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Origins of Earth's volatiles from experiments and modeling of accretion and core formation
No full textThis dissertation explores the two key processes– core formation and volatile loss– that shaped the geochemical signatures of the silicate Earth during its formation. We first improve existing models of core formation by incorporating a melt-scaling law to quantify the volume of melt produced by giant impacts. Volatile elements (H, C, and N) are integrated into these core formation models to investigate their distributions between core, mantle, atmosphere, and loss to space during Earth’s formation. Significant C, and potentially N, could be lost during the giant impact stage of Earth’s formation. The last two chapters focus on moderately volatile elements, beginning with high-pressure experiments on the metal–silicate partitioning of Pb. These experiments clarify the bulk Earth abundance of Pb, which confirms the plateau in moderately volatile element abundances with 50% condensation temperatures below ~750 K. Finally, isotopic chronometers that are sensitive to the timing of volatile loss (Pd–Ag, Mn–Cr, I–Xe, and U–Pb), are coupled with core formation models. The moderately volatile element budget of Earth and its precursors was likely set within the first few million years of the Solar System.Earth and Planetary Science
Decoding Development: Using Genetic Mutations to Understand Neurogenesis and Cell Fate
No full textNeurogenesis is the process by which new neurons are formed in the brain, and it is regulated by precise molecular and genetic programs that instruct the timing and order of neuronal birth. Mutations to genes that are essential for regulating the temporal pattern of cell divisions can disrupt neurogenesis, causing neurodevelopmental disease. One example is polymicrogyria (PMG), a congenital brain malformation that results in abnormal cortical folding and cortical disorganization due to altered neurogenesis and neuronal migration. Through functional investigations of PMG-causing mutations, we can characterize the molecular programs that govern cell proliferation in the human cortex. To this end, we functionally validated de novo missense variants found in Pannexin-1 (PANX1) in three individuals with severe PMG. PANX1 encodes a homo-heptameric ion channel that releases anions and ATP into the extracellular milieu. PMG-associated mutations in PANX1 were found to be gain of function, and their overexpression in mice and ferrets disrupted cell migration and cell fate through activity-dependent cell death. Through our findings, we establish a role for PANX1 in regulating neurogenesis by tuning the activity of progenitors and immature neurons.
While in the neocortex, neurogenesis is known to end around the time of birth, there remains a debate in the literature as to whether neurogenesis continues throughout life in the human hippocampus. In mice, extensive research has demonstrated protracted neurogenesis in a region of the hippocampus known as the dentate gyrus (DG). Whether this phenomenon of adult hippocampal neurogenesis (AHN) occurs in humans is unclear. One of the major challenges in investigating AHN is the difficulty of identifying newborn (or newer born) neurons. To address this challenge, we used whole genome sequencing of single DG neurons to probe a cell’s genome as a “barcode” for its development. Every cell acquires somatic mutations in its genome as a result of cell division and aging processes. Discrete mutational patterns can emerge based on specific mutational processes, such as cell proliferation. Thus, by sequencing the DNA of single DG neurons, we assessed mutational signatures consistent with neurogenesis, strengthening the evidence for AHN.Neuroscienc
Discovery and development of small molecule inhibitors of anaerobic microbial choline metabolism as potential therapeutics
No full textAnaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiota is a disease-associated pathway. The host’s impaired ability to oxidize TMA into the downstream metabolite trimethylamine-N-oxide (TMAO) results in trimethylaminuria, while TMAO is positively correlated with various metabolic diseases. Small molecule inhibition of bacterial choline metabolism has been shown to attenuate the development of chronic kidney disease and cardiovascular disease in mice, highlighting the therapeutic potential of modulating this pathway. Inhibitors previously developed to target this pathway are often substrate mimics of choline trimethylamine-lyase (CutC), the key enzyme involved in this transformation that is encoded within the choline utilization (cut) gene cluster. The close structural similarity of these inhibitors to choline raises potential safety concerns of off-target inhibition of host choline and acetylcholine receptors. This dissertation describes our efforts to discover and develop structurally distinct inhibitors of anaerobic microbial choline metabolism as potential therapeutics, by utilizing a combination of high-throughput screening (HTS), medicinal chemistry, quantitative proteomics, and in vivo experiments.
Chapter 2 describes the identification and optimization of structurally distinct inhibitors of anaerobic microbial choline metabolism, as well as preliminary investigations into their mode of action. Leveraging on our understanding of anaerobic choline metabolism in bacteria, we designed a growth-based phenotypic HTS that successfully identified two potential hits for further optimization. We used medicinal chemistry to improve upon the broad-spectrum TMA inhibitory activity and potency of the inhibitors, and reduced their antibacterial activity. Based on previous genetic studies of choline-metabolizing bacteria, we identified three potential modes of action in which inhibitors could exert their effects. After prioritizing the inhibitors based on their potency and toxicity, we assessed their ability to inhibit CutC activity in vitro, ability to repress the expression of the cut gene cluster, and their ability to inhibit choline uptake into the cell. These targeted mode of action assays pointed to a more complex mechanism of action for the inhibitors.
We then turned to a more unbiased approach to identify the targets of our inhibitors. In Chapter 3, we utilized knowledge from our inhibitor optimization efforts to design photo-crosslinking probes that we then used for photo-affinity labeling and quantitative proteomics. These probes labeled specific proteins in the proteome of Escherichia coli MS 200-1, a choline-metabolizing human gut isolate. Identification of these proteins by mass spectrometry revealed that they were homologs of outer membrane protein PagN, an adhesion/invasion protein involved in the virulence of Salmonella. Validation of the protein hit by genetic knockout suggested that these proteins, though binders of the photo-crosslinking probe, were likely not involved in anaerobic choline metabolism. These data suggests that the biologically relevant target may only be present in low abundance or is inaccessible to our probe in a cellular setting.
Finally, in Chapter 4, we evaluated the most promising inhibitors in vivo. In collaboration with the Rey Lab (University of Wisconsin–Madison), we confirmed that our inhibitor was able to reduce serum TMAO levels in both a gnotobiotic and conventional mouse model. We also characterized the shifts in gut microbial community composition of the gnotobiotic mice before and after treatment with our inhibitor and find that there was no significant change. This could imply that our inhibitor can selectively inhibit anaerobic choline metabolism without broader impacts on the gut microbiome. Lastly, we designed a panel of second-generation inhibitors aimed at increasing gut retention. Preliminary in vivo experiments with these inhibitors suggests that we may be able to modulate the bioavailability of the inhibitors by changing their physicochemical properties. Future studies will be focused on improving in vivo activity of these inhibitors and elucidating their mechanism of action in the gut microbiome.Chemistry and Chemical Biolog
Statistical models of protein mutational effects, directed evolution, and clinical chemistry
No full textRandomness is at the heart of life. For one, it mutates genes and thereby the properties of biomolecules like DNA, RNA, and proteins. Biomolecular changes can effect other changes at higher levels, causing variations that manifest in such states as disease. Randomness flows the other way too. Environments fluctuate, causing changes from the outside in. Living things are complex and diverse, and so are the forces that pervade them, genetically, physiologically, and environmentally.
Science progresses, in statistical terms, by inference and simulation: learning from data to predict aspects of different situations. But life's complexity and diversity make this difficult. There's a huge variety of possible proteins and many ways in which they might be improved toward a purpose or disrupted. There are many diseases, many possible markers thereof, and many different people with many different lives. Biology is in these and other ways a noisy science. When we interpret biological data and when we use biology to engineer and to make us healthier, we need to account for randomness, to learn kernels of truth and gently expand their scope.
Through questions I've asked during my PhD, I've taken a small part in this struggle. My approach has been to develop concise statistical models to identify underlying trends in biological data and overarching principles for applications in engineering and health. To better understand the effects of single amino acid substitutions on proteins, I ask in Chapter 1 to what degree these effects are explained by certain physicochemical features of the substitution. I ask in Chapter 2 how stringently experimenters should select variants while engineering biomolecules via directed evolution. And in Chapter 3, I formalize a statistical foundation for interpreting clinical chemistry tests with respect to health. It's been my hope that, beyond satisfying my curiosity, my answers are general enough to each problem that they are straightforward frameworks on which others can comfortably build.Systems Biolog
Escaping the Delphic Trap: Providing Variation Affordances to Foster Agency and Resilience in AI-Mediated Sensemaking
No full textWith emergent capabilities of generative AI, many systems have been eager to adopt features providing \textit{synthesis affordances}: properties that enable and entice users in engaging with AI-synthesized information. There are contexts where offering synthesis affordances may be appropriate---perhaps, even useful. However, approaches taken by popular design patterns in providing them are often not \textit{resilient}. They fail upon breakdowns stemming from AI limitations, human factors, or information quality issues. More concerningly, these design patterns distribute agency inappropriately between humans and AI by granting excessive agency to AI systems. Such configurations lure users into what we term the ``Delphic Trap,'' where users are enticed to satisfice to suboptimal information practice.
Drawing on theories from cognitive and ecological psychology and work in Human-Computer Interaction, we conceptualize \textit{variation affordances}, defining them as system properties that invite users to engage with the inherent variation within information collections. Systems can offer these affordances through steerable controls that support and invite users in engaging in productive friction during information seeking and sensemaking. We argue that a way to instantiate a more appropriate delegation of agency between humans and AI systems, in this context, is through providing variation affordances; doing so may help users engage in more intentional information actions. We design and evaluate several ways to provide these affordances.
Chapter 1 establishes the motivating background for this work. Chapter 2 reviews structure-mapping theory literature to inform approaches for helping users utilize variation. Chapter 3 presents an eye-tracking ablation study (n=24) examining how participants interact with different feature sets providing various variation affordances, discussing functional aspects to consider when implementing these affordances. Chapter 4 examines how common design patterns offering synthesis affordances lack resilience and may cause users to fall into the Delphic Trap. Addressing these risks, we propose a design intervention providing variation affordances through ``AI Highlighters''. Chapter 5 presents a formative study (n=24) assessing user interactions with our design intervention and its variation affordances.Computer Scienc
Deciphering the Role of Age/Timing on Type 2 Diabetes in Major Chronic Disease Precision Prevention and Mortality from a Life Course Perspective
No full textThe global disease burden of type 2 diabetes is substantial. There is a dramatically rising trend in incidence and prevalence of early-onset type 2 diabetes (diagnosed under 40 years of age), a more severe and aggressive phenotype characterized by exaggerated insulin resistance, rapid decline in β-cell function, aggressive disease course, poorer response to treatment, and potentially higher risk for complications. Also, here is a worrisome rising incidence of early-onset cancers across the globe, which is driven predominantly by obesity- and diabetes-related cancers. Mounting evidence has established a close link, epidemiologically and biologically, between type 2 diabetes and increased cancer incidence. To our knowledge, however, no prior study has evaluated the relationship between type 2 diabetes and risk of cancer according to their onset age and disentangled the influence of type 2 diabetes onset age and duration.
Type 2 diabetes is also strongly associated with excess risk of death and loss in life expectancy. The timing of diagnosis is critical, given that early-onset type 2 diabetes manifests as a more severe and aggressive phenotype. Moreover, the occurrence of type 2 diabetes at earlier ages increases the duration of diabetes over the life course. However, existing evidence on type 2 diabetes onset age and duration in relation to mortality risk has been limited by short follow-up, inadequate control for confounding, missing repeated measurements, and inability to cover the full spectrum of onset ages, durations, and major causes of death. Furthermore, data on how type 2 diabetes onset age and duration shape life expectancy remain scarce.
Suboptimal diet is the leading preventable cause of type 2 diabetes, with dietary insulinemic and inflammatory potential playing a pivotal role in its development. Identifying evidence-based optimal prevention strategies for type 2 diabetes is an urgent public health priority. The timing of dietary exposure across the lifespan may be critical in shaping type 2 diabetes risk. Despite this, no prior study has deciphered the influence of diet on type 2 diabetes risk across major life stages from a life course perspective.
In Chapter 1, we addressed the following unanswered research questions: Does the age of type 2 diabetes onset have an influence on cancer risk beyond type 2 diabetes duration? Is the association between early-onset type 2 diabetes and cancer risk inherently stronger than that of later-onset type 2 diabetes? We prospectively investigated the associations between incident early- (diagnosed under the age of 40 years) and later-onset type 2 diabetes and early- (diagnosed before age 50) and later-onset cancer risk based on 228,073 eligible participants in two large longitudinal cohorts: the Nurses’ Health Study and Nurses’ Health Study II. We reported that early-onset type 2 diabetes was associated with a substantially increased risk of early-onset total cancer, diabetes-related cancer, and obesity-related cancer, particularly among individuals with a higher BMI at age 18. Early-onset type 2 diabetes was also associated with a higher risk of later-onset diabetes-related and obesity-related cancers, specifically among those with a higher BMI at age 18. Later-onset type 2 diabetes was associated with a slightly increased risk of later-onset total cancer, diabetes-related cancer, and obesity-related cancer. In analyses based on refined timing, the hazard ratios attenuated substantially with aging. These findings suggest that cancer prevention efforts tailored to early-onset type 2 diabetes patients may need to focus on individuals with a higher BMI during adolescence or emerging adulthood. The influence of early-onset type 2 diabetes on cancer risk may be inherently stronger than that of later-onset type 2 diabetes.
In Chapter 2, we addressed the following unanswered research questions: What is the long-term magnitude of excess mortality risk and loss in life expectancy associated with type 2 diabetes across the full range of onset ages and durations, as well as the specific causes of death? Is the influence of early-onset type 2 diabetes on all-cause and cause-specific mortality risk and years of life lost greater than that of later-onset type 2 diabetes? We prospectively investigated these topics using data from 270,075 eligible participants in the Nurses’ Health Study, Nurses’ Health Study II, and the Health Professionals Follow-up Study. We reported that younger type 2 diabetes onset age and longer disease duration were associated with substantially increased risk of all-cause and cause-specific mortality and greater loss in life expectancy. The relative risk elevations declined rapidly with increasing type 2 diabetes onset age, though the absolute risk difference increased continuously. The influence of early-onset type 2 diabetes on mortality risk and years of life lost was stronger than that of later-onset type 2 diabetes. These findings highlight the imperative need for effective strategies in preventing or at least delaying the onset of type 2 diabetes in lowering mortality and improving life expectancy.
In Chapter 3, we addressed the following unanswered research questions: What are the associations of dietary insulinemic and inflammatory potential with type 2 diabetes risk across major life stages? What are their joint associations across major life stages? What are the associations between changes in dietary insulinemic and inflammatory potential from adolescence to adulthood and the risk of type 2 diabetes? Does lowering dietary insulinemic and inflammatory potential have immediate benefits in reducing the risk of type 2 diabetes in adulthood, or is there a time lag before the benefits become apparent? Leveraging data from 40,135 eligible participants in the Nurses’ Health Study II, we prospectively investigated, from a life course perspective in women, the associations of dietary insulinemic and inflammatory potential across different major life stages—adolescence, premenopausal adulthood, postmenopausal adulthood—and changes and cumulatively over the lifetime with the risk of incident type 2 diabetes. Empirical dietary index for hyperinsulinemia (EDIH) and empirical dietary inflammatory pattern (EDIP) scores were derived from validated adulthood food frequency questionnaires administered every 4 years and validated high school questionnaire. We reported that, over the life course in females, high dietary insulinemic and inflammatory potential during both premenopausal and postmenopausal adulthood—but not adolescence—was independently associated with a substantially increased risk of type 2 diabetes. Individuals with high adulthood dietary insulinemic and inflammatory potential had similar magnitudes of lifetime risk elevation, regardless of their adolescent dietary insulinemic and inflammatory potential status. Adolescent dietary insulinemic and inflammatory potential were associated with a slightly increased risk of premenopausal type 2 diabetes. These findings suggest that adulthood represents the most critical time window for dietary interventions to reduce lifetime type 2 diabetes risk, although adolescent diet may influence the risk of premenopausal type 2 diabetes. Furthermore, our analysis approximating the potential time window underscores the important message that it is never too late to reduce type 2 diabetes risk by lowering dietary insulinemic and inflammatory potential, as higher dietary insulinemic and inflammatory potential in adulthood were associated with an increased risk of type 2 diabetes with a very short time lag.Population Health Science
Clinical, Radiographic, Ultrasonographic and Histologic Outcomes of Alveolar Ridge Preservation using a Xenogeneic Collagen Plug with and without a Membrane: A Randomized Controlled Trial
No full textBackground: Conventional bone augmentation for dental implants typically involves grafting materials, with or without barrier membranes, to preserve ridge dimensions. This study compares the changes in horizontal ridge width in patients undergoing alveolar ridge preservation (ARP) with a xenogenic (bovine) collagen plug, with and without a collagen membrane.
Methods: A 6-month randomized clinical trial was conducted with 20 participants requiring ARP after tooth extraction. Participants were randomly assigned to two groups: Group I, which received a xenogenic plug alone, and Group II, which received a xenogeneic plug with a non-crosslinked collagen membrane. Both groups were allowed to heal by secondary intention. The outcomes of interest included clinical, radiographic, and ultrasonographic changes in hard and soft tissues, as well as histologic and histomorphometric evidence of new bone formation.
Results: All enrolled participants completed the study, with a mean age of 54.25 ± 17.08 years, including 17 premolars and 3 . Baseline buccal bone thickness was similar between the groups (Group 1: 1.02 ± 0.44 mm; Group 2: 0.93 ± 0.45 mm; p = 0.662). At 6 months, no significant differences were observed between groups for keratinized tissue width (Group 1: 4.80 ± 1.48 mm; Group 2: 4.80 ± 1.14 mm; p = 0.999), gingival thickness (Group 1: 1.22 ± 0.25 mm; Group 2: 1.20 ± 0.35 mm; p = 0.650), horizontal bone width at 3 mm from the crest (Group 1: 9.02 ± 2.09 mm; Group 2: 8.41 ± 1.45 mm; p = 0.464), and change in vertical bone at the buccal aspect (Group 1: -0.78 ± 0.59 mm; Group 2: -1.31 ± 1.20 mm; p = 0.244). Ultrasound evaluations were consistent with clinical measurements. Histologic analysis showed similar new bone formation between groups (Group 1: 25.80 ± 15.48%; Group 2: 27.89 ± 18.21%; p = 0.803).
Conclusion: The xenogeneic collagen plug alone yielded comparable ARP outcomes to its combination with a collagen membrane, simplifying the treatment process by reducing costs, time, and the need for additional materials.Periodontolog
Biochemical, Biophysical, and Computational Characterization of RAF Dimer Inhibition and Paradoxical Activation by Diverse RAF Inhibitors
No full textThe RAF family (ARAF, BRAF, and CRAF) of serine/threonine kinases are some of the most frequently mutated proteins in the human genome, and RAF alteration is frequently associated with a number of cancers and other developmental syndromes. The BRAFV600E mutation is particularly prevalent clinically, and, currently, the treatment of BRAFV600E cancers is co-administration of a BRAFV600E specific inhibitor with a MEK inhibitor, though this treatment regimen is only effective against BRAFV600E driven disease states, and even there, is not without issue. When given clinically, BRAFV600E inhibitors often lead to the development of secondary skin lesions, due to a phenomenon called paradoxical activation, where the inhibitors in question paradoxically activate RAF signaling, causing aberrant cell growth, and the aforementioned skin lesions. RAF inhibitors are now co-administered with a MEK inhibitor to more completely inhibit MAPK signaling and mitigate this effect. Here, I developed a reconstituted biochemical system to study RAF activity and RAF response to various inhibitors in vitro, in particular focusing on characterizing paradoxical activation. I find that specific classes of RAF inhibitor have specific isoform preferences for inhibition, and that type II RAF inhibitors inhibit RAF dimers with positive cooperativity, exhibiting tighter binding to the second RAF protomer than the first. We also report on crystal structures of BRAF bound to naporafenib and tovorafenib, two of these type II inhibitors. Notably, there is no evidence of paradoxical activation of these RAF dimers, regardless of inhibitor. I find that while RAF dimers do not exhibit paradoxical activation in this system, two of these same classes of inhibitor (I and II) are able to induce paradoxical activation of RAF monomers, in an isoform dependent fashion. In line with with the prevailing model for paradoxical activation, I find that it begins with inhibitor induced formation of active RAF dimers, from otherwise monomeric RAFs. However, my findings diverge from a crucial aspect of the prevailing model, which posits that the resulting inhibitor-induced RAF dimers escape inhibition due to negative cooperativity of inhibition: binding to one site of the dimer induces a kinase active but inhibitor resistant conformation in the other side of the dimer, which results in a buildup of half occupied RAF dimers that cause the inadvertent activation. I show here, via computational modeling of RAF dimerization, activation, and inhibition, that paradoxical activation can theoretically be induced by any ATP competitive inhibitor, regardless of cooperativity, but that the mechanism of activation can be affected by the type of inhibition cooperativity. Considering type II inhibitors exhibit positive cooperativity against RAF dimers, this computational modeling, in combination with my biochemical results, suggests that paradoxical activation by type II inhibitors is caused by inhibitor-free RAF dimers, which themselves arise because inhibitor induced dimers dissociate back into monomers more slowly than inhibitor itself dissociates from those aforementioned dimers. These findings deepen our understanding of RAF regulation, inhibition, and activation, granting valuable insights into what may be done to circumvent paradoxical activation entirely.Systems Biolog
Trading away the Future? The Winner's Curse and Overconfidence in Major League Baseball
No full textIt assumed in economics that agents perform rationally. However, there is a bevy of research across fields that show that agents are susceptible to biases which do not fit this assumption. One noted bias is time-inconsistency. In professional baseball, the incentives to reach the playoffs and win the World Series are such that teams may be susceptible to such an error. This paper finds that teams are willing to trade away future value for short-term gains in line with this error.Applied Mathematic
The Steel City Circuit: Reimagining Pittsburgh’s Steps, Slopes and Shifting Landscapes.
No full textFrederick Law Olmsted Jr.’s 1910 report drew attention to Pittsburgh’s incredible topography and hillside slopes yet overlooked its steps and landslides. This thesis serves as a contemporary addendum, by reframing the steps, once vital for
hillside connectivity, as dual-purpose infrastructure mitigating landslides while celebrating the city’s industrial heritage. The
Steel City Circuit, a 40-mile loop, is a physical and cultural stitch, linking neighborhoods on unbuildable land through
slope-stabilization strategies. Along the route, vantage points examine the observer and the observed in relationship to the
layered narratives of the city and its history. By filling the gaps in Olmsted’s framework, the project recasts Pittsburgh’s
topography as artifact and asset, ensuring steep hillsides become catalysts for social, ecological, and economic renewal
underscoring Pittsburgh’s capacity to preserve its past while ensuring a more resilient future.Department of Landscape Architectur