Theses: Recent submissions
Now showing items 1-20 of 897
Inkjet-Printed In-Vitro Organic Electronic Devices(2021-09) [Thesis]
Advisor: Inal, Sahika
Committee members: Baran, Derya; Salama, Khaled N.In-vitro electronic devices are promising to dynamically monitor minute-changes in biological systems. Electronic devices based on conducting polymers such as poly(3,4- ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) provide suitable and attractive substrates for biointerfacing. The soft polymer surface acts as a cushion for the living systems to interface while electronically detecting their properties. However, to this date, most bioelectronics devices have been fabricated via multi-step lithography techniques, which do not allow for mass fabrication and hence high throughput biosensing. Inkjet printing presents an alternative to fabricate organic bioelectronic devices. Besides being low-cost, inkjet printing allows to fabricate several devices in a short time with flexible design patterns and minimal material waste. Here, using inkjet printing, we fabricated PEDOT:PSS based organic electrochemical transistors (OECTs) for biomembrane interfacing. We optimized the deposition of various inks (silver nanoparticles (AgNPs), PEDOT:PSS, and the dielectric SU-8) used during the fabrication of these devices. We characterized the electrical characteristics of all-printed OECTs with various geometries and identified the high-performing ones. Due to the flexibility of ink optimization and design patterns, these all inkjet-printed electronic devices provide an alternative for mass production of biointerfacing platforms.
Stratigraphy of The Central Red Sea Margin: New Insights on the Tectono-stratigraphy of the Pre- and Syn- rift sedimentary sections and Arabian Plateau Uplift(2021-09) [Thesis]
Advisor: Alafifi, Abdulkader Musa
Committee members: Buchem, Frans van; Vahrenkamp, VolkerBroad uplift of the Red Sea margins has extensively eroded the pre-rift sedimentary section and exhumed the Proterozoic basement in the Arabian and Nubian Shields. However, some pre-rift sedimentary rocks are preserved within rift grabens along the coast, and on top of the Arabian plateau beneath syn-rift basalts of Harrat Hadan. Previous studies on outcrops of pre- and syn-rift sedimentary rocks near Jeddah assigned them various ages and Formations leading to confusion. Moreover, no attempts were made to correlate them to the section sitting on top of the Arabian plateau. This study redefines the stratigraphy of pre-rift sedimentary rocks in the Jeddah area (Usfan and Shumaysi Formations) and correlates them with similar rocks located 200 km east over the Arabian Shield (Khurma and Umm Himar Formations). Field work, petrographic investigation and satellite image mapping data from the central Red Sea are used to reveal new stratigraphic correlations for the pre-rift section and new insights about the uplift of the Arabian plate. The pre-rift sedimentary rocks rest uncomfortably on the Precambrian basement, consisting of sandstones, oolitic ironstone, shale, and bioclastic limestones. Their distinguishing characteristic is the textural and compositional maturity and total absence of basement-derived lithic pebbles. The pre-rift sedimentary rocks are disconformably overlain by a syn-rift section, reaching several kilometers thick, consisting of immature continental redbeds composed of basement-derived conglomerates, sandstones, and mudstones. They are distinguished by their brick-red color, poor sorting, and compositional immaturity. The presence of pre-rift marine sediments in Harrat Hadan over the Arabian shield and in the coastal plain of the Red Sea indicates that it was at or below sea level during the early Cenozoic. Subsequently, the rift was filled with immature continental syn-rift sediments eroded from the margins. Some key markers, particularly oolitic ironstones, define correlative units throughout the study area. Furthermore, the presence of 28 My old basaltic lava flows at the base of the syn-rift section in both the Jeddah and Harrat Hadan areas provides, for the first time, a reliable date for the start of rifting in the central Red Sea, and clear separation of pre-rift from syn-rift sedimentary rocks
Fracture Network Analysis for Carbon Mineralization in the Oligocene Jizan Volcanics, Saudi Arabia(2021-09) [Thesis]
Advisor: Alafifi, Abdulkader Musa
Committee members: Hoteit, Hussein; Van der Zwan, Froukje M.This study aims to characterize the fracture network in altered Oligocene-Early Miocene basalts of the Jizan Group, which accumulated in half grabens during the continental rift stage of Red Sea evolution. Unlike fresh basalts, the Jizan Group was affected by low temperature hydrothermal metamorphism, which plugged the original matrix porosity in vesicles, breccias, and interflow layers with alteration minerals. However, the basalts are pervasively shattered by closely spaced fractures in several directions, which provide fracture permeability. Characterization of these fractures is essential to reducing the fracture permeability uncertainty for mineral carbonation by the dissolved CO2 process such as Carbfix. Conventional fracture orientation and densities were initially taken at outcrops of the Jizan Group to characterize the fracture network. Terrestrial Digital Photogrammetry (TDP) and Unmanned Aerial Vehicle Digital Photogrammetry (UAVDP) surveys were conducted to acquire images covering larger areas to create 2D orthoimages and 3D models of the outcrops using Agisoft Metashape, which were analyzed for fracture geometries using QGIS and Cloud Compare, respectively. The automated analysis of fracture orientations and densities compared well with conventional manual measurements. Similar fracture geometries were observed at seven different sites along the outcrop belt of the Jizan Group, which suggests a common origin. This study found four dominating fracture sets in the Jizan Group volcanics, with a dominant trend of fractures in the NNW direction, similar to the general trend of the Red Sea. The Northern sites presented higher fracture intensity compared to the southern sites, indicating more suitable environments for carbon mineralization. Moreover, mineralogical composition of spatially distributed samples collected from the Jizan Group volcanics were collected to investigate spatial distributions of secondary alteration minerals in the Jizan Group basalts. Epidote was observed in samples collected from southern outcrops indicating hydrothermal alteration temperatures higher than 230 C, whereas the northern sites lacked epidote and contained calcite indicating lower hydrothermal alteration temperatures. The presence of sufficient amounts of Ca according to previous studies conducted by Torres (2020), along with potential 3D fracture networks in the subsurface indicate feasibility for the injection of CO2 charged fluids in the subsurface of the volcanics.
Hydrodynamics of a Gas-Solid Counter-Current Downer Reactor Using a Time-Resolved Planar Digital Particle Image Velocimetry and Digital Image Analysis Techniques(2021-08) [Thesis]
Advisor: Castaño, Pedro
Committee members: Gascon, Jorge; Thoroddsen, Sigurdur T; Ruiz-Martinez, JavierThis work analyzes the solid flow dynamics of gas-solid downer fluidized bed reactor in co-current and, particularly, in counter-current mode. This reactor is potentially interesting for catalytic applications where very short (sub second) and precise contact times are required between the solid catalyst and the gaseous reactants-products. To this aim, a 1.5 m and 36 mm ID downer reactor setup was built to replicate the conditions in a real unit in cold flow and using materials that enable the observation of the solid particle dynamics. Specifically, two state-of-the-art techniques have been used: Particle Image Velocimetry (PIV) and Digital Image Analysis (DIA). Three types of particles have been used: two commercial fluidized catalytic cracking (FCC) particles (ρp = 1300 kg/m3, dp = 75 and 56 μm) and sand (ρp=2600 kg/m3, dp= 370 μm). High-speed cameras were positioned in two axial positions: 70 and 140 cm from the top, to reveal the flow behavior across the reactor. It was found that the solid flow initially was segregated because of the solid feeding design. Thus, 3D printed re-distributer was used to even the solid flow. The solid particles in the counter-current downer was approaching the plug-flow behavior with 23% variation in the velocity gradient across the radial direction, compared with 40% for the co-current counterpart. A method to estimate solid hold-up based on images was developed, yielding values in a good agreement with literature. Keywords: Hydrodynamics, counter-current, downer, PIV, DIA, Solid hold-up
BranchNet: Tree Modeling with Hierarchical Graph Networks(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.
Photophysics of Poly(3-hexylthiophene):Non-Fullerene Acceptor Organic Solar Cells(2021-07-03) [Thesis]
Advisor: Laquai, Frédéric
Committee members: Anthopoulos, Thomas D.; McCulloch, IainInsight into the relationship between the Ionization Energy (IE) offsets between donor and acceptor materials and the performance of the organic solar cells (OSC) could improve the charge generation efficiency. Charge generation can proceed through two different paths in Bulk Heterojunction (BHJ) based OSCs which are electron transfer from donor to acceptor and hole transfer from acceptor to donor. Electron transfer can be controlled by electron affinities and hole transfer can be controlled by ionization energies. In this work, large IE offsets were investigated in poly(3-hexylthiophene-2,5-diyl)(P3HT):Non Fullerene Acceptor (NFA) based OSCs by fabricating and characterizing devices, also conducting several experiments to optimize the processing conditions for the devices. These results provide an overview of the charge transfer and IE offsets dependence, also a general picture of the photophysics in P3HT:NFAs based OSCs. Moreover, using wide bandgap polymer donor which has shallow IE such as P3HT with low-bandgap NFAs may provide sufficient IE offsets between donor and acceptors enabled us to reach the inverted Marcus regime. In this regime, the electron transfer rate decreases upon decreasing the charge transfer (CT) state energy compared to the exciton energy. The decrease of the internal quantum efficiency (IQE) upon increasing the IE offset suggests that we are in that regime.
Molecular Insights into the A. thaliana CDC48-NPL4-UFD1 Complex(2021-07) [Thesis]
Advisor: Arold, Stefan T.
Committee members: Hamdan, Samir; Blilou, IkramThe 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.
Geometry-based self-assembly of DNA origami-protein hybrid nanostructures(2021-07) [Thesis]
Advisor: Habuchi, Satoshi
Committee members: Liberale, Carlo; Frokjaer-Jensen, ChristianBiological 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.
Understanding the Genetic Basis for piRNA Silencing in the Soma and Germline of Caenorhabditis elegans(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.
The Unexpected Role of Uric Acid in Lifecycle Synchronicity and Symbiosis(2021-07) [Thesis]
Advisor: Aranda, Manuel
Committee members: Cui, Guoxin; Peixoto, RaquelFunctionality of Cnidarian symbiosis with Symbiodiniaceae is fundamental to reef ecosystem success. Symbiodiniaceae cells have a complex life history, which, in hospite, is controlled by the host. In addition to the endosymbiotic lifestyle, they can exist free-living cells which diurnally alternate between a coccoid, vegetative night-time form to a day-time motile, flagellated cell. Their cell division cycle is gated by external light cues, and correlates with transitions in cell morphology. In contrast, endosymbiotic cells have an elongated G1 phase – demonstrating a de-coupling of cell cycle from 24-hour cycle in response to symbiosis. Furthermore, daughters of dividing endosymbiotic Symbiodiniaceae remain as coccoid cells, de-coupling morphological and cell division cycles. How this occurs remains unknown. The answer may lie in crystalline uric acid deposits, which are present only in motile, daytime cells, correlating with G1 and S phase. These store excess nitrogen and are quickly metabolized in low nitrogen availability. They also function as an eyespot. The influence of uric acid on the life cycle of free-living and endosymbiotic Symbiodiniaceae is unknown. In this study, I treated cultures of B. minutum with allopurinol, an inhibitor of uric acid synthesis. Flow cytometry showed that allopurinol the reduced growth rate and ratio of coccoid:motile cell cultures. RNA sequencing and differential gene expression analysis identified biological processes enriched in allopurinol treatment. I hypothesize that an intracellular lack of nitrogen imposed lack of uric acid crystals stimulates the General Amino Acid Control pathway. This represses translation, explaining the downregulation of ribosomal proteins, and upregulates amino acid and purine de novo biosynthesis pathways. Repression of translation may slow cellular growth and the G1 phase of the cell cycle, reducing number of cells meeting the size threshold for G1/S transition. Without uric acid deposits, cells may lack a functioning eyespot and not receive light cues which usually trigger morphological transitioning. This may suppress the motile morphology of free-living Symbiodiniaceae and cells in hospite even though the cell division cycle progresses, albeit more slowly. Genes involved in biosynthesis of flagella, thecal plates and the eyespot are upregulated, suggesting suppression of the motile form may act downstream of transcription.
Environmental origin and compartmentalization of bacterial communities associated with Avicennia marina mangroves on the Red Sea coast(2021-07) [Thesis]
Advisor: Daffonchio, Daniele
Committee members: Marasco, Ramona; Soares, Alexandre; Pain, ArnabMangrove 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
Developing Production Methods for Different Microbial Strains and Beneficial Testing on Crop Species(2021-07) [Thesis]
Advisor: Hirt, Heribert
Committee members: Blilou, Ikram; Chodasiewicz, MonikaMicroorganisms 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.
Application of Physics-Informed Neural Networks to Solve 2-D Single-phase Flow in Heterogeneous Porous Media(2021-07) [Thesis]
Advisor: Hoteit, Hussein
Committee members: Sun, Shuyu; Ahmed, ShehabNeural networks have recently seen tremendous advancements in applicability in many areas, one of which is their utilization in solving physical problems governed by partial differential equations and the constraints of these equations. Physics-informed neural networks is the name given to such neural networks. They are different from typical neural networks in that they include loss terms that represent the physics of the problem. These terms often include partial derivatives of the neural network outputs with respect to its inputs, and these derivatives are found through the use of automatic differentiation. The purpose of this thesis is to showcase the ability of physics-informed neural networks to solve basic fluid flow problems in homogeneous and heterogeneous porous media. This is done through the utilization of the pressure equation under a set of assumptions as well as the inclusion of Dirichlet and Neumann boundary conditions. The goal is to create a surrogate model that allows for finding the pressure and velocity profiles everywhere inside the domain of interest. In the homogeneous case, minimization of the loss function that included the boundary conditions term and the partial differential equation term allowed for producing results that show good agreement with the results from a numerical simulator. However, in the case of heterogeneous media where there are sharp discontinuities in hydraulic conductivity inside the domain, the model failed to produce accurate results. To resolve this issue, extended physics-informed neural networks were used. This method involves the decomposition of the domain into multiple homogeneous sub-domains. Each sub-domain has its own physics informed neural network structure, equation parameters, and equation constraints. To allow the sub-domains to communicate, interface conditions are placed on the interfaces that separate the different sub-domains. The results from this method matched well with the results of the simulator. In both the homogeneous and heterogeneous cases, neural networks with only one hidden layer with thirty nodes were used. Even with this simple structure for the neural networks, the computations are expensive and a large number of training iterations is required to converge.
Metabolic Profiling Analysis of Four Date Palm (Phoenix dactylifera L.) Cultivars from Saudi Arabia and Tunisia Using LC-MS and GC–MS Analysis(2021-07) [Thesis]
Advisor: Jaremko, Mariusz
Committee members: Saikaly, Pascal; Arold, Stefan T.Date palm (Phoenix dactylifera L.) is a fruit-bearing tree with numerous potential sustainable applications. Since ancient times, it has been considered a stable, secure, and sustainable food. This work provides comprehensive metabolic profiling of both parts, flesh and seed, of four P. dactylifera cultivars; Ajwa, Anbara, Sukkari, and Degelt Nour, which originated from two countries, Saudi Arabia, Tunisia. The analysis performed using mass spectrometry-untargeted metabolomics approaches, included a combination of LC-MS and GC-MS coupled to multivariate statistical analysis to reveal the differences in metabolite compositions among date varieties. The LC-MS seed results showed several classes of metabolites that belong to the flavonoids, phenolic acids, and amino acids derivatives, including citric acid, malic acid, lactic acid, hydroxyadipic acid, caffeic acid, which were at high concentrations in AJS followed by DNS and ARS. The LC-MS flesh analysis displayed that DNF had a high level of Isoquercitrin (flavonoid compound) and sinapic acid, and AJF was high concentrations level in hydroxyadipic acid and ascorbic acid. GC-MS concluded that seed samples of four date varieties are richer in metabolites classes than the flesh samples. The metabolites contributed to the seed metabolite compositions included several classes of amino acids, hydrocinnamic acids (caffeic, ferulic and sinapic acids), antioxidant phenolics, and long-chain fatty acids. The PCA and its loading analysis demonstrated the discriminating metabolites that were responsible for date varieties segregation, as HCA displayed the metabolic patterns and groups of metabolites that drive the clustering of the date samples, two groups of dates clustered together (AR and AJ) and (SR and DN). These clusterings are based on the similarities and differences observed in the metabolite compositions of the studied date samples that could be explained by differences in various metabolic responses and the environmental conditions, genotypes and geographical regions. This extensive date palm information would increase the potential of date fruits and seeds as low-cost sources of natural diet that may provide nutritious and bioactive components in the food and pharmaceutical fields to produce value-added products.
Is Post Transplantation Performance Driven by the Variability of the Habitat of Origin?(2021-07) [Thesis]
Advisor: Aranda, Manuel
Committee members: Peixoto, Raquel; Schmidt-Roach, SebastianAs 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.
A Multi-platform Comparison of Phenology for Semi-automated Classification of Crops(2021-07) [Thesis]
Advisor: McCabe, Matthew
Committee members: Johansen, Kasper; Blilou, IkramRemote 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
A Synergy of Spatiotemporal Transcriptomic Techniques for Non-Model Organism Studies: Something Old, Something New, Something Borrowed, Something Ocean Blue(2021-07) [Thesis]
Advisor: Aranda, Manuel
Committee members: Peixoto, Raquel; Frøkjær-Jensen, ChristianIn 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.
Semi-Analytical Solution to Assess CO2 Leakage in the Subsurface through Abandoned Wells(2021-07) [Thesis]
Advisor: Hoteit, Hussein
Committee members: Patzek, Tadeusz; Sun, ShuyuGeological storage is an effective approach capable of reducing greenhouse gases emissions at significant scales by storing the CO2 underground. Subsurface reservoirs with sealing caprocks can provide long-term containment for the injected CO2. However, the leakage is a major concern in most storage sites. The presence of abandoned wells penetrating the reservoir caprock may cause leakage flow paths for CO2 to the overburden. To access the leakage in the subsurface, an analytical model for the time-varying leaky well is needed. In this thesis, we propose a new semi-analytical approach based on pressure-transient analysis to model the behavior of leakage and corresponding pressure distribution in multiple wells multiple layers system. Current solutions either take approximations on essential operations or requires numerical inversion for the solution in the Laplace domain. In this work, we employ the superposition in time and space to solve the diffusivity equation in 2D radial flow to approximate the transient pressure in the reservoirs. We use numerical simulations to verify the proposed time-dependent semi-analytical solution. The results show good agreement in both pressure and leakage rates. Sensitivity analysis is conducted to assess different CO2 leakage scenarios to the overburden. The equivalent injection rate is also proposed to release the single-phase assumption so that the solution can recover identical results as two-phase numerical simulation in the far-field.
Evaluation of Different Forward Osmosis Membrane Cleaning Strategies for Produced Water Streams Treatment(2021-07) [Thesis]
Advisor: Ghaffour, NorEddine
Committee members: Pinnau, Ingo; Vrouwenvelder, Johannes S.; Saqib Nawaz, MuhammadForward 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
Improving Formation Pressure Integrity Tests with Field-Wise Test Data Analysis and Hydraulic Impedance Testing(2021-07) [Thesis]
Advisor: Patzek, Tadeusz
Committee members: Finkbeiner, Thomas; Ahmed, ShehabDrilling 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.