Assistant Professor, Biological Sciences:
lmao@ben.edu

The recurrence of glioma tumors is the main cause of mortality for patients diagnosed with glioblastoma. Proper treatment depends on early detection of the possible recurrence of tumors. By conducting differential expression analysis on deep sequencing (RNA-seq and miRNA-seq) reads and alignments of recurrent versus non-recurrent glioma tumors, we seek to both confirm many of the previously identified and discover new candidate genes that are involved in glioma recurrence. More specifically, we aim to understand how miRNAs regulate and affect the expression of critical genes as measured by the transcriptome that may be responsible for the recurrence of gliomas. A secondary aim is to corroborate our findings with those found in cerebral spinal fluid or blood deep sequencing samples to ascertain whether these candidates may be used as biomarkers.

The summer projects will be conducted entirely online. As a group, we will check in together daily to troubleshoot issues and share progress. Previous coursework in Genetics and experience with R is preferred, but not required. Students will have the opportunity to continue work on this project during the academic year.

Dr. Grace Mirsky, Assistant Professor, Computer Science:
gmirsky@ben.edu
 

• Computer Vision / Robotics: Lightweight, inexpensive robots and drones have grown in popularity in a wide variety of applications. Being able to quickly locate and identify an object of interest using one of these platforms is challenging. These challenges arise from the limited processing capabilities of inexpensive hardware and the inability to include additional hardware due to weight requirements. This project involves designing algorithms to facilitate accurate object detection using a low-cost platform (robot or drone). Extensive programming experience is required (must have already completed CMSC 270/CMSC 274) as well as some hands-on hardware experience.
• Reconstruction of Absent or Corrupt Physiologic Signals: Signal corruption or dropout can cause issues in continuous patient monitoring in the ICU. As a result, the ability to accurately reconstruct absent or corrupt signals as well the ability to detect if a signal is becoming corrupt as a result of noise, drift, etc. can greatly enhance critical patient care. Continuous monitoring is important because in the ICU, patient condition can quickly degrade, and continuous monitoring is necessary in order to detect problems and administer treatment immediately. In this project, we will work with a variety of different signals (electrocardiogram (ECG), respiratory rate, blood pressure, etc.) to determine how to best reconstruct the lost signal data. An important application of this work, in addition to providing robust, continuous patient monitoring, is the continuous estimation of heart rate, even when the ECG signal is missing. This project will be accomplished using predictive analytics techniques from machine learning. Extensive programming experience is required (must have already completed CMSC 3270/CMSC 3274).
• Reduction of False Arrhythmia Alarms: Frequent false cardiac arrhythmia alarms in the ICU have been shown to result in reduced patient care by diminishing attentiveness of the staff, due to the so-called “crying wolf” effect. In addition, these alarms often negatively affect the patient’s ability to sleep, thus also interfering with the patient’s recovery. As such, reduction of false alarms could potentially greatly improve care, but the criterion of not removing any true alarms creates a difficult constraint. In this project, we will work with the electrocardiograms and their associated alarms to develop robust algorithms to reduce the frequency of false alarms, while ensuring that no true alarms are removed. This project will use Matlab to develop and test appropriate machine learning algorithms. Extensive programming experience is required (must have already completed CMSC 3270/CMSC 3274).

Research will be conducted remotely.
View Dr. Mirsky's home page

Dr. Madhavan Narayanan, Assistant Professor, Physical Sciences:
mnarayanan@ben.edu

Many natural phenomena are driven by light. The molecules that absorb the light energy and respond to them are called chromophores. Apart from their role in biological processes, they also provide researchers a way for tracking these processes. Various experimental and computational methods have been used characterize their chromophores. The summer projects that the students will be working on involves using computational chemistry to understand the electronic properties of molecules belonging to two classes of molecules: Fluorescent nucleic acid base analogs (FBAs) and flavins.

• Project 1: Fluorescent nucleic acid analogs (FBAs) are structural analogs of naturally occurring nucleic acids. When FBAs are included in DNA and RNA sequences and excited with appropriate wavelength of light, they light-up the DNA through fluorescence emission. The intensity of their emission is dependent on the base-pairing, base-stacking and the solvent environment. Their fluorescence properties can also be modulated when DNA/RNA sequences binding to various proteins. In this project, we will computationally explore the electronic and optical properties of the FBA, 6-Methyl Isoxanthopterin (6MI).
• Project 2: Flavins are naturally occurring compounds which are ubiquituous, and serve as important redox cofactors in biological enzymes. They exhibit characteristic absorption and fluorescence based on their oxidation states, which make them vital molecules in biological reactions. In this project, we will computationally explore the electronic and optical properties of the lumiflavin and lumichrome, using Time-dependent density functional theory.

The summer projects will be conducted predominantly online. Although, the student may be required to meet a few times on-campus in person to access certain software programs. Interested and motivated students who have completed two semesters of general chemistry and a semester of organic chemistry should be able to pick up the computational tools used in these projects. Students will have the opportunity to continue work on this project during the academic year.

Dr. Tiara Perez Morales, Assistant Professor, Biological Sciences:
tperezmorales@ben.edu

• Bacterial quorum sensing (QS) is a mechanism in which gene expression modulation is coordinated within a population. Bacterial populations can communicate and coordinate responses using small hydrophobic peptides or pheromones. QS regulates different genetic pathways in Gram-positive bacteria. The focus of our group is in unique stand-alone transcriptional regulators termed Rgg, and their pheromones.

  Rgg proteins contain an N-terminal DNA binding domain and a C-terminal peptide binding domain. The pheromones that interact with this domain are generally small hydrophobic peptides (termed SHP). Interaction leads to upregulation of target genes. Rgg QS pathways have been shown to regulate competence, biofilm formation, toxin production, and virulence in Gram-positive bacteria. We are interested in Rgg loci present in the probiotic and human commensal Lactobacillus acidophilus ATCC 4357.
  L. acidophilus ATCC 4357 contains three predicted Rgg proteins named herein as Rgg499, Rgg1765, and Rgg155. No pheromones have been listed for Lactobacillus species. rgg499 is in a predicted six gene operon which includes a second transcriptional regulator and it is found upstream of maltose transport genes. rgg155 is in a predicted five gene operon and all genes are of unknown function. However, rgg155 was found to have some sensitivity under stress conditions in L. acidophilus NCFM. Lastly, rgg1765 is surrounded by predicted drug transporters and cell envelope proteases. Our main research questions are: What are the QS pathways regulated by Rgg proteins in L. acidophilus ATCC 4357 and what are the signals that induce these Rgg pathways?
  Previous studies have shown Rgg positively or negatively regulate adjacent genes including itself. Most Rgg proteins are stand-alone and have been shown to be positive regulators. One negative regulator has been shown to be paired with positive regulators. Given the arrangement present in L. acidophilus, we hypothesize all Rgg(s) may be positive regulators. We have constructed luciferase transcriptional reporters to observe changes in transcription. In addition, our reporters will be used to perform phenotypic arrays to identify potential inducing environmental signals. These constructs will be expressed in L. acidophilus and a heterologous host. Results from this project will provide insight in Rgg regulation.

Research could be in-person or remote at Benedictine University.
View Dr. Perez Morales' home page

Dr. Stefan Stefanoski, Assistant Professor, Physics and Engineering:
sstefanoski@ben.edu
 

Students at Benedictine University are offered the opportunity to conduct a state-of-art research by using equipment and methodologies similar to that used in modern R&D laboratories across the industry, such as potentiostats/galvanostats and solar simulators. Their research activities will meet the following objectives: analyzing the benefits from the renewable energy technologies, understanding the fundamental scientific principles behind them, learning and applying theoretical knowledge in real-time applications, hands-on measurements by using state-of-art equipment, and preparing students to enter the job market as skilled professionals or enroll in graduate schools with an advanced knowledge and experience in designing and conducting experiments.

• Project 1: Batteries for biomedical applications: Batteries can be used as power sources for motorized wheelchairs, surgical tools, cardiac pacemakers and defibrillators, dynamic prostheses, sensors and monitors for physiological parameters, neurostimulators, devices for pain relief, iontophoresis, electroporation, and related devices for drug administration. Students will investigate the types of battery chemistries used for biomedical applications and test their properties (charge/discharge cycling, internal resistance, operation in hot and humid environments, etc.).
• Project 2: Batteries for electric vehicles: This project is suitable for students majoring in engineering, physics, and/or chemistry, as it focuses on testing batteries used in electric (EV) or hybrid-electric (HEV) vehicles. Even though this project involves testing batteries on a laboratory-scale, it is intended to mimic the activities of engineers in companies and national labs who design batteries for EVs. Properties such as battery capacity and voltage will be investigated as function of cycling (charge/discharge). The effects of temperature variations and mechanical stress on the performance of the battery will be analyzed. Impedance Spectroscopy and Nyquist plot-analysis will be implemented to measure the internal resistance and assess the “state of health” of a battery.
• Project 3: Dye-sensitized solar cells (DSSCs): This is one of the latest promising solar photovoltaic (PV) technologies, focused on the design of solar cells that are light, inexpensive, transparent, and have the potential of achieving desirable efficiencies. The DSSCs will be assembled and their electrical properties measured. Various types of dyes will be tested in order to identify the inexpensive and abundant ones that will help us pave the road toward the next-generation low-cost and high-efficiency solar PV technology.
• Project 4: Standalone solar PV system for health clinics or schools in remote areas: The project will focus on designing a solar PV system for a health clinic or a school in a remote area, where no alternative sources of power are available. The project will encompass understanding of the operation and properties of solar cells, the components of a typical solar PV system (solar panels, batteries, inverters, charge controllers, etc.), and incorporating them into a final design. This project is suitable for students across a range of disciplines and majors: those interested in the engineering aspects of the design, as well as those interested in its humanitarian aspect, for example by delivering power to areas in third-world countries where power is either inaccessible or prohibitively expensive.

Research could be in-person or remote at Benedictine University.
View Dr. Stefanoski's home page

Dr. Matt Wiesner, Assistant Professor, Physics:
mwiesner@ben.edu

• Extraordinary Merging Galaxies in the Sloan Digital Sky Survey  In this project we will look at data from the Sloan Digital Sky Survey. We will be looking especially for extraordinary merging galaxies, that is galaxies that are gravitationally interacting. We are interested in finding merging galaxies that exhibit significant tidal bridges of stars and gas, extensive star formation and other extraordinary morphologies. Much of this project will involve visual inspection of astronomical images as well as analysis of astronomical catalogs.
• First Light for the Jurica-Havlik Telescope  In this project, you will go through the manual and learn how to use all the functions of the new 16-inch telescope and the associated CCD imager. We will be working out all the bugs to get the telescope fully operational. This project will require some early mornings or nights in order to do on-sky observing. At the end of the summer session I hope to have some good images of the Ring Nebula and other summer sky objects.\
• Looking at Galaxy Cluster Populations  In this project we will look at a sample of about 18,000 galaxy clusters and measure richness (number of galaxies in the cluster) using two different methods and then compare the results. The first method is the Voronoi Tessellation method and the second is the red sequence method. This project will require learning a few computing techniques.
• Modeling the Propagation of Pseudoscience  In this project, we will attempt to mathematically model the propagation of pseudoscientific ideas. Following on research that has modeled how rumors spread, we will take data on how false scientific ideas propagate, with a particular eye to astronomical pseudoscience. We will be investigating how these ideas are communicated and try to describe the rate and method of communication of such ideas.

Updated 02/03/2020