• iMicrobe: Tools and Data-Driven Discovery Platform for the Microbiome Sciences

      Hurwitz, Bonnie; Youens-Clark, Charles Kenneth; U'Ren, Jana; Hartman, John (The University of Arizona., 2019)
      Background: Scientists have amassed a wealth of microbiome datasets making it possible to study microbes in biotic and abiotic systems on a population- or planetary-scale; however, this potential hasn’t been fully realized given that the tools, data sets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community. Findings: The iMicrobe platform brings together analysis tools and microbiome data sets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly-scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP). Conclusions: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.
    • Populus Fremontii Tree Ring Analysis and Semi-Arid River Water Source Variability over Time, San Pedro River, Arizona

      Meixner, Thomas; Stolar, Rebecca Ann; Hu, Jia; Niu, Guo-Yue (The University of Arizona., 2019)
      Summer floods are an important source of sustained streamflow in arid and semi-arid rivers of the American Southwest and Northwest Mexico. The degree to which natural function versus human alterations influence the system is subject to debate. Environmental information in the tree ring cellulose of Populus can be used to investigate the variation in water sources over time in these areas. Past research has shown that streamflow sources in the San Pedro Basin of Arizona vary isotopically between a source water of basin ground water and a summer flood water source. This study uses isotopic analyses of Populus fremontii and atmospheric data in the San Pedro Basin to estimate the water source of the trees and the river water source condition. After analyzing weather data within the basin, an inversion of the Barbour oxygen isotope model using tree ring cellulose isotopes was used to obtain the water source isotopic composition. The variation in water source composition inferred from the model was then compared to the river composition over time. It was initially found that each site’s water source isotopic composition was significantly different from the source water. However, several water source isotopic compositions were found to be more negative than the known basin groundwater signature in each of the study sites. Following sensitivity analyses on various parameters within the model, it was seen that relative humidity has a strong influence on the determination of source water. Therefore, relative humidity must be an accurate measurement and is not considered to be so in this study. Furthermore, in order to understand the degree to which natural function versus human alterations influence the system, older Populus fremontii tree ring isotopes are needed, posing a question regarding the reliability of the species.
    • But Wait, There’s More: On the Additions to Esther

      Friesen, Courtney; Bustamante, Angel Joseph; Wright, Ed; Bauschatz, John (The University of Arizona., 2019)
      This thesis examines the Greek Additions to the book of Esther. These Additions are found in both Greek versions of the book, but not in the Hebrew version. In Chapter 1 I discuss the history of the Hebrew (MT) and Greek texts (LXX, AT). The history of all three of the texts is too complicated to discuss in great detail, but a broad overview is necessary to understand the context of the Additions. In Chapter 2 I examine the Additions in depth. It seems that the Additions come in pairs, with one complementing the other. It is often very difficult to date the Additions, and most of the time nothing more than a terminus post quem or terminus ante quem can be offered. In the case of some of the Additions, it is uncertain whether they were originally written in Greek, Hebrew, or Aramaic. That said, two were clearly originally written in Greek, which demonstrates that the Additions were not composed by just one author. In the Conclusion I examine then asks why the Additions were written, determining that they were added both to heighten the drama and to include God explicitly in the text. I also conclude that, the authors of Esther and the Additions seem to be cautiously optimistic about relations between the Jews and the Hellenistic monarchs.
    • Holy Mother of Milk: Female Readers and the Function of Religious and Scientific Discourse in the Guidi Book of Hours

      Cuneo, Pia; Raymer, Katherine; Moore, Sarah; Soren, David (The University of Arizona., 2019)
      This thesis examines the Guidi Hours in the context of contemporaneous religious and medical teachings in regard to women of the early fifteenth century and the ways in which the narratives they create are visually articulated and actively promulgated through this book’s illustrations. The two virgo lactans and sacra cintola within this manuscript are analyzed through a fifteenth-century female reader’s perspective to investigate the ways in which women may have understood them and this prayer book. Based on medical and religious discourses surrounding the importance of these various aspects regarding the woman herself, our female reader’s understanding of this iconography went beyond an image of Mary and Christ, or of a mother and child, but imparted instructions on how to be a model for her gender.
    • Late Helladic Emulation: An Analysis of Palatial and Domestic Architecture and Construction Techniques in Mycenaean Greece

      Schon, Robert; Fricker, Laurel; Voyatzis, Mary E.; Romano, David G. (The University of Arizona., 2019)
      In this thesis, I investigate to what extent the architecture and constructions at the Mycenaean palaces are emulated at non-palatial sites, using methods and theories involving emulation, the power of architecture, and peer-polity interaction. I first compare the Palace at Mycenae with the Panagia Houses at Mycenae, houses at Korakou, and houses at Asine, to examine how distance from the palace and the time period affects the construction of houses in the Argolid and the Corinthia. Then I compare the Palace of Nestor at Pylos with Nichoria to see how distance, geographical boundaries, and site status affect the construction of houses in Messenia. A building is a statement, having the ability to form and communicate personal identities and communities, indicate social associations, highlight political organizations, and provide details for understanding aspects of life. Further, architecture can influence how people view their society and their community; the central unit (including the megaron hall with its hearth and columns) of the Mycenaean palaces, constructed on the monumental palatial scale, became a statement of power. The status of these constructions would have made them perfect candidates for locals at periphery sites attempting to emulate the authority of the palaces in LH III Greece. However, the dates of construction of the palaces and the residential structures, locally available materials, previous traditions of construction, and geographical boundaries all could have affected how much emulation was possible in LH IIIA-B Greece.
    • Single-Chip LiDAR by Multi-Order and Multi-Pulse Beam Steering with Digital Micro Mirror Device

      Takashima, Yuzuru; Rodriguez, Joshua Miguel; Kim, Dae Wook; Kim, Young Sik (The University of Arizona., 2019)
      We demonstrate the feasibility of enhancing the scanning rate for MEMS and diffraction based beam steering employing Digital Micromirror Device (DMD) by one to two orders of magnitude, which is configured as a programmable blazed grating. The tilt movement of micromirrors synchronizes with multiple pulses from multiple laser sources that sequen- tially redirect the pulses to multiple diffraction orders within μs. The approach opens up a pathway to achieve a LIDAR system with a scanning rate over 1M samples/s while leveraging a state of the art DMD and a moderate number of laser sources.
    • Theriomorphic Forms: Analyzing Terrestrial Animal-Human Hybrids in Ancient Greek Culture and Religion

      Voyatzis, Mary E.; Carter, Caroline LynnLee; Romano, David G.; Soren, David; Mahoney, Kyle W. (The University of Arizona., 2019)
      This thesis explores terrestrial theriomorphism (the ascription of animal characteristics to human figures) in ancient Greek culture and religion diachronically using literary and archaeological evidence, while focusing on the latter to supplement previous scholarship (Aston 2011). I analyze 13 consistently terrestrial theriomorphic beings (including eight deities) and iconography from the Greek historical period (Chapter 2). The unique scope of the thesis allows for a comprehensive examination, considering these hybrids’ possible origins in time and place, development through cultural interactions, geographical concentrations, iconographical representations, and overall significance (Chapter 3). The research and conclusions in this thesis offer new insights and developments towards furthering our understanding of the relationship between humans and animals in ancient Greece. Appendix A is a chart of cult sites to theriomorphic deities (which is complemented by a series of maps). It is the first of its kind to be published and reveals concentrations in both rural and urban locations across the Greek Mediterranean, but especially in Arcadia. In addition, I provide an analysis of (terrestrial) theriomorphism in the Bronze Age for the first time ever, showing that there are connections to later Greek culture and religion. This thesis sheds light on the extent to which animals were an essential aspect of Greek life as a means to express their relationship to man, nature, the landscape, and identity, especially in religious contexts. Numerous conclusions are made that challenge and supplement previous scholarships and generalized conceptions, such as theriomorphism being “primitive” and that the centaur existed in Greece continually though the Bronze Age and Early Iron Age.
    • Staging Shame: Constructing Aischunē in Menander’s Samia and Dyskolos

      Christenson, David M.; Ruprecht, Daniel Matthew; Groves, Robert; Friesen, Courtney (The University of Arizona., 2019)
      This thesis explores the Greek notion of aischunē as represented in Menander’s Samia and Dyskolos. The term aischunē conveys an emotion, a disposition, and an ethical code related to the concepts of shame, guilt, embarrassment, and dis/honor. I argue that aischunē cannot map directly onto any modern concept, but by analyzing how and why characters express aischunē in Menander’s family dramas, we can more fully understand the social frameworks underlying it and begin to understand how the emotion felt. Because part of aischunē is an expression of an emotion, Chapter 1 deals with emotional theory, how one can conduct a study into the history of emotions. Building on decades of interdisciplinary research, I argue that emotions are at least partially socially constructed, and, to study aischunē, one must investigate the constructs. I then lay out working definitions of three modern American emotional constructs—shame, guilt, and embarrassment—which are necessary touchstones to talk about ancient aischunē. Finally, I distinguish aischunē from aidōs, both of which denote sorts of shame/guilt/honor. In Chapter 2 and 3, I analyze each instance of aischunē in Menander’s Samia and Dyskolos, and I argue for a different translation to better convey complexities of meaning in each case.
    • ¡La Puebla Lucha! LGBTI Activism and Organizing against Violence in El Salvador

      Green, Linda B.; Gardella, Annalise; Pieper Mooney, Jadwiga; Bacelar da Silva, Antonio (The University of Arizona., 2019)
      Lesbian, Gay, Bisexual, Transgender, and Intersex (LGBTI) people in El Salvador face some of the highest rates of violence in the world. The modalities of violence impacting the LGBTI population span across many levels, including physical, economic, structural, and symbolic, and intersections of identity like gender, race, sexuality, and class within the population determine people’s proximity to and risk for violence. In response, local organizations, some with international ties and others working independently on a small-scale are attempting to organize the LGBTI population into a community that can work to redress this violence through community-building and support structures as well as make visible the oppression the community faces at a public and legislative level. This thesis outlines the historical formation of the Salvadoran LGBTI movement beginning in the 1980s through the present day, focusing on coalition-building and historical moments of unity that have led to the creation of a national Federación Salvadoreña LGBTI, or a federation of LGBTI organizations, to combat the most important issues facing the Salvadoran LGTBI population currently. Through an analysis of interviews and participant observation, this thesis examines the numerous and interconnected iterations of oppression and violence facing the Salvadoran LGBTI community and consequently explores the ways in which organizations and activists are strategically responding to the violence that devastates their community.
    • Design of Infrared Microscope

      Milster, Tom; Hu, Kai; McLeod, Euan; Kieu, Khanh (The University of Arizona., 2019)
      This thesis introduces a way to arrange the setup of infrared microscope so that it is theoretically feasible to realize the experimental infrared microscope. The most challenging problem mainly resolved in this paper is how to increase the really low SNR from {10}^{-8} to a measurable value. The process includes introducing an Optical Amplifier, such as Quantum Cascade Laser Amplifier, and applying sensitive detector, such as HgCdTe PD/APD with lock-in Amplifier. Finally, we also discuss about a way to arrange the infrared optical system and introduce a sample design of a high NA infrared objective (NA=3.7).
    • Condensed Chaos

      Zielinski, Angela; Dahlke, Ashley; Vaden, Cerese; Zielinski, Angela; Bradford, Carlton; Moore, Sarah; Leslie, Kelly (The University of Arizona., 2019)
      The relationship we have with objects is one that is often quite complex. Things that we own can bring us feelings of joy, nostalgia, comfort, melancholy, and can become burdensome. Objects that we choose to surround ourselves with gives insight into who we are and can become portals to our past experiences and memories. Condensed Chaos looks at objects found in thrift stores and resale shops and how their proximity to other objects creates a range of narratives about who the previous owners were and what the life of the object once was.
    • Exploring the Impact of TiO2 Surface Chemistry on Nucleation and Growth of Perovskite Active Layers for Photovoltaic Applications

      Armstrong, Neal R.; Saunders, Kara C.; Saavedra, S. Scott; Pemberton, Jeanne E. (The University of Arizona., 2019)
      We introduce lead ions adsorbed to TiO2 as a surface modification, which serves as a model system to begin understanding how the chemistry at the TiO2/perovskite interface influences nucleation and growth of mixed-halide cesium perovskites. The surface chemistry of TiO2 was incrementally changed by subjecting the thin films to both oxygen and argon plasma treatment and lead adsorption thereafter. A combination of x-ray photoelectron spectroscopy (XPS), x-ray diffraction (XRD), grazing-incidence wide-angle x-ray scattering (GIWAXS), and atomic force microscopy (AFM) were used to evaluate the surface chemistry, crystallinity, and morphology of both the modified TiO2 and the perovskite active layer on TiO2 with the hypothesis that lead adsorption on TiO2 would aid in the initial nucleation of the perovskite film by decreasing interfacial disorder by titrating away the reactive hydroxyl sites on the surface. By photoemission spectroscopy, we show that lead adsorbed from PbI2 preferentially binds to TiO2 at surface hydroxyl sites with a surface coverage ranging from 26-68% of a monolayer depending on the initial surface treatment. GIWAXS data reveals that perovskites on TiO2 exhibit crystal growth with greater preferential orientation of the (100) axis perpendicular to the surface normal and that the degree of preferential orientation depends on the availability of surface hydroxyl sites for the perovskite precursor materials to bind to. Moreover, perovskite films exhibited greater crystallinity and coherence lengths on substrates that have more available hydroxyl groups, such as as-deposited TiO2. AFM images evaluating the morphology of the perovskite films are consistent with findings acquired by XPS, XRD, and GIWAXS, demonstrating that atomic-scale changes to the interfacial region of this system result in changes visible at the top surface of the perovskite film. Although the data does not support the initial hypothesis, this work highlights the critical importance that adjacent hydroxyl groups have in the nucleation and growth of perovskite films. Passivation of these reactive sites by lead adsorption inhibits the initial crystal growth. Ultimately, understanding the importance of the reactive sites on TiO2 paves the way for future work on controlling hydroxyl density with the intent of controlling the nucleation and growth of perovskite active layers on TiO2 for photovoltaic applications.
    • Boom: Latinos, the Modern Pioneers

      González de Bustamante, Celeste; Lanuza, April; Relly, Jeannine; Duncan, Daniel; Newton, Kim (The University of Arizona., 2019)
      Latino dispersion is changing communities around the United States. Latinos are moving to and living in ‘non-traditional’ places around the country. The demographics of predominantly white, rural cities and states are changing. According to a PEW Research Study, Williams County, North Dakota, led the nation in Latino population growth from 2007 to 2014. For my thesis I visit Williston, the largest city in Williams County, to produce a documentary about the city’s growing Latino population in a post oil boom society. Williston suddenly had a surge in Latinos from 2007 to 2014 because of an oil boom and the increase in jobs that ensued afterwards. According to the US census of North Dakota (Cicha, 2015), as of 2015, every county in the state has a Latino population. Twenty-three percent indicated they were born in-state, sixty-one percent born out of state and sixteen-percent born outside of the country. However, even with the stabilization of the oil boom, a Latino community remains. The objective of my thesis is to investigate this shift in Latino migration and examine the networks that have been built as a result. Through the eyes of several Latinos in Williston, I have produced a documentary detailing their experiences in this city. Other people in the community give their perspectives about what the community is like and what is or isn’t supporting this new Latino population. As Latinos move away from ‘traditional’ places such as Miami and Los Angeles, rural, smaller, Anglo-American dominated communities are seeing an increase in native Spanish speakers that they had not seen before, thus influencing community dynamics. Using ethnographic research and the conceptual framework of moral geography, I will examine how the community perceives this new population. Keywords: Immigrant, Networks, North Dakota, Williams County, Hispanic, Latino/a, community, oil boom, Williston, moral geography
    • Accurate Trace Evidence Using Regression Approaches in Forensic Studies

      An, Lingling; Luo, Qianwen; Li, Haiquan; Hu, Chengcheng (The University of Arizona., 2019)
      Human microbiome data has become popular in forensic study due to its use in estimating the time since death, examination of trace evidence and human identification. The human microbiome is commonly presented independent of seasonal and environmental changes and is highly individual. With the growth of next-generation sequencing (NGS) technology, there are more human microbiome data available to use. 16S rRNA sequencing helps to detect and identify bacteria in human microbial communities. The wide use of human microbiome data in the forensic studies calls for powerful statistical and computational methods for analysis. Due to the human microbiome being highly individual, even varying in different body sites, it can serve as an alternative method for human identification and trace evidence in a criminal investigation, particularly, when human DNA samples are absent from the scene of the crime. In this research, we proposed a new analytic method FourStage to link the human microbiome (e.g., on palm) to the microbial evidence sample. The FourStage method has four procedures: 1) select the contributors from a pool of suspects and exclude the innocents at same time, 2) construct a “unknown” profile for possible missing suspect, 3) determine the status of a “missing” suspect, and 4) estimate proportions for each contributor. Through comprehensive simulation studies, we demonstrated that our new method surpasses the currently available approach, even for a situation in which a suspect was a contributor but is excluded from data analysis. This new method will be helpful for researchers/investigators in forensic area to analyze their own data and also provide them a new research angle/direction in trace evidence.
    • Regulation of Metal Transporters, ZIP14 and ZnT10, by Manganese Intake in Mice

      Zhao, Ningning; Felber, Danielle Maya; Teske, Jennifer; Marian, Mary (The University of Arizona., 2019)
      Manganese (Mn) is an essential trace mineral vital for many biological processes. ZIP14, ZnT10, and ZIP8 are proteins first identified as transporters for iron (Fe) and zinc (Zn). Current research now indicates a key role for these three metal transporters in regulating Mn homeostasis. However, there is still limited evidence to explain the regulatory mechanisms or how Mn status influences levels of Fe and Zn, which are believed to share several transport pathways with Mn. Here, we examined the effect of Mn intake on the regulation of these metal transporters by feeding mice a low-Mn diet, control diet, or high-Mn diet for 6 weeks. Levels of Mn, Fe, and Zn were measured using inductively coupled plasma mass spectrometry and protein levels of ZIP14, ZnT10, and ZIP8 were analyzed by Western Blot. While mice on the high-Mn diet exhibited significantly higher levels of Mn in the blood, liver, spleen, brain, and lungs, mice on the low-Mn diet did not display matching reductions, indicating Mn homeostasis is more challenging to maintain with high intake of Mn compared to low. Zn levels were not considerably altered and only minor reductions in Fe levels were observed in mice on the high-Mn diet, suggesting the regulation of these metals may not be as intertwined as previously believed. Interestingly, there was no difference in hepatic ZIP8 levels among the three diet groups. In response to the high-Mn diet, ZIP14 and ZnT10 were both upregulated in the liver, as well as in the small intestine, indicating a coordinated role for these two transporters in Mn excretion. Unexpectedly, this upregulation was only evident in male mice, with the exception of hepatic ZIP14, providing new insight into the mechanisms behind widely observed sex differences in Mn homeostasis.
    • Potential Application of Cosmic-Ray Neutron Sensors to Infer Precipitation Rates

      Zreda, Marek G.; Atwood, Joel Edwin; Meixner, Thomas; Zeng, Xubin (The University of Arizona., 2019)
      More studies are finding utility in using cosmic-ray neutron sensors (CRNS)s to understand hydrological processes within the environment. This study explores estimating precipitation by analyzing CRNS derived soil moisture time series data. A simple bucket model is employed to estimate precipitation from changes in soil moisture. Two soil moisture time series were simulated by iteratively weighting Hydrus-1D soil moisture profiles to estimate soil moisture observed by the CRNS. The simulated soil moisture time series were used to parameterize the model and better understand the system. The Kling-Gupta Efficiency metric was used to evaluate site performance where a value larger than 0.9 is desired. The model was evaluated at four field sites: Manitou (CO), Santa Rita Mesquite (AZ), Kendall-Walnut Gulch (AZ), and Silver Sword (HI). Due to apparent noise in time series data, temporal aggregation was used to improve performance. The 24-hour aggregated Kling-Gupta Efficiency metric for all sites was 0.92, 0.93, 0.87, and 0.62 respectively. The field results demonstrated some limitations using CRNS derived soil moisture due to environmental noise and uncertainty in measured precipitation. Further field investigations are needed to improve the performance of this method and better understand the nature of the precipitation measured. This method may be useful where direct measurements of precipitation are unavailable, unreliable or poorly represent the required scale.
    • Judean Cultural Resistance to the Persian and Hellenistic States: The Beginnings of a Jewish Kingdom

      Futrell, Alison; Delecki, Abram; Bauschatz, John; Johnstone, Steve (The University of Arizona., 2019)
      The date of 539 B.C.E. was significant for the people of ancient Judea for two reasons. First, it marked the rediscovery of and the rebuilding process for their sacred Temple in Jerusalem. Secondly it was the start of the inclusion of Judea into a large, cosmopolitan Persian Empire and then into the newer Hellenistic Kingdoms of the late 4th century B.C.E. As a result of this inclusion the Jews would be presented with a number of difficulties. A major one would be the cultural conflicts that would plague Judean society for centuries, mostly connected with marriages to non-Jews and various degrees of religious and cultural syncretism with (mostly) Greek neighbors. The other would be the questions of how Judea should function within the broader kingdom in which it was located, what kind of autonomy the Jews should receive and how this autonomy should be maintained. These questions would lead to disputes and, by the middle of the 2nd century B.C.E., outright revolt.
    • Development of a Microfluidic Model of a Human Prostate Gland for Cancer Research

      Zohar, Yitshak; Ivich, Fernando; Yoon, Jeong-Yeol; Jiang, Linan; Miranti, Cynthia (The University of Arizona., 2019)
      Prostate cancer is the second leading cause of cancer death in American men1. The prostate is a gland at the bladder base of males comprising a pseudo-stratified epithelium surrounded by a fibromuscular stroma2. Studies have shown that androgens regulate prostate development via signaling between the epithelium and the stroma2. We utilize a microfluidic-based system, prostate-on-a-chip (POC), developed for co-cultivation of human prostate epithelium and stroma to recapitulate the functions of a human prostate gland in vivo2 since it is difficult to establish a co-culture tissue in petri dishes. After successfully maintaining cultures of epithelial cells (iPECs) and stromal cells (BHPrSs) in fabricated microfluidic devices, epithelium differentiation was re-affirmed in epithelium/stroma co-cultures following 3 weeks incubation time. Some basal cells terminally differentiated into luminal cells, while acinus-like structures were formed in the epithelium, thereby confirming the PoC as a reliable in vitro model of the human prostate gland. Subsequently, the potential application of the PoC model for prostate cancer research was explored3. In cancerous epithelium/normal stroma (EMP/BHPrS) co-cultures, the cancerous epithelium was found to induce the initially normal stromal cells to assume a cancer-associated fibroblast (CAF) phenotype. In normal epithelium/cancerous stroma (iPEC/PIM1) co-cultures, Dox treatment of the PIM1 stroma induced the cells to over express biomarkers known to be associated with tumor progression. These results firmly establish the PoC not only as a superior model of the normal human prostate, especially in comparison with 2D cell cultures and animal models, but also as a promising platform to investigate biological mechanisms implicated in initiation, progression and proliferation of tumors in a human prostate cancer.
    • Une Etude de la Mondialisation en Tant qu'outil du Néocolonialisme en Afrique: Le cas du Sénégal et du Cameroun

      Taoua, Phyllis; Allihien, Anault Jean; Swanson, Lucy; Mouzet, Aurélia (The University of Arizona., 2019)
      Cette étude examine la mondialisation en tant qu’outil de la ‘‘recolonisation’’ de l’Afrique. Les différents aspects de la mondialisation—le plan économique, le plan politique et le plan socioculturel—seront examinés par rapport à leurs rôles dans l’établissement du néo-colonialisme. Ce mot problématique qui est la mondialisation sera sujet d’examen. Nous allons traiter de ses origines, ses significations et des problèmes liés à ce concept dans ces contextes Francophones.
    • Diurnal and Seasonal Proximally Sensed Photochemical Reflectance Index (PRI) in a High-Stress Semi-Arid Mixed Conifer Forest

      Barron-Gafford, Greg A.; Yang, Julia; Smith, William K.; van Leeuwen, Willem J.D (The University of Arizona., 2019)
      A lack of accurate, reliable data on coupled carbon and water fluxes for Earth’s expansive ecosystems remains a major barrier to a complete understanding of the terrestrial carbon cycle. The remotely sensed Photochemical Reflectance Index (PRI) measures deepoxidation of the xanthophyll cycle at wavelength 531nm and is one of the few pigment-based vegetation indices sensitive to rapid plant physiological responses. PRI presents new opportunities to study ecosystems on a diurnal time scale, as well as seasonal processes in evergreen systems where complex vegetation dynamics are not reflected by small annual changes in chlorophyll content or leaf structure. However, systematic PRI acquisition in conjunction with leaf and ecosystem flux measurements are needed in natural, diverse ecosystems. The growing field of proximal remote sensing affords the opportunity to bridge leaf, canopy and ecosystem scales, for a physiological inspection of whole ecosystem dynamics. The Southwest U.S. provides a natural setting for examining the influence of environmental drivers on the productivity of drought-sensitive forests, as well as for evaluating our ability to track these relationships using optical methods. We studied PRI in a semi-arid, sub-alpine mixed conifer forest, in order to assess its ability to serve as a proxy for dynamic photoprotection. We combined canopy spectral measurements with eddy covariance flux and sap flow methods to determine the sensitivity of PRI to seasonal changes in gross primary productivity (GPP) and the ecohydrological variability of a high stress environment. In addition, we combined top-of-canopy leaf-level gas exchange, chlorophyll fluorescence, and hyperspectral measurements to determine the sensitivity of PRI to diurnal changes in needle photosynthetic function, and confirm the extent to which canopy diurnal patterns reflect leaf physiology. At the canopy scale we found that the relationship between PRI and GPP was inconsistent over the course of the monsoon season, shifting from a negative relationship in July and August (R2=.62), to a positive relationship in September (R2=.48). Multiple linear regression with soil moisture and air temperature showed that PRI responded to dynamic water and energy limitations of this system (R2=.41). We report for the first time a relationship between seasonal PRI and sap flow in a natural forest (R2=.55). These results suggest that on a seasonal scale PRI is an effective indicator of photosynthetic response to ecohydrological constraints. On a diurnal scale we found that PRI remained constant throughout the day at both leaf and canopy scales, and we suggest that saturated light conditions drive retention of xanthophylls in a de-epoxidized state. We contribute evidence that remotely sensed PRI has potential to fill a major gap in our ability to distinguish how water availability influences forest productivity and associated carbon dynamics.