Recent Submissions

  • Inkjet-Printed In-Vitro Organic Electronic Devices

    Asghar, Hussain (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

    AlTammar, Ali J. (2021-09) [Thesis]
    Advisor: Alafifi, Abdulkader Musa
    Committee members: Buchem, Frans van; Vahrenkamp, Volker
    Broad 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

    Al Malallah, Murtadha (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.
  • High-resolution sedimentological, petrographic, and petrophysical analysis of Late Oxfordian - Early Kimmeridgian (?), Ulayyah Member, Hanifa Formation: Insights from behind-the-outcrop core WB-01

    Adigozalova, Teyyuba (2021-09) [Thesis]
    Advisor: Vahrenkamp, Volker
    Committee members: Buchem, Frans van; Ravasi, Matteo
    The Hanifa Formation has a high-economic value in Saudi Arabia and many middle-eastern countries where it exists both as a reservoir and source rock. A few examples of the super-giant oil and gas fields that have Hanifa reservoir in the subsurface include Berri and Khurais fields. In this project, an analogue core for Hanifa reservoir facies that was drilled behind-the-outcrop, ~ 150 km south of Riyadh, along the Tuwaiq Mountain escarpment is studied. The main objective of this study is to analyze the vertical facies heterogeneity of Ullayah Member of Hanifa Formation. Thus, for this study sedimentological, petrographical, and petrophysical data have been collected and analyzed at a very high resolution. Based on the sedimentological, petrophysical and petrographic interpretation, four different vertical facies associations can be defined, representing distinct depositional environments (vertically): 1) High energy-level proximal shoreline, intraclastic grainstones deposition with moderate-Vp, relatively low-GR signature ; 2) Relatively low energy-level lagoonal depositional setting with low-Vp, high-GR represented by wackestones/packstones that has lagoonal microfossils and dasyclad algae; 3) Back barrier reefal depositional setting with moderate Vp, low-GR signature represented by stromatoporoids and corals, and 4) Oncoidal depositional setting with moderate-Vp, low- GR signature, mainly composed of ellipsoidal oncoids. Overall, the facies from these environments have been systematically vertically stacked on top of each other (in core WB-01), representing a deepening upwards trend and followed by shallowing oncoidal facies. This interpretation is also well match in regional context (GR data) and can be used as correlation reference.
  • Hydrodynamics of a Gas-Solid Counter-Current Downer Reactor Using a Time-Resolved Planar Digital Particle Image Velocimetry and Digital Image Analysis Techniques

    Alzailaie, Abdulrahman (2021-08) [Thesis]
    Advisor: Castaño, Pedro
    Committee members: Gascon, Jorge; Thoroddsen, Sigurdur T; Ruiz-Martinez, Javier
    This 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

    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.
  • Photophysics of Poly(3-hexylthiophene):Non-Fullerene Acceptor Organic Solar Cells

    Althobaiti, Wejdan (2021-07-03) [Thesis]
    Advisor: Laquai, Frédéric
    Committee members: Anthopoulos, Thomas D.; McCulloch, Iain
    Insight 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.
  • 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
  • The Unexpected Role of Uric Acid in Lifecycle Synchronicity and Symbiosis

    Menzies, Jessica (2021-07) [Thesis]
    Advisor: Aranda, Manuel
    Committee members: Cui, Guoxin; Peixoto, Raquel
    Functionality 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.
  • 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.
  • 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.
  • 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.
  • Metabolic Profiling Analysis of Four Date Palm (Phoenix dactylifera L.) Cultivars from Saudi Arabia and Tunisia Using LC-MS and GC–MS Analysis

    Alsuhaymi, Shuruq (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.
  • 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
  • Rock mechanical characterization of the Upper Cretaceous carbonate mudrocks of Jordan

    Iakusheva, Regina (2021-07) [Thesis]
    Advisor: Vahrenkamp, Volker
    Committee members: Alafifi, Abdulkader Musa; Finkbeiner, Thomas
    Rock mechanical properties of subsurface strata, such as strength, hardness, brittleness, and elasticity, play an important role during reservoir development for wellbore stability, fracture prediction and generation, and the application of other engineering techniques. Specifically, for unconventional reservoir development characterization of the mechanical properties of organic-rich layered rocks is critical, including for the design of proper drilling, well completion, and production programs. This study evaluates rock mechanical properties of Jordanian Upper Cretaceous organic-rich carbonate mudrocks, which are comprised of carbonate mudstone, chalky marl and shale interlayers. They are characterized by high organic content, heterogeneous porosity (1.2%- 35%) and a nanodarcy permeability. The study mainly derives rock mechanical properties from core and laboratory investigations, with the aim to access the impact of compositional and sedimentary facies variation on rock mechanical properties. The rocks were examined for their lithology, mineralogy, and mechanical properties. Microscopic investigation allowed the definition of four different microfacies (organic-rich (OR) mudstone, OR wackestone, silica-rich packstone, OR packstone). X-Ray analysis shows that different microfacies types exhibit various mineralogical compositions, with carbonate, biogenic quartz, and apatite as the dominant components. All samples are rich in TOC content, ranging from 7.5 to 25.3% (average 16.6 wt.%). The data show that microfacies variation has a clear impact on the rock mechanical properties. Leeb Hardness (LH) is higher in silica-rich packstone and OR mudstone. Intrinsic specific energy (ISE) and wave velocities reach their maximum in OR mudstones. The average porosity values are much higher in OR wackestones (33.2%) and OR packstones (34.3%). The brittleness index (BI), which was calculated based on mineral composition, indicate that silica-rich packstones and OR mudstones are brittle, while the other two microfacies have properties of a ductile material. In addition, the good correlation between the ISE and BI suggests that ISE values are a useful proxy for brittleness. The present study improves the understanding of the relationships between stratigraphy, microfacies, TOC, and mechanical properties. These insights bear implications for improvement of exploitation of the JOS, understanding of rock mechanical properties of mature unconventional formations as well as provide the workflow for more efficient procedure to access the compressive strength
  • 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
  • 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.
  • 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.
  • 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

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