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  • Characterizing the role of the BIRD proteins in Solanum lycopersicum L.

    Farran, Ayman (2022-08-17) [Thesis]
    Advisor: Blilou, Ikram
    Committee members: Merzaban, Jasmeen; Rayapuram, Naganand
    The BIRD protein JACKDAW (JKD) belong to the INDETERMINATE DOMAIN (IDD) protein family shown to regulate many developmental processes in plants. JKD encodes a Zinc Finger Protein expressed in the root ground tissue and regulates root patterning in Arabidopsis thaliana (Arabidopsis). Recent and unpublished study indicates that JKD is involved in plant defense response in Arabidopsis. Here we study the JKD function in tomato plants (Solanum lycopersicum). We analyzed the tomato JKD orthologues (Solyc09g007550 (Solyc09) and Solyc10g084180 (Solyc10)) mutant lines, which were generated by Crispr-Cas and TILLING (Targeting Induced Local Lesions in Genomes). Our data indicate that, like in Arabidopsis, Solyc09 controls root ground tissue patterning; the mutant lines show extra cell division in the inner cortex and disturbed stem cell patterning. In addition, we found that both Solyc09 and Solyc10 control the root and stem thickness and regulate tomato leaf shape. To further investigate whether Solyc09 and Solyc10 have a function in tomato when subjected to biotic stress, we evaluated the mutants response to the necrotrophic fungi Botrytis cinerea. We found that the tomato bird mutants have less infection when compared to the control. Taken together our data show that Solyc09 and Solyc10 genes play an essential role in tomato root, shoot development, and in plant immune response to the pathogenic fungi.
  • rde-3 reduces piRNA-mediated silencing and abolishes inherited silencing in C. elegans.

    Priyadarshini, Monika; Al-Harbi, Sarah; Frøkjær-Jensen, Christian (Cold Spring Harbor Laboratory, 2022-08-15) [Preprint]
    Small RNA-mediated silencing of target genes can persist across generations and C. elegans is a well-established model for studying the molecular basis for epigenetic inheritance. We recently developed a piRNA-based inherited silencing assay that causes a high incidence of males by targeting him-5 and him-8. Acute gene silencing is determined in the presence of the piRNAi extra-chromosomal array and inherited silencing after loss of the piRNA trigger. This assay has the advantage of targeting endogenous genes that are easily scored in mutant backgrounds and obviates the need for mutant validation and genetic crosses, which can influence inherited silencing. Here we show an example of the assay by testing acute and inherited piRNA-mediated him-5 silencing in ribonucleotidyltransferase rde-3 (ne3370) mutant animals. In the absence of rde-3, acute silencing was reduced but still detectable, whereas inherited silencing was abolished.
  • Elucidating biofouling over thermal and spatial gradients in seawater membrane distillation in hot climatic conditions

    Elcik, Harun; Alpatova, Alla; Gonzalez-Gil, Graciela; Blankert, Bastiaan; Farhat, Nadia; Amin, Najat A.; Vrouwenvelder, Johannes S.; Ghaffour, NorEddine (Water Research, Elsevier BV, 2022-08-14) [Article]
    Biofouling is a hurdle of seawater desalination that increases water costs and energy consumption. In membrane distillation (MD), biofouling development is complicated due to the temperature effect that adversely affects microbial growth. Given the high relevance of MD to regions with abundant warm seawater, it is essential to explore the biofouling propensity of microbial communities with higher tolerance to elevated temperature conditions. This study presents a comprehensive analysis of the spatial and temporal biofilm distribution and associated membrane fouling during direct contact MD (DCMD) of the Red Sea water. We found that structure and composition of the biofilm layer played a significant role in the extent of permeate flux decline, and biofilms that built up at 45°C had lower bacterial concentration but higher extracellular polymeric substances (EPS) content as compared to biofilms that formed at 55 °C and 65°C. Pore wetting and bacterial passage to the permeate side were initially observed but slowed down as operating time increased. Intact cells in biofilms dominated over the damaged cells at any tested condition emphasizing the high adaptivity of the Red Sea microbial communities to elevated feed temperatures. A comparison of microbial abundance revealed a difference in bacterial distribution between the feed and biofilm samples. A shift in the biofilm microbial community and colonization of the membrane surface with thermophilic bacteria with the feed temperature increase was observed. The results of this study improve our understanding of biofouling propensity in MD that utilizes temperature-resilient feed waters.
  • The first case of artemisinin treatment failure of plasmodium falciparum imported to Oman from Tanzania

    Subudhi, Amit; Bienvenu, Anne-Lise; Bonnot, Guillaume; Abu-Shamma, Reem; Khamis, Faryal; Lawati, Hussain Ali Abdulhussain Al; Picot, Stephane; Petersen, Eskild; Pain, Arnab (Journal of Travel Medicine, Oxford University Press (OUP), 2022-08-12) [Article]
    We present the clinical and genomic epidemiological perspective of the first case of Artesunate treatment failure in an Omani citizen admitted to a hospital in Muscat who originally contracted P. falciparum malaria during travel to Dar Es Salaam, Tanzania.
  • Bubble-Size Distribution and Hydrogen Evolution from Pyrolysis of Hydrocarbon Fuels in a Simulated Ni0.27Bi0.73 Column Reactor

    Angikath Shamsudheen, Fabiyan; Pezzella, Giuseppe; Sarathy, Mani (Industrial & Engineering Chemistry Research, American Chemical Society (ACS), 2022-08-12) [Article]
    This study examines the modeling of hydrocarbon pyrolysis in a Ni0.27Bi0.73 molten metal alloy reactor. The model is executed in two stages. The first stage investigates the effect of the physical properties of the gas and molten liquid on the bubble-size distribution, and determines the Sauter mean bubble diameter in the Ni0.27Bi0.73 column. In this stage, a population-balance-based model using the Euler–Euler approach is coupled with nonreactive computational fluid dynamics in the ANSYS Fluent V17.2 software package. After estimating the Sauter mean diameter, the next stage computes the overall decomposition kinetics of hydrocarbons (gas phase + melt interface) and couples them with an existing hydrodynamic model to determine the final H2 output and selectivity. The Sauter mean diameter was found to increase with increasing superficial gas velocity (or flow rate), liquid density, surface tension, column diameter, and decrease with increasing liquid viscosity. The hydrogen selectivity improved when the model included the surface kinetics, and the hydrogen selectivity of higher hydrocarbons was comparable to (or even higher than) that of pure methane at 1000 °C.
  • Global beta diversity patterns of microbial communities in the surface and deep ocean

    Villarino, Ernesto; Watson, James R.; Chust, Guillem; Woodill, A. John; Klempay, Benjamin; Jonsson, Bror; Gasol, Josep M.; Logares, Ramiro; Massana, Ramon; Giner, Caterina R; Salazar, Guillem; Álvarez-Salgado, Xosé Antón; Catala, Teresa S.; Duarte, Carlos M.; Agusti, Susana; Mauro, Francisco; Irigoien, Xabier; Barton, Andrew D. (Global Ecology and Biogeography, Wiley, 2022-08-11) [Article]
    Aim Dispersal and environmental gradients shape marine microbial communities, yet the relative importance of these factors across taxa with distinct sizes and dispersal capacity in different ocean layers is unknown. Here, we report a comparative analysis of surface and deep ocean microbial beta diversity and examine how these patterns are tied to oceanic distance and environmental gradients. Location Tropical and subtropical oceans (30°N–40°S). Time period 2010–2011. Major taxa studied Prokaryotes and picoeukaryotes (eukaryotes between 0.2 and 3 μm). Methods Beta diversity was calculated from metabarcoding data on prokaryotic and picoeukaryotic microbes collected during the Malaspina expedition across the tropical and subtropical oceans. Mantel correlations were used to determine the relative contribution of environment and oceanic distance driving community beta diversity. Results Mean community similarity across all sites for prokaryotes was 38.9% in the surface and 51.4% in the deep ocean, compared to mean similarity of 25.8 and 12.1% in the surface and deep ocean, respectively, for picoeukaryotes. Higher dispersal rates and smaller body sizes of prokaryotes relative to picoeukaryotes likely contributed to the significantly higher community similarity for prokaryotes compared with picoeukaryotes. The ecological mechanisms determining the biogeography of microbes varied across depth. In the surface ocean, the environmental differences in space were a more important factor driving microbial distribution compared with the oceanic distance, defined as the shortest path between two sites avoiding land. In the deep ocean, picoeukaryote communities were slightly more structured by the oceanic distance, while prokaryotes were shaped by the combined action of oceanic distance and environmental filtering. Main conclusions Horizontal gradients in microbial community assembly differed across ocean depths, as did mechanisms shaping them. In the deep ocean, the oceanic distance and environment played significant roles driving microbial spatial distribution, while in the surface the influence of the environment was stronger than oceanic distance.
  • Photothermal Effects of Terahertz-band and Optical Electromagnetic Radiation on Human Tissues

    Reddy, Innem Venkata Anudeep Kumar; Jornet, Josep; Furlani, Edward (Research Square Platform LLC, 2022-08-11) [Preprint]
    The field of wireless communication has witnessed tremendous advancements in the past few decades, leading to more pervasive and ubiquitous networks. Human bodies are continually exposed to electromagnetic radiation, but typically this does not impact the body as the radiation is non-ionizing and the waves carry low power. However, with progress in the sixth generation (6G) of wireless networks and the adoption of the spectrum above 100~GHz in the next few years, higher power radiation is needed to cover larger areas, exposing humans to stronger and more prolonged radiation. Also, water has a high absorption coefficient at these frequencies and could lead to thermal effects on the skin. Hence, there is a need to study the radiation effects on human tissues, specifically the photothermal effects. In this paper, we present a custom-built, multi-physics model to investigate electromagnetic wave propagation in human tissue and study its subsequent photothermal effects. The proposed finite-element model consists of two segments -- the first one estimates the intensity distribution along the beam path, while the second calculates the increase in temperature due to the wave distribution inside the tissue. We determine the intensity variation in the tissue using the radiative transfer equation and compare the results with Monte Carlo analysis and existing analytical models. The intensity information is then utilized to predict the rise in temperature with a bio-heat transfer module, powered by Pennes' bioheat equation. The model is parametric, and we perform a systematic photothermal analysis to recognize the crucial variables responsible for the temperature growth inside the tissue, particularly for terahertz and near-infrared optical frequencies. Our numerical model can serve as a benchmark for studying the high-frequency radiation effects on complex heterogeneous media such as human tissue.
  • Mesopelagic fishes in a hurry at low latitudes

    Kaartvedt, S; Christiansen, S; Røstad, Anders; Aksnes, DL (Marine Ecology Progress Series, Inter-Research Science Center, 2022-08-11) [Article]
    We studied mesopelagic fishes in the Red Sea (22°N), hypothesizing that the rapid shifts between day and night at low latitudes would translate into rapid vertical migration speeds and brief near-surface ‘antipredation windows’. Using a bottom-moored echosounder, we found that diel vertical migration speeds of acoustical scattering layers were up to double that of the global average. Visits to upper water by some of the layers were strikingly brief, around 10 min, and included unusual rapid ascent and descent (up to 22 cm s-1), apparently with a high degree of behavioral plasticity. We suggest that the behavior of mesopelagic fishes in upper waters relates to their respective light sensitivities but is controlled by the arrival of predators. Rapid shifts between day and night appear to be an inherent factor in structuring marine ecosystems at low latitudes.
  • De novo assembly of the Tamarindus indica genome as part of the Kingdom of Saudi Arabia Native Genome Project

    Navarrete Rodriguez, Maria Eugenia (2022-08-10) [Thesis]
    Advisor: Wing, Rod Anthony
    Committee members: Blilou, Ikram; Merzaban, Jasmeen
    The Kingdom of Saudi Arabia Native Genome project aims to generate genomic resources for all the plants, animals, and associated microbiome species in the Kingdom. Tamarindus indica was pointed out by the MEWA as an endangered native species in the KSA and forms part of the first 15 plant species to be studied in the NGP. A voucher tree was identified in the Rijal Almaa region, from which leaf samples were collected. HMW DNA was extracted from this tissue and sequenced using CCS with the Pac-Bio Sequel II platform. The raw data obtained from the sequencing was assembled using HIFIASM, contaminant contigs were removed, and the 15 largest contigs were selected as the primary T. indica assembly. The genome sequence of Sindora glabra was used as reference guide for primary scaffolding, and T. indica optical maps were used for super-scaffolding. Secondary scaffolding utilized Hi-C data to produce a chromosome level assembly of the T. indica genome. Transposable element analysis and a preliminary annotation were performed on the final assembly. This project represents the first step in studying T. indica for the NGP. The final assembly can be used as a foundation for more genetic studies on this species, as a possible reference for other legume species from the Detarioideae family, and for Neo-domestication and reforestation. The pipeline developed for this project can also be used as a template for sequencing and assembling the remaining species in the NGP.
  • LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes

    Della Valle, Francesco; Reddy, Pradeep; Yamamoto, Mako; Liu, Peng; Saera-Vila, Alfonso; Bensaddek, Dalila; Zhang, Huoming; Prieto Martinez, Javier; Abassi, Leila; Celii, Mirko; Ocampo, Alejandro; Nuñez Delicado, Estrella; Mangiavacchi, Arianna; Aiese Cigliano, Riccardo; Rodriguez Esteban, Concepcion; Horvath, Steve; Belmonte, Juan Carlos Izpisua; Orlando, Valerio (Science Translational Medicine, American Association for the Advancement of Science (AAAS), 2022-08-10) [Article]
    Constitutive heterochromatin is responsible for genome repression of DNA enriched in repetitive sequences, telomeres, and centromeres. During physiological and pathological premature aging, heterochromatin homeostasis is profoundly compromised. Here, we showed that LINE-1 (Long Interspersed Nuclear Element-1; L1) RNA accumulation was an early event in both typical and atypical human progeroid syndromes. L1 RNA negatively regulated the enzymatic activity of the histone-lysine N-methyltransferase SUV39H1 (suppression of variegation 3-9 homolog 1), resulting in heterochromatin loss and onset of senescent phenotypes in vitro. Depletion of L1 RNA in dermal fibroblast cells from patients with different progeroid syndromes using specific antisense oligonucleotides (ASOs) restored heterochromatin histone 3 lysine 9 and histone 3 lysine 27 trimethylation marks, reversed DNA methylation age, and counteracted the expression of senescence-associated secretory phenotype genes such as p16, p21, activating transcription factor 3 (ATF3), matrix metallopeptidase 13 (MMP13), interleukin 1a (IL1a), BTG anti-proliferation factor 2 (BTG2), and growth arrest and DNA damage inducible beta (GADD45b). Moreover, systemic delivery of ASOs rescued the histophysiology of tissues and increased the life span of a Hutchinson-Gilford progeria syndrome mouse model. Transcriptional profiling of human and mouse samples after L1 RNA depletion demonstrated that pathways associated with nuclear chromatin organization, cell proliferation, and transcription regulation were enriched. Similarly, pathways associated with aging, inflammatory response, innate immune response, and DNA damage were down-regulated. Our results highlight the role of L1 RNA in heterochromatin homeostasis in progeroid syndromes and identify a possible therapeutic approach to treat premature aging and related syndromes.
  • PYK2 senses calcium through a disordered dimerization and calmodulin-binding element

    Momin, Afaque Ahmad Imtiyaz; Mendes, Tiago; Barthe, Philippe; Faure, Camille; Hong, Seungbeom; Yu, Piao; Kadaré, Gress; Jaremko, Mariusz; Girault, Jean Antoine; Jaremko, Lukasz; Arold, Stefan T. (Communications Biology, Springer Science and Business Media LLC, 2022-08-09) [Article]
    Multidomain kinases use many ways to integrate and process diverse stimuli. Here, we investigated the mechanism by which the protein tyrosine kinase 2-beta (PYK2) functions as a sensor and effector of cellular calcium influx. We show that the linker between the PYK2 kinase and FAT domains (KFL) encompasses an unusual calmodulin (CaM) binding element. PYK2 KFL is disordered and engages CaM through an ensemble of transient binding events. Calcium increases the association by promoting structural changes in CaM that expose auxiliary interaction opportunities. KFL also forms fuzzy dimers, and dimerization is enhanced by CaM binding. As a monomer, however, KFL associates with the PYK2 FERM-kinase fragment. Thus, we identify a mechanism whereby calcium influx can promote PYK2 self-association, and hence kinase-activating trans-autophosphorylation. Collectively, our findings describe a flexible protein module that expands the paradigms for CaM binding and self-association, and their use for controlling kinase activity.
  • Improving MFI-UF constant flux to more accurately predict particulate fouling in RO systems: Quantifying the effect of membrane surface porosity

    Abunada, Mohanad; Dhakal, Nirajan; Andyar, William Z.; Ajok, Pamela; Smit, Herman; Ghaffour, NorEddine; Schippers, Jan C.; Kennedy, Maria D. (Journal of Membrane Science, Elsevier BV, 2022-08-09) [Article]
    This study aimed to quantify the effect of membrane surface porosity on particulate fouling predicted by the MFI-UF method at constant flux. Firstly, the surface porosity of polyethersulfone UF membranes (5–100 kDa) was determined using ultra-high resolution SEM. Thereafter, the MFI-UF was measured using suspensions of polystyrene particles (75 nm), which were pre-washed to remove surfactant and particle fractions smaller than the pores of MFI-UF membranes, thus ensuring complete retention of particles during MFI-UF measurements. Consequently, the MFI-UF values of washed polystyrene particle suspensions were independent of the pore size and depended only on the surface porosity of MFI-UF membrane. The results showed that the membrane surface porosity decreased with MWCO from 10.5% (100 kDa) to 0.6% (5 kDa), and consequently the MFI-UF increased from 3700 to 8700 s/L2, respectively. This increase in MFI-UF was attributed to the non-uniform distribution of membrane pores, which is exacerbated as surface porosity decreases. Consequently, preliminary correction factors of 0.4–1.0 were proposed for MFI-UF measured with UF membranes in the range 5–100 kDa. Finally, the surface porosity correction was applied to predict particulate fouling in a full-scale RO plant. However, additional research is required to establish correction factors for different types of feed water.
  • Desalination at ambient temperature and pressure by a novel class of biporous anisotropic membrane

    Qtaishat, Mohammed Rasool; Obaid, Mohammed; Matsuura, Takeshi; Al-Samhouri, Areej; Lee, Jung-Gil; Soukane, Sofiane; Ghaffour, NorEddine (Scientific reports, Springer Science and Business Media LLC, 2022-08-09) [Article]
    Recent scientific advances have made headway in addressing pertinient issues in climate change and the sustainability of our natural environment. This study makes use of a novel approach to desalination that is environment friendly, naturally sustainable and energy efficient, meaning that it is also cost efficient. Evaporation is a key phenomenon in the natural environment and used in many industrial applications including desalination. For a liquid droplet, the vapor pressure changes due to the curved liquid-vapor interface at the droplet surface. The vapor pressure at a convex surface in a pore is, therefore, higher than that at a flat surface due to the capillary effect, and this effect is enhanced as the pore radius decreases. This concept inspired us to design a novel biporous anisotropic membrane for membrane distillation (MD), which enables to desalinate water at ambient temperature and pressure by applying only a small transmembrane temperature gradient. The novel membrane is described as a super-hydrophobic nano-porous/micro-porous composite membrane. A laboratory-made membrane with specifications determined by the theoretical model was prepared for model validation and tested for desalination at different feed inlet temperatures by direct contact MD. A water vapor flux as high as 39.94 ± 8.3 L m-2 h-1 was achieved by the novel membrane at low feed temperature (25 °C, permeate temperature = 20 °C), while the commercial PTFE membrane, which is widely used in MD research, had zero flux under the same operating conditions. As well, the fluxes of the fabricated membrane were much higher than the commercial membrane at various inlet feed temperatures.
  • Investigating calcification-related candidates in a non-symbiotic scleractinian coral, Tubastraea spp.

    Capasso, Laura; Aranda, Manuel; Cui, Guoxin; Pousse, Melanie; Tambutté, Sylvie; Zoccola, Didier (Scientific Reports, Springer Science and Business Media LLC, 2022-08-06) [Article]
    In hermatypic scleractinian corals, photosynthetic fixation of CO2 and the production of CaCO3 are intimately linked due to their symbiotic relationship with dinoflagellates of the Symbiodiniaceae family. This makes it difficult to study ion transport mechanisms involved in the different pathways. In contrast, most ahermatypic scleractinian corals do not share this symbiotic relationship and thus offer an advantage when studying the ion transport mechanisms involved in the calcification process. Despite this advantage, non-symbiotic scleractinian corals have been systematically neglected in calcification studies, resulting in a lack of data especially at the molecular level. Here, we combined a tissue micro-dissection technique and RNA-sequencing to identify calcification-related ion transporters, and other candidates, in the ahermatypic non-symbiotic scleractinian coral Tubastraea spp. Our results show that Tubastraea spp. possesses several calcification-related candidates previously identified in symbiotic scleractinian corals (such as SLC4-γ, AMT-1like, CARP, etc.). Furthermore, we identify and describe a role in scleractinian calcification for several ion transporter candidates (such as SLC13, -16, -23, etc.) identified for the first time in this study. Taken together, our results provide not only insights about the molecular mechanisms underlying non-symbiotic scleractinian calcification, but also valuable tools for the development of biotechnological solutions to better control the extreme invasiveness of corals belonging to this particular genus.
  • Performance and implications of forward osmosis-membrane distillation hybrid system for simultaneous treatment of different real produced water streams

    Saqib Nawaz, Muhammad; Alamoudi, Talal; Soukane, Sofiane; Soo Son, Hyuk; Jin, Yong; Medina, Sandra Constanza; Mustakeem, Mustakeem; Gudideni, Veerabhadraiah; Al-Qahtani, Ali; Ghaffour, NorEddine (Chemical Engineering Journal, Elsevier BV, 2022-08-06) [Article]
    This study investigates the simultaneous treatment of different real produced water streams using forward osmosis-membrane distillation (FO-MD) hybrid system. The water–oil separator outlet (WO) was used simultaneously as FO draw solution (DS) and MD feed solution (FS). The FO process generated stable average fluxes of 13.6 L/m2/h and 15.8 L/m2/h with desalter effluent (DE) and wash water (WW) as FO feed streams, while MD produced 13.2 L/m2/h and 11 L/m2/h, respectively. Monovalent ions induced internal concentration polarization and CaSiO3 colloidal scaling on the support layer reduced the FO flux. Further FO flux reduction was caused by CaSO4 and NaCl crystals on the active layer. Moreover, CaSO4 created partial pore covering while oil and grease depicted pore clogging of the MD membrane, which decreased the MD flux. Volatile fatty acids and organic nano pollutants reached MD permeate and FO FS. Humic acid scaling was fully recovered by ethylenediaminetetraacetic acid by masking calcium ions and reducing the pH. No membrane wetting was observed in the system. No bacteria were found in real streams as analyzed with Epifluorescence microscopy, eliminating the potential of microbial fouling. The hybrid system showed > 93 % removal of oil, inorganics and organics, making the permeate quality excellent for re-injection or industrial reuse. The FS streams were concentrated by 77–84 % resulting in smaller disposal volumes. No utilization of chemicals and water makes this hybrid concept practical and sustainable. The findings of this study can serve as design criteria for future onsite pilot plant applications.
  • Spectrochemistry of Firefly Bioluminescence

    Al-Handawi, Marieh B.; Polavaram, Srujana; Kurlevskaya, Anastasiya; Commins, Patrick; Schramm, Stefan; Carrasco-López, César; Lui, Nathan M.; Solntsev, Kyril M.; Laptenok, Siarhei; Navizet, Isabelle; Naumov, Panče (Chemical Reviews, American Chemical Society (ACS), 2022-08-04) [Article]
    The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.
  • A new species of Bathypathes (Cnidaria, Anthozoa, Antipatharia, Schizopathidae) from the Red Sea and its phylogenetic position

    Chimienti, Giovanni; Terraneo, Tullia Isotta; Vicario, Silvia; Marchese, Fabio; Purkis, Sam J.; Abdulla Eweida, Ameer; Rodrigue, Mattie; Benzoni, Francesca (ZooKeys, Pensoft Publishers, 2022-08-04) [Article]
    A black coral, Bathypathes thermophila Chimienti, sp. nov. is described from the Saudi Arabian coasts of the Gulf of Aqaba and north Red Sea (Neom area) using an integrated taxonomic approach. The morphological distinctiveness of the new species is confirmed by molecular analyses. The species thrives in warm and high salinity waters typical of the Red Sea at bathyal depths. It can form colony aggregations on muddy bottoms with scattered, small hard substrates. Colonies are monopodial, feather-like, and attached to a hard substrate through a thorny basal plate. Pinnules are simple, arranged biserially and alternately, and all the same length (up to approximately 20 cm) except for few, proximal ones. Spines are triangular, laterally compressed, subequal, smooth, and simple or rarely bifurcated. Polyps are elongated transversely, 1.5–2.0 mm in transverse diameter. Large colonies can have one or few branches, whose origin is discussed. The phylogenetic position of B. thermophila sp. nov. within the order Antipatharia, recovered using three mitochondrial markers, shows that it is nested within the family Schizopathidae. It is close to species in the genera Parantipathes, Lillipathes, Alternatipathes, and Umbellapathes rather than to the other available representatives of the genus Bathypathes, as currently defined based on morphology. In agreement with previous findings, our results question the evolutionary significance of morphological characters traditionally used to discriminate Antipatharia at higher taxonomic level.
  • Experimental and Numerical Investigation of Polymer Pore-Clogging in Micromodels

    Sugar, Antonia; Serag, Maged F.; Buttner, Ulrich; Fahs, Marwan; Habuchi, Satoshi; Hoteit, Hussein (Elsevier BV, 2022-08-04) [Preprint]
    Polymers have been used effectively in the Oil & Gas Industry for a variety of field applications, such as enhanced oil recovery (EOR), well conformance, mobility control, and others. Polymer intermolecular interactions with the porous rock, in particular, formation clogging and the associated alterations to permeability, is a common problem in the industry. In this work, fluorescent polymers and single-molecule imaging are presented for the first time to assess the dynamic interaction and transport behavior of polymer molecules utilizing a microfluidic device. Pore-scale simulations are performed to replicate the experimental observations. The microfluidic chip, also known as a "Reservoir-on-a-Chip" functions as a 2D surrogate to evaluate the flow processes that take place at the pore-scale. The pore-throat sizes of an oil-bearing reservoir rock, which range from 2 to 10 nm, are taken into consideration while designing the microfluidic chip. Using soft lithography, we created the micromodel from polydimethylsiloxane (PDMS). The conventional use of tracers to monitor polymers has a restriction due to the tendency of polymer and tracer molecules to segregate. For the first time, we develop a novel microscopy method to observe the dynamic behavior of polymer pore-clogging and unclogging processes. We provide direct dynamic observations of polymer molecules during their transport within the aqueous phase and their clustering and accumulations. Pore-scale simulations were carried out to simulate the phenomena using a finite-element simulation tool. The simulations revealed a decline in flow conductivity over time within the flow channels that experienced polymer accumulation and retention, which is consistent with the experimental observation of polymer retention. The performed single-phase flow simulations allowed us to assess the flow behavior of the tagged polymer molecules within the aqueous phase. Additionally, both experimental observation and numerical simulations are used to evaluate the retention mechanisms that emerge during flow and how they affect apparent permeability. This work provides new insights to assessing the mechanisms of polymer retention in porous media.
  • Coverage Enhancement of Underwater Internet of Things Using Multi-Level Acoustic Communication Networks

    Xu, Jiajie; Kishk, Mustafa Abdelsalam; Alouini, Mohamed-Slim (IEEE Internet of Things Journal, Institute of Electrical and Electronics Engineers (IEEE), 2022-08-03) [Article]
    Underwater acoustic communication networks (UACNs) are considered a key-enabler to the underwater internet of things (UIoT). UACN is regarded as essential for various marine applications such as monitoring, exploration, and trading. However, a large part of existing literature disregards the 3-dimensional (3D) nature of the underwater communication system. In this paper, we propose a K-tier UACN that acts as a gateway that connects the UIoT with the Space-Air-Ground-Sea Integrated System (SAGSIS). The proposed network architecture consists of several tiers along the vertical direction with adjustable depths. On the horizontal dimension, the best coverage probability (CP) is computed and maximized by optimizing the densities of surface stations (SSs) in each tier. On the vertical dimension, the depth of each tier is also optimized to minimize inter-tier interference and maximize overall system performance. Using tools from stochastic geometry, the total CP of the proposed K-tier network is analyzed. For given spatial distribution of UIoT device’s depth, the best CP can be achieved by optimizing the depths of the transceivers connected to the SSs through a tether. We verify the accuracy of the analysis using Monte-Carlo simulations. In addition, we draw multiple useful system-level insights that help optimize the design of underwater 3D networks based on the given distribution of UIoT device’s depths.
  • Differential role of neuronal glucose and PFKFB3 in memory formation during development

    Cruz, Emmanuel; Bessières, Benjamin; Magistretti, Pierre J.; Alberini, Cristina M (Glia, 2022-08-02) [Article]
    The consumption of glucose in the brain peaks during late childhood; yet, whether and how glucose metabolism is differentially regulated in the brain during childhood compared to adulthood remains to be understood. In particular, it remains to be determined how glucose metabolism is involved in behavioral activations such as learning. Here we show that, compared to adult, the juvenile rat hippocampus has significantly higher mRNA levels of several glucose metabolism enzymes belonging to all glucose metabolism pathways, as well as higher levels of the monocarboxylate transporters MCT1 and MCT4 and the glucose transporters endothelial-GLUT1 and GLUT3 proteins. Furthermore, relative to adults, long-term episodic memory formation in juvenile animals requires significantly higher rates of aerobic glycolysis and astrocytic-neuronal lactate coupling in the hippocampus. Only juvenile but not adult long-term memory formation recruits GLUT3, neuronal 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and more efficiently engages glucose in the hippocampus. Hence, compared to adult, the juvenile hippocampus distinctively regulates glucose metabolism pathways, and formation of long-term memory in juveniles involves differential neuronal glucose metabolism mechanisms.

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