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Recent Submissions

  • Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis (Cnidaria, Anthozoa) species complex

    Porro, Barbara; Zamoum, Thamilla; Mallien, Cédric; Hume, Benjamin; Voolstra, Christian R.; Röttinger, Eric; Furla, Paola; Forcioli, Didier (Molecular Ecology, Wiley, 2020-11-29) [Article]
    All metazoans are in fact holobionts, resulting from the association of several organisms, and organismal adaptation is then due to the composite response of this association to the environment. Deciphering the mechanisms of symbiont acquisition in a holobiont is therefore essential to understanding the extent of its adaptive capacities. In cnidarians, some species acquire their photosynthetic symbionts directly from their parents (vertical transmission) but may also acquire symbionts from the environment (horizontal acquisition) at the adult stage. The Mediterranean snakelocks sea anemone, Anemonia viridis (Forskål, 1775), passes down symbionts from one generation to the next by vertical transmission, but the capacity for such horizontal acquisition is still unexplored. To unravel the flexibility of the association between the different host lineages identified in A. viridis and its Symbiodiniaceae, we genotyped both the animal hosts and their symbiont communities in members of host clones in five different locations in the North Western Mediterranean Sea. The composition of within-host symbiont populations was more dependent on the geographical origin of the hosts than their membership to a given lineage or even to a given clone. Additionally, similarities in host symbiont communities were greater among genets (i.e. among different clones) than among ramets (i.e. among members of the same given clonal genotype). Taken together, our results demonstrate that A. viridis may form associations with a range of symbiotic dinoflagellates and suggest a capacity for horizontal acquisition. A mixed-mode transmission strategy in A. viridis, as we posit here, may help explain the large phenotypic plasticity that characterises this anemone.
  • Nocturnal Surface Urban Heat Island over Greater Cairo: Spatial Morphology, Temporal Trends and Links to Land-Atmosphere Influences

    El Kenawy, Ahmed M.; Hereher, Mohamed; Robaa, Sayed M.; McCabe, Matthew; Lopez-Moreno, Juan I.; Domínguez-Castro, Fernando; Gaber, Islam M.; Al-Awadhi, Talal; Al-Buloshi, Ali; Al Nasiri, Noura; Al-Hatrushi, Salim; Schuwerack, Petra-Manuela; Peña-Angulo, Dhais; Abdelaal, Mohamed M.; Vicente-Serrano, Sergio M. (Remote Sensing, MDPI AG, 2020-11-27) [Article]
    This study assesses the spatial and temporal characteristics of nighttime surface urban heat island (SUHI) effects over Greater Cairo: the largest metropolitan area in Africa. This study employed nighttime land surface temperature (LST) data at 1 km resolution from the Moderate Resolution Imaging Spectroradiometer (MODIS) Aqua sensor for the period 2003–2019. We presented a new spatial anomaly algorithm, which allowed to define SUHI using the most anomalous hotspot and cold spot of LST for each time step over Greater Cairo between 2003 and 2019. Results demonstrate that although there is a significant increase in the spatial extent of SUHI over the past two decades, a significant decrease in the mean and maximum intensities of SUHI was noted. Moreover, we examined the dependency between SUHI characteristics and related factors that influence energy and heat fluxes between atmosphere and land in urban environments (e.g., surface albedo, vegetation cover, climate variability, and land cover/use changes). Results demonstrate that the decrease in the intensity of SUHI was mainly guided by a stronger warming in daytime and nighttime LST in the neighborhood of urban localities. This warming was accompanied by a decrease in surface albedo and diurnal temperature range (DTR) over these areas. Results of this study can provide guidance to local urban planners and decision-makers to adopt more effective mitigation strategies to diminish the negative impacts of urban warming on natural and human environments.
  • Large deep-sea zooplankton biomass mirrors primary production in the global ocean

    Hernández-León, S.; Koppelmann, R.; Fraile-Nuez, E.; Bode, Antonio; Mompeán, C.; Irigoien, X.; Olivar, M. P.; Echevarría, Fidel; Fernández de Puelles, M. L.; González-Gordillo, J. Ignacio; Cózar, A.; Acuña, J. L.; Agusti, Susana; Duarte, Carlos M. (Nature Communications, Springer Science and Business Media LLC, 2020-11-27) [Article]
    AbstractThe biological pump transports organic carbon produced by photosynthesis to the meso- and bathypelagic zones, the latter removing carbon from exchanging with the atmosphere over centennial time scales. Organisms living in both zones are supported by a passive flux of particles, and carbon transported to the deep-sea through vertical zooplankton migrations. Here we report globally-coherent positive relationships between zooplankton biomass in the epi-, meso-, and bathypelagic layers and average net primary production (NPP). We do so based on a global assessment of available deep-sea zooplankton biomass data and large-scale estimates of average NPP. The relationships obtained imply that increased NPP leads to enhanced transference of organic carbon to the deep ocean. Estimated remineralization from respiration rates by deep-sea zooplankton requires a minimum supply of 0.44 Pg C y$^{−1}$ transported into the bathypelagic ocean, comparable to the passive carbon sequestration. We suggest that the global coupling between NPP and bathypelagic zooplankton biomass must be also supported by an active transport mechanism associated to vertical zooplankton migration.
  • Multiple wheat genomes reveal global variation in modern breeding

    Walkowiak, Sean; Gao, Liangliang; Monat, Cecile; Haberer, Georg; Kassa, Mulualem T.; Brinton, Jemima; Ramirez-Gonzalez, Ricardo H.; Kolodziej, Markus C.; Delorean, Emily; Thambugala, Dinushika; Klymiuk, Valentyna; Byrns, Brook; Gundlach, Heidrun; Bandi, Venkat; Siri, Jorge Nunez; Nilsen, Kirby; Aquino, Catharine; Himmelbach, Axel; Copetti, Dario; Ban, Tomohiro; Venturini, Luca; Bevan, Michael; Clavijo, Bernardo; Koo, Dal-Hoe; Ens, Jennifer; Wiebe, Krystalee; N’Diaye, Amidou; Fritz, Allen K.; Gutwin, Carl; Fiebig, Anne; Fosker, Christine; Fu, Bin Xiao; Accinelli, Gonzalo Garcia; Gardner, Keith A.; Fradgley, Nick; Gutierrez-Gonzalez, Juan; Halstead-Nussloch, Gwyneth; Hatakeyama, Masaomi; Koh, Chu Shin; Deek, Jasline; Costamagna, Alejandro C.; Fobert, Pierre; Heavens, Darren; Kanamori, Hiroyuki; Kawaura, Kanako; Kobayashi, Fuminori; Krasileva, Ksenia; Kuo, Tony; McKenzie, Neil; Murata, Kazuki; Nabeka, Yusuke; Paape, Timothy; Padmarasu, Sudharsan; Percival-Alwyn, Lawrence; Kagale, Sateesh; Scholz, Uwe; Sese, Jun; Juliana, Philomin; Singh, Ravi; Shimizu-Inatsugi, Rie; Swarbreck, David; Cockram, James; Budak, Hikmet; Tameshige, Toshiaki; Tanaka, Tsuyoshi; Tsuji, Hiroyuki; Wright, Jonathan; Wu, Jianzhong; Steuernagel, Burkhard; Small, Ian; Cloutier, Sylvie; Keeble-Gagnère, Gabriel; Muehlbauer, Gary; Tibbets, Josquin; Nasuda, Shuhei; Melonek, Joanna; Hucl, Pierre J.; Sharpe, Andrew G.; Clark, Matthew; Legg, Erik; Bharti, Arvind; Langridge, Peter; Hall, Anthony; Uauy, Cristobal; Mascher, Martin; Krattinger, Simon G.; Handa, Hirokazu; Shimizu, Kentaro K.; Distelfeld, Assaf; Chalmers, Ken; Keller, Beat; Mayer, Klaus F. X.; Poland, Jesse; Stein, Nils; McCartney, Curt A.; Spannagl, Manuel; Wicker, Thomas; Pozniak, Curtis J. (Nature, Springer Science and Business Media LLC, 2020-11-25) [Article]
    AbstractAdvances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome$^{1}$, and the lack of genome-assembly data for multiple wheat lines$^{2,3}$. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses$^{4,5}$. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1$^{6}$, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.
  • Host-directed editing of the SARS-CoV-2 genome.

    Mourier, Tobias; Sadykov, Mukhtar; Carr, Michael J; Gonzalez, Gabriel; Hall, William W; Pain, Arnab (Biochemical and biophysical research communications, Elsevier BV, 2020-11-25) [Article]
    The extensive sequence data generated from SARS-CoV-2 during the 2020 pandemic has facilitated the study of viral genome evolution over a brief period of time. This has highlighted instances of directional mutation pressures exerted on the SARS-CoV-2 genome from host antiviral defense systems. In this brief review we describe three such human defense mechanisms, the apolipoprotein B mRNA editing catalytic polypeptide-like proteins (APOBEC), adenosine deaminase acting on RNA proteins (ADAR), and reactive oxygen species (ROS), and discuss their potential implications on SARS-CoV-2 evolution.
  • Source Apportionment and Elemental Composition of Atmospheric Total Suspended Particulates (TSP) Over the Red Sea Coast of Saudi Arabia

    Cusack, Michael; Arrieta, J. M.; Duarte, Carlos M. (Earth Systems and Environment, Springer Science and Business Media LLC, 2020-11-24) [Article]
    AbstractThis work presents a comprehensive study on concentrations and elemental composition of total suspended atmospheric particulates for a semi-urban site on the Red Sea coast, and on-board a research vessel, which collected off-shore samples along the Red Sea. We conducted one of the most extended measurement campaigns of atmospheric particulates ever for the region, with continuous measurements over 27 months. The overall mean concentrations (± st. dev.) of TSP were 125 ± 197 µg m$^{−3}$ for the permanent semi-urban site, and 108 ± 193 µg m$^{−3}$ for the off-shore mobile site. The region is frequently severely impacted by both localised and widespread dust storms, which on occasion, can increase atmospheric particulate concentrations to levels above mg m$^{−3}$ (> 1000 µg m$^{−3}$). Median concentrations were not as variable between seasons, indicating a stable, permanent presence of atmospheric particulates independent of the time of year. The primary chemical elements contributing to particulate mass were Na, Ca, S, Al and Fe. We employed Positive Matrix Factorisation (EPA PMF v5.0.14) to identify different major sources of particulates, which were crustal, marine, fuel oil combustion/secondary sulphate and mixed anthropogenic. The crustal source was characterised by tracers Al, Fe, K, Mg and Sn, and was present to some extent in the other identified sources due to the permanent presence of dust particles in the atmosphere. The fuel oil combustion/secondary sulphate source was identifiable by the almost exclusive presence of S, and to a lesser extent V, emitted from oil combustion as primary emissions and also secondary sulphate formation following the release of S to the atmosphere. A mixed anthropogenic source was characterised by Zn, Ni, Cr, Cu and Pb, emitted from traffic, industry, power generation and water desalination. This study highlights that the natural sources of particulates in this desert region give rise to frequent episodes of extremely poor air quality, and this problem is compounded by significant emissions of anthropogenic pollution, which has an impact across the entire Red Sea basin. Further stringent measures should be adopted to improve air quality across the region and prevent long-term damage to the health of the local population and ecosystems.
  • A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris , representing a prototypic feature of neural evolution

    Noro, Yukihiko; Shimizu, Hiroshi; Mineta, Katsuhiko; Gojobori, Takashi (Cold Spring Harbor Laboratory, 2020-11-23) [Preprint]
    The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria are well conserved in Cnidaria. Thus, Cnidarian representative species, Hydra, is considered to be a living fossil and a good model organism for the study of the putative primitive nervous system in its last common ancestor. The diffuse nervous system of Hydra consists of several peptidergic neuron subsets. However, the specific functions of these subsets remain unclear. Using calcium imaging, here we show that the neuron subsets that express neuropeptide, Hym-176 function as motor neurons to evoke longitudinal contraction. We found that all neurons in a subset defined by the Hym-176 gene (Hym-176A) or its paralogs (Hym-176B) expression are excited simultaneously, which is then followed by longitudinal contraction. This indicates not only that these neuron subsets are motor neurons but also that a single molecularly defined neuron subset forms a single coactive motor circuit. This is in contrast with the Bilaterian nervous system, where a single molecularly defined neuron subset harbors multiple coactive circuits, showing a mixture of neurons firing with different timings. Furthermore, we found that the two motor circuits, one expressing Hym-176B in the body column and the other expressing Hym-176A in the foot, are coordinately regulated to exert region-specific contraction. Our results demonstrate that one neuron subset is likely to form a monofunctional circuit as a minimum functional unit to build a more complex behavior in Hydra. We propose that this simple feature (one subset, one circuit, one function) found in Hydra is a fundamental trait of the primitive nervous system.
  • Composition, uniqueness and connectivity across tropical coastal lagoon habitats in the Red Sea.

    Alsaffar, Zahra Hassan Ali; Curdia, Joao; Irigoien, Xabier; Carvalho, Susana (BMC ecology, Springer Science and Business Media LLC, 2020-11-23) [Article]
    BACKGROUND:Tropical habitats and their associated environmental characteristics play a critical role in shaping macroinvertebrate communities. Assessing patterns of diversity over space and time and investigating the factors that control and generate those patterns is critical for conservation efforts. However, these factors are still poorly understood in sub-tropical and tropical regions. The present study applied a combination of uni- and multivariate techniques to test whether patterns of biodiversity, composition, and structure of macrobenthic assemblages change across different lagoon habitats (two mangrove sites; two seagrass meadows with varying levels of vegetation cover; and an unvegetated subtidal area) and between seasons and years. RESULTS:In total, 4771 invertebrates were identified belonging to 272 operational taxonomic units (OTUs). We observed that macrobenthic lagoon assemblages are diverse, heterogeneous and that the most evident biological pattern was spatial rather than temporal. To investigate whether macrofaunal patterns within the lagoon habitats (mangrove, seagrass, unvegetated area) changed through the time, we analysed each habitat separately. The results showed high seasonal and inter-annual variability in the macrofaunal patterns. However, the seagrass beds that are characterized by variable vegetation cover, through time, showed comparatively higher stability (with the lowest values of inter-annual variability and a high number of resident taxa). These results support the theory that seagrass habitat complexity promotes diversity and density of macrobenthic assemblages. Despite the structural and functional importance of seagrass beds documented in this study, the results also highlighted the small-scale heterogeneity of tropical habitats that may serve as biodiversity repositories. CONCLUSIONS:Comprehensive approaches at the "seascape" level are required for improved ecosystem management and to maintain connectivity patterns amongst habitats. This is particularly true along the Saudi Arabian coast of the Red Sea, which is currently experiencing rapid coastal development. Also, considering the high temporal variability (seasonal and inter-annual) of tropical shallow-water habitats, monitoring and management plans must include temporal scales.
  • Eddy-induced transport and kinetic energy budget in the Arabian Sea

    Zhan, Peng; Guo, Daquan; Hoteit, Ibrahim (Geophysical Research Letters, American Geophysical Union (AGU), 2020-11-23) [Article]
    This study investigates the vertical eddy structure, eddy-induced transport, and eddy kinetic energy (EKE) budget in the Arabian Sea (AS) using an eddy-resolving reanalysis product. The EKE intensifies during summer in the western AS. Anticyclonic eddies (AEs) and cyclonic eddies (CEs) present warm-fresh and cold-salty cores, respectively, with interleaved salinity structures. The eddy-induced swirl transport is larger in the western AS and tends to compensate for heat transport by the mean flow. Zonal drift transport by AEs and CEs offset each other, and meridional transport is generally weaker. Eddies also produce notable upward heat flux during summer in the western AS, where ageostrophic circulations are induced to maintain a turbulent thermal wind balance. Plausible mechanisms for EKE production are governed by baroclinic and barotropic instabilities, which are enhanced in summer in the western basin, where signals are quantitatively one order larger than the turbulent wind inputs.
  • Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems

    Garcias-Bonet, Neus; Eguíluz, V. M.; Díaz-Rúa, Rubén; Duarte, Carlos M. (Environmental Microbiology, Wiley, 2020-11-22) [Article]
    The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyze the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9 and 74.8 % of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.
  • A new approach for quantifying epigenetic landscapes.

    Fischle, Wolfgang (The Journal of biological chemistry, American Society for Biochemistry & Molecular Biology (ASBMB), 2020-11-20) [Article]
    ChIP-Seq is a widespread experimental method for determining the global enrichment of chromatin modifications and genome-associated factors. Whereas it is straightforward to compare the relative genomic distribution of these epigenetic features, researchers have also made efforts to compare their signal strength using external references for normalization. New work now suggests that these "spike-ins" could lead to inaccurate conclusions due to intrinsic issues of the methodology and instead calls for new criteria of experimental reporting that may permit internal standardization when certain parameters are fulfilled.
  • Counterintuitive Wetting Transitions in Doubly Reentrant Cavities as a Function of Surface Make-Up, Hydrostatic Pressure, and Cavity Aspect Ratio

    Arunachalam, Sankara; Ahmad, Zain; Das, Ratul; Mishra, Himanshu (Advanced Materials Interfaces, Wiley, 2020-11-20) [Article]
    Surfaces that entrap air underwater serve numerous practical applications, such as mitigating cavitation erosion and reducing frictional drag. These surfaces typically rely on perfluorinated coatings. However, the non-biodegradability and fragility of the coatings limit practical applications. Thus, coating-free, sustainable, and robust approaches are desirable. Recently, a microtexture comprising doubly reentrant cavities (DRCs) has been demonstrated to entrap air on immersion in wetting liquids. While this is a promising approach, insights into the effects of surface chemistry, hydrostatic pressure, and cavity dimensions on wetting transitions in DRCs remain unavailable. In response, Cassie-to-Wenzel transitions into circular DRCs submerged in water are investigated and compared with those in cylindrical “simple” cavities (SCs). It is found that at low hydrostatic pressures (≈50 Pa), DRCs with hydrophilic (θo ≈ 40°) and hydrophobic (θo ≈ 112°) make-ups fill within 105 and 107 s, respectively, while SCs with hydrophilic make-up fill within <10−2 s. Under elevated hydrostatic pressure (P ≤ 90 kPa), counterintuitively, DRCs with hydrophobic make-up fill dramatically faster than the commensurate SCs. This comprehensive report should provide a rational framework for harnessing microtexturing and surface chemistry toward coating-free liquid repellency.
  • VLG-Net: Video-Language Graph Matching Network for Video Grounding

    Qu, Sisi; Soldan, Mattia; Xu, Mengmeng; Tegner, Jesper; Ghanem, Bernard (arXiv, 2020-11-19) [Preprint]
    Grounding language queries in videos aims at identifying the time interval (or moment) semantically relevant to a language query. The solution to this challenging task demands the understanding of videos' and queries' semantic content and the fine-grained reasoning about their multi-modal interactions. Our key idea is to recast this challenge into an algorithmic graph matching problem. Fueled by recent advances in Graph Neural Networks, we propose to leverage Graph Convolutional Networks to model video and textual information as well as their semantic alignment. To enable the mutual exchange of information across the domains, we design a novel Video-Language Graph Matching Network (VLG-Net) to match video and query graphs. Core ingredients include representation graphs, built on top of video snippets and query tokens separately, which are used for modeling the intra-modality relationships. A Graph Matching layer is adopted for cross-modal context modeling and multi-modal fusion. Finally, moment candidates are created using masked moment attention pooling by fusing the moment's enriched snippet features. We demonstrate superior performance over state-of-the-art grounding methods on three widely used datasets for temporal localization of moments in videos with natural language queries: ActivityNet-Captions, TACoS, and DiDeMo.
  • Hollow Fibers with Encapsulated Green Amino Acid-Based Ionic Liquids for Dehydration

    Gebreyohannes, Abaynesh Yihdego; Upadhyaya, Lakshmeesha; Silva, Liliana P.; Falca, Gheorghe; Carvalho, Pedro J.; Nunes, Suzana Pereira (ACS Sustainable Chemistry & Engineering, American Chemical Society (ACS), 2020-11-18) [Article]
    Dehydration technologies with low energy consumption using non-toxic materials are important in industrial, residential, and transport applications. Herein, nanocomposite polymeric hollow fibers with high dehydration capability were demonstrated with the incorporation of green amino acid-based ionic liquids. The ionic liquid was encapsulated in designed submicrometer carbon capsules (ENILs) and dispersed in thin polydimethylsiloxane (PDMS) coating layers. The effect of different coating compositions and operation conditions on the water vapor permeance and selectivity of water vapor over nitrogen was investigated using vacuum and sweep gas. Both sorption and permeation results suggested strong interactions between the water vapor and the encapsulated ionic liquid. The selectivity greatly depends on the PDMS coating and the amount of loaded ENIL. A linear increase of the water vapor over nitrogen selectivity was observed up to 50% ENIL loading in PDMS. The membrane systems had water vapor permeance up to 10,600 GPU and selectivity of 4500, which are promising characteristics for application in membrane air dehumidification and other dehydration processes
  • Molecularly-porous ultrathin membranes for highly selective organic solvent nanofiltration

    Huang, Tiefan; Moosa, Basem; HOANG, PHUONG; Liu, Jiangtao; Chisca, Stefan; Zhang, Gengwu; Alyami, Mram Z.; Khashab, Niveen M.; Nunes, Suzana Pereira (Nature Communications, Springer Science and Business Media LLC, 2020-11-18) [Article]
    AbstractEngineering membranes for molecular separation in organic solvents is still a big challenge. When the selectivity increases, the permeability tends to drastically decrease, increasing the energy demands for the separation process. Ideally, organic solvent nanofiltration membranes should be thin to enhance the permeant transport, have a well-tailored nanoporosity and high stability in harsh solvents. Here, we introduce a trianglamine macrocycle as a molecular building block for cross-linked membranes, prepared by facile interfacial polymerization, for high-performance selective separations. The membranes were prepared via a two-in-one strategy, enabled by the amine macrocycle, by simultaneously reducing the thickness of the thin-film layers (<10 nm) and introducing permanent intrinsic porosity within the membrane (6.3 Å). This translates into a superior separation performance for nanofiltration operation, both in polar and apolar solvents. The hyper-cross-linked network significantly improved the stability in various organic solvents, while the amine host macrocycle provided specific size and charge molecular recognition for selective guest molecules separation. By employing easily customized molecular hosts in ultrathin membranes, we can significantly tailor the selectivity on-demand without compromising the overall permeability of the system.
  • Millimeter-Deep Detection of Single Shortwave-Infrared-Emitting Polymer Dots through Turbid Media

    Piwonski, Hubert Marek; Wang, Yang; Li, Wei; Michinobu, Tsuyoshi; Habuchi, Satoshi (Nano Letters, American Chemical Society (ACS), 2020-11-18) [Article]
    Fluorescence imaging at longer wavelengths, especially in the shortwave-infrared (SWIR: 1000-1700 nm) region, leads to a substantial decrease in light attenuation, scattering, and background autofluorescence, thereby enabling enhanced penetration into biological tissues. The limited selection of fluorescent probes is a major bottleneck in SWIR fluorescence imaging. Here, we develop SWIR-emitting nanoparticles composed of donor-acceptor-type conjugated polymers. The bright SWIR fluorescence of the polymer dots (primarily attributable to their large absorption cross-section and high fluorescence saturation intensity (as high as 113 kW·cm-2)) enables the unprecedented detection of single particles as small as 14 nm through millimeter-thick turbid media. Unlike most SWIR-emitting nanomaterials, which have an excited-state lifetime in the range of microseconds to milliseconds, our polymer dots exhibit a subnanosecond excited-state lifetime. These characteristics enable us to demonstrate new time-gated single-particle imaging with a high signal-to-background ratio. These findings expand the range of potential applications of single-particle deep-tissue imaging.
  • Divergent expression of hypoxia response systems under deoxygenation in reef-forming corals aligns with bleaching susceptibility

    Alderdice, Rachel; Suggett, David J.; Cardenas, Anny; Hughes, David J.; Kühl, Michael; Pernice, Mathieu; Voolstra, Christian R. (Global Change Biology, Wiley, 2020-11-16) [Article]
    Exposure of marine life to low oxygen is accelerating worldwide via climate change and localized pollution. Mass coral bleaching and mortality have recently occurred where reefs have experienced chronic low oxygen events. However, the mechanistic basis of tolerance to oxygen levels inadequate to sustain normal functioning (i.e. hypoxia) and whether it contributes to bleaching susceptibility, remain unknown. We therefore experimentally exposed colonies of the environmentally resilient Acropora tenuis, a common reef-building coral from the Great Barrier Reef, to deoxygenation–reoxygenation stress that was aligned to their natural night–day light cycle. Specifically, the treatment involved removing the ‘night-time O2 buffer’ to challenge the inherent hypoxia thresholds. RNA-Seq analysis revealed that coral possess a complete and active hypoxia-inducible factor (HIF)-mediated hypoxia response system (HRS) homologous to other metazoans. As expected, A. tenuis exhibited bleaching resistance and showed a strong inducibility of HIF target genes in response to deoxygenation stress. We applied this same approach in parallel to a colony of Acropora selago, known to be environmnetally susceptible, which conversely exhibited a bleaching phenotype response. This phenotypic divergence of A. selago was accompanied by contrasting gene expression profiles indicative of varied effectiveness of their HIF-HRS. Based on our RNA-Seq analysis, we propose (a) that the HIF-HRS is central for corals to manage deoxygenation stress and (b) that key genes of this system (and the wider gene network) may contribute to variation in coral bleaching susceptibility. Our analysis suggests that heat shock protein (hsp) 70 and 90 are important for low oxygen stress tolerance and further highlights how hsp90 expression might also affect the inducibility of coral HIF-HRS in overcoming a metabolic crisis under deoxygenation stress. We propose that differences in coral HIF-HRS could be central in regulating sensitivity to other climate change stressors—notably thermal stress—that commonly drive bleaching.
  • Hypothesis: Potentially Systemic Impacts of Elevated CO2 on the Human Proteome and Health

    Duarte, Carlos M.; Jaremko, Mariusz; Jaremko, Lukasz (Frontiers in Public Health, Frontiers, 2020-11-16) [Article]
    Uniform CO2 during human evolution (180 to 280 ppm) resulted, because of the role of the CO2-bicarbonate buffer in regulating pH, in rather constant pH (7.35 to 7.45) in human fluids, cells and tissues, determining, in turn, the narrow pH range for optimal functioning of the human proteome. Here we hypothesize that chronic exposure to elevated pCO2 with increasing atmospheric CO2 (>400 ppm) and extended time spent in confined, crowded indoor atmospheres (pCO2 up to 5,000 ppm) with urban lifestyles may be a major, largely overlooked, driver of changes in the performance of the human proteome. The reduced pH (downregulated from 0.1 to 0.4 units below the optimum pH) of extant humans chronically exposed to elevated CO2 is likely to lead to proteome malfunction due to protein misfolding, aggregation, charge distribution and altered interaction with other molecules (e.g. nucleic acids, metals, proteins, and drugs). Such alterations would have systemic effects helping explain the prevalence of syndromes (obesity, diabetes, respiratory diseases, osteoporosis, cancer, and neurological disorders) characteristic of the modern lifestyle. The risks chronic exposure to elevated CO2 poses to human health are too profound to be ignored and require testing with fit-for-purpose equipment and protocols along with indoor carbon capture technologies to bring CO2 levels to those (180 to 280 ppm) under which the humans proteome evolved.
  • Mesomorphic, Optical and DFT Aspects of Near to Room-Temperature Calamitic Liquid Crystal

    Zaki, Ayman A.; Hagar, Mohamed; Alnoman, Rua B.; Jaremko, Mariusz; Emwas, Abdul-Hamid M.; Ahmed, Hoda A. (Crystals, MDPI AG, 2020-11-16) [Article]
    A new liquid crystalline, optical material-based Schiff base core with a near to room-temperature mesophase, (4-methoxybenzylideneamino)phenyl oleate (I), was prepared from a natural fatty acid derivative, and its physical and chemical properties investigated by experimental and theoretical approaches. The molecular structure was confirmed by elemental analysis, FT-IR (Fourier-Transform-Infrared Spectroscopy) and NMR (nuclear magnetic resonance) spectroscopy. Optical and mesomorphic activities were characterized by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The results show that compound (I) exhibits an enantiotropic monomorphic phase comprising a smectic A phase within the near to room-temperature range. Ordinary and extraordinary refractive indices as well as birefringence with changeable temperatures were analyzed. Microscopic and macroscopic order parameters were also calculated. Theoretical density functional theory (DFT) calculations were carried out to estimate the geometrical molecular structures of the prepared compounds, and the DFT results were used to illustrate the mesomorphic results and optical characteristics in terms of their predicted data. Three geometrical isomers of the prepared compound were investigated to predict the most stable isomer. Many parameters were affected by the geometrical isomerism such as aspect ratio, planarity, and dipole moment. Thermal parameters of the theoretical calculations revealed that the highest co-planar aromatic core is the most stable conformer.
  • T cell receptor repertoire as a potential diagnostic marker for celiac disease.

    Yao, Ying; Zia, Asima; Neumann, Ralf Stefan; Pavlovic, Milena; Balaban, Gabriel; Lundin, Knut E A; Sandve, Geir Kjetil; Qiao, Shuo-Wang (Clinical immunology (Orlando, Fla.), Elsevier BV, 2020-11-16) [Article]
    An individual's T cell repertoire is skewed towards some specificities as a result of past antigen exposure and subsequent clonal expansion. Identifying T cell receptor signatures associated with a disease is challenging due to the overall complexity of antigens and polymorphic HLA allotypes. In celiac disease, the antigen epitopes are well characterised and the specific HLA-DQ2-restricted T-cell repertoire associated with the disease has been explored in depth. By investigating T cell receptor repertoires of unsorted lamina propria T cells from 15 individuals, we provide the first proof-of-concept study showing that it could be possible to infer disease state by matching against a priori known disease-associated T cell receptor sequences.

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