Bacteria are constantly evolving to become more resistant to antibiotic treatment. Pseudomonas aeruginosa, a harmful facultative anaerobic bacterium, is a prime example of this phenomenon. P. aeruginosa can affect many life forms and is found in the lungs of people with cystic fibrosis. The bacterium has evolved to become naturally resistant to many antibiotics, making its infections extremely difficult to treat. While its mechanisms of survival are unknown, P. aeruginosa can switch between aerobic and anaerobic respiration based on the availability of oxygen and other terminal electron acceptors. Under anaerobic conditions, P. aeruginosa relies on a catalyst called periplasmic nitrate reductase, or NAP, for energy generation. NAP seems to be integral to the function of P. aeruginosa in anaerobic growth conditions.
Amanda Myles, a senior in Biomedical Sciences, aims to characterize the role of NAP in Pseudomonas aeruginosa and its function in anaerobiosis. Her preliminary data suggest that NAP may be involved in the oxidation-reduction cycle of the bacterium. Amanda plans to attend medical school next year and says that her undergraduate research experience has caused her to consider a career as a research-active physician. She claims her research fellowship has been one of the most rewarding experiences of her college career. Her advice for prospective future research fellows is to “focus on research areas that interest you because doing research in an area that you find interesting or enjoy will make your experience so much better!”
In almost all mammals, females mobilize their bones during lactation. This can cause serious issues including bone fragility, compromised bone quality, and increased mortality rate. Kayla Frey, a recent graduate in Biomedical Sciences, examined how the number of pregnancies and the total number of young produced impacts the bone quality of female mice. Frey used the femurs from age-matched mice to determine variation in morphology and mineral composition. Because the mice were kept under semi-natural settings, Frey was able to assume that the animals’ bones experienced a level of strain that is comparable to wild mice.
Frey notes that her career opportunities have been broadened by her experience in research saying, “Before participating in the laboratory, I had never even considered that research might be a part of my future. After my experience with undergraduate research, I am open to a career in both research and medicine. I am looking forward to remaining involved in research throughout my time in medical school and I am hoping to continue researching well into my career as a physician.” Frey has been working with Dr. Wendy Hood in the College of Sciences and Mathematics for over two years and recently presented her research at the Auburn University “2018 This is Research: Student Symposium,” as well as the National Conference on Undergraduate Research at the University of Central Oklahoma this past spring.
Phillip Wang, a senior in the College of Science and Mathematics- Biomedical Sciences, is investigating whether organic pigments, known as carotenoids, can serve as antioxidants in living systems. Wang asserts that the study is important because most research done on this topic comes from studies outside of living systems. During his research, Wang used a zooplankton to test if carotenoid supplementation causes reduce mortality and reduced deactivation of aconitase, an important metabolic enzyme that, when exposed to a chemical called tBHP, can induce oxidative damage.
Wang has been an undergraduate research fellow for the past two years and is continuing in the fellowship for the 2018-2019 year. When asked what he would tell an undergraduate student who was considering undergraduate research, Wang said, “I would definitely encourage him/her to do undergraduate research! It enhances your critical thinking skills, is an excellent way to develop a relationship with a professor, and looks great on a resume.” Wang also talked about how rewarding his undergraduate research experience has been and how he feels accomplished to see his research pay off after many trial and error tests.
In addition to his time in the Undergraduate Research Fellowship Program, where he is mentored by Dr. Geoffrey Hill, Wang has also been a recipient in the Fund for Excellence scholarship program and received third place in the STEM poster category at the Auburn University “2018 This is Research: Student Symposium.” He also presented his research at the National Conference on Undergraduate Research in Oklahoma City this past spring.
Steatohepatitis, or fatty liver disease, causes harmful and sometimes deadly fibrosis of the liver. Although steatohepatitis can be a product of genetic predisposition, not much is known about the genes that play a role in its development.
Peyton Kuhlers, a junior majoring in Biochemistry, is researching a mechanism that can screen for potentially steatohepatitis-causing genes. His model used the CRISPR-Cas9 system which utilizes the Cas-9 enzyme to cut and mutate specific genes that could play a role in the development of liver fibrosis. Peyton experimented with this model by infecting mouse liver cells with a virus containing Cas-9 genes, and from there, grew an entire colony of Cas-9 cells. Continuing this research will lead to a better understanding of steatohepatitis and will hopefully help researchers to identify potential therapeutic targets.
Kuhlers, who now plans to pursue a research career, says that the best part of his project was improving his ability to work independently in the laboratory and to put into practice the techniques learned in the classroom. He advises future student researchers to find a professor whose work genuinely interests them!
Due to the increasing demand for energy, researchers have been looking for alternative renewable sources of energy and better means of energy transport. Polythiophene, a conductive polymer, has been found useful in this search because of its optoelectronic properties. Polythiophenes show potential to improve energy transport because of their ability to transition between semiconducting and conducting states. Jihyuk Kim, a senior majoring in Chemical Engineering, is working on synthesizing a derivative of a thiophene monomer and will soon be polymerizing the monomer into what he has titled PTEMA to investigate the thermal, optoelectrical, halochromic, and solution properties. So far, Kim has been able to verify each polymer intermediaries using 1H NMR spectroscopy.
When asked what was the most rewarding thing about his undergraduate research experience, Kim replied, “Having the opportunity to work on my own personal project, I get to see my progress as I spend many long hours of work. At first, many things went wrong, and I had barely any idea what I was doing. However, after many hours of research, I can now scientifically explain some of the phenomena that happen when I do chemistry. It thrills me to know that the polymer I am dealing with is something nobody has made before.” He went on to explain that this experience has allowed him to add context to his engineering courses. By using fundamentals that he learned from his organic chemistry class, Kim was able to relate his coursework to real-life circumstances. Kim also discussed how his undergraduate research experience has reaffirmed his career goals and has helped him develop a love for research.
Jihyuk Kim was a 2017-18 Undergraduate Research Fellow mentored by Dr. Bryan S. Beckingham in the Samuel Ginn College of Engineering.
Sushil Bhavnani, Associate Department Chair and Endowed Professor for Auburn University’s Mechanical Engineering program, began conducting research during his graduate studies at the Indian Institute of Technology Bombay. Bhavnani said he was blessed with excellent mentors for both his masters and doctorate who had a tremendous impact on his research journey.
“Those interactions at an impressionable age have helped guide my actions with my mentees,” Bhavnani says.
Bhavnani’s primary research focuses on the cooling of electronics. Bhavnani’s main research goal is to keep cell phones and large computers that are in data centers like Google, Walmart, eBay, and Amazon operating at low temperatures. The purpose of Bhavnani’s research is to guarantee these electronics are the most efficient they can be and last longer.
When mentoring students, Bhavnani identifies goals he wants his undergraduate students to accomplish. Bhavnani said he expects outstanding students not only to accomplish the goals he assigns, but to show independence and take ownership of projects by creating additional goals using their own creativity.
“My principle for research has always been to recognize that it is a service activity. It is a service activity to prepare younger minds to enter the field of research,” Bhavnani says.
With more than 30 years at Auburn University Bhavnani, said he has had the privilege of interacting with approximately 400 students in a research capacity.
According to the Centers for Disease Control and Prevention, one-fourth of the world’s population is infected with Tuberculosis (TB). KatG is an enzyme responsible for the activation of the pro-drug isoniazid which treats TB. Patrick Sahrmann, a junior majoring in Biochemistry, is investigating the role of a specific amino acid (M377) by studying a corresponding mutated version of the protein.
For his approach, Sahrmann performed a series of kinetic studies on the mutated protein for comparison to that of the normal enzyme. Since KatG converts H2O2 to O2 in its catalytic pathway, an oxygen-sensitive electrode was used to measure substrate conversion.
As a result of Sahrmann’s study, Sahrmann discovered the mutated protein displays similar kinetic parameters to that of a wild-type but becomes inactive after fewer substrate turnovers. This suggests that while M377 is not directly related to catalase turnover, it is necessary for mechanisms of catalytic recovery from oxidized protein.
Sahrmann said his undergraduate research experience with his mentor, Dr. Douglas Goodwin, has solidified his decision to pursue enzymology research in graduate school, specifically through a biophysical lens.
Sahrmann has been awarded the Marks Family Scholarship for Undergraduate Research and presented his research at the 2018 Southeast Enzyme Conference in Atlanta, Georgia, earlier this month.
Polymerase chain reaction, or PCR, is a method used to make many copies of a small section of DNA, typically a part of a larger gene. This copied fragment can then be sequenced and identified, but there are shortcomings to the most commonly used methods, such as a lack of taxonomic resolution and distortion of microbial abundance. Sara Odom, a senior majoring in Microbial, Cellular and Molecular Biology, is working to develop a new PCR procedure that allows researchers to address these shortcomings, so they are able to produce more detailed and accurate information from environmental DNA.
The first step of Odom’s approach was the development of degenerate primers that could target gyrB across a wide range of bacteria. While Odom did not develop the primers, she did get to see the process of how they are designed and was involved in testing them against DNA sequences via primer mapping software. Next, Odom tested them in lab. PCR consists of two stages: the linear stage where the targeted section of template DNA is initially copied and the exponential stage where the copied DNA segments, also known as amplicons, are also copied.
Odom has seen consistent production of amplicons from these primers and new PCR procedure on both mixed culture and environmental DNA samples. Soon, she will start sequencing the amplicons, which will allow her to confirm the identity of the amplicons and compare amplified ratios to known ratios, allowing for confirmation of the procedure’s goal.
Odom said the most rewarding part of doing undergraduate research is getting to be involved with active science and interacting with other students and professors involved in research.
“I feel like my experience with undergraduate research has helped me to both understand certain topics, like PCR, better than when I just learned about them in class, as well as given me a deeper understanding and appreciation of the scientific process and the research field as a whole,” Odom said.
Odom is working alongside her mentor Dr. Mark Liles, and Ph.D. candidate Cody Rasmussen-Ivey.
People who experience “cold hands” often do not have enough blood flowing to their hands and fingertips. Jack McDaniel and Franklin Roberts, both seniors studying Biomedical Sciences, conducted a case study to investigate acral hand tissue response to varying environmental temperatures from 10-32°C (50-90°F).
McDaniel and Roberts studied college aged individuals – 4 with “cold hands” and 4 normal response individuals. The individuals were scheduled for five randomly assigned environmental sessions at 10°C, 16°C, 21°C, 26°C, and 32°C (50°F, 60°F, 70°F, 80°F, 90°F) with the relative humidity held constant at 35%. The sessions were separated by 24 hours and performed during the same time of day. The environmental exposure consisted of standing in the environmental chamber during which infrared images of the anterior and posterior hands were taken after an equilibration period (before) and 20 minutes (after).
The duo did not discover the mechanism behind the response of the individuals with “cold hands.” However, based on their case study observations, “cold hand” individuals maintain vasoconstriction below 21°C, while normal participants released vasoconstriction above 16°C. These observations suggest that thermographic evaluations of cold hand individuals may show discrepant results for both ambient, exercise, and cold water environmental testing procedures.
McDaniel and Roberts hope their research will spark interest for others, so that in the future other researchers may find the mechanism behind “cold hands.”
“The most rewarding thing for us was seeing something we had been working on for months finally come to completion and be accepted for multiple presentations,” McDaniel said.
McDaniel and Roberts will present their research in London at the 14th European Association of Thermology Congress in July. The conference is called “Thermology in Medicine: Clinical Thermometry and Thermal Imaging.”
Dr. David Pascoe served as the mentor during this Undergraduate Research Fellowship.
Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of death in the United States. Andrew Lenzie, a senior majoring in Chemical Engineering, is working to figure out if the newly discovered collapse of the central airway, Expiratory Central Airway Collapse, in patients with COPD adds resistance to airflow in the airways. Lenzie is working alongside his mentor, Dr. Vrishank Raghav an Assistant Professor in the Department of Aerospace Engineering. They will share their findings with their collaborators at the University of Alabama at Birmingham (UAB) Medical School for further study.
Lenzie’s approach has been to design and build a benchtop lung simulator, such that the collapse of the central airway can be mimicked in a model outside of the body. He is currently installing the pressure and flow probes which will measure the changes in pressure and flowrate across the flexible tubing that represents the central airway. Instead of air, water is used in the simulated airway for ease of pumping and measurement. The pumping of water through the system is controlled by software to mimic the force and rate of an average diaphragm.
Lenzie said his undergraduate research experience has helped him succeed at other endeavors like applying for medical school and suggests others give undergraduate research a try.
“The most rewarding thing is knowing that the design and construction of this device followed by experimentation could help so many people with this disease,” Lenzie said.