Office of Undergraduate Research Undergraduate research will set you apart.

The Potential Role of Inflammation in Oocyte Health and Developmental Potential

By: Sara A. Gorman, Casey C. Read, Kaitlyn M. Phillips, Terry D. Brandebourg, and Paul W. Dyce



Evaluation of Açaí and Maca Extracts for CYP3A4 Enzyme Induction

By: Elizabeth Lopez, Yilue Zhang, Da Jung, Kodye Abbott, Satyanarayana R. Pondugula, Angela I. Calderon


Development of an in vitro model to evaluate novel genes regulating inflammation and fibrosis



The Biofluid Mechanics of Expiratory Central Airway Collapse in Patients with Chronic Obstructive Pulmonary Disease

Student Author: Andrew Lenzie

Co-Authors: Dr. Vrishank Raghav; Surya Bhatt, M.D. (Pulmonologist at the University of Alabama at Birmingham)

Over 11 million people in the U.S. suffer from chronic obstructive pulmonary disease (COPD), the third leading cause of death. COPD is a progressive disease that irritates, inflames, and weakens the lungs. An excess of mucus is produced that obstructs the lungs and makes breathing difficult. Smoking is the primary cause of COPD; with no cure, much of the medicine is preventative [1]. Collapse of the central airway of greater than 50% has been associated with cigarette smoking and COPD. This condition has been named expiratory central airway collapse (ECAC), because the collapse occurs upon exhalation. This has been shown to result in an overall reduction of respiratory health of the COPD patient [2]. It is hypothesized that this collapse results in additional resistance to air flow and hence amenable to interventional therapy. The aim of this project was to develop a bench-top lung simulator to mimic the collapse of the central airway and measure the resistance to fluid flow.

The lung simulator was designed as a flow loop with water as the medium. Using water instead of air allows for the use of pumps, and the water can be measured more easily. A bladder pump allows for compressed air to pressurize the chamber within which it is held, thus allowing the bladder full of water to compress and push water through the loop. Therefore, the bladder pump allows for controlled beating similar to both cardiac and pulmonary rhythms. Water is held approximately three feet above the pump and flexible tubing models the central airway, thus providing a pressure head on the system. The reservoir allows for water to be pumped continuously in the piping of the system. The flexible tubing is necessary to model the collapse of the central airway. A box was designed to contain the tubing and to be air tight. Air is compressed into the box with a modified sphygmomanometer. The tubing within the box is collapsed by positive pressure. The bladder pump, reservoir, and chest cavity box are connected in series to complete the flow loop. The bladder pump is controlled by a computer system and controller to provide successive compressions. This drives the water through the flexible tubing in the chest cavity box and up into the reservoir. Pressure and flow sensors have been installed and are being calibrated.

The flow loop design has been finalized, but sensor calibration is required to begin experimentation. Further investigation with the measurement of the changes to pressure and flow rate across the collapsed tubing (airway) compared to no collapse is necessary. This study will help physicians determine corrective measures by evaluating the effectiveness of interventional therapies, such as stenting of the trachea to stop the airway from collapsing. Future endeavors include patient specific 3D-printed airways from CT scans.

Statement of Research Advisor: “Andrew’s research focused on understanding the bio-mechanics of the recently discovered problem of expiratory central airway collapse among smokers who are suffering from chronic obstructive pulmonary disorder. He worked towards developing a bench-top physiological analog to study the mechanics of central airway collapse.”—Vrishank Raghav, Aerospace Engineering


  1. Lung Health and Diseases. American Lung Association. December 18, 2017.
  2. Bhatt SP, et al. Association Between Expiratory Central Airway Collapse and Respiratory Outcomes Among Smokers. 2016;315(5):498–505.doi:10.1001/jama.2015.19431

Lenzie Figure


Figure 1. (A and B) CT images of ECAC patient (see reference [2]), (C) bladder pump, (D) reservoir, (E and F) pressure sensor system, (G) trachea box with modified sphygmomanometer, (H) collapsed tubing, (I) respiratory simulation flow loop.


Anaerobic Digestion of Food Waste and Poultry Litter for Biogas Production

Student Author: Matthew Preisser

Co-Author: Brendan Higgins

Millions of pounds of food waste are generated in the United States every year, and Auburn is no exception. This food waste burdens the environment by contributing to pollution associated with landfills and is an inefficient use of natural and economic resources. Alabama alone produces over 1.5 million pounds of poultry litter per year. Poultry litter contains harmful bacteria (e.g., salmonella) and high concentrations of nutrients that can contribute to water pollution. Currently, most of this litter is applied on the surface, but concerns about nutrient build-up in soils may soon limit this practice. A possible solution to divert poultry litter and other forms of food waste from the landfill is through the anaerobic digestion process. Anaerobic digestion has the potential to divert food waste and convert it into methane-rich biogas that can be used as a heat and electricity source.

The objective of this research project was to determine if locally sourced poultry litter and food waste are viable feedstocks for anaerobic digestion at Auburn University. It was hypothesized that both locally sourced poultry litter and food waste from on campus dining venues (the Village Dining) could produce biogas with high concentrations of methane, which can be used to generate heat. To test this, 160 mL batch reactors were loaded with varying amounts of inoculum containing methane-producing bacteria, water, and waste. They were then left in an incubator at 35oC for close to a month (Figures 1). Pressure readings were taken every two days to measure the gas buildup inside the reactors. In reactors loaded with a 1:1 ratio of waste to inoculum by volatile solids, a bio-methane potential (BMP) of 80.8 mL-CH4/gram of food waste and 183.5 mL-CH4/gram of poultry litter was achieved.

Through this research project, it was determined that a more efficient way to measure biogas production, other than measuring pressure changes, was needed in the laboratory. This is because the build-up of biogas (the metabolic end-points) in the headspace can inhibit further digestion. A more suitable approach is to allow biogas to leave the reactor while measuring its flow rate. A low-flow gas measurement device that monitors water displacement over time was consequently constructed. This device uses a time of flight (ToF) infrared ranging sensor and Arduino, a commercially available microprocessor, to monitor six different bioreactors at a single time. A Matlab™ code was also developed to be able to convert water displacement into a volumetric flow rate. Future students in the lab will be able to calibrate this device and use it to monitor larger scale reactors.

Moving forward, there is a desire to use the anaerobic digestion process in conjunction with food waste generated by TigerDining. A closed-loop food cycle that converts uneaten and wasted food into heat for greenhouses on campus has the potential to reduce Auburn University’s natural gas needs. The application of this technology can have a direct impact on Auburn University’s energy needs.

Statement of Research Advisor: Matt has carried out a project on anaerobic digestion of poultry litter and food waste in satisfaction of the requirements of his Undergraduate Research Fellowship. This research holds the potential to advance the conversion of waste materials into renewable energy and organic fertilizer. Closer to home, Matt’s project can have a transformative impact on food waste management practices at TigerDining on the AU campus. His results and development of a gas monitoring system have laid the groundwork for testing of fed-batch reactors operated over a long-time horizon. —Brendan Higgins, Biosystems Engineering

Preisser image

Figure 1: 160 mL bioreactor containing inoculum, waste, and water (left) placed in an incubator at 35oC (right).


A Shape-Memory Alloy Actuated Hand Exoskeleton

Student Author: Sean Vincent Herrera

Co-Author: Dr. Michael Zabala

Many musculoskeletal disabilities restrict motor hand movement to a degree that limits day-to-day function. The purpose of my research was to create a biomechanical glove that aides in finger movement for those with such disabilities. This was achieved by heating and cooling of shape memory alloy (SMA) wire laced into a finger of a glove.  SMA wires have a unique ability in which they contract in length under a heated condition, and return to their original length under a cooled condition, producing a “shape memory” effect. The exoskeleton fingers can thus curl from wire contraction with resistive heating of the wires. 

Two applications were tested with motion capture: (1) a 3D-printed finger and (2) a custom designed biomechanical glove. Data were also collected from a human finger to serve as an anatomical standard. For each finger, the angle that the mid phalange makes with the proximal phalange was calculated as a function of time. Motion capture data were processed so that the flexion of the 3D-printed finger and the biomechanical glove could be compared to that of the human finger.

The time to reach full flexion for the human finger, the 3D-printed finger, and the glove-assisted finger was approximately 1.2 s, 2.1 s, and 1.85 s, respectively; the change in the mid phalange joint angle over this time was 33.2 degrees, 64.7 degrees, and 29.8 degrees, respectively. Data from the 3D-printed finger and the human finger both show increasing values over time, indicating that the SMA wire in the 3D-printed finger was successful in actuating finger movement in the correct direction. The shape of the human finger flexion curve was different from that of the 3D-printed finger (linear vs exponential). This might be a result of greater joint friction in the printed finger than in the human finger, thus creating irregularity in the rate at which the 3D-printed finger actuates. The glove’s flexion curve and the human finger’s flexion curve were very similar in shape and range. The glove-assisted finger flexed at a similar rate as did the human finger. The similarity of the human finger flexion and the glove-assisted flexion demonstrates the glove’s capability of actuating an impaired user’s finger to produce natural, human-like movement.

This study demonstrates the performance of a custom-designed biomechanical glove that assists finger flexion through the controlled heating and cooling of SMA laced into the ring finger. Kinematic data of the 3D printed finger validate use of SMA wires for such finger actuation. The data from the glove-assisted finger and the human finger demonstrates that the glove can produce human-like finger flexion on an immobile hand. Future studies involve increasing actuation speed, load-carrying capabilities, and implementing a feedback control system for position and speed control of the fingers of the glove.

Statement of Research Advisor: Sean has designed, built, and tested a powered hand exoskeleton that is actuated with shape memory alloy wire laced within a glove. His design has the potential to aid in hand movement rehabilitation and to provide strength augmentation to the user. —Michael Zabala, Mechanical Engineering

Herrera Figure

Figure 1. The joint angle that the mid phalange makes with the proximal phalange as a function of time during the flexion process of a human finger, 3D-printed finger, and glove-assisted finger.

Electron-hole hopping as catalytic self-preservation: how catalase-peroxidase from Mycobacterium tuberculosis avoids the perils of peroxide decomposition

Student Author: Patrick Sahrmann

Co-Authors: Kirklin McWhorter, Jessica R. Krewall, Dr. Douglas C. Goodwin

Catalase-peroxidase (KatG), an enzyme produced by bacteria and fungi, is especially prominent among some of the world’s most prolific pathogens (e.g., Mycobacterium tuberculosis). These organisms use KatG to defend against H2O2 produced by host immune responses. Contrary to all other members of its enzyme superfamily, KatG is bifunctional, capable of catalase and peroxidase activities. Further, against long-standing predictions that its two activities would be mutually antagonistic, we have shown that peroxidatic electron donors (PxEDs) stimulate KatG’s catalase activity.

A narrow active site access channel prevents PxEDs from directly reducing KatG’s heme cofactor, suggesting that the protein itself must facilitate free radical transfer from within the active site and channel this absence of an electron to the periphery of the enzyme via oxidizable amino acids (i.e., electron-hole hopping) to prevent irreversible inactivation). This links the active site to the solvent-accessible surface of KatG. In this manner, peroxidase activity (i.e., the use of PxEDs) serves to uphold KatG’s robust catalase activity. We have shown that one prominent electron hole-hopping pathway begins with oxidation of an active site tryptophan (W321). A methionine (M377), an amino acid which contains an oxidizable sulfur, 3.9 Å away from W321 is a prime candidate for the next step in this mechanism.

To investigate this possibility, we used site-directed mutagenesis to generate M377I KatG, replacing methionine with the non-oxidizable amino acid isoleucine. M377I KatG variant displays similar catalase activity to that of wild type, indicating M377 is not directly involved in catalase turnover. Subsequent additions of substrate after an initial reaction with H2O2 in the presence of ABTS, a peroxidatic electron donor, show a decreased initial rate, suggesting M377 is pertinent in the mechanisms of catalase recovery. M377I is incapable of aiding in through-protein radical transfer from W321, leading to irreversible inactivation of enzyme due to advanced oxidation of the protein even in the presence of ABTS. As with both wild-type and W321F KatG, a variant of KatG with the previously mentioned tryptophan replaced with a non-oxidizable phenylalanine, inclusion of a PxED sustains the catalase activity of the M377I variant to the complete consumption of H2O2. We propose that possible pathways for through-protein radical transfer expand as the distance from the active-site heme cofactor increases, thereby producing a corresponding decrease in contribution from any particular oxidizable amino acid in catalase activity preservation. Future research will focus on generation of more variants of KatG to identify amino acids involved in the hole-hopping mechanism, as well as a definitive look at the iron oxidation states of the heme cofactor using Mössbauer spectroscopy.

Statement of Research Advisor: Patrick Sahrmann’s research has helped to elucidate how redox enzymes protect themselves from inactivation by the highly reactive intermediates they must generate as part of the chemical reactions they catalyze. Redox enzymes are essential in every realm of biology, and the particular enzyme Patrick worked on is central to how pathogens like Mycobacterium tuberculosis defend themselves from host defenses. —Douglas Goodwin, Biochemistry

Sahrmann Figure

Figure 1. Possible hole-hopping routes from the KatG active site. Blue amino acids indicate possible starting points for hole-hopping routes, while red amino acids indicate possible continuations of each route.