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Undergraduate Research Opportunities Program

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Publication Search Results

Now showing 1 - 10 of 154

Production of ryanodine receptor calcium release channel ATP-binding site mutants

(Georgia Institute of Technology, 2023-01-18) Cutter, Catarina Santos

Ryanodine receptors (RyRs) are a class of mammalian ion channels which are the primary efflux pathways for the release of Ca2+ from the sarcoplasmic reticulum. They play a critical role in muscle excitation-contraction coupling (ECC). Because it is the largest known ion channel, the mechanisms for its activation are not fully understood. ATP is a well characterized channel activator. However, its mechanism of activation has not been determined and the importance of ATP regulation of RyRs in vivo is not clear. In 2016, des George, et al. published a structure of RyR1 with ATP bound. The adenosine group of ATP is contained within a hydrophobic cleft while the triphosphate tail is extended and interacts with positively charged residues. The goal of this study was to identify residues important for ATP binding to the channel. Site-directed mutagenesis of the receptor was used to substitute specific residues in order to change their size and or charge. After transfection with recombinant DNA, HEK293 cells were harvested for isolation of microsomal membranes. Two of the largest hydrophobic residues of the cleft were replaced with alanine with the goal of drastically reducing or abolishing ATP binding to RyR1. The selected mutations F4960A and L4985A were expected to impair channel activation by both ATP and adenosine. After initial verification of wild type channel expression in HEK293 cells, later transfections with wild type and mutant RyR1 DNA failed to produce detectable amounts of protein. Low DNA transfection efficiency combined with the low yield of microsomal membrane likely contributed to the inability to detect channels in these preparations. Optimizing DNA transfections and scaling up the cell culture may increase the likelihood of successful protein production.
Interaction between Burkholderia ceoncepacia and Staphylococcus aureus in Presence of Meropenem

(Georgia Institute of Technology, 2022-05) Wang, Runyi

In recent decades, chronic pulmonary infections have become the leading cause of death among patients with cystic fibrosis. Despite the large number of available studies that explore the effects of single-species bacterial infections, the dynamics of polymicrobial infections are not as well-understood. Initial pulmonary infections in patients with cystic fibrosis often involve multiple species. Therefore, it is important to identify the interactions between multiple bacterial species and the potential effects to patients during treatment. β-lactam antibiotics such as meropenem, are often prescribed by clinicians for infection treatment and management. However, Burkholderia cenocepacia is capable of producing β-lactam degrading enzymes β-lactamases. In this study, we show that B. cenocepacia’s production of β-lactamases has potential to rescue nearby bacteria that would be susceptible to the β-lactam antibiotics, such as Staphylococcus aureus. The study shows that S. aureus does not grow better in the presence of B. cenocepacia. This finding suggests that S. aureus is not being rescued by B. cenocepacia despite the β-lactamases produced. While it is probable that such relationship is detrimental to traditional treatment options, additional studies need to be conducted to definitively conclude its effects on treatment outcomes.
Hsp90 and the Evolution of Novel Cellular Differentiation

(Georgia Institute of Technology, 2022-05) Cheng, Vivian

Cellular differentiation is a prerequisite for complex multicellular life, yet little is known about how it evolves de novo. Several mechanisms may explain how early multicellular organisms evolved to perform cell-specific roles. In this work, I explore the potential role of cellular aging in driving age-dependent differences that evolve to become co-opted for a novel role in cellular differentiation. Specifically, I am examining how, in the snowflake yeast model system of nascent multicellularity, the Hsp90 class chaperone proteins have evolved to act in a novel age-dependent manner, thus driving the emergence of adaptive differences in protein activity among cells.
Modeling health and developmental effects of particulate matter exposure using C. elegans

(Georgia Institute of Technology, 2022-05) Thompson, Carys

Particulate matter (PM) is air pollution comprised of tiny particles suspended in the air. Exposure to PM is a major global health concern, contributing to 9 million deaths annually. Fine PM can break down protective cellular barriers and cause systemic inflammation, leading to damage of the central nervous and respiratory systems. Children are especially vulnerable to prolonged PM exposure due to breathing in toxins at a faster rate. Due to the limitations in the current approaches (e.g., cultured cells and mice models), specific biological mechanisms linking PM exposure to health hazards are still largely unknown. In this work, the microscopic nematode C. elegans is proposed to model the systemic and multi-tissue effects of PM at the cellular level. C. elegans is an excellent model organism due to its small size and fast life and reproductive cycles. Here we examined the oxidative stress response caused by prolonged oxygenated polycyclic aromatic hydrocarbons (oxy-PAH) exposure in larval C. elegans using a reporter strain for cellular redox status. Oxy-PAH has been recognized as a toxic component of PM. We find that although oxy-PAH exposure causes delay in larval growth, it does not affect redox activity, suggesting that oxy-PAH toxicity occurs through other biological pathways. The results of this study establish lab-manufactured oxy-PAH as a positive control and serve as a pilot study for ambient PM. Future work will focus on the health and developmental effects of ambient PM throughout larval worm development.
Reproduction and recruitment in perennial Vespula squamosa yellowjacket was colonies

(Georgia Institute of Technology, 2022-05) Crossley, Henry G.

Many people are all too familiar with social wasps of the genus Vespula, more commonly known as yellowjackets. What many people may not know is that recently, the nesting behavior of these wasps has begun to shift from a yearly cycle to a prolonged multiyear state. These perennial nests are becoming more and more common in areas with warmer climates. Using repetitive sequences of DNA known as microsatellites, allele frequencies, and strategies such as PCR, gel electrophoresis, and fragment sequencing, we worked to genotype eight perennial southern yellow jacket, Vespula squamosa, colonies from Auburn, Alabama to get a better understanding of the reproductive and genetic structure in these colonies. We then compared our data to that of annual colonies of the same species. We found that the relatedness is lower in perennial colonies than in annual colonies, and there is evidence in the genetic structure showing that perennial colonies contain more than one reproductive queen.
Analysis of Tympanum and Columella Constructions in the Family Incilius (Anura: Bufonidae: Incilius)

(Georgia Institute of Technology, 2022-05) Shinn, Ollie

Toad ears are usually composed of a tympanic membrane, tympanic annulus, columella, and inner ear, and vary greatly across species. In order to investigate the state and evolutionary history of ears within the toad family Incilius, I compiled information on the tympanum and columella presence and shape from first hand CT scans and observations as well as previously documented descriptions. I applied this information to the phylogeny presented by Mendelson et al (2011) and reviewed them for changes throughout evolutionary history. I concluded that the common ancestor of Incilius had both a tympanum and a columella, and both had been lost and regained at least once in evolutionary history, most likely around the same point in evolution. Based on those conclusions, I predicted the most likely state of columella for species I did not have data on. While hearing is important for many toads’ social behaviors, it is important to recognize that several studies have shown that amphibians without complete ears can still perceive sounds.
The True Cost: An Analysis of Course Registration Patterns in the College of Sciences

(Georgia Institute of Technology, 2022-05) Ciaccia, Julia

In the United States, less than half of college students who enroll in a STEM program will graduate with a STEM degree (Chen 2013). Attrition rates are disproportionately high for marginalized students, leading to a homogenous STEM workforce (Simon et al. 2021). This study, completed at an R1 midsized southeastern university, investigates course registration patterns and student opinions to determine what factors contribute to students leaving STEM majors through the lens of the Deep Teaching model (Dewsbury 2019). Through survey and course enrollment data, we determined that 1) students feel overwhelmingly negative about textbook costs, 2) financially insecure students are significantly more likely to consider course material costs when registering for courses and 3) students add and drop courses for a wide variety of personal, course, and university level reasons. These results indicate that implementing Deep Teaching in the classroom, specifically focused on self-awareness and empathy, can increase retention in STEM and reduce attrition rates.
Prediction and Visualization of RNA Secondary Structures

(Georgia Institute of Technology, 2022-05) McCann, Holly

Non-coding RNAs play key roles in cellular systems such as transcription and translation. Computational predictive methods provide insight into the secondary structures of non-coding RNAs from diverse organisms for which there are no high-quality crystal structures. This research project builds upon the existing framework of the R2DT (RNA 2D Templates) tool developed by the RNAcentral consortium with collaboration from Georgia Tech researchers. R2DT predicts RNA secondary structures and displays them in the form of a 2D topology diagram by using known, related structures as templates for prediction and visualization. The automated template-based approach, however, often ignores unique species-specific regions such as ribosomal RNA expansion segments.   To improve the functionality of R2DT, the secondary structures of insertion regions which are not found in any template structure are now predicted using the RNAfold algorithm developed by ViennaRNA. This hybrid approach can generate more accurate structures for various types of RNA molecules with unique features across entire phylogeny. In addition to improvements to the folding algorithm, a new front-end for R2DT has also been developed which builds on the PDBe RNA Viewer. The generated topology diagrams now display RNA secondary structures represented either as a contour line or as individual nucleotides. The improved RNA Viewer provides support for visualization of both canonical and non-canonical base pairs (using the symbolism proposed by Leontis and Westhof), and includes interactive features such as object highlighting and a tooltip. These developments improve the accuracy and functionality of computationally predicted RNA topology diagrams. The applet further enables users to visualize various structural and evolutionary data and to easily generate publication-quality images of data mapped onto secondary structures. This applet has been integrated with the PDB MSA and Mol* viewers to display non-coding RNA molecules and associated data in three dimensions on the RiboVision2 webserver.
A submaximal normalization of EMG signals in trunk muscle groups

(Georgia Institute of Technology, 2022-05) Jones, Tamia M.

The accuracy of control and strength of contraction for muscles of the trunk, the muscles between our neck and groin, can vary significantly with conditions like hemiparesis, multiple sclerosis, or low back pain. Such medical conditions can contribute to an inability of our trunk muscles to perform at full capacity. A typical normalization method for applied physiologists includes finding a given muscle’s maximum voluntary isometric contraction (MVIC), and many individuals with muscle weakness or control-limiting conditions are unable to efficiently participate in this method. To properly assess the severity of muscle weakness or loss of control, there is a need for research on normalizing EMG signals produced from contractions in trunk muscles at a fraction of an individual’s MVIC. In order to contribute to this normalization, healthy participants in this study performed a muscle contraction task based on a submaximal MVIC. Participants attempted to reach and hold a contraction for a specific muscle group (i.e., deltoids, pectoralis major, external obliques, and latissimus dorsi) at a target contraction level defined as 25%, 12%, and 6% of their MVIC. The objective of this study was to characterize normalization of EMG signals from trunk muscle contractions with variability and offset error. The standardized measures supported the use of the 25% and 12% contraction levels as submaximal EMG signal normalization. In future studies, the 6% contraction level and the external obliques potentially require refinement in contraction maneuvers for a more accurate normalization. Nevertheless, future experiments may use the results of this study as a submaximal reference point within healthy populations acting as a measure of comparison for patients demonstrating muscle weakness.
Effects of Muscle-Based Control and Electrical Stimulation of Residual Sensory Nerve on Biomechanics of Locomotion with Transtibial Prosthesis

(Georgia Institute of Technology, 2022-05) Zhang, Celina

This study examines the use of muscle activity and nerve stimulation for trans-tibial prosthetic control. We tested various modes of an osseointegrated prosthesis – in a cat subject – that varied in their implementation of control using soleus EMG activity as well as residual nerve stimulation to see if these factors would improve locomotor biomechanics in level and sloped walking. The results indicate that there were varying effects of EMG-based control and nerve stimulation on locomotor variables. It was found that the prosthesis was able to reduce asymmetry of locomotion, but there were still compensations from remaining portions of the ipsilateral limb. The EMG-based prosthetic control with communication of sensory motion-dependent information from the prosthesis still requires further studying and adjustment but show promise in improving locomotion.