Evaluating women in Ancient History could be difficult as patriarchal societies limited the representation of women, which resulted in little or biased documentation. Another obstacle was evaluating the accuracy of evaluating the authenticity and accuracy of reported events when there is such limited evidence of certain figures and events in Ancient History . However, regarding the feminist martyr narrative, I was able to evaluate the effects of the representation in martyrdom and how they could be applied to modern feminist narratives. To investigate the significance of the texts of women and martyrdom to values in the Patristic Era of Christianity, I analyzed women in the context of the Roman Empire compared to the Early Christian Church using primary sources. Introducing the consequences of martyrdom, I addressed the etymology of the word “martyr” and the connotations associated with the term. As my primary sources, I used the accounts of Perpetua and Blandina because their narratives were among the most well-known. Studying the divergence of feminine virtues of the Roman Empire and Early Christianity, I explained how the differences influenced the divisions and spread of the Early Christian Church. I also studied the retelling of their stories throughout history, which illustrated society’s expectations of women as opposed to the possible motivations of the martyred women. I discovered that the stories of martyred women were altered throughout history to perpetuate different ideals of femininity but at a closer look, the original narratives depicted a progressive depiction of women. This research exposed how the representation of women could be altered to fit an agenda and revealed the values of the authors of the narratives as well as the surrounding culture. This could be used to evaluate the representation of influential women figures today as well as the consequences of altering feminist narratives.

Although the relationship between the structure, function, and physiology of organs is well documented, the mechanisms by which cells collectively coordinate into three-dimensional tissues and organ components remains unknown.The countless factors that inform the morphogenesis of mammalian organs poses a challenge to understand organogenesis from first principles. However, the Malpighian tubules of the fruit fly Drosophila offer an excellent model system for investigating this question due to their rapid development, relative simplicity, and the degree to which scientists can manipulate variables that affect their development. These tubules are the renal equivalent of the fruit fly excretory system; further, many of the genes involved in sculpting these tubules are conserved from flies to humans. One conserved gene is the fly homolog of β-catenin, which is known to play an essential role in cell-cell adhesion. The goal of my research is to define how β-catenin impacts organ morphogenesis. To do this, I use fluorescence microscopy and live imaging to compare wildtype Drosophila to those with decreased β-catenin expression. Using tissue-specific fluorescent protein tagging, I can differentiate Malpighian tubule cells from other embryonic cells under the microscope so that their shapes can be analyzed, and I control the level of β-catenin expression specifically in Malpighian tubule cells using RNAi. Due to β-catenin’s integral role in cell-cell adhesion, I expect to find localization of β-catenin to the cell membranes of the tubules, with high concentration along membranes undergoing the greatest adhesion or motion, and interrupted tubule morphogenesis in reduced-expression lines. I also suspect that cells may completely fail to adhere and will be unable to transmit tension effectively along the tissue. The results of this experiment will contribute to our understanding not only of Malpighian tubule morphogenesis, but of one of the components of morphogenesis in general.

How do organs have such consistent and reproducible shape, form, and volume? One factor of this complex phenomena is cell-cell adhesion. Cell-cell adhesion plays a vital role in organ formation, as it is an essential driver of cell shape, cell arrangements, and tissue structure. To determine the role of adhesion in organ formation, I define the role of E-Cadherin, a cell-cell junction projection that adheres neighboring cells. The developing renal system of Drosophila, Malpighian tubules, are an excellent system because I can selectively manipulate expression of E-Cadherin in the organ and can utilize fluorescence microscopy to observe how these changes affect tubule morphogenesis. I observe where the adhesion protein is located during organ growth, and what happens to organ growth when expression of the adhesion protein is reduced. To track the dynamic localization of E-Cadherin, I take measurements of specific location of E-Cadherin between cells and concentration of E-Cadherin throughout organ development. I expect the concentration of E-Cadherin to increase during elongation, and that it will be enriched in more looped parts of the organ. To define the requirement of E-cadherin during organ formation, I use RNA interference to reduce E-Cadherin expression. Because of how vital E-Cadherin is in other developmental morphogenetic processes, I expect a decrease of expression to have profound impacts, leading to severe organ developmental defects. I measure these defects by comparing cell shape change and organ shape in control and E-Cadherin reduced organs. The results of this study will not only help us understand Malpighian tubule morphogenesis, but it will also help us understand organogenesis more generally. Elucidating the precise mechanisms behind cell behavior, shape, and cell-cell interaction has important human health implications and will enable work in many other fields such as cancer, regenerative treatments, tissue growth, and organ synthesis.

Infants perceive speech and acquire language amidst noisy and complex auditory environments. Thus, elucidation of the cognitive mechanisms governing speech perception under noisy conditions is crucial. Cortical encoding of the speech envelope has been one approach used to study speech-in-noise perception in adults. For infants, research shows that Infant Directed Speech (IDS) facilitates cortical encoding of the speech envelope in quiet conditions more than adult direct speech. However, it is unclear whether infants are able to track the IDS speech envelope amidst competing speech. To investigate this, we recorded the neural responses from 40 typically-hearing infants (20 seven-month-olds, 20 eleven-month-olds) to continuous IDS using electroencephalography (EEG) in three conditions: Quiet, Co-located Noise, and Separated Noise. The target stimuli consisted of naturally recorded IDS produced by two female English speakers. The noise stimuli consisted of a four-person babble constructed from audiobooks read by 2 male and 2 female English speakers. We presented stimuli at an overall level of 70 dB SPL via speakers placed at 0°, +90°, and -90° azimuth to infants sitting on a caregiver’s lap in a sound-attenuated booth. Our team analyzed EEG signals using the Multivariate Temporal Response Function (mTRF) toolbox in MATLAB. This backward modeling approach assesses whether the stimulus envelope can be reconstructed based on the recorded neural responses. Reconstruction accuracies greater than chance were observed in all three conditions for the majority of infants, suggesting that we were able to decode the speech envelope in both quiet and noise. Participants demonstrated the capacity to process speech, even amidst competing auditory stimuli, emphasizing speech perception competencies from an early developmental stage. These results support using the envelope model and mTRF method as a feasible method for investigating the development of speech-in-noise perception in infants and young children.

As global urbanization accelerates, wildlife habitats are increasingly lost and fragmented, exacerbating the ongoing biodiversity crisis. Within urban ecosystems, remaining wildlife face multifaceted challenges. The heterogeneity of urban environments arises not only from ecological characteristics but also from social factors. This study addresses these complexities by deploying transects of baited tracking tunnels and camera traps in Seattle parks to assess indices of abundance for squirrels, mice, rats, and rabbits—integral components of urban small mammal communities. This investigation centers on comprehensive identification of primary predictors of small mammal abundance citywide, encompassing habitat variables like canopy cover and social factors such as median household income and environmental health. Leveraging statistical analyses, we delineate the relationships between these predictors and small mammal abundance, offering insight into urban wildlife population dynamics. These findings provide guidance for urban planners, wildlife managers, and policymakers endeavoring to foster coexistence between humans and wildlife in shared landscapes.

Addressing bias in artificial intelligence (AI) and machine learning (ML) systems is crucial for ensuring fairness, transparency, and ethical integrity. This study introduces a pioneering interdisciplinary approach, blending advanced computational methods with social sciences insights to tackle the multifaceted nature of bias. Through a mixed methods strategy that combines quantitative and qualitative data, we scrutinize algorithmic outcomes and conduct different case studies of stakeholders—developers, users, and communities affected by AI/ML biases. Our initial findings indicate that bias transcends technical boundaries, manifesting as a complex socio-technical dilemma that demands both algorithmic adjustments and societal reforms. We highlight specific biases, such as gender and racial disparities in recruitment algorithms and facial recognition technologies, underscoring the critical need for our research. To address these biases, we propose adopting data enhancement techniques, fairness-focused learning algorithms, and promoting explainable AI practices. Inspired by influential figures like Joy Buolamwini, founder of the Algorithmic Justice League, and Cathy O'Neil, author of Weapons of Math Destruction, we emphasize the importance of inclusive datasets and critically examining opaque algorithms. Our future efforts concentrate on developing comprehensive guidelines to reduce AI/ML biases and exploring the broader societal impacts of establishing unbiased AI and ML systems. By cultivating more equitable and ethical AI and ML frameworks, our research aims to meet the diverse needs of global communities, setting a new standard for responsible AI development.

Marine microbial communities produce and cycle organic matter in the ocean. Some of this organic matter is in the form of metabolites, small, organic biomolecules that are present both inside of microbial cells and dissolved in seawater. Studying metabolite dynamics provides insights into the fate of a significant portion of marine primary production as well as microbial community interactions that influence short and long term carbon storage in the ocean. Here I analyzed both dissolved (extracellular) and particulate (intracellular) metabolites from the 2019 Gradients 3 (G3) research cruise that were collected along a latitudinal transect. Sampling stations spanned the North Pacific Subtropical Gyre, an area with low nutrients and primary productivity, to the North Pacific Subpolar Gyre, an area with higher nutrients and primary productivity. I extracted particulate metabolites using a modified Bligh and Dyer extraction and dissolved metabolites using cation-exchange solid phase extraction. I acquired metabolite data using liquid chromatography mass spectrometry and processed the data using Skyline software. In both dissolved and particulate samples, metabolite pools were dominated by compatible solutes, compounds organisms use for handling osmotic stress, as well as amino acids. Metabolite abundances in both phases largely increased traveling northwards along the transect, reflecting increases in productivity, microbial biomass, and nutrients. However, certain metabolite concentrations did not follow this trend, suggesting that differences in microbial community composition or physiology may play an important role in regulating the synthesis of these compounds. These results show how varying environmental conditions affect the composition of organic matter produced by marine microbial communities. This information can be used in to predict how marine primary producers will store and use carbon in a future changed ocean.

Science is rapidly evolving, yet its advances do not enter classrooms at the same rate. Systems Education Experiences (SEE) is a program in the Baliga Lab at the Institute for Systems Biology (ISB) that accelerates the transfer of scientific knowledge and practices to classrooms. One active area of Baliga Lab research is elucidating the level of resilience organisms have, when faced with complex environmental changes. My role is to design laboratory experiments that investigate this with the model organism Halobacterium salinarum (Halo) and to connect this to broader rules governing natural systems for use in high school classrooms. My first experiment probes the resiliency of Halo with the introduction of a combination of stressors (salt and hydrogen peroxide) and its recovery after population collapse. The second measures the long term phenotypic changes in the population. I wanted to see if after being exposed to a new environment if there was an advantage to having gas vesicles and if it is an irreversible trait that allows Halo to be resilient across a variety of environmental conditions. This relates to broadly applicable rules governing resilience across many systems. This project serves as a model for how all organisms respond to stress. Combinations of stressors in human lives can make us less resilient. However, strategies to quickly prepare, respond, and react can improve outcomes for individuals and the overall population. This project connects to a goal of K-12 science education which is to not just teach academic concepts but to equip students with knowledge that can be applied to all parts of life. Our knowledge on the mechanisms that control how organisms respond to stress is extremely limited. By understanding the biological stress response we can promote resilience in the earth's most vulnerable systems in the wake of climate change.

The world is in dire condition and our energy and environmental future need to be secured. Through a historical look at the field of Futures Studies, the World's Fairs, the Hanford Site, and solar power, we will gain insights on how to implement R. Buckminster Fuller's framework of Comprehensive Anticipatory Design Science to address future energy and environmental challenges. This literature review analyzes Fuller's essay "Humanity's Critical Path: From Weaponry to Livingry" (1983) and its implications for the future. Comprehensive Anticipatory Design Science, as conceptualized by R. Buckminster Fuller, is an approach that begins with the entirety of a system, anticipates future needs, and applies accumulated knowledge to create an omnicooperative society. Examining two of Fuller's artifacts — the World Game and Dymaxion Map — we gain insight into how to give everyone access to a global accounting system of resources available to inform future policy decisions. From this research, we learn how to leverage Design Science to change our projected future. Through an exploration of the Hanford Site, we gain an understanding of what dangers nuclear technology poses. A detailed overview of the World's Fairs and those involved in strategic national planning projects informs how past decisions were made that led to this dire situation. This work seeks to determine whether observing the development of solar energy technology can conserve our petroleum reserves, fissionable materials, and transition our society to the participatory, sustainable, and renewable future that Fuller envisioned. This research unveils the significance of Fuller's ideas by addressing the risks and benefits of nuclear technologies and alternative renewable energy sources that could be employed. Further research into Fuller's concepts at the intersection of complex energy solutions and sustainability will provide us with feasible options to our dire climate crisis.

The human genome is associated with numerous variations, some of which can be pathogenic. Any variations larger than 50 base pairs (bp) are considered structural variants (SVs), and SVs impacting copy number of the genome are termed copy number variants (CNVs). By studying CNVs, we can understand the underlying mechanisms of damage and repair within DNA, which can help work towards prevention and cure in other fields, such as cancer genomics. My project investigates a CNV on chromosome 2 of a pediatric patient, who presents with tetralogy of Fallot, global development delay, and multiple other congenital anomalies. Using array comparative genomics hybridization (aCGH), we identified a 3.2 megabase (Mb) complex genomic rearrangement (CGR) spanning the 2q31 region of the proband’s chromosome 2. Detailed analysis of the short-read whole genome sequencing (WGS) allowed us to locate the exact coordinates of each junction, or the beginning and end points of each extra copy. PacBio long-read genome sequencing and optical genome mapping detected the same junctions and facilitated confirmation of the overall structure. The CGR can be characterized as a duplication-triplication-duplication-triplication-duplication (DUP-TRP-DUP-TRP-DUP), meaning this segment of the genome contains a segment of alternating 1 and 2 extra copies of this region. The CGR is de novo, or not inherited from the proband’s parents. Due to the nature of this variant, it is likely to be impacting the phenotype of our patient. To establish a genotype-phenotype correlation, I did a literature review of patients with overlapping CGRs, comparing their phenotypes to our proband, as well as reviewing any known disease-associated genes in the region using the online catalog of human genes and genetic disorders (OMIM). Patient and disease comparison revealed the extreme rarity of our patient’s CGR, leading us to believe the phenotype of the proband results from impact of multiple genes in the affected region.

Gastrointestinal symptoms are a common comorbidity of autism spectrum disorder (ASD), and individuals with the disorder tend to have a distinct gut microbial community composition and circulating metabolomes. My work in the Rajakovich Group focuses on a gut-derived metabolite, 4-ethylphenolsulfate (4-EPS), found in higher abundance in ASD mouse models and children with ASD. 4-Ethylphenol (4-EP), its precursor, is produced by gut microbiota before host-mediated sulfation, but the microbial biosynthetic pathway is unknown. A proposed metabolic pathway suggests the microbial stepwise conversion of plant-derived complex polysaccharides to 4-EP. My project goal is to identify a gut microbial enzyme responsible for the first step of this proposed pathway: a hydroxycinnamoyl esterase. I used literature searches and bioinformatics tools to identify characterized bacterial cinnamoyl esterases and candidate enzymes. I designed plasmids for two candidate enzymes (both from E. faecium, known to colonize the gut) and one characterized esterase (from L. plantarum). Currently, I am working on expressing the proteins in E. coli cells and purifying them by affinity chromatography. Once purified, I will assess the enzymes for their anticipated cinnamoyl esterase activity by incubating them with dietary hydroxycinnamic acid esters and detecting products with high-performance liquid chromatography (HPLC) and UV/Vis spectroscopy. Since the candidate enzymes are homologs of confirmed esterases and have conserved catalytic motifs, I hypothesize that they will have hydrolytic activity. If correct, I will see consumption of the substrate (no detection) and detect the anticipated products. Positive results from these assays would complement ongoing work by the lab to identify other E. faecium enzymes in this proposed pathway. Though it is debated if 4-EPS is causal to the disorder or simply a biomarker, elucidating its biosynthetic pathway and studying the biochemistry of gut microbes will contribute to detangling the gut’s role in ASD.

The heart is one of the most mechanically active organs in the body. In a mechanism known as the “Bainbridge Reflex”, the heart rate accelerates in response to the mechanical stretch induced by the increase in venous return. The cardiac pacemaker controls heart rate, and while stretch-activated channels have been identified in cardiac tissue, their molecular identity remains unknown. We hypothesize that PIEZO channels are the molecular determinant of the stretch-dependent heart rate acceleration responsible for the Bainbridge reflex. Using quantitative polymerase chain reaction (qPCR), we assessed the presence of Piezo1 and Piezo2 transcripts in the pacemaker, atrium, and ventricle of the mouse heart. Our findings revealed that both Piezo1 and Piezo2 are present in the three regions with significantly higher expression in the pacemaker and atria. Combining immunohystochemistry, tissue clearing, and super-resolution microscopy, we analyzed the distribution of Piezo1 and Piezo2 in mouse pacemaker explants. Our results show that Piezo2 is uniformly expressed in the pacemaker and surrounding atrial tissue, whereas Piezo1 exhibits higher expression levels outside the pacemaker. These results were further confirmed at the single-cell level, with immunostaining of Piezo1 and Piezo2 in isolated pacemaker cells (HCN4+) and transitional cells (HCN4-). We observed similar expression levels of Piezo2 in both cell types and increased Piezo1 expression in transitional cells. In addition, we observed distinct localization patterns for Piezo1 and Piezo2 at the subcellular level. Piezo1 predominantly localizes to the sarcolemma, while Piezo2 exhibits a striated distribution that colocalizes alternately with both the Z- and the M- line of the sarcomere. Given this pattern, half of the Piezo2 bands colocalize with the RyR. These results set the starting point to evaluate the functional role of PIEZO channels in the cardiac pacemaker.

The modification of tRNA plays a significant role in the efficiency and accuracy of translation during protein synthesis. A modification that plays a direct role in reading cognate codons of mRNA in E. coli is the 5-oxyacetic acid methyl ester (mcmo5) modification. This modification occurs on the uracil base at position 34 (U34). The biosynthetic pathway of this modification is initiated via a hydroxylation reaction. Previous in vivo studies demonstrate the enzyme TrhP, tRNA hydroxylation protein, performs this hydroxylation reaction in anaerobic conditions. No in vitro work has been done to study this enzyme and its mechanistic function. TrhP is known to coordinate an iron-sulfur cluster, a metallic cofactor known to contribute to a variety of critical cellular processes, however, the necessity of an iron-sulfur cluster for a hydroxylation reaction is unique to this newly discovered protein family. The goal of this research project is to spectroscopically characterize TrhP’s iron-sulfur cluster to understand the importance of the FeS cluster. Site-directed mutagenesis is utilized to study the coordination of the iron-sulfur cluster. Changes to iron-sulfur cluster coordination are monitored via UVVIS, electron paramagnetic resonance (EPR), and colorimetric assays. These experiments determine how the loss of cysteine, a known iron-sulfur cluster ligand, impacts the iron-sulfur cluster coordination. Coordination of a [2Fe2S] cluster by 4 conserved cysteines is expected, and UVVIS data agrees with that hypothesis. Colorimetric assays show the cysteine to alanine mutants contain less iron than wild-type TrhP, indicating each cysteine has a significant role in cluster binding. Learning more about the specific coordination will establish the site of cluster-binding within TrhP and shed light on the cluster’s role in TrhP’s stability, geometry, and redox properties which all contribute to the enzyme’s modification activity.