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Recent Submissions

  • Synthesis of Chitosan-La2O3 Nanocomposite and Its Utility as a Powerful Catalyst in the Synthesis of Pyridines and Pyrazoles

    Khalil, Khaled D.; Riyadh, Sayed M.; Jaremko, Mariusz; Farghaly, Thoraya A.; Hagar, Mohamed (Molecules, MDPI AG, 2021-06-17) [Article]
    Recently, the development of nanocatalysts based on naturally occurring polysaccharides has received a lot of attention. Chitosan (CS), as a biodegradable and biocompatible polysaccharide, is considered to be an excellent template for the design of a hybrid biopolymer-based metal oxide nanocomposite. In this case, lanthanum oxide nanoparticles doped with chitosan at different weight percentages (5, 10, 15, and 20 wt% CS/La2O3) were prepared via a simple solution casting method. The prepared CS/La2O3 nanocomposite solutions were cast in a Petri dish in order to produce the developed catalyst, which was shaped as a thin film. The structural features of the hybrid nanocomposite film were studied by FTIR, SEM, and XRD analytical tools. FTIR spectra confirmed the presence of the major characteristic peaks of chitosan, which were modified by interaction with La2O3 nanoparticles. Additionally, SEM graphs showed dramatic morphological changes on the surface of chitosan, which is attributed to surface adsorption with La2O3 molecules. The prepared CS/La2O3 nanocomposite film (15% by weight) was investigated as an effective, recyclable, and heterogeneous base catalyst in the synthesis of pyridines and pyrazoles. The nanocomposite used was sufficiently stable and was collected and reused more than three times without loss of catalytic activity.
  • Uncertainty Quantification and Bayesian Inference of Cloud Parameterization in the NCAR Single Column Community Atmosphere Model (SCAM6)

    Pathak, Raju; Dasari, Hari Prasad; El Mohtar, Samah; Subramanian, Aneesh; Sahany, Sandeep; Mishra, Saroj K; Knio, Omar; Hoteit, Ibrahim (Frontiers in Climate, Frontiers, 2021-06-16) [Article]
    Uncertainty quantification (UQ) in weather and climate models is required to assess the sensitivity of their outputs to various parameterization schemes and thereby improve their consistency with observations. Herein, we present an efficient UQ and Bayesian inference for the cloud parameters of the NCAR Single Column Atmosphere Model (SCAM6) using surrogate models based on a polynomial chaos expansion. The use of a surrogate model enables to efficiently propagate uncertainties in parameters into uncertainties in model outputs. We investigated eight uncertain parameters: the auto-conversion size threshold for ice to snow (dcs), the fall speed parameter for stratiform cloud ice (ai), the fall speed parameter for stratiform snow (as), the fall speed parameter for cloud water (ac), the collection efficiency of aggregation ice (eii), the efficiency factor of the Bergeron effect (berg_eff), the threshold maximum relative humidity for ice clouds (rhmaxi), and the threshold minimum relative humidity for ice clouds (rhmini). We built two surrogate models using two non-intrusive methods: spectral projection (SP) and basis pursuit denoising (BPDN). Our results suggest that BPDN performs better than SP as it enables to filter out internal noise during the process of fitting the surrogate model. Five out of the eight parameters (namely dcs, ai, rhmaxi, rhmini, and eii) account for most of the variance in predicted climate variables (e.g., total precipitation, cloud distribution, shortwave and longwave cloud forcing, ice and liquid water path). A first-order sensitivity analysis reveals that dcs contributes approximately 40–80% of the total variance of the climate variables, ai around 15–30%, and rhmaxi, rhmini, and eii around 5–15%. The second- and higher-order effects contribute approximately 20% and 11%, respectively. The sensitivity of the model to these parameters was further explored using response curves. A Markov chain Monte Carlo (MCMC) sampling algorithm was also implemented for the Bayesian inference of dcs, ai, as, rhmini, and berg_eff using cloud distribution data collected at the Southern Great Plains (USA). Our study has implications for enhancing our understanding of the physical mechanisms associated with cloud processes leading to uncertainty in model simulations and further helps to improve the models used for their assessment.
  • Integrated solar-driven PV cooling and seawater desalination with zero liquid discharge

    Wang, Wenbin; Aleid, Sara; Shi, Yifeng; Zhang, Chenlin; Li, Renyuan; Wu, Mengchun; Zhuo, Sifei; Wang, Peng (Joule, Elsevier BV, 2021-06-16) [Article]
    Utilizing the ‘‘waste heat’’ of solar cells for desalination enables the simultaneous production of freshwater and electricity and represents low barrier-of-entry electricity and freshwater supplies to off-grid communities for point of consumption. Herein, guided by theoretical modeling, this project demonstrated that a higher freshwater production rate and a lower solar cell temperature could be achieved simultaneously. With a five-stage photovoltaics-membrane distillation-evaporative crystallizer (PME), we experimentally demonstrated a high and stable freshwater production rate of 2.45 kg m2 h1 and a reduced solar cell temperature of 47 C under 1 sun irradiation, as compared to 62 C of the same solar cell working alone. The reduced solar cell temperature led to an 8% increase in its electricity production. Moreover, the concentrated brine produced in the process was fully evaporated by the underlying evaporative crystallizer, achieving zero liquid discharge. We expect that our work will have important implications for the understanding and advancement of solar distillation.
  • Synthesis, Structural Studies, and Anticancer Properties of [CuBr(PPh3)2(4,6-Dimethyl-2-Thiopyrimidine-κS]

    Babgi, Bandar A.; Alsayari, Jalal; Davaasuren, Bambar; Emwas, Abdul-Hamid M.; Jaremko, Mariusz; Abdellattif, Magda H.; Hussien, Mostafa A. (Crystals, MDPI AG, 2021-06-16) [Article]
    CuBr(PPh3)2(4,6-dimethylpyrimidine-2-thione) (Cu-L) was synthesized by stirring CuBr(PPh3)3 and 4,6-dimethylpyrimidine-2-thione in dichloromethane. The crystal structure of Cu-L was obtained, and indicated that the complex adopts a distorted tetrahedral structure with several intramolecular hydrogen bonds. Moreover, a centrosymmetric dimer is formed by the intermolecular hydrogen bonding of the bromine acceptor created by symmetry operation 1−x, 1−y, 1−z to the methyl group (D3 = C42) of the pyrimidine–thione ligand. HSA-binding of Cu-L and its ligand were evaluated, revealing that Cu-L binds to HSA differently than its ligand. The HSA-bindings were modeled by molecular docking, which suggested that Cu-L binds to the II A domain while L binds between the I B and II A domains. Anticancer activities toward OVCAR-3 and HeLa cell lines were tested and indicated the significance of the copper center in enhancing the cytotoxic effect; negligible toxicities for L and Cu-L were observed towards a non-cancer cell line. The current study highlights the potential of copper(I)-phosphine complexes containing thione ligands as therapeutic agents.
  • Latitudinal variation in monthly-scale reproductive synchrony among Acropora coral assemblages in the Indo-Pacific

    Bouwmeester, Jessica; Edwards, Alasdair J.; Guest, James R.; Bauman, Andrew G.; Berumen, Michael L.; Baird, Andrew H. (Coral Reefs, Springer Science and Business Media LLC, 2021-06-15) [Article]
    Early research into coral reproductive biology suggested that spawning synchrony was driven by variations in the amplitude of environmental variables that are correlated with latitude, with synchrony predicted to break down at lower latitudes. More recent research has revealed that synchronous spawning, both within and among species, is a feature of all speciose coral assemblages, including equatorial reefs. Nonetheless, considerable variation in reproductive synchrony exists among locations and the hypothesis that the extent of spawning synchrony is correlated with latitude has not been formally tested on a large scale. Here, we use data from 90 sites throughout the Indo-Pacific and a quantitative index of reproductive synchrony applied at a monthly scale to demonstrate that, despite considerable spatial and temporal variation, there is no correlation between latitude and reproductive synchrony. Considering the critical role that successful reproduction plays in the persistence and recovery of coral reefs, research is urgently needed to understand the drivers underpinning variation in reproductive synchrony
  • Latitudinal variation in monthly-scale reproductive synchrony among Acropora coral assemblages in the Indo-Pacific

    Bouwmeester, Jessica; Edwards, Alasdair J.; Guest, James R.; Bauman, Andrew G.; Berumen, Michael L.; Baird, Andrew H. (Coral Reefs, Springer Science and Business Media LLC, 2021-06-15) [Article]
    Early research into coral reproductive biology suggested that spawning synchrony was driven by variations in the amplitude of environmental variables that are correlated with latitude, with synchrony predicted to break down at lower latitudes. More recent research has revealed that synchronous spawning, both within and among species, is a feature of all speciose coral assemblages, including equatorial reefs. Nonetheless, considerable variation in reproductive synchrony exists among locations and the hypothesis that the extent of spawning synchrony is correlated with latitude has not been formally tested on a large scale. Here, we use data from 90 sites throughout the Indo-Pacific and a quantitative index of reproductive synchrony applied at a monthly scale to demonstrate that, despite considerable spatial and temporal variation, there is no correlation between latitude and reproductive synchrony. Considering the critical role that successful reproduction plays in the persistence and recovery of coral reefs, research is urgently needed to understand the drivers underpinning variation in reproductive synchrony
  • Plateau–Rayleigh Instability Induced Self-Assembly of Nano-Cubes in Stretched DNA Molecules

    Zhang, Peng; Yang, Zi Qiang; Thoroddsen, Sigurdur T; Di Fabrizio, Enzo (Submitted to MNE2021 - 47th international conference on Micro and Nano Engineering, 2021-06-13) [Preprint]
  • An integrative investigation of sensory organ development and orientation behavior throughout the larval phase of a coral reef fish.

    Majoris, John E.; Foretich, Matthew A; Hu, Yinan; Nickles, Katie R; Di Persia, Camilla L; Chaput, Romain; Schlatter, E; Webb, Jacqueline F; Paris, Claire B; Buston, Peter M (Scientific reports, Springer Science and Business Media LLC, 2021-06-12) [Article]
    The dispersal of marine larvae determines the level of connectivity among populations, influences population dynamics, and affects evolutionary processes. Patterns of dispersal are influenced by both ocean currents and larval behavior, yet the role of behavior remains poorly understood. Here we report the first integrated study of the ontogeny of multiple sensory systems and orientation behavior throughout the larval phase of a coral reef fish-the neon goby, Elacatinus lori. We document the developmental morphology of all major sensory organs (lateral line, visual, auditory, olfactory, gustatory) together with the development of larval swimming and orientation behaviors observed in a circular arena set adrift at sea. We show that all sensory organs are present at hatch and increase in size (or number) and complexity throughout the larval phase. Further, we demonstrate that most larvae can orient as early as 2 days post-hatch, and they swim faster and straighter as they develop. We conclude that sensory organs and swimming abilities are sufficiently developed to allow E. lori larvae to orient soon after hatch, suggesting that early orientation behavior may be common among coral reef fishes. Finally, we provide a framework for testing alternative hypotheses for the orientation strategies used by fish larvae, laying a foundation for a deeper understanding of the role of behavior in shaping dispersal patterns in the sea.
  • Nutrient and temperature constraints on primary production and net phytoplankton growth in a tropical ecosystem

    López-Sandoval, Daffne C.; Duarte, Carlos M.; Agusti, Susana (Limnology and Oceanography, Wiley, 2021-06-12) [Article]
    The Red Sea depicts a north–south gradient of positively correlated temperature and nutrient concentration. Despite its overall oligotrophic characteristics, primary production rates in the Red Sea vary considerably. In this study, based on five cruises and a 2-year time series (2016–2018) sampling in the Central Red Sea, we determined phytoplankton photosynthetic rates (PP) by using 13C as a tracer and derived phytoplankton net growth rates (μ) and chlorophyll a (Chl a)-normalized photosynthesis (PB). Our results indicate a ninefold variation (14–125 mgC m−2 h−1) in depth-integrated primary production and reveal a marked seasonality in PP, PB, and μ. Depth-integrated PP remained <30 mg C m−2 h−1 during spring and summer, and peaked in autumn–winter, particularly in the southernmost stations (~17°N). In surface waters, phytoplankton grew at a slow rate (0.2 ± 0.02 d−1), with the population doubling every 3.5 days, on average. However, during the autumn–winter period, when Chl a concentrations peaked in the central and southern regions, μ increased to values between 0.60 and 0.84 d−1, while PB reached its maximum rate (7.8 mgC [mg Chl a]−1 h−1). We used path analysis to resolve direct vs. indirect components between correlations. Our results show that nutrient availability modulates the photosynthetic performance and growth of phytoplankton communities and that PB and μ fluctuations are not directly associated with temperature changes. Our study suggests that similarly to other oligotrophic warm seas, phosphorus concentration exerts a key role in defining photosynthetic rates and the biomass levels of phytoplankton communities in the region.
  • Living with the enemy: from protein-misfolding pathologies we know, to those we want to know

    Emwas, Abdul-Hamid; Alghrably, Mawadda; Dhahri, Manel; Sharfalddin, Abeer; Alsiary, Rawiah; Jaremko, Mariusz; Faa, Gavino; Campagna, Marcello; Congiu, Terenzio; Piras, Monica; Piludu, Marco; Pichiri, Giuseppina; Coni, Pierpaolo; lachowicz, joanna izabela (Ageing Research Reviews, Elsevier BV, 2021-06-11) [Article]
    Conformational diseases are caused by the aggregation of misfolded proteins. The risk for such pathologies develops years before clinical symptoms appear, and is higher in people with alpha-1 antitrypsin (AAT) polymorphisms. Thousands of people with alpha-1 antitrypsin deficiency (AATD) are underdiagnosed. Enemy-aggregating proteins may reside in these underdiagnosed AATD patients for many years before a pathology for AATD fully develops. In this perspective review, we hypothesize that the AAT protein could exert a new and previously unconsidered biological effect as an endogenous metal ion chelator that plays a significant role in essential metal ion homeostasis. In this respect, AAT polymorphism may cause an imbalance of metal ions, which could be correlated with the aggregation of amylin, tau, amyloid beta, and alpha synuclein proteins in type 2 diabetes mellitus (T2DM), Alzheimer’s and Parkinson’s diseases, respectively.
  • Antiviral activities of flavonoids

    Badshah, Syed Lal; Faisal, Shah; Muhammad, Akhtar; Poulson, Benjamin Gabriel; Emwas, Abdul-Hamid M.; Jaremko, Mariusz (Biomedicine & Pharmacotherapy, Elsevier BV, 2021-06-11) [Article]
    Flavonoids are natural phytochemicals known for their antiviral activity. The flavonoids acts at different stages of viral infection, such as viral entrance, replication and translation of proteins. Viruses cause various diseases such as SARS, Hepatitis, AIDS, Flu, Herpes, etc. These, and many more viral diseases, are prevalent in the world, and some (i.e. SARS-CoV-2) are causing global chaos. Despite much struggle, effective treatments for these viral diseases are not available. The flavonoid class of phytochemicals has a vast number of medicinally active compounds, many of which are studied for their potential antiviral activity against different DNA and RNA viruses. Here, we reviewed many flavonoids that showed antiviral activities in different testing environments such as in vitro, in vivo (mice model) and in silico. Some flavonoids had stronger inhibitory activities, showed no toxicity & the cell proliferation at the tested doses are not affected. Some of the flavonoids used in the in vivo studies also protected the tested mice prophylactically from lethal doses of virus, and effectively prevented viral infection. The glycosides of some of the flavonoids increased the solubility of some flavonoids, and therefore showed increased antiviral activity as compared to the non-glycoside form of that flavonoid. These phytochemicals are active against different disease-causing viruses, and inhibited the viruses by targeting the viral infections at multiple stages. Some of the flavonoids showed more potent antiviral activity than the market available drugs used to treat viral infections.
  • Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea

    Abdulrahman Ashy, Ruba; Suttle, Curtis A.; Agusti, Susana (Microorganisms, MDPI AG, 2021-06-11) [Article]
    Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL−1 and 1.9 to 3.2 × 105 bacteria mL−1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.
  • Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start

    Conchouso Gonzalez, David; Alma’abadi, Amani D.; Behzad, Hayedeh; Alarawi, Mohammed; Hosokawa, Masahito; Nishikawa, Yohei; Takeyama, Haruko; Mineta, Katsuhiko; Gojobori, Takashi (Institute of Electrical and Electronics Engineers (IEEE), 2021-06-11) [Preprint]
    <p>Droplet microfluidics techniques have shown promising results to study single-cells at high throughput. However, their adoption in laboratories studying “-omics” sciences is still irrelevant because of the field’s complex and multidisciplinary nature. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single-cells in droplets at a rate of ~ 250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescent activated droplet sorting (FADS) systems to integrate the use of 4 independent fluorescence-exciting lasers (e.g., 405, 488, 561, 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger was also integrated into our method to enable adding new reagents to already made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput (> 50,000 cells/day) capabilities to mining and bioprospecting metagenomic data.</p>
  • Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization

    Abd El Ghany, Moataz; Barquist, Lars; Clare, Simon; Brandt, Cordelia; Mayho, Matthew; Joffre´, Enrique; Sjöling, Åsa; Turner, A. Keith; Klena, John D.; Kingsley, Robert A.; Hill-Cawthorne, Grant A.; Dougan, Gordon; Pickard, Derek (Microbial Genomics, Microbiology Society, 2021-06-10) [Article]
    Enterotoxigenic Escherichia coli (ETEC) expressing the colonization pili CFA/I are common causes of diarrhoeal infections in humans. Here, we use a combination of transposon mutagenesis and transcriptomic analysis to identify genes and pathways that contribute to ETEC persistence in water environments and colonization of a mammalian host. ETEC persisting in water exhibit a distinct RNA expression profile from those growing in richer media. Multiple pathways were identified that contribute to water survival, including lipopolysaccharide biosynthesis and stress response regulons. The analysis also indicated that ETEC growing in vivo in mice encounter a bottleneck driving down the diversity of colonizing ETEC populations.
  • G3BPs in Plant Stress

    Abulfaraj, Aala A.; Hirt, Heribert; Rayapuram, Naganand (Frontiers in Plant Science, Frontiers Media SA, 2021-06-10) [Article]
    The sessile nature of plants enforces highly adaptable strategies to adapt to different environmental stresses. Plants respond to these stresses by a massive reprogramming of mRNA metabolism. Balancing of mRNA fates, including translation, sequestration, and decay is essential for plants to not only coordinate growth and development but also to combat biotic and abiotic environmental stresses. RNA stress granules (SGs) and processing bodies (P bodies) synchronize mRNA metabolism for optimum functioning of an organism. SGs are evolutionarily conserved cytoplasmic localized RNA-protein storage sites that are formed in response to adverse conditions, harboring mostly but not always translationally inactive mRNAs. SGs disassemble and release mRNAs into a translationally active form upon stress relief. RasGAP SH3 domain binding proteins (G3BPs or Rasputins) are “scaffolds” for the assembly and stability of SGs, which coordinate receptor mediated signal transduction with RNA metabolism. The role of G3BPs in the formation of SGs is well established in mammals, but G3BPs in plants are poorly characterized. In this review, we discuss recent findings of the dynamics and functions of plant G3BPs in response to environmental stresses and speculate on possible mechanisms such as transcription and post-translational modifications that might regulate the function of this important family of proteins.
  • Evolution of memory system-related genes

    Bajaffer, Amal A.; Mineta, Katsuhiko; Gojobori, Takashi (FEBS Open Bio, Wiley, 2021-06-10) [Article]
    Memory has an essential function in human life as it helps individuals remember and recognize their surroundings. It is also the major form of cognition that controls behavior. As memory is a function that is highly characteristic of humans, how it was established is of particular interest. Recent progress in the field of neurosciences, together with the technological advancement of genome-wide approaches, has led to the accumulation of evidence regarding the presence and similar/distinct mechanisms of memory among species. However, the understanding of the evolution of memory obtained utilizing these genome-wide approaches remains unclear. The purpose of this review is to provide an overview of the literature on the evolution of the memory system among species and the genes involved in this process. This review also discusses possible approaches to study the evolution of memory systems to guide future research.
  • CubeSats deliver new insights into agricultural water use at daily and 3 m resolutions

    Aragon Solorio, Bruno Jose Luis; Ziliani, Matteo G.; Houborg, Rasmus; Franz, Trenton E.; McCabe, Matthew (Scientific Reports, Springer Science and Business Media LLC, 2021-06-09) [Article]
    Earth observation has traditionally required a compromise in data collection. That is, one could sense the Earth with high spatial resolution occasionally; or with lower spatial fidelity regularly. For many applications, both frequency and detail are required. Precision agriculture is one such example, with sub-10 m spatial, and daily or sub-daily retrieval representing a key goal. Towards this objective, we produced the first cloud-free 3 m daily evaporation product ever retrieved from space, leveraging recently launched nano-satellite constellations to showcase this emerging potential. Focusing on three agricultural fields located in Nebraska, USA, high-resolution crop water use estimates are delivered via CubeSat-based evaporation modeling. Results indicate good model agreement (r2 of 0.86–0.89; mean absolute error between 0.06 and 0.08 mm/h) when evaluated against corrected flux tower data. CubeSat technologies are revolutionizing Earth observation, delivering novel insights and new agricultural informatics that will enhance food and water security efforts, and enable rapid and informed in-field decision making.
  • Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

    Yoshitake, Kazutoshi; Kimura, Gaku; Sakami, Tomoko; Watanabe, Tsuyoshi; Taniuchi, Yukiko; Kakehi, Shigeho; Kuwata, Akira; Yamaguchi, Haruyo; Kataoka, Takafumi; Kawachi, Masanobu; Ikeo, Kazuho; Tan, Engkong; Igarashi, Yoji; Ohtsubo, Masafumi; Watabe, Shugo; Suzuki, Yutaka; Asakawa, Shuichi; Ishino, Sonoko; Tashiro, Kosuke; Ishino, Yoshizumi; Kobayashi, Takanori; Mineta, Katsuhiko; Gojobori, Takashi (Scientific Reports, Springer Science and Business Media LLC, 2021-06-09) [Article]
    AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.
  • Hydroxycarboxylic Acid Receptor 1 and Neuroprotection in a Mouse Model of Cerebral Ischemia-Reperfusion.

    Buscemi, Lara; Blochet, Camille; Magistretti, Pierre J.; Hirt, Lorenz (Frontiers in physiology, Frontiers Media SA, 2021-06-07) [Article]
    Lactate is an intriguing molecule with emerging physiological roles in the brain. It has beneficial effects in animal models of acute brain injuries and traumatic brain injury or subarachnoid hemorrhage patients. However, the mechanism by which lactate provides protection is unclear. While there is evidence of a metabolic effect of lactate providing energy to deprived neurons, it can also activate the hydroxycarboxylic acid receptor 1 (HCAR1), a Gi-coupled protein receptor that modulates neuronal firing rates. After cerebral hypoxia-ischemia, endogenously produced brain lactate is largely increased, and the exogenous administration of more lactate can decrease lesion size and ameliorate the neurological outcome. To test whether HCAR1 plays a role in lactate-induced neuroprotection, we injected the agonists 3-chloro-5-hydroxybenzoic acid and 3,5-dihydroxybenzoic acid into mice subjected to 30-min middle cerebral artery occlusion. The in vivo administration of HCAR1 agonists at reperfusion did not appear to exert any relevant protective effect as seen with lactate administration. Our results suggest that the protective effects of lactate after hypoxia-ischemia come rather from the metabolic effects of lactate than its signaling through HCAR1.
  • A new Lagrangian-based short-term prediction methodology for high-frequency (HF) radar currents

    Solabarrieta, Lohitzune; Hernández-Carrasco, Ismael; Rubio, Anna; Campbell, Michael F; Esnaola, Ganix; Mader, Julien; Jones, Burton; Orfila, Alejandro (Ocean Science, Copernicus GmbH, 2021-06-04) [Article]
    Abstract. The use of high-frequency radar (HFR) data is increasing worldwide for different applications in the field of operational oceanography and data assimilation, as it provides real-time coastal surface currents at high temporal and spatial resolution. In this work, a Lagrangian-based, empirical, real-time, short-term prediction (L-STP) system is presented in order to provide short-term forecasts of up to 48 h of ocean currents. The method is based on finding historical analogs of Lagrangian trajectories obtained from HFR surface currents. Then, assuming that the present state will follow the same temporal evolution as the historical analog, we perform the forecast. The method is applied to two HFR systems covering two areas with different dynamical characteristics: the southeast Bay of Biscay and the central Red Sea. A comparison of the L-STP methodology with predictions based on persistence and reference fields is performed in order to quantify the error introduced by this approach. Furthermore, a sensitivity analysis has been conducted to determine the limit of applicability of the methodology regarding the temporal horizon of Lagrangian prediction. A real-time skill score has been developed using the results of this analysis, which allows for the identification of periods when the short-term prediction performance is more likely to be low, and persistence can be used as a better predictor for the future currents.

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