Tag: Biology

Investigation of Training Methods Used for Mice to Perform Auditory Discrimination Tasks

Presenter: Sean Kyne – Biology

Faculty Mentor(s): Santiago Jaramillo

Session: (In-Person) Oral Panel—Stimuli and Response

The auditory system has a tremendous capacity to interpret all the surrounding sounds in the environment and help make sense of the world around us. To understand how our brains interpret and process complex sounds, we need a new method for studying auditory cognition. Researchers have created head-fixed rigs where mice run on a wheel while their head remains stationary and perform auditory discrimination tasks. This setting will allow us to study how the auditory system discriminates complex sounds using electrophysiological techniques that would be more challenging to apply in a freely-moving setting. Previous work in the lab suggests that it is more challenging to train mice in a head-fixed setting than in the more well-known freely moving setting. To improve our understanding of how to train head-fixed mice, they were trained to discriminate sounds of varying complexity. In each project, a new training protocol was implemented to increase our understanding of the best methods for training mice. The training protocols had varying success in teaching the task which provided helpful insights into teaching head-fixed mice auditory discrimination tasks.

Taking what was learned will allow us to teach mice more efficiently on future tasks using more complex sounds. Studying the methodology of how to train mice will allow for future experiments to use electrophysiological techniques to increase our understanding of the neural circuits used in auditory cognition.

DiversiPhi29—An Orthogonal System for the Continuous Directed Evolution of Genes In Vivo

Presenter: Amanda Kreppel − Biology

Faculty Mentor(s): Nora Kearns, Calin Plesa

Session: (In-Person) Poster Presentation

Directed evolution is a method for protein engineering which allows scientists to impose novel functions on proteins through the random and progressive introduction of mutations to their encoding gene. Traditional directed evolution approaches are inefficient, alternating cycles of manual in vitro mutation and in vivo expression and selection until a desirable advancement in protein function occurs. This limits the throughput and depth at which a protein’s mutational landscape can be explored. By eliminating in vitro mutagenesis and allowing an orthogonal error-prone polymerase to replicate a gene of interest over several generations in E. coli, we are able to push the boundaries of evolution and create large libraries of desirable mutants in vivo. Here we propose DiversiPhi29, which repurposes the replication machinery of bacteriophage ɸ29 to continuously replicate a linear plasmid (pL) carrying a gene of interest in vivo independently of host replication. Once orthogonal replication of pL is established, we will implement a system capable of tuning the mutation rate of the linear construct’s replication by altering the ratio of two ɸ29 DNA Polymerases, one of which contains error-prone mutations. This approach will enable high throughput molecular evolution in the best understood host organism.

Does plant community diversity change with terrain steepness in southwestern Oregon?

Presenter: Delaney Kleiner − Biology, Environmental Science

Faculty Mentor(s): Lucas Silva, Brooke Hunter

Session: (In-Person) Poster Presentation

Southwestern Oregon is characterized by complex patterns of plant communities across environmental gradients. Previous research has found the structure and composition of vegetation to be related to the complex geology of this region. In this study, we explore the relation between topography and plant communities by asking if and how vegetation changes across ridgelines of varying steepness. We selected six ridgelines with a gradient of slope steepness (steep to gentle) in Rabbit Mountain, Riddle, Oregon and used quadrat and line-point intercept techniques to quantify vegetation cover by species at each site. We assessed the differences and similarities between plant communities with NMDS (non-metric multidimensional scaling) analysis. We found plant communities on steep ridgelines are significantly different than communities on gentle ridgelines. Studying how landscapes exist in relation to vegetation deepens our understanding of the connectedness of Earth’s processes, emphasizes the interdisciplinary nature of environmental science, and further informs forestry management practices in a time of increasing climate change.

Development of new uroflowmetry techniques for pediatric patients

Presenter: Myrriah Jones − Biology

Faculty Mentor(s): Molly Jud, Edouard Hay

Session: (In-Person) Poster Presentation

Uroflowmetry measures data points like the max and average flow rate, volume, and duration of urination. Pediatric urologists use uroflowmetry to aid in diagnosing disorders of the urinary system like pediatric voiding dysfunction, a disorder that affects the sphincter control of the urethra.

Our purpose is to create a cost-effective tool for urologists to use to collect these data points more frequently and more accurately, in a more comfortable environment for patients. We used a combination of machine learning techniques and audio recordings of simulated urinations to train an algorithm to accurately predict the data points in people who urinate in a standing position. The data from the simulated urinations had similar trends in the data as the machine learning predictions and could reasonably work as a tool for urologists. By having a tool like this app, we can work towards increasing accessibility for necessary medical testing and improve both the accuracy and precision of uroflowmetry testing which helps provide better differential diagnoses and proper treatment to pediatric patients with similar symptoms yet distinct disorders.

How Cooler Temperatures Affect Scavenger Visitation and Decomposition of Sows

Presenter: Laila Johansson − Biology

Co-Presenter(s): Breanna Johnston

Faculty Mentor(s): Richard Glover

Session: (In-Person) Poster Presentation

Taphonomy is the study of what happens to an organism’s remains after death, and it can provide information on many factors, including what facets affect decay, determining the post-mortem interval, organismal interactions with the remains, etc. Lane Community College has a “taphonomy lab” comprising of 7 hog carcasses placed at different times and locations. This study analyzed 3 out of the 7 hogs over 18 weeks, from October to February, to see how cooler temperatures and scavengers may affect the rate of decay. 2 of the 3 hogs were placed in July 2021, and 1 was placed in November 2021. Trail cameras monitored the subjects and were used to examine animal visitation and the progression of decay. Average daily temperatures were recorded via the Eugene Weather Station. We hypothesized that as the temperature decreased, scavenger prevalence would increase, and the hogs’ decomposition rates would fall. Data showed decreased average daily temperatures and increased animal visitation as the study progressed, with a correlation coefficient of -0.6 between them. This allowed us to acknowledge the hypothesis as fairly well supported. Comparison of the decay of the July 2021 hogs to the November 2021 hog showed that the November hog was less decomposed at the 2.5 post-mortem mark than the July hogs were at their 2.5 post-mortem mark. Because of this, we assume the lower temperatures influenced the decreased decomposition rate. Scavengers may have aided in aspects of the hogs’ decay.

Mechanisms of 3D genome organization by condensin and its interactors

Presenter(s): Yukiko Gaudreault — Biology

Faculty Mentor(s): Osamu Iwasaki

Session: Oral Panel—Bio-Zebrafish and DNA

It is known that eukaryotic genomes are organized in differently sized chromatin domains, including topologically associating domains (TADs) which organize active and inactive chromatin domains and therefore coregulate transcription. This structure is of great interest because when defective, it can lead to developmental abnormalities and human disease. The in situ Hi-C method has been applied to fission yeast cells to show that the protein complex condensin forms ~500kbp chromosomal domains that are required for proper chromosome segregation during mitosis. However, it is still unclear how condensin domains are formed and regulated during the cell cycle. Here we show several potential condensin interactors involved in the regulation of condensin-mediated domains. To do so, we applied the auxin-inducible degron system to 9 condensin interactor genes that were previously found via yeast-two hybrid screening. Performing in situ Hi-C on these conditional knock-out strains showed that Clc1/ clathrin and Sds3/ histone deacetylase promote the formation of condensin domain and that Fyu1/ UTP-glucose-1-phosphate uridylyltransferase and Pfk1/ 6-phosphofructokinase negatively regulate condensin function. We anticipate these results to drive further investigation into the involvement of metabolic proteins in genome organization, as well as the further understanding of chromosome organization mediated by condensin and its interactors.

Design and Characterization of BMP-2 Protein Binders to Augment Non-Union Fracture Healing

Presenter(s): Karly Fear — Biology

Faculty Mentor(s): Parisa Hosseinzadeh

Session: (In-Person) Oral Panel—Daily Dose of Proteins

Each year, over 630,000 people in the US suffer from non-union bone fractures, or fractures that do not heal completely without further medical intervention. To improve bone healing in non-union fractures, researchers have shown that bone morphogenetic protein 2 (BMP-2) improves bone regeneration. However, it is critical to fine tune the physiological dose and spatiotemporal control of BMP-2 release from a delivery biomaterial to avoid adverse side effects such as abnormal bone growth. I leverage the structural and biophysical insight of molecular modeling and design to generate protein binders predicted to control the release of BMP-2 into a fracture site via affinity interactions. I characterize subsequent protein binder designs using yeast surface display and flow cytometry. Over 1,000 designs are tested using this high-throughput computational and experimental pipeline and I will further characterize the toxicity, stability, and structure of a subset of these designs for practical application.

The Role of the Primary Visual Cortex in Processing Complex Environments

Presenter(s): Yichen Fan — Biology

Faculty Mentor(s): Denise Niell

Session: (In-Person) Poster Presentation

To survive, animals have evolved visual systems fit for extracting relevant information from complex, natural environments. In mammals, visual information flows from the eyes to the brain via two dominant gateways. First, the primary visual cortex (V1) is a higher-order structure well-studied using simple, artificial stimuli. However, its role under more complex visual conditions remains unclear. Inactivation of the cortex have surprisingly little effect on many perceptual discrimination tasks, prompting the question: what is the fundamental role of the visual cortex? Second, the superior colliculus (SC) is highly conserved across vertebrates, including mammals and lower-order animals such as fish, which lack a cortex but can still use vision for important behaviors. To ultimately elucidate the integrated role of SC and V1, we must first understand the role of V1. We hypothesized that V1 is required for object identification in complex visual scenes, but not under simple environments. We investigated this in mice using prey capture, an ethological, visually guided behavior. We optogenetically inactivated bilateral binocular V1 neurons while mice captured cricket prey in 8 environments of varying visual complexity. We found that while V1 is not necessary for prey capture in a simple visual environment, it becomes increasingly necessary as the scene becomes more complex. We will next inactivate layer 5 cortico-collicular neurons to study the integrated role of SC and cortex.

Meiotic recombination is regulated by dosage of synaptonemal complex proteins

Presenter: Amelia Dayton — Biology

Faculty Mentor(s): Cori Cahoon, Diana Libuda

Session: (In-Person) Oral Panel—Daily Dose of Proteins

Meiosis is a specialized cell division that produces haploid gametes, such as sperm and eggs. To ensure each parental genome is inherited properly, cells must pair homologous chromosomes, induce DNA double-strand breaks, repair these breaks as crossovers, and segregate the chromosomes. The synaptonemal complex (SC), a large protein structure, assembles between homologs and facilitates crossing over, which ensures accurate chromosome segregation. Using Caenorhabditis elegans, previous work in the Libuda lab showed that two SC proteins, SYP-2 and SYP-3, have dosage-dependent functions in regulating crossing over. SYP-2 dosage is critical for regulating early crossover steps, while SYP-3 dosage influences the timing of crossover establishment. Crossovers are nonrandomly positioned on chromosomes, and whether SYP dosage influences crossover position remains unclear. To this end, I am using single nucleotide polymorphisms to characterize the positions and rates of crossovers in cells with altered SYP-2 and SYP-3 dosages. Preliminary data on Chromosome X shows that SYP-dosage is crucial for proper crossover positioning. Since the sex chromosomes often behave differently from autosomes, I am also determining the effect of SYP- dosage on crossovers across Chromosome II to establish whether autosomes show similar changes in crossover positioning. Overall, these experiments will define the dosage-dependent manner that SYP-2 and SYP-3 regulate recombination to promote fertility.

A Novel Zebrafish Mutant Reveals New Insight into Cilia Motility Regulation and Body Axis Formation

Presenter: Craig Samuel — Biology

Faculty Mentor(s): Daniel Grimes, Zoe Irons

Session: (In-Person) Oral Panel—Bio-Zebrafish and DNA

Motile cilia are responsible for critical functions in development, including left-right patterning and cerebrospinal fluid flow. Their motility depends on the assembly of outer dynein arms: ATPases which power ciliary beating. Defects in dynein arm function occur in Primary Ciliary Dyskinesia, a disorder affecting 1:15,000–30,000 human births. Daw1 is a cytoplasmic protein thought to be required for cilia beating by controlling import of dynein arms into cilia. Here, I use zebrafish as a model to understand Daw1 function during development and growth. I characterize daw1b1403 mutants, a new daw1 mutant line harboring a 2-amino acid deletion in a conserved region of the protein generated by CRISPR mutagenesis. Defects associated with motile cilia dysfunction in daw1b1403 mutants, including otolith abnormalities, left-right patterning defects, and abnormal body axis curvature are observed. Surprisingly, daw1b1403 mutants exhibit recovery of body curve defects later in development. Consequently, we hypothesize that Daw1 is not essential for cilia motility per se, but only for timely onset of beating over developmental timescales. Importantly, this Daw1 model of delayed cilia motility and body straightening provides an opportunity to study how early embryos can sense, or correct, shape deformations, which is an exciting and relatively unknown aspect of developmental morphogenesis. Ultimately, understanding these processes may help inform our treatments of congenital disorders.