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  • Integrative systematics of the scleractinian coral genera Caulastraea , Erythrastrea and Oulophyllia

    Arrigoni, Roberto; Huang, Danwei; Berumen, Michael L.; Budd, Ann F.; Montano, Simone; Richards, Zoe; Terraneo, Tullia Isotta; Benzoni, Francesca (Zoologica Scripta, Wiley, 2021-03-02) [Article]
    Modern systematics integrating molecular and morphological data has greatly improved our understanding of coral evolutionary relationships during the last two decades and led to a deeply revised taxonomy of the order Scleractinia. The family Merulinidae (Cnidaria: Scleractinia) was recently subjected to a series of revisions following this integrated approach but the phylogenetic affinities of several genera ascribed to it remain unknown. Here, we partially fill this gap through the study of 89 specimens belonging to all 10 valid species from four genera (Caulastraea, Erythrastrea, Oulophyllia and Dipsastraea) collected from 14 localities across the Indo-Pacific realm. Four molecular loci (histone H3, COI, ITS and IGR) were sequenced, and a total of 44 skeletal morphological characters (macromorphology, micromorphology and microstructure) were analysed. Molecular phylogenetic analyses revealed that the phaceloid Caulastraea species are split into two distinct lineages. A species previously ascribed to the genus Dipsastraea, Dipsastraea maxima, is also recovered in one on these lineages. Furthermore, Erythrastrea is nested within Oulophyllia. The molecular reconstructions of evolutionary relationships are further corroborated by multiscale morphological evidence. To resolve the taxonomy of these genera, Astraeosmilia is resurrected to accommodate Astraeosmilia connata, Astraeosmilia curvata, Astraeosmilia tumida and Astraeosmilia maxima, with Caulastraea retaining Caulastraea furcata and Caulastraea echinulata. Based on the examination of type material, Erythrastrea flabellata is considered an objective synonym of Lobophyllia wellsi, which is transferred to Oulophyllia following the obtained morpho-molecular results. This work further confirms that an integrated morpho-molecular approach based on a rigorous phylogenetic framework is fundamental for an objective classification that reflects the evolutionary history of scleractinian corals.
  • Enabling a large-scale assessment of litter along Saudi Arabian red sea shores by combining drones and machine learning.

    Martin, Cecilia; Zhang, Qiannan; Zhai, Dongjun; Zhang, Xiangliang; Duarte, Carlos M. (Environmental pollution (Barking, Essex : 1987), Elsevier BV, 2021-03-02) [Article]
    Beach litter assessments rely on time inefficient and high human cost protocols, mining the attainment of global beach litter estimates. Here we show the application of an emerging technique, the use of drones for acquisition of high-resolution beach images coupled with machine learning for their automatic processing, aimed at achieving the first national-scale beach litter survey completed by only one operator. The aerial survey had a time efficiency of 570 ± 40 m2 min-1 and the machine learning reached a mean (±SE) detection sensitivity of 59 ± 3% with high resolution images. The resulting mean (±SE) litter density on Saudi Arabian shores of the Red Sea is of 0.12 ± 0.02 litter items m-2, distributed independently of the population density in the area around the sampling station. Instead, accumulation of litter depended on the exposure of the beach to the prevailing wind and litter composition differed between islands and the main shore, where recreational activities are the major source of anthropogenic debris.
  • Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods.

    Sysoev, Maksim; Grötzinger, Stefan W.; Renn, Dominik; Eppinger, Jörg; Rueping, Magnus; Karan, Ram (Frontiers in microbiology, Frontiers Media SA, 2021-03-01) [Article]
    Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
  • Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline

    Michoud, Gregoire; Ngugi, David; Barozzi, Alan; Merlino, Giuseppe; Calleja Cortes, Maria de Lluch; Delgado-Huertas, Antonio; Moran, Xose Anxelu G.; Daffonchio, Daniele (The ISME Journal, Springer Science and Business Media LLC, 2021-03-01) [Article]
    AbstractDeep-sea hypersaline anoxic basins are polyextreme environments in the ocean’s interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine–seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.
  • Seaweed farms provide refugia from ocean acidification.

    Xiao, Xi; Agusti, Susana; Yu, Yan; Huang, Yuzhou; Chen, Weizhou; Hu, Jing; Li, Chao; Li, Ke; Wei, Fangyi; Lu, Yitian; Xu, Caicai; Chen, Zepan; Liu, Shengping; Zeng, Jiangning; Wu, Jiaping; Duarte, Carlos M. (The Science of the total environment, Elsevier BV, 2021-02-28) [Article]
    Seaweed farming has been proposed as a strategy for adaptation to ocean acidification, but evidence is largely lacking. Changes of pH and carbon system parameters in surface waters of three seaweed farms along a latitudinal range in China were compared, on the weeks preceding harvesting, with those of the surrounding seawaters. Results confirmed that seaweed farming is efficient in buffering acidification, with Saccharina japonica showing the highest capacity of 0.10 pH increase within the aquaculture area, followed by Gracilariopsis lemaneiformis (ΔpH = 0.04) and Porphyra haitanensis (ΔpH = 0.03). The ranges of pH variability within seaweed farms spanned 0.14-0.30 unit during the monitoring, showing intense fluctuations which may also help marine organisms adapt to enhanced pH temporal variations in the future ocean. Deficit in pCO2 in waters in seaweed farms relative to control waters averaged 58.7 ± 15.9 μatm, ranging from 27.3 to 113.9 μatm across farms. However, ΔpH did not significantly differ between day and night. Dissolved oxygen and Ωarag were also elevated in surface waters at all seaweed farms, which are benefit for the survival of calcifying organisms. Seaweed farming, which unlike natural seaweed forests, is scalable and is not dependent on suitable substrate or light availability, could serve as a low-cost adaptation strategy to ocean acidification and deoxygenation and provide important refugia from ocean acidification.
  • The Importance of Thermal Treatment on Wet-Kneaded Silica–Magnesia Catalyst and Lebedev Ethanol-to-Butadiene Process

    Chung, Sang-Ho; Galilea, Adrian; Shoinkhorova, Tuiana; Mukhambetov, Ildar; Abou-Hamad, Edy; Telalovic, Selevedin; Gascon, Jorge; Ruiz-Martinez, Javier (Nanomaterials, MDPI AG, 2021-02-26) [Article]
    The Lebedev process, in which ethanol is catalytically converted into 1,3-butadiene, is an alternative process for the production of this commodity chemical. Silica–magnesia (SiO2–MgO) is a benchmark catalyst for the Lebedev process. Among the different preparation methods, the SiO2–MgO catalysts prepared by wet-kneading typically perform best owing to the surface magnesium silicates formed during wet-kneading. Although the thermal treatment is of pivotal importance as a last step in the catalyst preparation, the effect of the calcination temperature of the wet-kneaded SiO2–MgO on the Lebedev process has not been clarified yet. Here, we prepared and characterized in detail a series of wet-kneaded SiO2–MgO catalysts using varying calcination temperatures. We find that the thermal treatment largely influences the type of magnesium silicates, which have different catalytic properties. Our results suggest that the structurally ill-defined amorphous magnesium silicates and lizardite are responsible for the production of ethylene. Further, we argue that forsterite, which has been conventionally considered detrimental for the formation of ethylene, favors the formation of butadiene, especially when combined with stevensite.
  • The global network of ports supporting high seas fishing

    Rodríguez, J. P.; Fernández-Gracia, Juan; Duarte, Carlos M.; Irigoien, Xabier; Eguíluz, V. M. (Science Advances, American Association for the Advancement of Science (AAAS), 2021-02-26) [Article]
    Fisheries in waters beyond national jurisdiction (“high seas”) are difficult to monitor and manage. Their regulation for sustainability requires critical information on how fishing effort is distributed across fishing and landing areas, including possible border effects at the exclusive economic zone (EEZ) limits. We infer the global network linking harbors supporting fishing vessels to fishing areas in high seas from automatic identification system tracking data in 2014, observing a modular structure, with vessels departing from a given harbor fishing mostly in a single province. The top 16% of these harbors support 84% of fishing effort in high seas, with harbors in low- and middle-income countries ranked among the top supporters. Fishing effort concentrates along narrow strips attached to the boundaries of EEZs with productive fisheries, identifying a free-riding behavior that jeopardizes efforts by nations to sustainably manage their fisheries, perpetuating the tragedy of the commons affecting global fishery resources.
  • Superconductivity and High-Pressure Performance of 2D Mo2C Crystals

    Zhang, Junli; Cao, Zhen; He, Xin; Liu, Wenhao; Wen, Yan; Cavallo, Luigi; Ren, Wencai; Cheng, Huiming; Zhang, Xixiang (The Journal of Physical Chemistry Letters, American Chemical Society (ACS), 2021-02-26) [Article]
    Two-dimensional (2D) materials have attracted significant attention for their ability to support novel magneto-electrical transport and their optical and magnetic properties, of which their superconductivity is particularly of interest. Here we report on the behavior of superconductivity in 2D Mo2C crystals when hydrostatic pressure is applied, which has not yet been described in the literature. We found that the localization of boundary atoms disorder-induced Cooper pairs can suppress the superconducting transition temperature (Tc) as effectively as a magnetic field and current. We observed that the Tc initially decreased as the pressure increased to 1.75 GPa but then began to increase as the pressure increased further to 2.5 GPa. Our density functional theory calculations revealed that this behavior was linked to the modulation of the strength of the electron-phonon coupling and the electron property, which was triggered by compression of the lattice under high pressure. We attributed the inflection point in the hydrostatic pressure-dependent Tc curve to the structural phase transition of Mo2C from a hexagonal to an orthorhombic structure. This work presents a new avenue for the study of the superconductivity of Mo2C, which can be extended to apply to other 2D superconductors to modulate their electronic states.
  • Layer number dependent ferroelasticity in 2D Ruddlesden–Popper organic-inorganic hybrid perovskites

    Xiao, Xun; Zhou, Jian; Song, Kepeng; Zhao, Jingjing; Zhou, Yu; Rudd, Peter Neil; Han, Yu; Li, Ju; Huang, Jinsong (Nature Communications, Springer Science and Business Media LLC, 2021-02-26) [Article]
    AbstractFerroelasticity represents material domains possessing spontaneous strain that can be switched by external stress. Three-dimensional perovskites like methylammonium lead iodide are determined to be ferroelastic. Layered perovskites have been applied in optoelectronic devices with outstanding performance. However, the understanding of lattice strain and ferroelasticity in layered perovskites is still lacking. Here, using the in-situ observation of switching domains in layered perovskite single crystals under external strain, we discover the evidence of ferroelasticity in layered perovskites with layer number more than one, while the perovskites with single octahedra layer do not show ferroelasticity. Density functional theory calculation shows that ferroelasticity in layered perovskites originates from the distortion of inorganic octahedra resulting from the rotation of aspherical methylammonium cations. The absence of methylammonium cations in single layer perovskite accounts for the lack of ferroelasticity. These ferroelastic domains do not induce non-radiative recombination or reduce the photoluminescence quantum yield.
  • Surrogate formulation and molecular characterization of sulfur species in vacuum residues using APPI and ESI FT-ICR mass spectrometry

    Abdul Jameel, Abdul Gani; Alquaity, Awad B.S.; Campuzano, Felipe; Emwas, Abdul-Hamid M.; Saxena, Saumitra; Sarathy, Mani; Roberts, William L. (Fuel, Elsevier BV, 2021-02-26) [Article]
    Vacuum residues (VR) are the bottom of the barrel products left after vacuum distillation of crude oils. VR are primarily used as feedstock for production of syn-gas and hydrogen via gasification; and heavy fuel oil (HFO) for use as fuel in power generation and shipping. However, VR contain relatively large amounts of sulfur (upto 8% by mass) and require the removal of varying amounts depending on the emission norms (eg. International Maritime Organization 2020 sulfur regulations). Understanding the fuel molecular structure and, in particular, the structure of sulfur species enables the adoption and optimization of suitable desulfurization strategies. In the present work, detailed molecular characterization of the sulfur species in VR was performed using positive ion atmospheric pressure photoionization (APPI) and electrospray ionization (ESI) coupled to Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS). Ions possessing mass to charge (m/z) in the range of 100 to 1200 were detected using the ultra-high resolution instrument and were resolved into unique chemical formulas (CcHhSsNnOo). The assigned masses were then divided into molecular classes based on the presence of heteroatoms, and plots of carbon number versus double bond equivalency (DBE) were made for each molecular class. The molecular classes were further sub-divided based on the presence of sulfur families like sulfides (Su), thiophenes (Th), benzothiophenes (BT), dibenzothiophenes (DBT) and benzonaphthothiophene (BNT) and their derivatives. A single surrogate molecule that represents the average structure of the VR sample was then designed based on the average molecular parameters (AMP) obtained from APPI and ESI FT-ICR MS. Plausible core skeletal structures of VR were drawn from the average DBE value, and then a symmetrical, alkylated, polyaromatic sulfur heterocycles (PASH) molecule was formulated as the VR surrogate. A number of physical and thermo-chemical properties of the VR surrogate were then predicted using quantitative structure property relationships (QSPR). The VR surrogate proposed here will enable high-fidelity computational studies, including chemical kinetic modeling, property estimation, and emissions modeling.
  • NMR-based metabolomics with enhanced sensitivity

    Chandra, Kousik; Al-Harthi, Samah; Sukumaran, Sujeesh; Almulhim, Fatimah F.; Emwas, Abdul-Hamid M.; Atreya, Hanudatta S.; Jaremko, Lukasz; Jaremko, Mariusz (RSC Advances, Royal Society of Chemistry (RSC), 2021-02-25) [Article]
    NMR-based metabolomics, which emerged along with mass spectrometry techniques, is the preferred method for studying metabolites in medical research and food industries. However, NMR techniques suffer from inherently low sensitivity, regardless of their superior reproducibility. To overcome this, we made two beneficial modifications: we detuned the probe to reach a position called “Spin Noise Tuning Optimum” (SNTO), and we replaced the conventional cylindrical 5 mm NMR tube with an electric field component-optimized shaped tube. We found that concerted use of both modifications can increase the sensitivity (signal to noise ratio per unit volume) and detection of metabolites and decrease the measurement time by order of magnitude. In this study, we demonstrate and discuss the achieved signal enhancement of metabolites on model non-human (bovine serum, amino acid standard mixture) and human urine samples.
  • Effect of Zinc-doping on the Reduction of the Hot-carrier Cooling Rate in Halide Perovskites

    Xing, Guichuan; WEI, Qi; Yin, Jun; Bakr, Osman; Wang, Ze; Wang, Chenhao; Mohammed, Omar F.; Li, Mingjie (Angewandte Chemie, Wiley, 2021-02-25) [Article]
    Fast hot-carrier cooling process in the solar-absorbers fundamentally limits the photon-energy conversion efficiencies. It is highly desirable to develop the solar absorber with long-lived hot-carriers at sun-illumination level, which can be used to develop the hot-carrier solar cells with enhanced efficiency. Herein, we reveal that zinc-doped (0.34%) halide perovskites have the slower hot-carrier cooling compared with the pristine sample through the transient absorption spectroscopy measurements and theoretical calculations. The hot-carrier energy loss rate at the low photoexcitation level of 10 17 cm -3 is found to be ~3 times smaller than that of un-doped perovskites for 500-K hot carriers, and up to ten times when the hot-carrier temperature approaching the lattice temperature. The incorporation of zinc-dopant into perovskites can reduce the nonadiabatic couplings between conduction bands, which retards the photogenerated hot-carriers relaxation process. Our findings present a practical strategy to slow down the hot-carrier cooling in perovskites at low carrier densities, which are valuable for the further development of practical perovskite hot-carrier photovoltaics .
  • One-step conversion of crude oil to light olefins using a multi-zone reactor

    Alabdullah, Mohammed A.; Rodriguez Gomez, Alberto; Shoinkhorova, Tuiana; Dikhtiarenko, Alla; Chowdhury, Abhishek Dutta; Hita, Idoia; Kulkarni, Shekhar Rajabhau; Vittenet, Jullian; Sarathy, Mani; Castaño, Pedro; Bendjeriou-Sedjerari, Anissa; Abou-Hamad, Edy; Zhang, Wen; Ali, Ola S.; Morales-Osorio, Isidoro; Xu, Wei; Gascon, Jorge (Nature Catalysis, Springer Science and Business Media LLC, 2021-02-25) [Article]
    With the demand for gasoline and diesel expected to decline in the near future, crude-to-chemicals technologies have the potential to become the most important processes in the petrochemical industry. This trend has triggered intense research to maximize the production of light olefins and aromatics at the expense of fuels, which calls for disruptive processes able to transform crude oil to chemicals in an efficient and environmentally friendly way. Here we propose a catalytic reactor concept consisting of a multi-zone fluidized bed that is able to perform several refining steps in a single reactor vessel. This configuration allows for in situ catalyst stripping and regeneration, while the incorporation of silicon carbide in the catalyst confers it with improved physical, mechanical and heat-transport properties. As a result, this reactor–catalyst combination has shown stable conversion of untreated Arabian Light crude into light olefins with yields per pass of over 30 wt% with a minimum production of dry gas.
  • Single-Crystalline Ultrathin 2D Porous Nanosheets of Chiral Metal–Organic Frameworks

    Liu, Yuhao; Liu, L. M.; Chen, Xu; Liu, Yan; Han, Yu; Cui, Yong (Journal of the American Chemical Society, American Chemical Society (ACS), 2021-02-23) [Article]
    Two-dimensional (2D) materials with highly ordered in-plane nanopores are crucial for numerous applications, but their rational synthesis and local structural characterization remain two grand challenges. We illustrate here that single-crystalline ultrathin 2D MOF nanosheets (MONs) with intrinsic porosity can be prepared by exfoliating layered metal-organic frameworks (MOFs), whose layers are stabilized by sterically bulky groups. As a result, three three-dimensional (3D) isostructural lanthanide MOFs possessing porous layer structures are constructed by coordinating metal ions with an angular dicarboxylate linker derived from chiral 1,1'-biphenyl phosphoric acid with pendant mesityl groups. The Eu-MOF is readily ultrasonic exfoliated into single-crystalline nanosheets with a thickness of ca. 6.0 nm (2 layers) and a lateral size of 1.5 × 3.0 μm2. The detailed structural information, i.e., the pore channels and individual organic and inorganic building units in the framework, is clearly visualized by a low-dose high-resolution transmission electron microscopy (HRTEM) technique. Benefiting from their ultrathin feature, the nanosheets are well embedded into the polymer matrix to form free-standing mixed-matrix membranes. In both the solution and membrane phase, the fluorescence of the MONs can be effectively quenched by a total of 17 chiral terpenes and terpenoids through supramolecular interactions with uncoordinated chiral phosphoric acids, leading to a chiral optical sensor for detecting vapor enantiomers, which is among the most challenging molecular recognition tasks.
  • A Brief Review of Solar Indoor Lighting System Integrated with Optofluidic Technologies

    Chen, Qian; Burhan, Muhammad; Oh, Seung Jin (Energy Technology, Wiley, 2021-02-23) [Article]
    Indoor lighting system incorporating daylighting effectively provides potential energy savings as well as meaningful spatial and temporal variation in illuminance beneficial to human well-being and performance. Integration of the tunable liquid prisms driven by optofluidic technologies will further improve the solar indoor lighting systems to achieve better illumination performance and higher solar energy utilization efficiency. This paper provides an overview of the state-of-the-art investigations over different aspects of the solar indoor lighting system enhanced by optofluidic liquid prisms, including (1) theoretical background, design, fabrication, and operation of liquid prisms, (2) advances in solar collectors and solar trackers, and (3) major tools for indoor lighting simulation and ray-tracing simulation. These studies form a solid foundation for future solar indoor lighting systems integrated with optofluidic technologies. The prospective study will focus on laboratory and on-site testing of the integrated system.
  • Replacing Thymine with a Strongly Pairing Fifth Base: a Combined Quantum Mechanics and Molecular Dynamics Study

    Chawla, Mohit; Gorle, Suresh; Shaikh, Abdul Rajjak; Oliva, Romina; Cavallo, Luigi (Computational and Structural Biotechnology Journal, Elsevier BV, 2021-02-23) [Article]
    The non-natural ethynylmethylpyridone C-nucleoside (W), a thymidine (T) analogue that can be incorporated in oligonucleotides by automated synthesis, has recently been reported to form a high fidelity base pair with adenosine (A) and to be well accommodated in B-DNA duplexes. The enhanced binding affinity for A of W, as compared to T, makes it an ideal modification for biotechnological applications, such as efficient probe hybridization for the parallel detection of multiple DNA strands. In order to complement the experimental study and rationalize the impact of the non-natural W nucleoside on the structure, stability and dynamics of DNA structures, we performed quantum mechanics (QM) calculations along with molecular dynamics (MD) simulations. Consistently with the experimental study, our QM calculations show that the A:W base pair has an increased stability as compared to the natural A:T pair, due to an additional CH-π interaction. Furthermore, we show that mispairing between W and guanine (G) causes a distortion in the planarity of the base pair, thus explaining the destabilization of DNA duplexes featuring a G:W pair. MD simulations show that incorporation of single or multiple consecutive A:W pairs in DNA duplexes causes minor changes to the intra- and inter-base geometrical parameters, while a moderate widening/shrinking of the major/minor groove of the duplexes is observed. QM calculations applied to selected stacks from the MD simulations also show an increased stacking energy for W, over T, with the neighboring bases.
  • A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples

    Mandujano, Gerardo Ramos-; Salunke, Rahul Pandurang; Mfarrej, Sara; Rachmadi, Andri Taruna; Hala, Sharif; Xu, Jinna; Alofi, Fadwa S.; Khogeer, Asim; Hashem, Anwar M.; Almontashiri, Naif A. M.; Alsomali, Afrah; Shinde, Digambar; Hamdan, Samir; Hong, Pei-Ying; Pain, Arnab; Li, Mo (Global Challenges, Wiley, 2021-02-22) [Article]
    Molecular diagnosis and surveillance of pathogens such as SARS-CoV-2 depend on nucleic acid isolation. Pandemics at the scale of COVID-19 can cause a global shortage of proprietary commercial reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. An open-source method, magnetic-nanoparticle-aided viral RNA isolation from contagious samples (MAVRICS), built upon readily available reagents, and easily assembled in any basically equipped laboratory, is thus developed. The performance of MAVRICS is evaluated using validated pathogen detection assays and real-world and contrived samples. Unlike conventional methods, MAVRICS works directly in samples inactivated in phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. MAVRICS allows wastewater biomass immobilized on membranes to be directly inactivated and lysed in TRIzol followed by RNA extraction by magnetic nanoparticles, thereby greatly reducing biohazard risk and simplifying processing procedures. Using 39 COVID-19 patient samples and two wastewater samples, it is shown that MAVRICS rivals commercial kits in detection of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. Therefore, MAVRICS is safe, fast, and scalable. It is field-deployable with minimal equipment requirements and could become an enabling technology for widespread testing and wastewater monitoring of diverse pathogens.
  • Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species

    Selmoni, Oliver; Lecellier, Gaël; Magalon, Hélène; Vigliola, Laurent; Oury, Nicolas; Benzoni, Francesca; Peignon, Christophe; Joost, Stéphane; Berteaux-Lecellier, Véronique (Molecular Ecology, Wiley, 2021-02-22) [Article]
    Anomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that had been exposed to recurrent thermal stress over the years and whose corals appeared tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known. In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single nucleotide polymorphisms (SNPs) of which frequencies associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic region. In each of the studied species, we found heat stress associated SNPs located in proximity of genes involved in pathways well-known to contribute to the cellular responses against heat, such as protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways and DNA damage-repair. In some cases, the same candidate molecular targets of heat stress adaptation recurred among species. Together, these results underscore the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.
  • Efficient alkane oxidation under combustion engine and atmospheric conditions

    Wang, Zhandong; Ehn, Mikael; Rissanen, Matti P.; Garmash, Olga; Quéléver, Lauriane; Xing, Lili; Monge Palacios, Manuel; Rantala, Pekka; Donahue, Neil M.; Berndt, Torsten; Sarathy, Mani (Communications Chemistry, Springer Science and Business Media LLC, 2021-02-18) [Article]
    AbstractOxidation chemistry controls both combustion processes and the atmospheric transformation of volatile emissions. In combustion engines, radical species undergo isomerization reactions that allow fast addition of O2. This chain reaction, termed autoxidation, is enabled by high engine temperatures, but has recently been also identified as an important source for highly oxygenated species in the atmosphere, forming organic aerosol. Conventional knowledge suggests that atmospheric autoxidation requires suitable structural features, like double bonds or oxygen-containing moieties, in the precursors. With neither of these functionalities, alkanes, the primary fuel type in combustion engines and an important class of urban trace gases, are thought to have minor susceptibility to extensive autoxidation. Here, utilizing state-of-the-art mass spectrometry, measuring both radicals and oxidation products, we show that alkanes undergo autoxidation much more efficiently than previously thought, both under atmospheric and combustion conditions. Even at high concentrations of NOX, which typically rapidly terminates autoxidation in urban areas, the studied C6–C10 alkanes produce considerable amounts of highly oxygenated products that can contribute to urban organic aerosol. The results of this inter-disciplinary effort provide crucial information on oxidation processes in both combustion engines and the atmosphere, with direct implications for engine efficiency and urban air quality.
  • ADAM10 hyperactivation acts on piccolo to deplete synaptic vesicle stores in Huntington's disease.

    Cozzolino, Flora; Vezzoli, Elena; Cheroni, Cristina; Besusso, Dario; Conforti, Paola; Valenza, Marta; Iacobucci, Ilaria; Monaco, Vittoria; Birolini, Giulia; Bombaci, Mauro; Falqui, Andrea; Saftig, Paul; Rossi, Riccardo L; Monti, Maria; Cattaneo, Elena; Zuccato, Chiara (Human molecular genetics, Oxford University Press (OUP), 2021-02-18) [Article]
    Synaptic dysfunction and cognitive decline in Huntington's disease (HD) involve hyperactive A disintegrin and metalloproteinase domain-containing protein 10 (ADAM10). To identify the molecular mechanisms through which ADAM10 is associated with synaptic dysfunction in HD, we performed an immunoaffinity purification-mass spectrometry (IP-MS) study of endogenous ADAM10 in the brains of wild-type and HD mice. In the normal brain, proteins implicated in synapse organization, synaptic plasticity, and vesicle and organelles trafficking interact with ADAM10, suggesting that it may act as a hub protein at the excitatory synapse. Importantly, the ADAM10 interactome is enriched in presynaptic proteins and ADAM10 coimmunoprecipitates with piccolo (PCLO), a key player in the recycling and maintenance of synaptic vesicles (SVs). In contrast, reduced ADAM10/PCLO immunoprecipitation occurs in the HD brain, with decreased density of SVs in the reserve and docked pool at the HD presynaptic terminal. Conditional heterozygous deletion of ADAM10 in the forebrain of HD mice reduces active ADAM10 to wild-type level, and normalizes ADAM10/PCLO complex formation and SVs density and distribution. The results indicate that presynaptic ADAM10 and PCLO are a relevant component of HD pathogenesis.

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