Recent Submissions

  • The Effect of Increasing Temperature on Greenhouse Gas Emissions by Halophila stipulacea in the Red Sea

    Burkholz, Celina (2018-12)
    Seagrass ecosystems are intense carbon sinks, but they can also emit greenhouse gases (GHG), such as carbon dioxide (CO2) and methane (CH4), to the atmosphere. Yet, GHG emissions by seagrasses are not considered when estimating global CH4 production rates by natural sources, although these estimations will help predict future scenarios and potential changes in CH4 emissions. In addition, the effect of warming on GHG emissions by seagrasses has not yet been reported. The present study aims to assess the CO2 and CH4 production rates by vegetated and adjacent bare sediment of a monospecific seagrass meadow (Halophila stipulacea) located in the central Red Sea. We measured CH4 and CO2 fluxes and their isotopic signatures by cavity ringdown spectroscopy on chambers containing vegetated and bare sediment. The fluxes were measured at temperatures from 25 °C (winter seawater temperature) to 37 °C to cover the natural thermal range and future seawater temperatures in the Red Sea. Additional parameters analyzed included changes in the sediment microbial community composition, sediment organic matter, organic carbon, nitrogen, and phosphorus concentration. We detected up to 100-fold higher CH4 (up tp 571.65 µmol CH4 m−2 d−1) and up to six-fold higher CO2 (up to 13,930.18 µmol CO2 m−2 d−1) fluxes in vegetated sediment compared to bare sediment, and an increase in CH4 and CO2 production with increasing temperature. In contrast, CH4 and CO2 production rates decreased in communities that were maintained at 25 °C, while communities that were exposed to prolonged darkness showed a decrease in CH4 and an increase in CO2 production rates. However, only minor changes were seen in the microbial community composition with increasing temperatures. These results show that GHG emissions by seagrasses might be affected by natural temperature extremes and warming due to climate change in the Red Sea. The findings will have critical implications for the estimation of natural GHG sources, especially when predicting future changes in the global CH4 budget.
  • Modeling and Analysis of Hybrid Aerial-Terrestrial Networks: A Stochastic Geometry Approach

    Alshaikh, Khlod K. (2018-12)
    The ever-increasing demand for better mobile experiences is propelling the research communities to look ahead at how future networks can be geared up to meet such demands. It is likely that the next-generation of wireless communications will be revolutionary, outpacing the current systems capabilities in terms connectivity, reliability and intelligence. These trends and predictions will cause a revolutionary change in the wireless communications. In this context, the concept of Ultra-Dense Network (UDN) is poised to be the cornerstone of the development of fifth generation(5G) systems, whereby a massive number of base stations (BSs) are deployed for enhancing the network performance metrics. Though such densification might be economically viable in urban areas, it is mostly unfavorable in rural ones due to the sheer complexity and the various factors involved the planning and installation processes; all of which trigger the need for cost-effective, flexible and easily-implementable solutions. As a result, unmanned aerial vehicles (UAVs) emerge as a promising alternative solution for enhancing wireless coverage. Due to their mobility capabilities, UAVs are of particular importance in events of (i) terrestrial-based cellular systems dilapidation, (ii) infrastructure absence in remote and suburban areas, or (iii) limited-duration events or activities wherein there is a short-term need for supplementary network resources to handle the overload. While a growing body literature works towards characterizing and providing insights into the performance of UAVs-only networks (serving the first two purposes), understanding the performance of such networks when coupled with existing terrestrial BSs remains a challenging, yet interesting, open research venue. Towards this direction, this thesis provides a rigorous analysis of the downlink coverage probability of hybrid aerial-terrestrial networks using tools from Stochastic Geometry. The thesis presents a mathematical model that characterizes the coverage probability metric under different network environments. The proposed model is validated against intensive simulations so as to substantiate the analytical results. The developed work is essential to understanding the premises of one possible solution to the UDNs of tomorrow, capture its key performance metrics and, most importantly, to uncover key design insights and reveal new directions for the wireless communication industry.
  • A Biocomputational Study of Water-Nucleobase Stacking Contacts in Functional RNAs

    Kalra, Kanav (2018-12)
    Recent structural studies evidenced the presence of a recurring well-known interaction between an oxygen atom and an aromatic nucleobase ring in structural motifs of nucleic acids. In particular, this type of interaction is observed between the O4' atom of the (deoxy)ribose moiety and the aromatic nucleobase in Z-DNA molecules and in a variety of structural RNA molecules. In this thesis, we comprehensively examine the hitherto undetected stacking interactions between an oxygen atom of a water (Ow) molecule and the aromatic nucleobase ring, using structural bioinformatics along with quantum mechanics. On the basis of the structural analysis of the high-resolution X-ray structures, we found out that the stacking distance between the Ow atom and the nucleobase plane varies between 3.1 and 4.0 Å. Further, the contact between the Ow-nucleobase plane can be categorized either as a lonepair-π type, where the Ow atom interacts directly with the aromatic surface of the nucleobase, or as an OH-π interaction, where one of the hydrogen atoms of the Ow points towards the nucleobase. Our quantum chemical analysis evidenced that the OH-π interaction is clearly favored in terms of energetics when compared to the lonepair-π, except for the uracil, where the lonepair-π kind of interaction seems to be energetically more stable, as also supported by electrostatic potential map calculations.
  • Preparation of modified DNA molecules for multi-Spectroscopy Application

    zhang, xinyu (2018-11-29)
    Hot Electron Nanoscopy and Spectroscopy (HENs) is a current-sensing AFM technique recently developed in our lab, which have proven a new kind of response on conduction at the nanometer scale, casting a new light for the comprehension of electronic states in nanomaterials. Direct imaging of DNA structure has long been investigated, with the development of HENs technology, more structural information about DNA could be revealed by simultaneous measurements of height, phase, Raman signal, and conductivity. With the aim of applying it for the first time on biological molecules, customized double-stranded DNA sequences, including thiol-modified oligonucleotides are designed to create preferential conductive paths through the basis as a benchmark system for the technique on biomolecules. This work aims to a final goal to characterize hot-electron current between gold tip and thiol modified DNA which ideally is covalently bonded to the gold surface and optimized for the application. In this work, high density of DNA absorbed by SERS active gold surface with atomic flat islands has been prepared for HENs application. The samples have been characterized by AFM, SKPM and Raman Spectroscopy, as non-destructive and controlled interactive image analysis. High-resolution images of DNA have been acquired, S-S and Au-S bonding of DNA anchored on SERS active gold substrate are also visible with Surface-enhanced Raman and Tip-enhanced Raman signals. A submolecular feature has also been found in both topographical and electrical results. Herein, we report the synthesis and characterization steps to obtain the optimized operation standard.
  • Prediction of Active and Inactive Chemical Compounds from High-Throughput Assays

    Islam, Elaf J. (2018-11-28)
    This study considers chemical compounds that can exert their activity by interacting with a target protein or other molecular receptors. Our aim is to develop machine learning models that can predict if a chemical compound will be active in a particular test/assay. We will use data from assays that are present in the PubChem knowledgebase, specifically in its segment called BioAssays which reports the results of many high-throughput screening experiments. PubChem BioAssays is a valuable resource that contains information from a large number of experiments. In one assay, sometimes many hundreds or even many thousands of chemicals are tested. Data from these experimental assays contain information about chemicals that are active as well as chemicals that are not active in the assay. These represent an interesting resource of experimental data that are well suited for classification purposes. We will approach the problem by evaluating different ways that chemical compounds can be numerically described by means of so-called fingerprints, and then apply different machine learning (ML) and deep learning (DL) models to classify active and inactive chemicals for a number of assays. In this study, we will make comprehensive comparisons of the types of ML/DL models and types of fingerprint features that describe chemicals, and evaluate combinations of models and fingerprints that work best for the problem in question. Our focus is on finding those combinations which are useful for distinguishing active from inactive compounds in single PubChem assays. We will evaluate the methods across 10 assays and will examine the effects of 11 types of fingerprints. For example, PubChem fingerprints and MACCS keys fingerprints. For the evaluation, up to now we performed 88 experiments for each dataset and 968 in total for all 10 PubChem assays. These experiments involved approximately 6,000 interactions between chemicals and their targets. The implementation of this project has been done using MATLAB. Based on these and additional experiments, we will be in a position to propose which combination of fingerprints and ML/DL models works best in the above mentioned task. Such modeling will be useful to predict activity for chemicals that are not yet tested.
  • Visualization and Simulation of Variants in Personal Genomes With an Application to Premarital Testing (VSIM)

    Althagafi, Azza Th. (2018-11-28)
    Interpretation and simulation of the large-scale genomics data are very challenging, and currently, many web tools have been developed to analyze genomic variation which supports automated visualization of a variety of high throughput genomics data. We have developed VSIM an automated and easy to use web application for interpretation and visualization of a variety of genomics data, it identifies the candidate diseases variants by referencing to four databases Clinvar, GWAS, DIDA, and PharmGKB, and predicted the pathogenic variants. Moreover, it investigates the attitude towards premarital genetic screening by simulating a population of children and analyze the diseases they might be carrying, based on the genetic factors of their parents taking into consideration the recombination hotspots. VSIM supports output formats based on Ideograms that are easy to interpret and understand, which makes it a biologist-friendly powerful tool for data visualization, and interpretation of personal genomic data. Our results show that VSIM can efficiently identify the causative variants by referencing well-known databases for variants in whole genomes associated with different kind of diseases. Moreover, it can be used for premarital genetic screening by simulating a population of offspring and analyze the disorders they might be carrying. The output format provides a better understanding of such large genomics data. VSIM thus helps biologists and marriage counsellor to visualize a variety of genomic variants associated with diseases seamlessly.
  • Suspended dsDNA/Rad51 on super-hydrophobic devices: Raman spectroscopy characterization

    Morello, Maria Caterina (2018-11-22)
    The novel method herein proposed, aims to study Deoxyribonucleic acid (DNA) and Rad51 repair protein in its resting state after their interaction by using a combination of biological preparation and physical measures. Rad51 is a highly conserved protein; it is involved in eukaryotes genome stability and can interact with single strand (ss) and double strands (ds) DNA. In our work, a droplet of the solution containing the dsDNA/Rad51 complexes was deposited on micro-fabricated super-hydrophobic substrates (SHS) to obtain self-organized and suspended fibers. The silicon-based SHS were designed to incorporate a regular circular array of pillars and to maintain a high contact angle with the drop. The samples were let dehydrate at controlled temperature and humidity conditions. At the end of the buffer evaporation process, non-suspended material and salt excess are concentrated on the top of a few micro-pillars in a limited area (drop residual) of the device while ordered and self-assembled DNA/Rad51 fibers are suspended between micro-pillars. To find the ideal conditions to obtain and suspend the nucleic acid/protein complexes, several parameters were investigated: saline buffer, DNA and protein concentrations were widely titrated and showed a significant effect on the biomolecule suspension on SHS. The samples were then preliminarily checked by microscopy techniques and then described by the Raman spectra acquired. Several techniques were used: optical microscopy, Energy Dispersive X-Ray Spectroscopy (EDAX), Scanning Electron Microscopy (SEM) and Raman Spectroscopy. Protein expressions, DNA suspension, micro-fabrication and characterization were all performed in KAUST Core Labs and Structural Molecular Imaging Light Enhanced Spectroscopies (SMILEs) Lab. The novel approach presented in this work is highly multidisciplinary and comprises physical measurements (Raman spectroscopy and EM imaging), chemistry and biology. In future the method can be used further expanded supporting the data with HRTEM direct imaging to elucidate the nucleic acids/proteins behavior in the multiple phases of the genome repair processes. Also, it and can serve as a fingerprint of the biological molecules involved in biological interactions, their localization and structural characterization, providing a new tool for structural analysis, screening and diagnostics.
  • Micro-fabricated super-hydrophobic substrate for amyloid fibers characterization

    Ricco, Andrea (2018-11-22)
    In recent years super-hydrophobic micro-patterned substrates (SHS) have been successfully used for the suspension of a few biological molecules, allowing the further characterization in a background-free environment by label-free techniques such as Raman spectroscopy, SEM and TEM in one device. This result is due to the combined action of laminar flow and shear stress exerted on the molecules contained in a drop that is spotted on top of the SHS and slowly evaporates. This new method is here proposed for the label-free formation and background-free characterization of amyloid fibers. Amyloids are insoluble aggregates formed by proteins that convert from a misfolded form into highly-organized β-sheet structures that could accumulate in different organs and compromise their normal physiological functions. Known amyloid-related diseases, named amyloidosis, are for instance Alzheimer, Parkinson, and type 2 diabetes. In classical crystallography, the study of the amyloid aggregates structure is often hampered by the laborious and time consuming sample preparation techniques. Therefore the need of a quick reproducible technique, has emerged. The amyloid fibers investigated in this work are derived from a lysozyme protein and a Tau-derived short peptide, both known to be related to two forms of amyloidosis. With this technique we demonstrate that threads of protein fibers are deposited on the substrate helped by the patterning of the SHS and its properties, and by characterizing them with Raman spectroscopy technique we revealed that they are anisotropic structures of amyloid nature. This type of sample preparation technique arises from the effect of the evaporation on the SHS, and opens up new possibilities for the formation of oriented fibers of amyloids and more in general, of proteins, ready for a substrate-free characterization, while classic crystallographic methods could have a limitation.
  • Variants Prioritization in Cancer: Understanding and Predicting Cancer Driver Genes and Mutations

    Althubaiti, Sara (2018-11-08)
    Millions of somatic mutations in human cancers have been identified by sequenc- ing. Identifying and distinguishing cancer driver genes amongst the millions of candi- date mutations remains a major challenge. Accurate identification of driver genes and mutations is essential for the progress of cancer research and personalizing treatment based on accurate stratification of patients. Because of inter-tumor genetic hetero- geneity, numerous driver mutations within a gene can be found at low frequencies. This makes them difficult to differentiate from other non-driver mutations. Inspired by these challenges, we devised a novel way of identifying cancer driver genes. Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, function, and whole body physiological phenotypes as features. We demonstrate that our method can accurately identify known cancer driver genes and distinguish between their role in different types of cancer. In ad- dition to identifying known driver genes, we identify several novel candidate driver genes. We provide an external evaluation of the predicted genes using a dataset of 26 nasopharyngeal cancer samples that underwent whole exome sequencing. We find that the predicted driver genes have a significantly higher rate of mutation than non-driver genes, both in publicly available data and in the nasopharyngeal cancer samples we use for validation. Additionally, we characterize sub-networks of genes that are jointly involved in specific tumors.
  • Quantifying the Ionized Dopant Concentrations of InGaN-based Nanowires for Enhanced Photoelectrochemical Water Splitting Performance

    Zhang, Huafan (2018-11-04)
    III-nitride nanowires (NWs) have been recognized as efficient photoelectrochemical (PEC) devices due to their large surface-to-volume ratio, tunable bandgap, and chemical stability. Doping engineering can help to enhance the PEC performance further. Therefore, addressing the effects of Si and Mg doping on the III-nitride NW photoelectrodes is of great interest. In this study, doping levels of NWs were tuned by the dopant effusion cell temperature of the molecular beam epitaxy (MBE) growth. The successful doping of the III-nitride NWs was confirmed using photoluminescence (PL), Raman spectroscopy, and open circuit potential (OCP) measurements. The ionized dopant concentrations of Si-doped InGaN/GaN NWs were systematically quantified by electrochemical impedance studies (EIS). Due to the three dimensional surfaces of NWs, modified Mott-Schottky formulas were induced to improve the accuracy of ionized dopant concentrations. The highest dopant concentration of Si-doped InGaN NWs can reach 2.1x1018 cm-3 at Tsi = 1120 oC. Accordingly, the estimated band edge potentials of the tested NWs straddled the redox potential of water splitting. The PEC performance of these devices was investigated by linear scan voltammetry (LSV), chronoamperometry tests, and gas evolution measurements. The results were consistent with the quantified dopant concentrations. The current density of n-InGaN NWs doped at TSi = 1120 oC was nine times higher than the undoped NWs. Additionally, the doped NWs exhibited stoichiometric hydrogen and oxygen evolution. By doping Mg into InGaN and GaN segments separately, the p-InGaN/p-GaN NWs demonstrated improved PEC performance, compared with undoped-InGaN/p-GaN and n-InGaN/n-GaN NWs. The p-InGaN/p-GaN NWs exhibited a highly stable current density at ~-9.4 mA/cm2 for over ten hours with steady gas evolution rates (~107 μmol/cm2/hr for H2) at near a stoichiometric ratio (H2: O2~ 1.8:1). This study demonstrated that optimizing the doping level and appropriate band engineering of III-nitride NWs is crucial for enhancing their PEC water splitting performance.
  • Catalytically Generating and Utilizing Hydrogen to Reduce NOx Emissions in Automobile Applications

    Alghamdi, Nawaf (2018-11)
    Heterogeneous catalysis is a powerful chemical technology because it can enhance the conversion of reactants, promote selectivity to a desired product, and lower the reaction temperature requirements. The breaking and forming of chemical bonds in heterogeneous catalysis is facilitated on a solid surface where adsorbed gas-phase species react and form products. This study is concerned with utilizing heterogeneous catalysis in the automobile industry via the generation and utilization of hydrogen to reduce NOx emissions. In spark ignition engines, the three-way-catalyst technology is ineffective at the more efficient, lean-burn conditions. In compression-ignition engines, an ammonia-based technology is implemented but has associated high cost and ammonia slip challenges. This motivates providing an alternative technology, such as hydrogen selective catalytic reduction (H2-SCR). In this study, four catalysts were investigated for the lean-burn selective catalytic reduction of NO using hydrogen. The catalysts were platinum (Pt) and palladium (Pd) noble metals supported on cerium oxide (CeO2) and magnesium oxide (MgO). Additionally, finding a source of hydrogen for H2-SCR on board a vehicle is a challenge due to the issues associated with hydrogen storage. A numerical study was performed to investigate the utilization of the partial oxidation of natural gas on a rhodium surface to synthesis gas, CO and H2. A kinetic understanding of natural gas demands an understanding of its components. While methane and ethane have been extensively studied, propane partial oxidation on rhodium has only been kinetically examined at low temperatures. The aim of the numerical study was to obtain an improved understanding of propane partial oxidation kinetics by extending the surface reactions mechanism to high temperatures and developing a gas phase mechanism to capture the effects of gas-phase reactions. Moreover, the optimal temperature and pressure for H2 generation were determined, and the kinetic simulation results were analyzed by temperature sensitivity, chemical path flux and hydrogen production sensitivity analyses.
  • Multiple stressor interaction of nutrient enrichment and crude oil pollution on benthic recruitment on a Red Sea coral reef

    Hulver, Ann (2018-11)
    The Red Sea is one of the warmest, saltiest, and most oligotrophic seas in the world that supports a healthy and extremely diverse coral reef ecosystem. Increasing development along the Saudi Arabian coast may increase eutrophication due to impacts of human population and also oil pollution from increased shipping traffic and refinery activity. The risk of oil pollution combined with increased eutrophication due to coastal development provides a clear stressor interaction which is vastly understudied. Individually, these stressors are known to negatively impact coral reproduction, recruitment, and growth. This study focuses on reef settlement and recovery following experimentally-simulated disturbance scenarios. Carbonate recruitment tiles were placed on the reef and exposed to four treatments: control, nutrient enrichment with slow-release fertilizer, tiles soaked in crude oil, and a combination treatment of nutrient enrichment and oil-coated tiles. At periods of 3, 6, 9, 14, and 17 weeks, tiles were collected to classify the settled community and measure oxygen production. Oil, nitrate, and phosphate were the biggest determining factors predicting settlement and oxygen production of the different treatments. The oil treatment had the least overall settlement and oxygen production, whereas the nutrient treatment had the most turf algal recruitment and oxygen production. The combination treatment had an antagonistic effect on algal growth: the nutrients facilitated growth on the otherwise toxic oiled tiles.
  • A path towards high efficiency using Argon in an HCCI engine

    Mohammed, Abdulrahman (2018-11)
    Argon replacing nitrogen has been examined as a new engine cycle to reach high efficiency. Experiments were carried out under Homogeneous Charge Compression Ignition (HCCI) conditions using a single cylinder variable compression ratio Cooperative Fuel Research (CFR) engine. Isooctane has been used as the fuel for this study. All the parameters were kept fixed but the compression ratio to make the combustion phasing constant. Typical engine outputs and emissions were compared to conventional cycles with both air and synthetic air. It has been found that the compression ratio of the engine must be significantly reduced while using argon due to its higher specific heat ratio. The resulting in-cylinder pressure was lower but combustion remains aggressive. However, greater in-cylinder temperatures were reached. To an end, argon allows gains in fuel efficiency, in unburned hydrocarbon and carbon monoxide, as well as in indicated efficiency. A higher nitrogen oxide concentration while replacing nitrogen by argon was observed but the origin remains to be identified. The concept should therefore be able to reach zero-NOx emissions as no nitrogen should be present.
  • Modeling of Arabian Light Crude Oil Cracking in Two-Zone Fluidized Bed Reactors

    Hijazi, Nibras (2018-11)
    Abstract embargoed until 2023-11-27
  • Atmospheric Water Harvesting by an Anhydrate Salt and Its Release by a Photothermal Process Towards Sustainable Potable Water Production in Arid Regions

    Alsaedi, Mossab K. (2018-11)
    Only 2.5% of the water on Earth is fresh water and only less than 1% is accessible to human consumption. Landlocked and desert communities and communities that are not wealthy enough to provide clean drinking water via conventional water treatment technologies are facing severe water shortages and tend to rely on long distance transportation to supply fresh water for their daily use. As a lot of the water-scarce countries have abundant annual solar irradiation and relatively high humidity, this project proposes a technology that harvests water from ambient air using an anhydrate salt and releases it for collection using sunlight. This technology is designed to be potentially deployed in night-day cycles, as the humidity at night is at its peak, and solar irradiation during the day is also at its peak. In this work, a mesoporous silica powder filled with CuCl2 and coated with carbon nanotubes is used. The water capture performance of this material was investigated with different relative humidity environments. Furthermore, the powder agglomeration sizes of this material were also investigated for each relative humidity environment. Water release was investigated under 1 kW/m2 simulated solar light in an in-lab ~60% relative humidity environment. The results show that this mesoporous material was able to capture water at 12% relative humidity conditions, low enough to capture water from the air in the Sahara Desert. At relative humidity of 15% and 35%, the material was able to absorb 0.12 and 0.25 kg/kg of water, respectively, within 100 minutes, which indicates its fast water harvesting kinetics. A fully hydrated sample released 0.26 kg/kg of water in almost half an hour under 1 kW/m2 simulated sunlight. This project sheds more light on utilizing the atmosphere as an alternative water source.
  • Sand temperature profiles at turtle nesting sites in the Red Sea: implications for hatchling sex ratios

    Tanabe, Lyndsey K. (2018-11)
    Climate change poses a serious threat to species that demonstrate temperature dependent sex determination (TDS), including marine turtles. Increased temperatures can result in highly female skewed sex ratios and decreased hatchling success. In situ sand temperature data was collected from the nesting depth of hawksbill and green turtles at five study sites along the coast of the Red Sea. The sand temperature profile at four of the sites exceeded the pivotal temperature of 29.2°C (commonly cited in literature) throughout the study duration, which suggests feminization of turtles could be occurring, but further studies need to identify the pivotal temperature in this region. The percentage of days exceeding the commonly cited maximum thermal threshold (33 and 35°C) was calculated for each site at 30 and 50 cm. Sand temperature recordings were as high as 36.0°C at 30 cm depth, and 35.3°C at 50 cm. This suggests that the turtle hatchlings in some areas of the Red Sea could already have high mortality rates due to high temperatures, unless they are locally adapted to these high temperatures. The Red Sea is home to five out of the seven extant species of marine turtles in the world, but not much is known about these populations. The Red Sea is an understudied region of the world, but it has the potential to provide insight on how species might adapt to future climate change due to its high and variable water temperatures (range of 20°C to 35°C) and high salinity (40 PSU). Sites with lower sand temperatures (and lower risk of feminization) may represent priority areas for conservation efforts, particularly in regions facing imminent coastal development.
  • How does light affect the heat stress response in Arabidopsis?

    Kim, Eunje (2018-11)
    Light and temperature are two of the most important environmental factors regulating plant development. Although heat stress has been well studied, little is known about the interaction between light and temperature. In this study, we performed phenotypic assays comparing seedling responses to heat under light and dark conditions. Seedlings exposed to heat in the dark show lower survival rates than seedlings stressed in the light. To identify transcriptional changes underlying light-dependent heat tolerance, we used RNA-sequencing. The light-dependent heat stress responses involved a plethora of genes which could be potential candidate genes for light-induced heat tolerance, including transcription factors (bHLH) and genes commonly associated with biotic stress. By using the latest high-throughput phenotyping facility, we found that the light-dependent heat tolerance is reflected more on the maintenance of photosynthetic capacity, rather than leaf temperature. These results provide insights into how light increases heat stress tolerance in Arabidopsis seedlings and suggest its underlying mechanisms.
  • Biological and Biochemical Properties of Two KDM1A Associated Alternatively Spliced SWIRM Domains

    Fadaili, Yara (2018-11)
    LSD1 is the first described histone demethylase which demethylates H3K4me1/2 (Shi et el., 2004), thus, causing transcriptional repression. Alternatively, LSD1 was demonstrated to have H3K9me1/2 demethylase activity when bound by androgen receptor, hence, causing transcriptional activation (Schule et al., 2005). LSD1 is commonly recruited by the so called CoREST core complex including: RCOR1, HDAC1 and HDAC2 among others and therefore is coupled with histone deacetylation and transcriptional repression (Foster et al., 2010). It is an important regulator of pluripotency in early development and it occupies, along with pluripotency factors NANOG and OCT4, the promoters of major lineage determining genes that are poised for activation in the pluripotent state, (Adamo et al., 2011). There are four described isoforms for LSD1: LSD1, LSD1-E2a, LSD1-8a and LSD1-E2a/E8a (Zibetti et al., 2010). While the Cterminus of LSD1 is extensively studied and the function of the isoforms LSD1-E8a and LSD1-E8aE2a is described, there is scarce knowledge on LSD1 N-terminus unstructured region and the SWIRM domain. In this project I examined the role of the differently spliced exon 2a on the function of the SWIRM domain through generation of eight constructs coding for the N-terminal portion of LSD1 SV1 and SV2 fused with a C- or N-terminus FLAG tag. I then performed an immunoprecipitation experiment followed by mass spectrometry and proteomics analysis that led to the identification of previously unknown binding partners to the LSD1 SWIRM domain: NONO and IGF2B3.
  • Single-Copy Insertion of Split-GFP for the Restriction of Germline Expression in Caenorhabditis elegans

    Al Johani, Mohammed (2018-11)
    Gene regulation in C. elegans germ cells depend on transgenerational chromatin modification and small RNA pathways. Germline silencing mechanisms evolved to repress foreign DNA from compromising the transfer of genetic information to progeny. Effective genetic tools that circumvent the silencing machinery will facilitate studies using this model organism. Specifically, translation of heat-shock inducible transgenes is inhibited in the germline making it challenging to transiently express enzymes to modify the genome. Here, we describe a genetic screen design that can be used to identify pathways that prevent germline expression of heat-shock induced transgenes. We use split-GFP (GFP1-10 and GFP11) to confine a genetic screen to germ cells. Stable transgenic lines with germline expression of single-copy integrated GFP11 were produced using MosSCI. The insertion lines will be used in RNAi or chemical mutagenesis screens for the germline de-repression of GFP1-10 expressed under heat-shock promoters. The screen is likely to identify candidate RNAi or chromatin factors involved in repressing heat-shock expression in the germline, particularly from extrachromosomal arrays. Inducible high-level expression in the germline from extrachromosomal arrays would be a valuable tool for large-scale genome engineering.
  • Underwater wireless optical communication system under reciprocal turbulence

    Guo, Yujian (2018-11)
    Underwater communication systems are in high demanded for subaquatic environment activities as the sea is an enormous and mostly unexplored place. The ten-meter long and few giga-bit per second range optical communication technique is feasible and has bright future compared to the mature but low data rate (few kilobits per second) acoustic technology and short distance (several meters) radio-frequency signaling schemes. The underwater wireless optical communication (UWOC) technique takes advantage of wide bandwidth, low attenuation effect in the visible range for multiple applications such as seafloor and offshore exploration, oil pipe control and maintenance, and pipeline leak detection. Nowadays, visible light-emitting diode (LED)-based and laser diode (LD)-based UWOC system are attractive and much related research is being conducted in the field. However, the major challenges of developing UWOC systems are the attenuation, scattering and turbulence effects of the underwater environment. The temperature gradient, salinity gradient, and bubbles make underwater optical channel predictable challenging and degrade the optical beam propagating distance and quality. Most studies focus on the statistical distribution of intensity fluctuations in underwater wireless optical channels with random temperature and salinity variations as well as the presence of air bubbles. In this thesis, we experimentally investigate the reciprocity nature of underwater turbulence caused by the turbidity, air bubbles, temperature variations, and salinity. Bit error rate measurement and statistical data analysis reveal the high reciprocal nature of turbulence that can be induced by the presence of bubbles, temperature, and salinity. The mitigation strategies for the different turbulence scenarios are discussed.

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