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  • Shape Matching and Map Space Exploration via Functional Maps

    Ren, Jing (2021-07-29) [Dissertation]
    Advisor: Wonka, Peter
    Committee members: Ovsjanikov, Maks; Ghanem, Bernard; Pottmann, Helmut; Solomon, Justin
    Computing correspondences or maps between shapes is one of the oldest problems in Computer Graphics and Geometry Processing with a wide range of applications from deformation transfer, statistical shape analysis, to co-segmentation and exploration among a myriad others. A good map is supposed to be continuous, as-bijective-as-possible, accurate if there are ground-truth corresponding landmarks given, and lowdistortionw.r.t. different measures, for example as-conformal-as-possible to preserve the angles. This thesis contributes to the area of non-rigid shape matching and map space exploration in Geometry Processing. Specifically, we consider the discrete setting, where the shapes are discretized as amesh structure consisting of vertices, edges, and polygonal faces. In the simplest case, we only consider the graph structure with vertices and edges only. In this thesis, we design algorithms to compute soft correspondences between discrete shapes. Specifically, (1)we propose different regularizers, including orientation-preserving operator and the Resolvent Laplacian Commutativity operator, to promote the shape correspondences in the functional map framework. (2) We propose two refinement methods, namely BCICP and ZoomOut, to improve the accuracy, continuity, bijectivity and the coverage of given point-wisemaps. (3)We propose a tree structure and an enumeration algorithm to explore the map space between a pair of shapes that can update multiple high-quality dense correspondences.
  • Stationary and Cyclostationary Processes for Time Series and Spatio-Temporal Data

    Das, Soumya (2021-07-10) [Dissertation]
    Advisor: Genton, Marc G.
    Committee members: Stenchikov, Georgiy L.; Ombao, Hernando; Pourahmadi, Mohsen
    Due essentially to the difficulties associated with obtaining explicit forms of stationary marginal distributions of non-linear stationary processes, appropriate characterizations of such processes are worked upon little. After discussing an elaborate motivation behind this thesis and presenting preliminaries in Chapter 1, we characterize, in Chapter 2, the stationary marginal distributions of certain non-linear multivariate stationary processes. To do so, we show that the stationary marginal distributions of these processes belong to specific skew-distribution families, and for a given skew-distribution from the corresponding family, a process, with stationary marginal distribution identical to that given skew-distribution, can be found. While conventional time series analysis greatly depends on the assumption of stationarity, measurements taken from many physical systems, which consist of both periodicity and randomness, often exhibit cyclostationarity (i.e., a periodic structure in their first- and second-order moments). Identifying the hourly global horizontal irradiances (GHIs), collected at a solar monitoring station of Saudi Arabia, as a cyclostationary process and considering the significant impact of that on the energy production in Saudi Arabia, Chapter 3 provides a temporal model of GHIs. Chapter 4 extends the analysis to a spatio-temporal cyclostationary modeling of 45 different solar monitoring stations of the Kingdom. Both the proposed models are shown to produce better forecasts, more realistic simulations, and reliable photovoltaic power estimates in comparison to a classical model that fails to recognize the GHI data as cyclostationary. Chapter 5 extends the notion of cyclostationarity to a novel and flexible class of processes, coined evolving period and amplitude cyclostationary (EPACS) processes, that allows periods and amplitudes of the mean and covariance functions to evolve and, therefore, accommodates a much larger class of processes than the cyclostationary processes. Thereafter, we investigate its properties, provide methodologies for statistical inference, and illustrate the presented methods using a simulation study and a real data example, from the heavens, of the magnitudes of the light emitted from the variable star R Hydrae. Finally, Chapter 6 summarizes the findings of the thesis and discusses its significance and possible future extensions.
  • Reconfigurable Snapshot HDR Imaging Using Coded Masks

    Alghamdi, Masheal M. (2021-07-10) [Dissertation]
    Advisor: Heidrich, Wolfgang
    Committee members: Wonka, Peter; Ghanem, Bernard; Myszkowski, Karol
    High Dynamic Range (HDR) image acquisition from a single image capture, also known as snapshot HDR imaging, is challenging because the bit depths of camera sensors are far from sufficient to cover the full dynamic range of the scene. Existing HDR techniques focus either on algorithmic reconstruction or hardware modification to extend the dynamic range. In this thesis, we propose a joint design for snapshot HDR imaging by devising a spatially varying modulation mask in the hardware combined with a deep learning algorithm to reconstruct the HDR image. In this approach, we achieve a reconfigurable HDR camera design that does not require custom sensors, and instead can be reconfigured between HDR and conventional mode with very simple calibration steps. We demonstrate that the proposed hardware-software solution offers a flexible, yet robust, way to modulate per-pixel exposures, and the network requires little knowledge of the hardware to faithfully reconstruct the HDR image. Comparative analysis demonstrated that our method outperforms the state-of-the-art in terms of visual perception quality. We leverage transfer learning to overcome the lack of sufficiently large HDR datasets available. We show how transferring from a different large scale task (image classification on ImageNet) leads to considerable improvements in HDR reconstruction
  • BranchNet: Tree Modeling with Hierarchical Graph Networks

    Zhang, Jiayao (2021-07-04) [Thesis]
    Advisor: Michels, Dominik L.
    Committee members: Wonka, Peter; Elhoseiny, Mohamed H.
    Research on modeling trees and plants has attracted a great deal of attention in recent years. Early procedural tree modeling can be divided into four main categories: rule-based algorithms, repetitive patterns, cellular automata, and particle systems. These methods offer a very high level of realism; however, creating millions of varied tree datasets manually is not logistically possible, even for professional 3D modeling artists. Trees created using these previous methods are typically static and the controllability of these procedural tree models is low. Deep generative models are capable of generating any type of shape automatically, making it possible to create 3D models at large scale. In this paper, we introduce a novel deep generative model that generates 3D (botanical) tree models, which are not only edible, but also have diverse shapes. Our proposed network, denoted BranchNet, trains the tree branch structures on a hierarchical Variational Autoencoder (VAE) that learns new generative model structures. By directly encoding shapes into a hierarchy graph, BranchNet can generate diverse, novel, and realistic tree structures. To assist the creation of tree models, we create a domain-specific language with a GUI for modeling 3D shape structures, in which the continuous parameters can be manually edited in order to produce new tree shapes. The trees are interpretable and the GUI can be edited to capture the subset of shape variability.
  • Produced Water Pretreatment Prior to Filtration with Forward Osmosis and Membrane Distillation Integrated System

    Alqulayti, Abdullah (2021-07) [Thesis]
    Advisor: Ghaffour, NorEddine
    Committee members: Saikaly, Pascal; Fortunato, Luca; Saqib Nawaz, Muhammad
    The simultaneous treatment of different produced water streams with the forward osmosis membrane distillation hybrid system (FO-MD) has been suggested recently. This work investigates the need for pretreatment of produced water prior to filtration with FO-MD in order to reduce the level of fouling and scaling in the system. The desalter effluent (DE) stream was selected as FO feed solution, and the water oil separator (WO) stream was used as FO draw solution/MD feed solution, and a significant flux decline was observed in FO and MD within the first 5 hours of operations. SEM and EDX analysis indicated that the formation of scale layer on both membranes was the main reason for the sharp flux decline. Silica was the major contributor to the scaling of the support layer of the FO membrane. While the scaling layer on MD membrane consisted mainly of CaSO4 crystals with some deposition of Silica. Therefore, electrocoagulation (EC) was selected for the pretreatment of produced water to target the removal of Ca, SiO2 and SO4 ions in order to reduce the likelihood of inorganic fouling in FO-MD. The different parameters of EC, namely, the current density, electrolysis time, and initial pH were tested at a wide range of values of 7-70 mA/cm2 , 10-60 minutes, 5-9, respectively. calcium and sulfate ions were not effectively removed at the relatively high applied current density of 70 mA/cm2 , while high removal of silica was achieved even at low applied current densities. The optimum conditions of EC for silica removal were found to be 7 mA/cm2 for the current density and 10 minutes for the electrolysis time which resulted in a 97% removal of silica. it was found that due to pretreatment, the average FO and MD fluxes increased by 49% (9.93 LMH) and 39% (8.55 LMH), respectively. Therefore, even though EC did not show promising results in terms of the removal of calcium and sulfate, efficient silica removal was achieved with minimum energy requirements which suggests that it could have a potential to be integrated with the FO-MD hybrid system for the treatment and reclamation of produced water.
  • Improving Formation Pressure Integrity Tests with Field-Wise Test Data Analysis and Hydraulic Impedance Testing

    Abilov, Elmir (2021-07) [Thesis]
    Advisor: Patzek, Tadeusz
    Committee members: Finkbeiner, Thomas; Ahmed, Shehab
    Drilling operations without issues and non-productive time are highly desired by operators. Circulation loss is one of the common issues faced during drilling when a formation is fractured by mud weight or by Equivalent Circulating Density (ECD) exceeding the formation fracture gradient. This makes it necessary to obtain information about in-situ stress and rock strength. Formation Pressure Integrity Tests (FPITs) determine directly the fracture pressure of the formation or test the formation for a safe drilling mud weight window and kick tolerance. Although FPIT is a routine test conducted before drilling each hole section, previous studies and field experience have demonstrated several problems and a lack of unique operational procedures for these tests. This study examines some of the main issues faced during operation and interpretation of FPITs and possible solutions to eliminate them. We generated a unique database of FPITs which includes all necessary technical and non-technical details about each test and analyzed the discrepancy between surface and downhole pressure data generated while conducting FPITs. We also analyzed pressure build-up behavior versus pumped fluid volume and its similarities with Casing Integrity Tests (CIT). Furthermore, we investigated pressure loss rates after shut-in, and the application of hydraulic impedance testing to improve test quality. Our analysis of the discrepancy trends indicated that Reservoir Drilling Fluid (RDF) causes more pressure transmission losses than Oil-Based Mud (OBM). We examined more than 50 tests based on pressure build-up behavior versus pumped fluid volume and obtained an empirical equation that only requires the measured depth to give an estimation for the pressure build-up rate. In addition, comparing CIT with FPIT based on pressure build-up rate shows similarities between the tests, and CIT build-up rate values can potentially be used as an initial assumption for FPIT build-up rate. Our findings reveal that pressure loss rate after pump-off is less than 6 psi/min in more than 65% of the Formation Integrity Tests (FITs). We also suggest to use Hydraulic Impedance Testing (HIT) method together with formation strength tests to give a qualitative indication of fracture initiation and a quantitative estimation of fracture dimensions.
  • Characterization of a Red Multimode Vertical-Cavity Surface-Emitting Laser for Intrinsic Parameters

    Wagstaff, Jonathan (2021-07) [Thesis]
    Advisor: Ooi, Boon S.
    Committee members: Salama, Khaled N.; Schwingenschlögl, Udo; Ng, Tien Khee
    Compared to single-mode VCSELs, multimode VCSELs have not received much attention in models and characterizations for functional parameters, despite making up the majority of commercially available VCSELs [1]. In particular, the extraction of the linewidth enhancement factor for multimode VCSELs has been overlooked, likely due to difficulties in measurement. Additionally, multimode models for VCSELs have, until recently, omitted spectral characteristics such as linewidth [2]. This is the first work to report a measured linewidth enhancement factor value (lower bound) for a multimode VCSEL. A characterization for the functional parameters of a red multimode vertical-cavity surface-emitting laser (VCSEL) is shown herein. The extracted values form a complete working set of parameters for the laser rate equations. The techniques employed for extracting values include frequency responses, power versus current fittings, and optical spectral measurements. From the frequency responses at various bias currents, the relaxation oscillation frequency and damping factor are found. The power versus current curve is fitted to find parameters including the modal spontaneous emission rate and carrier density at threshold. The spectral measurements are used for evaluating the linewidth enhancement factor (LEF) also known as the alpha factor or Henry factor. These 5 methods have been applied previously to characterizing single-mode VCSELs [3]–[5]. The experimentally extracted parameters herein are important for creating accurate models and simulations for multimode VCSELs. Improved multimode VCSEL models are necessary for improving optical communication, especially for short-range optical interconnects [2]. The measured parameters for the characterized VCSEL are comparable to similar single-mode VCSELs characterized in other works. This is promising because multi-mode VCSELs have higher output power than their single-mode counterparts, thus these results may aid in improving short-range optical interconnects.
  • Evaluation of Different Forward Osmosis Membrane Cleaning Strategies for Produced Water Streams Treatment

    Alamoudi, Talal (2021-07) [Thesis]
    Advisor: Ghaffour, NorEddine
    Committee members: Pinnau, Ingo; Vrouwenvelder, Johannes S.; Saqib Nawaz, Muhammad
    Forward osmosis (FO) as a novel membrane separation technology has recently been investigated in various water treatment applications. The natural mass transfer process between two solutions driven by the osmotic pressure difference leads to many operational advantages in the FO process, such as low energy consumption and minimal fouling problems. It makes FO a feasible technology for the treatment of produced water (PW). Although previously, the treatment of PW using FO has been investigated, osmotic backwashing (OB) is not systematically examined for water flux recovery of the PW fouled FO membranes. Moreover, the cleaning of FO membranes used for the simultaneous treatment of different PW streams was never previously attempted. In this study, OB was thoroughly investigated for the cleaning of PW-fouled FO membranes. Also, FO membrane chemical cleaning using SDS and NaOH solutions was examined too. To investigate OB, the cleaning efficiency of a 60 min OB cleaning protocol was examined under different FO operating modes in (5 x 20 h) experiments using synthetic desalter effluent as FO feed solution (FS) and 1.2 M NaCl solution or water-oil separator outlet (WO) as draw solutions (DS). The AL-FS (active layer facing FS) mode outcompeted the AL-DS (active layer facing DS) mode, achieving a flux of 12.9 LMH and 80.1% water reclamation when using WO as a DS. Therefore, this FO configuration 5 was selected when evaluating the cleaning protocols. Moreover, after evaluating different OB methods, the 30 min OB protocol achieved the highest system efficiency rate of 95% and was studied for the treatment of real PW streams. The SDS and NaOH chemical cleaning methods achieved flux recovery rates of 99% and 98% by the end of the third treatment cycle, respectively, outperforming the 89% flux recovery rate of the optimized OB protocol. Although the investigated cleaning methods were able to restore the system performance, a substantial increase in RSF was observed due to mainly irreversible colloidal fouling. This study demonstrates the feasibility of OB and chemical cleaning in restoring FO system performance for the simultaneous treatment of PW streams
  • Is Post Transplantation Performance Driven by the Variability of the Habitat of Origin?

    Golding, Victoria C. (2021-07) [Thesis]
    Advisor: Aranda, Manuel
    Committee members: Peixoto, Raquel; Schmidt-Roach, Sebastian
    As rising sea temperatures and increases in the frequency, duration, and intensity of marine heatwaves threaten coral survival at a global scale, research on the capacity of corals to acclimatize and adapt to changing environments has become a high priority. Understanding how environmental parameters shape coral thermal performance across habitats is crucial to identify populations with high vulnerability or high thermal tolerance to future ocean warming. In recent studies, corals from high temperature variable environments (HVE) have shown increased thermal tolerance compared to corals from low temperature variable environments (LVE). Here, I investigate if these phenotypes are shaped by acclimatization, habitat-specific adaptation, or a combination of both, in the branching coral, Acropora hemprichii, by reciprocally transplanting individuals between a back (HVE) and front reef (LVE). After ten months of acclimatization, comparisons of photosynthetic efficiency (photosystem II), mortality, and bleaching recovery was assessed for > 2 months between coral ramets following a natural bleaching event in the central Red Sea. In tandem, coral bleaching severity and recovery in each reef environment was assessed to genus level by photographic surveys of fixed belt transects. Bleaching between reef sites was compared against bleaching in treatments to differentiate the role of habitat specific adaptation and acclimatization in the corals. This study aims to elucidate the evolutionary mechanisms driving coral habitat-specific thermal stress tolerances, which may inform coral reef management and restoration efforts.
  • New Algorithms to Solve the Positioning Problem of Outdoor Localization Using Constrained and Unconstrained Optimization Techniques

    Alsaif, Muhanned (2021-07) [Thesis]
    Advisor: Al-Naffouri, Tareq Y.
    Committee members: Feron, Eric; Wittum, Gabriel
    The demand for outdoor precise location is increasing with the development of new applications such as autonomous vehicles, exploration robots and wireless sensor networks. Global Navigation Satellite System (GNSS) is the go-to system for outdoor localization. This thesis focuses on developing new methods for GNSS single-point positioning (SPP) model, where no access to a reference station or precise GNSS parameters is needed. We investigated the limitations of the standard method, least- squares adjustment (LSA), and we derived the Cramer-Rao bounds for the SPP estimation problem. We also investigated different techniques to formulate the positioning problem with the goal to increase the accuracy. A new method is developed by reformulating the problem as difference-of-convex program (DC program) and utilizing convex-concave procedure (CCCP) to solve the positioning problem without linearizing the observation equations. In addition, we examined the potential of multiple-receiver systems in increasing the accuracy. We formulated the multiple- receiver SPP estimation problem, and we proposed to configure the multiple receivers in a fixed equilateral triangle to exploit the symmetry and the geometrical constraints of the configuration. We extended the use of LSA in multiple-receiver system. We also developed a modification of LSA algorithm, named least-squares adjustment extension (LSAE), that utilizes attitude information and the constraints of the multiple-receiver system. In addition, we developed a new algorithm to optimizes the SPP estimates over the equilateral triangles Riemannian manifold, which enforces the geometrical constraints of the multiple-receiver system. Furthermore, we derived the constrained and the unconstrained Cramer-Rao bounds (CRB and CCRB) for the multiple-receiver SPP problem. Moreover, we investigated the influence of both attitude information and the equilateral triangle baseline length on the algorithms’ performances and the derived CCRB. Finally, we carried out a numerical analysis by implementing the algorithms and the bounds in MATLAB, where we tested the algorithms on simulated GNSS scenarios. The proposed multiple-receiver methods provide more precise estimates for the SPP problem in comparison to the single receiver methods.
  • Environmental origin and compartmentalization of bacterial communities associated with Avicennia marina mangroves on the Red Sea coast

    Escobar prieto, Juan david (2021-07) [Thesis]
    Advisor: Daffonchio, Daniele
    Committee members: Marasco, Ramona; Soares, Alexandre; Pain, Arnab
    Mangrove forests are highly productive ecosystems widespread in tropical and subtropical coastlines, with a coverage of 75% of the world’s tropical shorelines. Mangrove plants developed specific physiological and morphological adaptation to thrive in such unique environments. Together with plant adaptations, mangroves develop a tight partnership with microorganisms, mainly bacteria and fungi, that form the so-called mangrove-microbiome. Plant-associated microorganisms are generally recruited by the root system (root tissues and rhizosphere) and the colonization process starts with the release of root-related exudates detected by the surrounding edaphic microorganisms that are attracted in the rhizosphere zone. Then, root surface selects those microorganisms that can enter the tissues as endophytes. The microorganisms recruited belowground can migrate through the plant tissues by using the plant vessels and may colonize the aboveground compartments of the plant. Here, I aimed to evaluate the environmental origin and compartmentalization of the mangrove microbiome. To do this, I sampled bulk sediments, sea water, and mangrove plant compartments (root rhizosphere and endosphere, pneumatophores, shoot, leaves, flowers and propagules) of 20 gray mangrove trees (Avicennia marina L.) across two sites on the Red Sea coast of the King Abdullah University of Science and Technology (KAUST), Saudi Arabia. By high-throughput sequencing of the bacterial 16S rRNA gene, I showed that the bacterial assembly in A. marina plant compartments follows a clear niche partition process in which bacterial communities are actively recruited from the surrounding ecosystem (sediment and sea water) by the root system, and further distributed across the different plant organ and compartments. Moreover, the composition of microbiome detected had many similitudes with others previously described around the world, suggesting that certain bacteria represent a mangrove “core microbiome”. The conservation of microbiome composition, mainly driven by environmental and host selection, that beneficial bacteria provide to the plant and contribute to its growth and fitness by several mechanisms. Thus, the characterization and identification of mangrove microbiome can meliorate our knowledge regarding plant–microbe interactions, as well as put the bases for the development of Nature-based Solution (NBS) to enhance reforestation and rehabilitation of mangrove ecosystems
  • A Synergy of Spatiotemporal Transcriptomic Techniques for Non-Model Organism Studies: Something Old, Something New, Something Borrowed, Something Ocean Blue

    Watson, Kelly (2021-07) [Thesis]
    Advisor: Aranda, Manuel
    Committee members: Peixoto, Raquel; Frøkjær-Jensen, Christian
    In situ hybridization (ISH) has played a crucial role in developing a spatial transcriptomic understanding of emerging model organisms in the past, but advancing high-throughput RNA-sequencing (RNA-seq) technology has pushed this method into the shadows, leading to a loss of data resolution. This shift in research towards the exclusive use of RNA-seq neglects essential considerations for transcriptomic studies including the spatial and temporal expression of transcripts, available budget, experimental design needs, and validation of data. A synergy of spatiotemporal transcriptomic techniques is needed, using the bulk and unbiased analysis of RNA-seq and the visual validation and spatiotemporal resolution of ISH. Integration of this synergistic approach can improve our molecular understanding of non-model organisms and establish the background data needed for advancing research techniques. A prime example lies within an emerging model of the marine science and symbiosis fields, where I present a case study on a threatened coral reef keystone – the cnidarian-dinoflagellate symbiosis. Establishing a whole-mount ISH protocol for the emerging cnidarian model Aiptasia (sea anemone) will help future studies reveal the gene regulation underpinning the establishment, persistence, and breakdown of this complex symbiotic relationship.
  • Impact of Different Cleaning Methods on Biofilm Removal in Membrane Distillation

    Amin, Najat A. (2021-07) [Thesis]
    Advisor: Ghaffour, NorEddine
    Committee members: Vrouwenvelder, Johannes S.; Alpatova, Alla
    Membrane distillation (MD) is an emerging thermal separation technology which proved its efficiency in desalination of highly saline waters, including seawater, brines and impaired process waters. In a long-term prospective, MD can reinforce sustainability of the clean water production and mitigate the water-energy stress caused by lacking suitable freshwater recourses. However, just like in any other membrane separation process, MD membrane is susceptible to biofouling which presents a significant challenge by substantially reducing its performance and deteriorating permeate quality. This study evaluated different cleaning methods aimed at controlling biofilm development on a surface of hydrophobic MD membrane in a direct contact MD (DCMD) process fed by the Red Sea water. This was achieved by applying physical (hydraulic) cleaning and chemical cleanings with a range of chemicals utilized in membrane separation processes including citric acid (mineral acid), ethylenediaminetetraacetic acid (EDTA, metal-chelating agent) and sodium hypochlorite (NaOCl, oxidant). Flux recovery and changes in biofilm morphology, including its thickness and structure as well as microbial and extracellular polymeric substances (EPS) contents before and after cleanings have been analyzed to elucidate cleaning mechanisms and suggest effective strategies of biofilm removal. The results showed that 0.3% EDTA exhibited the best cleaning performance resulting in the highest permeate flux recovery (93%), followed by 0.3% NaOCl (89%), 3% citric acid (76%), and hydraulic (66%) cleanings. Application of EDTA and NaOCl has also resulted in the lowest number of bacterial cells and substantial reduction of the peak intensities caused by protein-like compounds and tyrosine-containing proteins present on the membrane surface after its treamtent. The observed trends are in a good correlation with the optical coherence tomography (OCT) observations which revealed substation changes in biofilm morphology leading to a significant reduction of biofilm thickness which followed the order of hydraulic cleaning < citric acid cleaning < NaOCl cleaning < EDTA cleaning. This study suggests that selection of an appropriate cleaning type and formulation is critical for achieving sustainable MD plant operations, both technically and economically.
  • Bottled Drinking Water: Assessment of Physical-Chemical and Microbiological Parameters and Biological Stability of 19 Different Brands Available in Saudi Arabia

    Nadreen, Yasmeen (2021-07) [Thesis]
    Advisor: Vrouwenvelder, Johannes S.
    Committee members: Gonzalez-Gil, Graciela; Saikaly, Pascal
    Bottled drinking water is a common form of water consumption that has grown in popularity and dependency. With countless types and brands available, there are factors to consider regarding the variations in mineral content and microbiological quality, and environmental consequences associated with importing natural bottled waters. Saudi Arabia is the largest desalinated water producer, and although there are scarce natural water resources, consuming locally produced water can alleviate environmental pressures, so long as local bottled water is of good quality and provides the basic function of drinking water. The objective of this study is to scrutinize the variations in bottled waters available in the Saudi market and compare local and imported waters regarding water quality and compliance with health regulations. Surveying local bottled waters revealed that over 60% were imported, adding to the environmental significance. Results from inductively coupled plasma-atomic emission spectroscopy, ion chromatography, and pH meters indicate most bottled waters were compliant with health standards. Flow Cytometry (FCM) was used to determine microbial cell densities. Purified waters, on average, contained significantly lower concentrations than other water types, while mineral waters contained the most cells per milliliter. Microbiological stability was examined through incubating samples at 30°C to promote microbial growth, and results were analyzed using an online FCM system. Purified waters had the least amount of growth and to a lesser degree than mineral and sparkling, which varied in microbial growth responses. DNA extractions and microbial community analyses were performed on select mineral waters before and after incubation. Results showed microbial genera found were similar between samples from the same country and some were unique. All samples exhibited some change in microbial community composition after incubation, signifying that certain communities thrived more than others. Proteobacteria was the most common abundant phylum among samples. Although analysis was restricted to the genera level, there were no health concern associated with types of bacteria discovered. In conclusion, local purified waters had greater microbiological quality and stability than imported waters, and mineral compositions were within the healthy range. Reducing reliance on foreign natural waters may help alleviate environmental consequences and improve local economy
  • Understanding the Genetic Basis for piRNA Silencing in the Soma and Germline of Caenorhabditis elegans

    Peng, Yuli (2021-07) [Thesis]
    Advisor: Frøkjær-Jensen, Christian
    Committee members: Lauersen, Kyle J.; Krattinger, Simon G.
    C. elegans is a commonly used genetic model organism due to the ease of genetic screens, transgenesis, and microscopy. Here, I describe methods that improve transgenesis in C. elegans and the development of a genetic screen to identify genes involved in the piRNA pathway. Transgenesis is commonly used for most laboratories that utilize C. elegans and improvements are therefore likely to facilitate research across many research areas. In the first chapter, I characterized a pan-muscular promoter that drives fluorophore expression to help identify C. elegans transgenesis. This promoter is an improved co-injection marker as it drives bright fluorescence with low toxicity and high efficiency. In the second chapter, I study piRNAs which are a large class of non-coding RNA that play important roles in protecting the genome from transposable elements in most animals. The study of piRNAs has mostly focused on their function in the germline, but recent evidence suggests functions in somatic cells such as neurons. To identify genes involved in the piRNA pathway in C. elegans, I performed a chemical genetic screen. I identified one mutant with a somatic phenotype and six mutants with a germline phenotype. I have focused on the germline and sequenced two strains and identified candidate genes involved in the piRNA pathway. Future work will focus on validating and identifying the remaining mutants.
  • A Multi-platform Comparison of Phenology for Semi-automated Classification of Crops

    Kanee, Sarah (2021-07) [Thesis]
    Advisor: McCabe, Matthew
    Committee members: Johansen, Kasper; Blilou, Ikram
    Remote sensing has enabled unprecedented earth observation from space and has proven to be an invaluable tool for agricultural applications and crop management practices. Here we detect seasonal metrics indicating the start of the season (SOS), the end of the season (EOS) and maximum greenness (MAX) based on vegetation spectral signatures and the normalized difference vegetation index (NDVI) for a time series of Landsat-8, Sentinel-2 and PlanetScope imagery of potato, wheat, watermelon, olive and peach/apricot fields. Seasonal metrics were extracted from NDVI curves and the effect of different spatial and temporal resolutions was assessed. It was found that Landsat-8 overestimated SOS and EOS and underestimated MAX due to its low temporal resolution, while Sentinel-2 offered the most reliable results overall and was used to classify the fields in Aljawf. Planet data reported the most precise SOS and EOS, but proved challenging for the framework because it is not a radiometrically normalized product, contained clouds in its imagery, and was difficult to process because of its large volume. The results demonstrate that a balance between the spatial and temporal resolution of a satellite is important for crop monitoring and classification and that ultimately, monitoring vegetation dynamics via remote sensing enables efficient and data-driven management of agricultural system
  • Monitoring crop development and health using UAV-based hyperspectral imagery and machine learning

    Angel, Yoseline (2021-07) [Dissertation]
    Advisor: McCabe, Matthew
    Committee members: Hong, Pei-Ying; Tester, Mark A.; Zarco-Tejada, Pablo
    Agriculture faces many challenges related to the increasing food demands of a growing global population and the sustainable use of resources in a changing environment. To address them, we need reliable information sources, like exploiting hyperspectral satellite, airborne, and ground-based remote sensing data to observe phenological traits through a crops growth cycle and gather information to precisely diagnose when, why, and where a crop is suffering negative impacts. By combining hyperspectral capabilities with unmanned aerial vehicles (UAVs), there is an increased capacity for providing time-critical monitoring and new insights into patterns of crop development. However, considerable effort is required to effectively utilize UAV-integrated hyperspectral systems in crop-modeling and crop-breeding tasks. Here, a UAV-based hyperspectral solution for mapping crop physiological parameters was explored within a machine learning framework. To do this, a range of complementary measurements were collected from a field-based phenotyping experiment, based on a diversity panel of wild tomato (Solanum pimpinellifolium) that were grown under fresh and saline conditions. From the UAV data, positionally accurate reflectance retrievals were produced using a computationally robust automated georectification and mosaicking methodology. The resulting multitemporal UAV data were then employed to retrieve leaf-chlorophyll (Chl) dynamics via a machine learning framework. Several approaches were evaluated to identify the best-performing regression supervised methods. An investigation of two learning strategies (i.e., sequential and retraining) and the value of using spectral bands and vegetation indices (VIs) as prediction features was also performed. Finally, the utility of UAVbased hyperspectral phenotyping was demonstrated by detecting the effects of salt-stress on the different tomato accessions by estimating the salt-induced senescence index from the retrieved Chl dynamics, facilitating the identification of salt-tolerant candidates for future investigations. This research illustrates the potential of UAV-based hyperspectral imaging for plant phenotyping and precision agriculture. In particular, a) developing systematic imaging calibration and pre-processing workflows; b) exploring machine learning-driven tools for retrieving plant phenological dynamics; c) establishing a plant stress detection approach from hyperspectral-derived metrics; and d) providing new insights into using computer vision, big-data analytics, and modeling strategies to deal effectively with the complexity of the UAV-based hyperspectral data in mapping plant physiological indicators.
  • Geometry-based self-assembly of DNA origami-protein hybrid nanostructures

    Al-Zarah, Hajar A. (2021-07) [Thesis]
    Advisor: Habuchi, Satoshi
    Committee members: Liberale, Carlo; Frokjaer-Jensen, Christian
    Biological nanomaterials are defined as materials with sizes within the nanoscale range of 1 - 100 nm. The fundamental functionalities and biocompatibility of these materials can be tailored for biotechnology applications. In 1983, Ned Seeman successfully developed the first customized DNA nanostructures, Holliday junctions. Since then, the field has continued to expand rapidly and various 2D and 3D nanostructures has been designed. Although the high predictability of DNA base-pairing is essential for the design of complex DNA nanostructures, it greatly limits its functional versatility; therefore, proteins are conjugated with DNA nanostructures to compensate for that. DNA origami-protein hybrid nanostructures were introduced in 2012. However, the structural units based on DNA origami-protein hybrid nanostructures are still limited, and the majority are constructed by covalent or sequence-specific non-covalent interactions. Here we utilize the inherent, non-sequence-specific interaction between DNA and histones to present sequence-independent self-assembled DNA origami-protein hybrid nanostructures. We demonstrated using various molecular biology and imaging techniques that ssDNAs and histone proteins self-assemble into structurally well-defined complexes. We successfully assembled DNA origami–histone hybrid nanostructures using two different shapes of DNA origami: rectangular (PF-3), and rectangular with central aperture (PF-2) nanostructures. We observed precise localization of nucleosome-like histone-ssDNA nanostructures at the edge (PF-3) or the center (PF-2) of the DNA origami. In addition, we demonstrated that this DNA origami-histone interaction results in the assembly of larger DNA origami complexes, including a head-to-head type dimer and a cross-shape complex. Our results suggest the successful self-assembly of the DNA origami–histone hybrid nanostructures provide a principal structural unit for constructing higher-order nanostructures. Given the reversible nature of the geometry-based noncovalent interaction between the DNA origami and the nucleosome-like histone-ssDNA nanostructures, the self-assembly/disassembly of DNA-histones hybrid nanostructures may open new opportunities to construct stimuli-responsive DNA-protein hybrid nanostructures.
  • Developing Production Methods for Different Microbial Strains and Beneficial Testing on Crop Species

    Alghanmi, Linah Y. (2021-07) [Thesis]
    Advisor: Hirt, Heribert
    Committee members: Blilou, Ikram; Chodasiewicz, Monika
    Microorganisms will play a significant role in the agricultural revolution in the coming decades and help meet the growing population's needs. Hence, understanding the impact of beneficial bacteria on crop development is key to the future of developing microbial products. The ability of PGPB to increase crop yields has been recently investigated in agriculture, as PGPB can support and protect plants under different stresses. Since PGPB interactions occur naturally, finding a method to apply beneficial bacteria while maintaining their efficiency and quality is a topic of interest. PGPB have been used as microbial inoculants, biofertilizers, and also as seed coatings. Preservation of microorganisms through desiccation has been used as the preferred method for long-term storage of microbial culture. The use of dry powders is favored over liquid cultures due to their ease of transportation and better quality control. For microbial preservation, freeze-drying has been defined as the most convenient and satisfactory preservation method for long-term storage. Freeze-drying is generally preferred over other drying techniques as it gives a high-quality dehydrated product. However, to reach a high-quality product, many parameters need to be monitored, such as bacterial cell concentration, growth medium, lyophilization buffer, rehydration, and duration of freeze-drying. In this research, SA190 was freeze-dried with 10% sucrose mixed with 5% trehalose as lyophilization buffer. Pseudomonas argentinensis SA190 was isolated from the root nodules of the desert plant Indigofera argentae in Saudi Arabia, specifically Jizan. The SA190 freeze-dried product was examined by several tests to assess the product viability and quality, such as accelerated test and water stability test. For future work, the effect of freeze-dried SA190 on plant growth and crop yield will be investigated. Moreover, optimization of the freeze-drying process, formulation, and packaging for commercial will be considered. In addition, bacterial strains isolated in DARWIN21 project with promising effects on plant growth, will be subjected to freeze-drying process.
  • Molecular Insights into the A. thaliana CDC48-NPL4-UFD1 Complex

    Zahodnik-Huntington, Brandon D. (2021-07) [Thesis]
    Advisor: Arold, Stefan T.
    Committee members: Hamdan, Samir; Blilou, Ikram
    The maintenance of protein homeostasis as a response to changing external conditions is crucial for cellular survival and proper function. Since plants cannot adapt by changing location, their need for a rapid intracellular response is accentuated. The AAA ATPase CDC48 maintains protein homeostasis in conjunction with NPL4 and UFD1 by coupling ATP hydrolysis with mechanical force to extract and unfold ubiquitylated proteins from organelle membranes, chromatin, or protein complexes. Our bioinformatic analysis revealed considerable domain and binding motif differences in A. thaliana NPL4 compared to its orthologs in animals and fungi. Using ITC, MST, and SEC-MALS, we found that NPL4 and UFD1 did not heterodimerize, NPL4 bound to CDC48A in the absence of UFD1, and the complex was not stable in vitro. Additionally, we provided the first medium-high-resolution reconstructions of CDC48A in both an AMP-PNP bound and apo state, using cryo-EM. AMP-PNP bound CDC48A was reconstructed in both a tense (3.3 Å) and relaxed (3.5 Å) conformation with the N domain was positioned above or coplanar with the D1 ring, respectively. Our heterogeneity analysis using CryoDRGN revealed continuous flexibility of the N domains between the two conformations. The apo state was reconstructed as a single conformation at 4.4 Å resolution. A cryo-EM reconstruction of the complex was also obtained at a resolution of ~6 Å, which showed expected cofactor stoichiometry and binding positions. Through our efforts, we have observed differences in the interaction between A. thaliana CDC48A and its cofactors UFD1 and NPL4 that may correspond to functional differences between kingdoms.

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