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.

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.

As part of the National Science Foundation funded Washington Resurvey of Pierids (WARP) project in the Buckley lab, I am conducting a comparison between the temperature dependent growth rates of Pieris rapae caterpillars collected 25 years ago and this past summer. Pieris rapae, the cabbage white butterfly, is a recently introduced, abundant, and invasive crop pest across North America that is active in the warm spring and summer months (May to September) with 4-5 generations each year. This species has been previously studied as a model for insect thermophysiology, as ectotherms and insects in particular rely on permissive thermal environmental conditions for many core life processes. Our goal is to investigate if evolution has occurred in these caterpillars over more than 100 generations to take advantage of their new, warmer thermal environment compared to a historical baseline. We hypothesize that the temperature sensitivity of relative growth rates (RGRs) has shifted due to increasing temperatures during their season of activity, and predict that contemporary caterpillars grow faster at high temperatures than their historical counterparts did. We caught female butterflies in the Seattle area and reared their caterpillar offspring in a standardized thermal environment (10-30॰C). We then measured short term (2-24hr) RGRs by exposing caterpillars in their 4th developmental stage to 5 different temperature conditions in sequence (11-35॰C), observing their mass after each treatment. I am performing an analysis of variance (ANOVA) test of the data using two covariates of interest, temperature and time period (current or historical), to test for differences within each temperature treatment across time. Understanding how insects, especially pollinators, are evolving in response to climate change is vitally important to building accurate models for future population ranges and densities, as without this evolutionary and mechanistic knowledge, our predictions will be unreliable.

 After someone suffers from a heart attack, heart tissue can become scarred. Scarred heart tissue cannot regenerate, leading to many dangerous outcomes, including dysrhythmia, chronic heart failure, and even sudden cardiac death. Therefore, there is a need in tissue engineering to create a “band-aid” that could functionally replace damaged heart tissue. Utilizing open microfluidic patterning techniques, we can generate suspended heart tissue that could reinforce and replace unviable heart tissue. Towards this aim, we designed an open microfluidic patterning removable rail that interfaces between two posts such that an open channel is formed around the posts. Combining human vein endothelial cells (HUVECs) and enzyme-degradable polyethylene glycol (PEG) hydrogel, we pattern the cell-gel solution through the open channel. After the hydrogel has gelled, the rail can then be removed from the posts, revealing a suspended tissue model, acting as the vasculature of the heart tissue. Then, a second patterning rail that has a larger open channel can be placed around the first generated suspended tissue. We will then pattern human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM) in fibrin (a physiologically relevant extracellular matrix of heart cells) such that the hiPSC-CM laden fibrin gel will completely encapsulate the first HUVEC laden PEG gel. Once the complete tissue is made, the construct can be treated with an enzyme that specifically degrades PEG, resulting in a hollow core within the hiPSC-CM gel, releasing the HUVECs into the newly formed cavity. The HUVECs can then localize around the walls, thus generating an endothelized vascular chamber. Overall, this platform models the inner walls and lumen of a blood vessel, thereby representing an endothelium. Eventually, to further this project, I intend to integrate this blood vessel within a thick, multilayered engineered heart tissue patch and test its efficiency in providing structural support and useful circulation.

Many microorganisms that are crucial to the human body and environment need to use highly controlled electron transfer processes to catalyze challenging chemistry under a variety of oxygen levels. The under-studied anaerobic ubiquinone-8(UQ-8) biosynthesis pathway, found across multiple bacterial classes, uses unprecedented oxidation chemistry with proteins containing [4Fe-4S] clusters. Understanding the electron flow and mechanism of control in this pathway is key to understanding microbial adaptation to anoxic conditions. Two recently identified proteins, UbiU and UbiV, catalyze the oxygen-free hydroxylation in UQ-8 synthesis. Preliminary in vivo evidence shows the following highly conserved redox-active amino acids, Tyrosine 177,181 in UbiU and Tyrosine 281 and Tryoptophan 282 in UbiV are necessary to complete the reaction. I hypothesize that these amino acids facilitate electron transport from the active site to an external electron acceptor. UbiU/NHis-UbiV heterodimers containing Y177F, Y181F, Y281F, and W282F were expressed in E. coli and purified using his-tag affinity chromatography, then analyzed via size-exclusion chromatography to evaluate the impact of the mutations on structure. The mutations have had a variety of impacts on the oligomeric state implying some level of disruption to the dimer-interface, however, the majority of protein remains in dimerized form. Spectroscopic characterization of these mutants via EPR and UV-Vis is consistent with the identification of the metallocofactors as [4Fe-4S] clusters, although site occupancy is consistently lower than for the wild type. In vitro protein assays test observed catalysis of octaprenyl phenyl(OPP) to UQ-8 to illuminate the mutations impact on activity. Structural data gathered thus far forms a foundation for future work with radical-trap synthetic amino acids and further activity assays.

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 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.