Biology Lab

Summer CoRPS Project Descriptions

The following faculty projects are eligible for Summer CoRPS student collaboration:

Mechanistic Studies of Laser-induced Color Changes in the Model Visual Pigment Bacteriorhodopsin

Judit K. Beagle, Chemistry, College of Arts and Sciences
Angela Mammana, Chemistry, College of Arts and Sciences
Mark B. Masthay, Chemistry, College of Arts and Sciences

Bacteriorhodopsin (BR) is a purple trans-membrane protein that is responsible for the color and function of the purple membrane (PM) found in the bacterium H. Salinarium. BR is structurally and functionally similar to the human visual pigments rhodopsin and iodopsin found in the rod and cone cells of the eye. We have identified an irreversible purple-to-blue color change which PM undergoes upon irradiation with green laser pulses. In the proposed research, we will (1) synthesize a novel conformationally-locked BR chromophore, (2) reconstitute PM with this novel chromophore, and (3) characterize the role of BR chromophore conformation in this color change by irradiating the reconstituted PM. The broad, long-term objective of the proposed research is to characterize the mechanisms underlying the photodegradation of BR, with the ultimate goal of gaining insights into the mechanisms by which light damages the human retina, as rhodopsin and iodopsin are believed to mediate photochemical damage which contributes to degenerative diseases of the retina. This research may thus result in new strategies for the prevention and treatment of retinal disease. It should also provide new strategies for preventing or mitigating photodamage to BR-based optical data storage devices and BR-based artificial retinas.

Candidates must have completed CHM 123 & 124. Previous chemical research experience is preferred but not required. 

Effect of climate change on lake water balance: A case study at the Grand Lake St. Mary's, Ohio

Zelalem Bedaso, Geology, College of Arts and Sciences
Shuang-Ye Wu, Geology, College of Arts and Sciences

Climate change has an unprecedented effect on the hydrologic cycle with profound implications for water resources. Global warming has the potential to alter the frequency and intensity of precipitation, evaporation and soil moisture, runoff and stream flow, lake water balance, and groundwater recharge. These are all important issues for the Grand Lake St. Mary's in western Ohio, the largest inland lake in Ohio, which particularly vulnerable to toxic algal blooms because of its shallow depths. Therefore, this project aims to both establish the water balance for the Grand Lake St. Mary's drainage basin using water isotope and climate data, and examine the past and potential future changes of the lake water balance. It has four major objectives: (1) collect data on the stable isotopic composition of water for precipitation, river inflows, groundwater and lake water in the drainage basin; (2) build a hydrological model to establish the lake water balance; (3) examine past changes in the lake water balance; (4) investigate the potential future changes on lake water balance under different climate change scenarios. This study will enable us to understand the effect of climate change (temperature and precipitation) on the physical, chemical, and biological characteristics of the lake. Students will develop a wide range of skills such as (1) collection of environmental data in the field (i.e., temperature, pH, dissolved oxygen, conductivity), (2) water sampling from lake, surface and groundwater, (3) isotope and geochemical laboratory analysis, (4) climate data collection and analysis, (5) hydrological modelling for water balance, and (6) use of climate models to project future changes.

Students are required to have taken at least one introductory geology course, have basic computer skills including Microsoft word and excel, and a drivers license. Priority will be given to students with GIS knowledge and computer programming skills. The expected outcome of the summer fellowship is that the student will be trained 1) to perform environmental data collection and water sampling techniques for geochemical and isotope analysis, 2) to analyze water isotope in the lab, 3) to use GIS and the R programming language to analyze climate data, and climate modeling. Upon successful completion of the summer fellowship the student will write summary report and present the result in UD seminars as well as at national scientific conferences such as the Geological Society America annual meeting and/or the American Geophysical Union fall meeting.

Comparison of physiochemical properties of recombinant and native foot proteins

Don Comfort, Chemical and Materials Engineering, School of Engineering
Doug Hansen, Corrosion Science and Engineering, UDRI

This project will combine molecular biology techniques to clone and recombinantly express one of the adhesive proteins from the foot of the blue mussel Mytilus edulis and analysis of the native protein with physiochemical and/or protein folding computer analysis. The adhesive proteins that M. edulis produces comprise the attachment structure (byssus) which allows the organism to remain adhered to surfaces within the tidal zone. A number of these proteins are located at the substrate-byssus interface, and have been shown to coordinate with metals, such as iron, which makes the foot proteins of interest for biotechnological applications such as rust inhibitors.

The challenge to applying these proteins to biotechnological applications has been that they are harvested from the mussels, which results in only small yields of purified proteins. The use of molecular biology to clone and produce these proteins creates a means to generate significantly larger quantities of protein for study and potential commercial applications. The proteins generated as part of this study will be compared against native (from mussels) proteins to understand differences that may exist between the recombinant protein expressed in bacteria (E. coli) and those from M. edulis.

The cloning and expression of proteins in Dr. Comfort's lab will be complemented with detailed physiochemical analysis (polyacrylamide gel electrophoresis for visualization of protein purification, acid hydrolysis and amino acid analysis), comparing the native and recombinant proteins in Dr. Hansen's lab. In addition, 3-dimensional modeling of the protein(s) based upon their amino acid composition and sequence may be analyzed using protein folding software to gain greater understanding of the molecular mechanism of adhesion and metal coordination.

Over the course of the summer, students will work on various phases of the project, potentially learning highly transferable skills such as basic molecular biology skills for gene cloning, microbial cell culture for protein expression, and/or protein purification, characterization and analysis techniques.

Identifying oncogenic pathways in Drosophila tumor models

Madhuri Kango-Singh, Biology, College of Arts and Sciences
Pothitos Pitychoutis, Biology, College of Arts and Sciences

Glioblastoma multiforme (GBM) is a devastating form of primary brain cancer with poor prognosis. Current standard of care extends life by a few months. Thus, it is important to explore the mechanisms (oncogenic pathways) that drive glioma growth and find pharmacological inhibitors (drugs) that target these pathways to find better tools for glioma therapy. We have established a glioma model in a simpler organism - the fruit fly Drosophila. Our model coactivates the genetic lesions most commonly associated with human gliomas and therefore is clinically relevant. We propose to use this model to find molecular inhibitors of glioma growth using a chemical library of tyrosine kinase inhibitors (Aim 1), and study oncogenic pathways activated by genetic lesions commonly found in human patients in fly glioma models (Aim 2). Overall, data from these studies will provide 'proof of concept' for investigating the molecular signaling involved in glioma growth, therapy resistance and recurrence of GBM, and provide data that will facilitate applications to national agencies for research funds.

We are looking for students with interest in genetics and biochemical signaling interaction mechanisms, and familiarity with basic Mendelian concepts. A prior experience with laboratory safety practices (e.g., in handling chemicals) and Drosophila genetics is not required but desirable.

At the completion of this project we expect to:

  1. Identify oncogenic pathways that are activated with and without drug treatment
  2. Identify inhibitors of tumor growth using a chemical library
  3. Validate the drugs found in the initial primary screen by secondary screens

These studies will provide the framework for applying to extramural funding for the PIs, and for students to develop research projects (e.g., Honors' or independent research) that are expected to lead to enriching outcomes (e.g., presentations in local/national research symposia and/or authorship in peer-review research publication).

Insectile Neurochemistry: developing a novel HPLC-based method to assess neurotransmitters in the grasshopper brain

Chelse Prather, Biology, College of Arts and Sciences
Pothitos Pitychoutis, Biology, College of Arts and Sciences

In the context of this collaborative, interdisciplinary research project our team will develop a novel assay to quantify neurotransmitter levels (i.e., dopamine, serotonin, glutamate) in the grasshopper brain. Ex vivo neurochemical analysis will be conducted using state-of-the-art high-performance liquid chromatography (HPLC) with coulometric detection. This assay will be useful to determine whether grasshopper diet quality affects neurotransmitter activity. Dr. Prather's lab has documented changes in grasshopper communities in relation to certain nutrients, and this would help to determine whether these changes are resulting from changes to brain chemistry, as has been suggested in the literature. The successful applicant should have demonstrated interest in the fields of neuroscience and/or ecology, prior laboratory research experience, and be proficient with the use of HPLC analytical techniques.

Finding new targets of amyloid plaque mediated neurodegeneration using Drosophila eye model

Amit Singh, Biology, College of Arts and Sciences
Muhammad Usman, Mathematics, College of Arts and Sciences

Alzheimer's disease (hereafter, AD), a fatal progressive neurodegenerative disorder with no cure to-date, manifests as a gradual decline in cognitive functions and finally the death of the patient. In AD, accumulation of hydrophobic human amyloid-beta-42 (Aß42) plaques trigger neurodegeneration (death of neurons) by unknown molecular-genetic mechanisms. Drosophila, with a large repository of genetic tools and similar genetic makeup to humans, is used for genome-wide screens, and therapeutic target-compounds screening for human disease. We developed a humanized fly model where we misexpress high levels of human-Aß42 polypeptides in the retinal/eye neurons, which exhibit AD like neuropathology in nearly 100% of flies. Our long-term goal is to employ our Drosophila eye model to identify (a) downstream target genes, (b) look for chemical inhibitors of Aß42-mediated Alzheimer's neuropathology. In a genetic screen, we identified highly conserved growth regulatory Hippo signaling pathway as a dominant modifier of AD Neurodegeneration. We will investigate the role of its reporters/sensors as biomarkers in Aß42 mediated-Alzheimer's neuropathology. We will screen the chemical inhibitors of Hippo pathway in their efficacy to block Aß42-mediated neurodegeneration. These potential gene and drug targets could be developed as diagnostic/therapeutic tools for neurodegeneration. We will use mathematical approaches to derive rescue percentages of neuronal population from neurodegeneration as a function of drug dosage.

The project requires disciplined individuals with a desire to learn modern day cutting edge biological techniques and mathematical modeling. A basic aptitude in biology and mathematics will be a great help to understand the project and prior training in handling Drosophila may be an added advantage.

Establishing analytical methods to measure short chain fatty acids in fecal samples

Yvonne Sun, Biology, College of Arts and Sciences
Erick Vasquez, Chemical and Materials Engineering, School of Engineering
Judit Beagle, Chemistry, College of Arts and Sciences

This project aims to test and establish analytical methods to obtain reproducible measurements of short chain fatty acids (SCFAs) in fecal samples from mice. SCFAs are a group of metabolites generated by the intestinal microbiota and have received increasing attention for their significant contribution to human health. The student on this project will work with fresh fecal samples generated from mice in Dr. Sun's lab, extract metabolites from fecal samples, and assess different analytical methods using available instruments in the Department of Chemical Engineering and the Department of Chemistry. The student will work with Dr. Sun's research team to collect fresh fecal samples from two mouse cohorts: aging mice and high alcohol preferring mice. The student will also help identify working protocols from published research, adapt available methods for our use, and perform data analysis-under the primary mentorship of Dr. Sun and collaborating mentorship from Dr. Vasquez and Dr. Beagle. We expect the student to work for approximately 35 hours a week for 10 weeks, participate in Dr. Sun's weekly lab meetings, and present at the Summer Science Research Symposium in August 2018 or the Stander Symposium in April 2019. Preferred qualifications for the student include: the ability to perform literature search and work independently when necessary; the ability to take initiatives in approaching faculty and asking questions; the basic understanding of analytical chemistry instrumentations; and the motivation to learn and practice scientific communication.

Collaborative research to study the evolution of bacterial antibiotic resistance

Yvonne Sun, Biology, College of Arts and Sciences
Timothy Reissman, Mechanical and Aerospace Engineering, School of Engineering

Antibiotic resistance is a worldwide threat to human health. This student project will focus on developing an automatic image capturing system to investigate environmental factors that influence the development of antibiotic resistance. The student will first work with Dr. Reissman to build and optimize an automatic image capturing device to take pictures of growing bacterial colonies. Then, the student will work with Dr. Sun to design different environmental conditions that may influence the development of antibiotic resistance. We expect the student to work for approximately 35 hours a week for 10 weeks, participate in Dr. Sun's weekly lab meetings, and present at the Summer Science Research Symposium in August 2018 and/or the Stander Symposium in April 2019. Preferred qualifications for the student include: the ability to perform literature search and work independently when necessary; the ability to take initiatives in approaching faculty and asking questions; strong organization skills; and the motivation to learn and practice scientific communication.

Computational modeling of ecosystems

Alan Veliz-Cuba, Mathematics, College of Arts and Sciences
Catherine Kublik, Mathematics, College of Arts and Sciences

This project is about the modeling of biological systems. The focus will be on nonlinear systems with applications to ecosystems, as well as the implementation of examples and algorithms in Matlab. We are interested in how the individual components of a system and the way they interact can give rise to complex behavior. To this end, we can represent each biological component as a variable, and the way the components interact can be represented by equations. The resulting mathematical object can be used to study the original biological system, to test hypotheses, and to gain theoretical understanding. This mathematical object can take many forms depending on the theoretical framework used, ranging from qualitative models such as Boolean networks to quantitative models such as differential equations.

The tentative systems we will study are ecosystems where humans participate (such as marine ecosystems) and ecosystems of cells (such as bacterial populations). In the first case we are interested in how human intervention can be modified to achieve a healthy equilibrium in the ecosystem. In the second case we are interested in how cell-to-cell communication can be modified to achieve complex patterns.

The selected student will design the appropriate mathematical representation to study the ecosystem and will use the model to make predictions. An ideal candidate for this project would have previously taken a course in differential equations and have a basic knowledge of Matlab.