Cunningham, Eric. Zen Past and Present. Key Issues in Asian Studies, no. 8. Ann Arbor: Association for Asian Studies, 2011.

Review of Zen Past and Present by Eric Cunningha

Investigation into the mechanisms of size-resolved particle dry deposition across three environments

2022 Summer.Includes bibliographical references.Airborne particulate matter, or aerosols, have significant impacts on radiative forcing through both their direct - scattering and absorbing light - and indirect effects- acting as cloud condensation nuclei and altering the lifetime of clouds. The magnitude of these effects is largely determined by particle lifetime, which is defined by their rate of removal through wet and dry deposition. Dry deposition, specifically of accumulation mode aerosols (0.1 – 1 µ), is one of the largest sources of uncertainty in global models. The processes that influence deposition are poorly constrained and few comprehensive measurements are available to improve our understanding. Characterizing these mechanisms is vital for predicting spatial and temporal trends in particle dry deposition and lifetime. While there have been improvements in quantifying and understanding dry deposition, large gaps in our knowledge still exist that make predicting the impacts of aerosols on Earth's climate difficult. To improve understanding of the underlying mechanisms that determine the rate of particle deposition in an environment this dissertation reports size-resolved dry deposition measurements from three distinct environment types. First, we report measurements from a test house which identify dilution and deposition as the most important factors influencing particle concentrations indoors. This analysis also shows that deposition indoor is governed by the same fundamental process that we consider for outdoor environments. Second, we present particle flux and deposition measurements from a Ponderosa pine forest over four seasons where significant enhancement in deposition during the wintertime was observed. This is attributable to changes in interception, caused by changes in plant physiology and surface structure during the winter that leads to an increase in their ability to uptake particles. Finally, we show particle and black carbon deposition from a low Arctic tundra during snow-cover that are elevated compared to predictions of dry deposition in that region. Incorporating interception into the model parameterizations improved model measurement agreement and provides evidence to suggest that surface structure and microroughness impact deposition even when there is snow-cover

Strength in numbers? Not always!

We propose a simple model to compute the probability of success under a quorum sensing strategy. We show that a quorum sensing strategy has a higher probability of success than an individualistic strategy when, for instance, the probability of success for a single individual is low and the cost of building a quorum is not too high. On the other hand if the cost of building a quorum is too high then the probability of success under quorum sensing always decreases as a function of the quorum

Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria

A canonical quantitative view of transcriptional regulation holds that the only role of operator sequence is to set the probability of transcription factor binding, with operator occupancy determining the level of gene expression. In this work, we test this idea by characterizing repression in vivo and the binding of RNA polymerase in vitro in experiments where operators of various sequences were placed either upstream or downstream from the promoter in Escherichia coli. Surprisingly, we find that operators with a weaker binding affinity can yield higher repression levels than stronger operators. Repressor bound to upstream operators modulates promoter escape, and the magnitude of this modulation is not correlated with the repressor-operator binding affinity. This suggests that operator sequences may modulate transcription by altering the nature of the interaction of the bound transcription factor with the transcriptional machinery, implying a new layer of sequence dependence that must be confronted in the quantitative understanding of gene expression

Theoretical and Experimental Dissection of DNA Loop-Mediated Repression

Transcriptional networks across all domains of life feature a wide range of regulatory architectures. Theoretical models now make clear predictions about how key parameters describing those architectures modulate gene expression, and the ability to construct genetic circuits with tunable parameters enables precise tests of such models. We dissect gene regulation through DNA looping by tuning network parameters such as repressor copy number, DNA binding strengths, and loop length in both thermodynamic models and experiments. Our results help clarify the short-length mechanical properties of DNA

Modeling Multispecies Gene Flow Dynamics Reveals the Unique Roles of Different Horizontal Gene Transfer Mechanisms

Horizontal gene transfer within diverse bacterial populations occurs through multiple mechanisms of exchange. The most established routes of gene transfer, transduction, transformation, and conjugation, have been characterized in detail, revealing the advantages and limitations of each mechanism. More recently, interspecies gene exchange via extracellular vesicles has been reported and characterized, making vesicle-mediated exchange a fourth, general mechanism of gene transfer. Despite an understanding of each individual pathway, how all of these mechanisms act in concert has not been explored. Here we develop a model of gene exchange in a multispecies bacterial community that takes into account the rates and limitations of all four gene transfer mechanisms. Our results reveal unique roles for each gene exchange mechanism, and highlight how multiple pathways working together are required for widespread gene exchange within diverse bacterial populations