2,453 Works

Data from: Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment

Eva Aylagas, Angel Borja, Xabier Irigoien & Naiara Rodriguez-Ezpeleta
Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing represents an alternative to rapidly, accurately and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive...

Data from: Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

Weipeng Zhang, Renmao Tian, Yang Bo, Huiluo Cao, Lin Cai, Lianguo Chen, Guowei Zhou, Jin Sun, Xixiang Zhang, Abdulaziz Al-Suwailem & Pei-Yuan Qian
The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep-sea environments. Using artificial surface-based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment...

Data from: Ecomorphological convergence in planktivorous surgeonfishes

Sarah T. Friedman, Samantha A. Price, Andrew S. Hoey & Peter C. Wainwright
Morphological convergence plays a central role in the study of evolution. Often induced by shared ecological specialization, homoplasy hints at underlying selective pressures and adaptive constraints that deterministically shape the diversification of life. Though midwater zooplanktivory has arisen in adult surgeonfishes (family Acanthuridae) at least four independent times, it represents a clearly specialized state, requiring the capacity to swiftly swim in midwater locating and sucking small prey items. While this diet has commonly been associated...

Insights into bacterial community changes following heat and salinity treatments in Aiptasia

Janna L. Randle
Coral bleaching, i.e. the loss of photosynthetic algal symbionts, caused by ocean warming is now the main factor driving reef decline, but not all corals are affected equally. Corals from the Arabian Seas have unusually high temperature tolerances, and recently studies implicated salinity as one of the contributing factors. In particular, a recent heat stress experiment at different salinities using the model system Aiptasia and Red Sea corals, showed that cnidaria at large bleach less...

Investigating Spatial Patterns of Variability in Bacterial Communities Inhabiting Arid Avicennia marina Forests

Timothy Thomson
Mangrove forests provide a suite of critical ecosystem services ranging from local to global scales.Soil conditions and associated micro-organisms play a fundamental role in maintaining these services, that include nutrient cycling, carbon sequestration and plant growth-promoting properties. Despite its importance, the microbial abundance and function of mangrove soil has received little effort in current research. On the ecotone between the land and the sea, mangrove soils are subject to high variability of geomorphological and ecological...

Comparative metabolic modeling and analysis of human pathogens

Alyaa M. Abdel-Haleem
Infectious diseases continue to be major health concerns worldwide. Although major advances have led to accumulation of genomic data about human pathogens, there clearly exists a gap between genome information and studies aiming at identifying potential drug targets. Here, constraint-based modeling (CBM) was deployed to integrate disparate data types with genome-scale metabolic models (GEMs) to advance our understanding of the pathogenesis of infectious agents with respect to identifying and prioritizing drug targets. Specifically, genome-scale metabolic...

Improving the Quality of Seismic Images by Deterministic Inversion and Machine Learning Methods

Yuqing Chen
This thesis develops five novel methods for seismic imaging and inversion to improve both their computational efficiency and accuracy. Three of them improve the accuracy of the final inverted images by novel preconditioning strategies, and the other two are machine learning (ML) methods applied to seismic data. 1. Conventional viscoacoustic least-squares reverse time migration, also denoted as Q-LSRTM, suffers from slow-convergence and low-resolution problems due to the attenuative property of the adjoint Q propagators. To...

Real-Space Imaging of Charge Carrier Dynamics in Photoactive Materials by 40 Scanning Ultrafast Electron Microscopy

Basamat S. Shaheen
Surfaces of photoactive materials play a pivotal role in determining the interfacial properties and the photoconversion efficiency of optoelectronic devices. On the other hand, the fundamental photophysical processes of photo-generated carriers and their transport and recombination occur at extremely short timescales ranging from femtoseconds to nanoseconds. In order to provide a complete picture about the best working conditions of photoactive materials to improve their device performance, it is very essential to explore and decipher the...

Advanced MTJ Sensory Devices for Industrial and Healthcare Applications

Yousof Mashraei
Magnetic sensors are deployed in many applications such as automotive, consumer electronics, navigation and data storage devices. Their market’s growth is driven by demands of higher performance; primarily to assist in the advancement of the Internet of Things (IoT) and smart systems. Challenging obstacles of miniaturization and power consumptions must be overcome. A leading sensor that has the potential to accelerate the development is the magnetic tunnel junction (MTJ) devices. Corrosion causes catastrophic consequences for...

Identification of MALAT1 as a PRC2-Ezh1 Associated lncRNA Essential for Epigenetic Control of Skeletal Muscle Adaptation and Plasticity

Nadine H. El Said
Polycomb Proteins (PcG) are chromatin proteins that control the maintenance of “transcriptional memory” and cell identity by fixing the repressed state of developmentally regulated genes. This function has been linked to interaction with RNA moieties, in particular long non-coding RNAs (lncRNAs). However, specificity of PcG-RNA interactions has been controversial (Beltran et al., 2016; Chen Davidovich, Leon Zheng, Karen J. Goodrich, & Thomas R. Cech, 2013). In this study we took advantage of recent work published...

Additively Manufactured Conformal Microwave Sensors for Applications in Oil Industry

Muhammad Akram Karimi
Depleting oil reserves and fluctuating oil prices have necessitated to increase the efficiency of oil production process. This thesis is focused on developing low-cost sensors, which can increase oil production efficiency through real-time monitoring of oil wells and help in safe transport of oil products from the wells to the refineries. Produced fluid from an oil well is a complex mixture of oil, water and gases, which needs to be quantified for various strategic and...

Interactive High-Quality Visualization of Large-Scale Particle Data

Mohamed Ibrahim
Large-scale particle data sets, such as those computed in molecular dynamics (MD) simulations, are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles can be perceived well in close-up views. However, for large-scale simulations with millions of particles, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to...

Towards Supported Nitrogen Containing Fragments on Silica Surface for Catalytic Applications

Maha A. Aljuhani
This thesis shed lights on metal-nitrogen organometallic fragments supported on silica surface for catalytic applications. It Focuses on group IV and V metal transition as a well-defined single-site catalysts, specifically titanium, hafnium, and tantalum to utilize them in the development of selective heterogeneous catalysis for imine metathesis, hydroamination and hydroaminoalkylation of olefins and alkynes. Developing new metal-nitrogen containing fragments by using easily available and abundant precursors which is silica SiO2 and metal amides complexes. Here,...

Organic Semiconductor Nanoparticle Photocatalysts for Hydrogen Evolution from Water

Jan Kosco
Photocatalytic water splitting using solar irradiation has the potential to produce sustainable hydrogen fuel on a large scale. Practical solar energy conversion requires the development of new, stable photocatalysts that operate efficiently under a broad range of visible wavelengths. Organic semiconductors are increasingly being employed as photocatalysts due to their earth abundance, aqueous stability, and optical absorptions that can be tuned to the solar spectrum. However, much remains unknown about the mechanism of organic semiconductor...

Spectro-Electrochemical Study of Staging in Graphitic Electrodes for Aluminum Batteries

Shianlin Wee
After three decades of commercialization, graphite remains the preferred active material for intercalation-type Li-ion battery anodes. Still, the characterization of staging continues to be elusive at the sub-micro- and nano-scales, the typical dimensions of graphite crystallites. Here, the intercalation of Al-based anions in graphitic materials was studied using X-ray powder diffraction (XRD) and Raman spectroscopy. While, in the first case, the analysis was done ex-situ and in mm3-samples, a more localized view was provided by...

Investigating The Molecular Functions of The Os-Sc106 Spliceosomal Protein Via CRISPR/Cas9 System

Abdulrahman Alhabsi
Plants employ sophisticated molecular machineries to fine-tune their responses to growth, developmental, and stress cues. Plants cellular response influences gene expression through regulating processes like transcription and splicing. To increase the genome coding potential and further regulate the expression, pre-mRNA is alternatively spliced. Serine/Arginine-rich (SR) proteins, a family of pre-mRNA splicing factors, recognize splicing cis-elements and regulate both constitutive and alternative splicing. Recent studies reported only 22 SR proteins encoded in the genome of rice...

Atomically Precise Silver Nanoclusters: Controlled Synthesis and Assembly into Structurally Diverse Frameworks with Tailored Optical Properties

Mohammad Jaber Alhilaly
Ligand-protected metal nanoclusters (NCs), which are ultra-small nanoparticles marked by their atomic precision, are distinctly importance for contemporary nanomaterials. NCs have attracted significant research attention for utilizing their novel optical and physicochemical properties in various applications, including fluorescence sensing, catalysis, and biomedical applications. This dissertation deals with ligand-protected atomically precise silver NCs and is divided into two main parts. The first part is focused on the exploration and design of well-defined silver NCs through surface...

Drag reduction by gas layers and streamlined air cavities attached to free-falling spheres

Aditya Jetly
The general objective of this thesis is to conduct experiments on sphere free-falling in liquid that advance our understanding of the drag reduction on solids moving in liquid by means of lubricating gas layers and attached streamlined air cavities. Part I of the thesis investigates the effect of thin air layers, naturally sustained on superhydrophobic surfaces, on the terminal velocity and drag force of metallic spheres free- falling in water. The surface of 20 mm...

Design and evaluation of hybrid plasmonic nanostructures towards materialization of SERS sensors

Phuong Hoang
Optical sensors based on Surface-enhanced Raman scattering (SERS) effect are among the most versatile sensors due to their ability to characterize samples in various states of matter. The appeal of the SERS sensors lies in the molecular “fingerprint” specificity, sensitivity, and the non-invasive nature of the analysis. Although the current state of art SERS sensors have advanced toward ultrasensitivity with single-molecule detection limit, ultrafast analysis at femtosecond and sub-nanometer resolution, the application of these innovations...

Designing Electrochemical Systems for Energy Conversion

Keisuke Obata
Electrochemical water splitting to hydrogen and oxygen is an attractive approach to store and convert intermittent renewable energy sources. Energy efficient, cost effective and durable electrochemical systems are highly required. Firstly, CeOx coated oxygen evolution electrocatalysts were developed to improve the stability. Unique permselectivity of the CeOx layer was disclosed, which helps to prevent dissolution of active metal site. Because oxygen evolution reaction requires a higher overpotential than hydrogen evolution reaction, kinetically facile oxidation of...

Simultaneous Lightwave Information and Power Transfer (SLIPT)

José Ilton De Oliveira Filho
Harvesting energy became one of the most prominent research topics around the world, not only for research institutes and universities but also for technology companies as well. Mainly focused on internet of things (IoT) applications, harvesting energy is a crucial factor for reducing costs that come with the use of batteries and increasing the devices’ working time. Simultaneous lightwave information and power transfer is a technique that seeks to use wireless optical communication to achieve...

Designing Surfaces for Enhanced Water Condensation and Evaporation

Yong Jin
With the increasing pressure of providing reliable potable water in a sustainable way, it is important to understand water phase change phenomena (condensation and evaporation) as the water phase change is involved in many processes such as membrane distillation and solar still which can be a feasible choice of supplementing the present potable water access. In the present thesis, we first elucidate the role of wettability of water condensation substrate by combining the droplet growth...

Determining Signaling Pathways involved in Migration of Hematopoietic Stem Cells upon binding of E-selectin

Ioannis Isaioglou
E-selectin is a transmembrane endothelium adhesion protein involved in rolling, arrest and migration of leukocytes as well as in the metastasis of many cancer types. Previous reports suggested that the interactions between E-selectin and its ligands transduce signals into migrating leukocytes and in E-selectin expressing endothelial cells. This study investigates the signaling pathways involved in E-selectin binding to ligands on leukocytes. Using recombinant soluble E-selectin constructs, we simulated the binding of E-selectin to its ligand(s)...

Antibiotic resistance genes and antibiotic resistant bacteria as emerging contaminants in wastewater: fate and persistence in engineered and natural environments

David Mantilla Calderon
The emergence and rapid spread of antimicrobial resistance (AMR) is a phenomenon that extends beyond clinical settings. AMR has been detected in multiple environmental compartments, including agricultural soils and water bodies impacted by wastewater discharges. The purpose of this research project was to evaluate what factors could influence the environmental persistence of antibiotic resistance genes (ARGs), as well as to identify potential strategies employed by human pathogens to survive in secondary environment outside the host....

A functional group approach for predicting fuel properties

Abdul Gani Abdul Jameel
Experimental measurement of fuel properties are expensive, require sophisticated instrumentation and are time consuming. Mathematical models and approaches for predicting fuel properties can help reduce time and costs. A new approach for characterizing petroleum fuels called the functional group approach was developed by disassembling the innumerable fuel molecules into a finite number of molecular fragments or ‘functional groups’. This thesis proposes and tests the following hypothesis, Can a fuels functional groups be used to predict...

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