The immune system persists in a sensitive equilibrium, necessarily avoiding overreaction to illegitimate threats while watchfully waiting for any bona fide harms that might come along. Fortunately, myriad cell extrinsic and intrinsic mechanisms have evolved to fortify this steady state. Amongst these regulatory forces, three distinct yet interdependent signals lie at the heart of immune activation. This first signal – engagement of the B or T cell receptor by cognate antigen – has significant diagnostic and therapeutic potential. After the emergence of SARS-CoV-2 and its associated clinical syndrome, COVID-19, we led a nationwide, multi-disciplinary scientific and clinical team to systematically benchmark numerous serological assays testing for effective “signal 1” responsiveness to SARS-CoV-2-associated antigens. Establishing accuracy of these tests had significant implications on governmental policies relating to the pandemic, as well as efforts to employ these serology tests to understand COVID-19 seroprevalence and protective immunity. Next, we applied computational tools to improve the performance of these serological tests through combinatorial application and companion analyses. Lastly, we followed these studies of serology diagnostics (corresponding to signal 1) with systematic molecular studies of costimulation: the second signal influencing T cell activation. This critical next step is indispensable to immune responsiveness, but the intricacies of regulatory factors influencing each step have yet to be systematically studied. Our labs have pioneered the use of functional genomic screening using CRISPR/Cas9 to thoroughly explore the regulatory landscape of various immunological phenotypes. Thus, we leveraged recent molecular advances to functionally define the cis and trans regulators converging on the human costimulatory locus harboring CD28, CTLA4, and ICOS at scale. This work uncovered gene-, cell subset-, and stimulation-specific cis-regulatory elements (CREs) bound by validated trans regulators to influence costimulatory gene expression. Finally, deep characterization of genomic architecture in the locus defined critical insulator elements reinforcing CRE activation of true targets while also preventing spurious activation of flanking genes. Ultimately, similar demonstrations of collaborative science to study the human immune system whether in the form of fundamental genomic immunology or translational immune diagnostics will aid our collective transition to the next generation of more precise biomedicine.

The University of California (UC), California State University (CSU), and California Investor-Owned Energy Utilities are collaborating in an innovative new program to retro-commission campus facilities with the assistance of permanently installed energy monitoring equipment and trending capability. This monitoring-based commissioning (MBCx) effort spans 25 campuses, with nine projects for plant systems and 37 projects for buildings. Half of the buildings include laboratory or other energy-intensive space. The program is a part of the implementation of the UC Green Building and Clean Energy Policy, the similar CSU policy, and the California Investor Owned Utility (IOU) customer funded Energy Efficiency Program.

Monitoring-Based Commissioning (MBCx) employs remote energy system metering with trend log capability to identify previously unrecognized inefficiencies in energy system operations, facilitate the application of diagnostic protocols, document energy savings from operationalimprovements, and ensure persistence of savings through ongoing recommissioning. The program emphasizes training of campus staff in commissioning techniques includingmonitoring and diagnostic protocols. The program is also demonstrating the potential for MBCx to identify previously unrecognized cost-effective retrofit opportunities. In addition, the monitoring equipment will provide enhanced benchmarking capability for campuses—aiding in overall energy management efforts, as wells as design of new buildings and infrastructure.

Based on the success of preceding efforts on university campuses and supported by research and development efforts, this synergy of retro commissioning practices and enhanced permanent monitoring results in a robust energy efficiency program. The monitoring supports persistence of savings for the commissioning effort, while the commissioning makes the monitoring action-oriented with energy savings the end-result.

The first project results indicate more energy use reduction than expected, making this a promising approach for California universities and indicating potential for other programs as well. The 2004-05 effort is serving as a pilot —with the identification of best practices to form the basis for an expansion of the program to a large portion of the 160 million gross square feet of floor area in the two university systems.

Whereas the human fetal immune system is poised to generate immune tolerance and suppress inflammation in utero, an adult-like immune system emerges to orchestrate anti-pathogen immune responses in post-natal life. Compared to their adult counterparts, fetal naïve T cells more readily differentiate into tolerance-prone regulatory T cells (Tregs) upon stimulation, and fetal monocytes exhibit distinct responses to cytokine stimulation and impaired antigen presentation capacity. It is believed that tolerogenic responses across various immune cells are adaptations that allow the fetal immune system to suppress responses to non-inherited maternal antigens that might otherwise lead to pregnancy complications. After birth, the balance between tolerance versus protection must shift. It has been posited that cells of the adult immune system arise as a discrete ontological “layer” of hematopoietic stem-progenitor cells (HSPCs) and their progeny; evidence supporting this model in humans has, however, been inconclusive. Although it has been shown that various immune cell transitions during early gestation may be modeled by the layering hypothesis, it is unknown whether the transition from fetal-to-adult follows a similar mechanism. Here, we combine bulk and single-cell transcriptional profiling of lymphoid, myeloid, and HSPCs from fetal, perinatal, and adult developmental stages to demonstrate that the fetal-to-adult transition occurs progressively along a continuum of maturity—with a substantial degree of interindividual variation at the time of birth—rather than via a transition between discrete waves. We find that (1) newborn immune cells are relatively homogenous, each with an intermediate transitional phenotype, rather than having either a fetal or adult phenotype, (2) UCB HSPCs are not fully adult-transitioned, (3) the progression of transition at birth shows a high degree of inter-individual variability, and (4) pathways known to affect T cell polarization are among those expressed more highly in newborn than adult naïve CD4 T cells. These findings have important implications in the design of strategies for prophylaxis against infection in the newborn, and for the use of umbilical cord blood (UCB) in the setting of transplantation. I also present dittoSeq, a universal bulk and single-cell visualization toolkit that powered the analysis of these data. dittoSeq visualizations are color blindness-friendly by default, robustly documented to power ease-of-use by both novice and experienced coders, and allow highly customizable generation of both daily-use and publication-quality figures.

This dissertation examines the settler colonial, multispecies, and microbial politics of Atlantic salmon aquaculture in what is now British Columbia, Canada. Salmon aquaculture production systems enable 18 million Atlantic salmon to be raised in nets that are anchored to the seafloor in the coastal waters of British Columbia each year. Aquaculture is recognized as the fastest growing method of food production worldwide and is often positioned as a “blue revolution” capable of providing sustainable, affordable seafood in the midst of salmon population declines. In British Columbia, however, the raising of Atlantic salmon in critical Pacific salmon migration routes has engendered concerns about emerging industrial uses of the waterscape and the ability for farm-borne viruses to move between species. By investigating how industrial aquaculture is encountered, negotiated, and resisted on-the-ground, particularly by Indigenous communities in whose waters the practice is occurring, I instead propose that aquaculture is not a radical departure or a revolutionary break from the past, but is steeped within and dependent upon histories of colonialism, industrialization, and capitalism that have long transformed salmon and waterscapes into sites of state and economy-building.

Stemming from ongoing uncertainties regarding the potential for pathogens to transfer between Atlantic and Pacific salmon, this dissertation particularly focuses on historic, scientific, and political controversies that surround salmon viruses. In the absence of state monitoring for salmon pathogens like Piscine orthoreovirus (PRV), Indigenous leaders and their allies travel to sites of aquaculture production to monitor the daily operations of farms and gather underwater video footage from within farm sites. Campaigns to enact stronger fish health protections and document the spread of viruses and pollution also become part of broader political movement aimed at reclaiming territory and restoring Indigenous forms of governance within coastal waterscapes. While pathogens come to reflect and reinforce colonial structures of dispossession, I argue that Indigenous-led efforts to track pathogens throughout salmon bodies and ecosystems are shifting power dynamics in ways that offer new possibilities for the “blue revolution.”

This research brings scholarship on pathogens and industrial landscapes into conversation with enduring concerns about the material consequences of environmental injustice and colonialism. In situating aquaculture as part of an under-explored extension of settler colonial logics, structures, and governance into marine space, I suggest that the dominant framing of settler colonialism as land-based leaves large openings for understanding how colonialism and sovereignty are enacted in water-centered and maritime regions. Illuminating how industrial aquaculture and efforts to track pathogens take place within a broader politics of asserting sovereignty “at sea” reveals how historical inequalities and ongoing power dynamics become inscribed within oceans, with important implications for understanding contemporary ocean politics in the 21st century.

Thymic central tolerance is a critical process that prevents autoimmunity, but also presents a challenge to the generation of anti-tumor immune responses. Medullary thymic epithelial cells (mTECs) eliminate self-reactive T cells by displaying a diverse repertoire of tissue-specific antigens (TSAs) that are also shared by tumors. Therefore, while protecting against autoimmunity, mTECs simultaneously limit the generation of tumor-specific effector T cells by expressing tumor self-antigens. This ectopic expression of TSAs largely depends on autoimmune regulator (Aire), which is expressed in mature mTECs. Thus, therapies to deplete Aire-expressing mTECs represent an attractive strategy to increase the pool of tumor-specific effector T cells. Recent work has implicated the TNF family members RANK and RANK-Ligand (RANKL) in the development of Aire-expressing mTECs. Here, we show that in vivo RANKL blockade selectively and transiently depletes Aire and TSA expression in the thymus to create a window of defective negative selection. Further, we demonstrate that RANKL blockade can rescue melanoma-specific T cells from thymic deletion and that persistence of these tumor-specific effector T cells promoted increased host survival in response to tumor challenge. These results indicate that modulating central tolerance through RANKL can alter thymic output and potentially provide therapeutic benefit by enhancing anti-tumor immunity. Finally, in an effort to identify novel genes and signaling pathways required for thymic function, we demonstrate that canonical microRNAs (miRNAs) are required in TECs to maintain proper thymic architecture and to support the maintenance of central tolerance. By understanding which miRNAs are important for these functions, we hope to uncover new targets and regulatory pathways for therapeutic intervention in the thymus.