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  • A zero liquid discharge system integrating multi-effect distillation and evaporative crystallization for desalination brine treatment

    Chen, Qian; Burhan, Muhammad; Shahzad, Muhammad Wakil; Ybyraiymkul, Doskhan; Akhtar, Faheem; Li, Yong; Ng, Kim Choon (Desalination, Elsevier BV, 2021-01-13) [Article]
    With growing global desalination capacity, brine from desalination plants has become an environmental threat to the ecosystems. One sustainable method for brine treatment is to develop zero liquid discharge systems that completely convert seawater into freshwater and salts. This paper presents a zero liquid discharge system, which consists of multi-effect distillation and evaporative crystallization, to treat desalination brine with a salinity of 70 g/kg. A thermodynamic analysis is firstly conducted for the proposed system. The specific heat consumption, specific heat transfer area, and Second-law efficiency are found to be 600–1100 kJ/kg, 110–340 m2/(kg/s), and 10–17%, respectively. The heat consumption can be effectively reduced by increasing the number of MED stages, while the specific heat transfer area decreases significantly with higher heat source temperatures. Based on the thermodynamic performance, a techno-economic analysis is conducted for the proposed system, and the specific cost is calculated to be $4.17/m3. Cost reduction can be achieved via employing cost-effective heat sources, reducing heat consumption, and scaling up the system. By selling the freshwater and salt crystals, the system will be more competitive than other existing brine treatment methods.
  • Impacts of hypoxic events surpass those of future ocean warming and acidification

    Sampaio, Eduardo; Santos, Catarina; Rosa, Inês C.; Ferreira, Verónica; Pörtner, Hans-Otto; Duarte, Carlos M.; Levin, Lisa A.; Rosa, Rui (Nature Ecology & Evolution, Springer Science and Business Media LLC, 2021-01-11) [Article]
    Over the past decades, three major challenges to marine life have emerged as a consequence of anthropogenic emissions: ocean warming, acidification and oxygen loss. While most experimental research has targeted the first two stressors, the last remains comparatively neglected. Here, we implemented sequential hierarchical mixed-model meta-analyses (721 control–treatment comparisons) to compare the impacts of oxygen conditions associated with the current and continuously intensifying hypoxic events (1–3.5 O2 mg l−1) with those experimentally yielded by ocean warming (+4 °C) and acidification (−0.4 units) conditions on the basis of IPCC projections (RCP 8.5) for 2100. In contrast to warming and acidification, hypoxic events elicited consistent negative effects relative to control biological performance—survival (–33%), abundance (–65%), development (–51%), metabolism (–33%), growth (–24%) and reproduction (–39%)—across the taxonomic groups (mollusks, crustaceans and fish), ontogenetic stages and climate regions studied. Our findings call for a refocus of global change experimental studies, integrating oxygen concentration drivers as a key factor of ocean change. Given potential combined effects, multistressor designs including gradual and extreme changes are further warranted to fully disclose the future impacts of ocean oxygen loss, warming and acidification.
  • The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals

    Le Roy, Nathalie; Ganot, Philippe; Aranda, Manuel; Allemand, Denis; Tambutté, Sylvie (BMC Ecology and Evolution, Springer Science and Business Media LLC, 2021-01-11) [Article]
    Abstract Background The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. stony corals) in comparison to the subclass Octocorallia (i.e. red corals); the two diverged approximately 600 million years ago. The precious Mediterranean red coral, Corallium rubrum, is an octocorallian species, which produces two distinct high-magnesium calcite biominerals, the axial skeleton and the sclerites. In order to gain insight into the red coral biomineralization process and cnidarian biomineralization evolution, we studied the protein repertoire forming the organic matrix (OM) of its two biominerals. Results We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. We identified a total of 102 OM proteins, 52 are found in the two red coral biominerals with scleritin being the most abundant protein in each fraction. Contrary to reef building corals, the red coral organic matrix possesses a large number of collagen-like proteins. Agrin-like glycoproteins and proteins with sugar-binding domains are also predominant. Twenty-seven and 23 proteins were uniquely assigned to the axial skeleton and the sclerites, respectively. The inferred regulatory function of these OM proteins suggests that the difference between the two biominerals is due to the modeling of the matrix network, rather than the presence of specific structural components. At least one OM component could have been horizontally transferred from prokaryotes early during Octocorallia evolution. Conclusion Our results suggest that calcification of the red coral axial skeleton likely represents a secondary calcification of an ancestral gorgonian horny axis. In addition, the comparison with stony coral skeletomes highlighted the low proportion of similar proteins between the biomineral OMs of hexacorallian and octocorallian corals, suggesting an independent acquisition of calcification in anthozoans.
  • Metabolomic and Biochemical Analysis of Two Potato (Solanum tuberosum L.) Cultivars Exposed to In Vitro Osmotic and Salt Stresses.

    Hamooh, Bahget Talat; Sattar, Farooq Abdul; Wellman, Gordon; Mousa, Magdi Ali Ahmed (Plants (Basel, Switzerland), MDPI AG, 2021-01-09) [Article]
    Globally, many crop production areas are threatened by drought and salinity. Potato ($\textit{Solanum tuberosum}$ L.) is susceptible to these challenging environmental conditions. In this study, an in vitro approach was employed to compare the tolerance of potato cultivars 'BARI-401' (red skin) and 'Spunta' (yellow skin). To simulate ionic and osmotic stress, MS media was supplemented with lithium chloride (LiCl 20 mM) and mannitol (150 mM). GC-MS and spectrophotometry techniques were used to determine metabolite accumulation. Other biochemical properties, such as total phenols concentration (TPC), total flavonoids concentration (TFC), antioxidant capacity (DPPH free radical scavenging capacity), polyphenol oxidase (PPO), and peroxidase (POD) activities, were also measured. The two cultivars respond differently to ionic and osmotic stress treatments, with Spunta accumulating more defensive metabolites in response, indicating a higher level of tolerance. While further investigation of the physiological and biochemical responses of these varieties to drought and salinity is required, the approach taken in this paper provides useful information prior to open field evaluation.
  • Generation of iPSC lines (KAUSTi011-A, KAUSTi011-B) from a Saudi patient with epileptic encephalopathy carrying homozygous mutation in the GLP1R gene.

    Alowaysi, Maryam; Astro, Veronica; Fiacco, Elisabetta; AlZahrani, Fatema; Alkuraya, Fowzan S; Adamo, Antonio (Stem cell research, Elsevier BV, 2021-01-09) [Article]
    Glucagon-like peptide-1 receptor (GLP1R) is a seven-transmembrane-spanning helices membrane protein expressed in multiple human tissues including pancreatic islets, lung, brain, heart and central nervous system (CNS). GLP1R agonists are commonly used as antidiabetic drugs, but a neuroprotective function in neurodegenerative disorders is emerging. Here, we established two iPSC lines from a patient harboring a rare homozygous splice site variant in GLP1R (NM_002062.3; c.402 + 3delG). This patient displays severe developmental delay and epileptic encephalopathy. Therefore, the derivation of these iPSC lines constitutes a primary model to study the molecular pathology of GLP1R dysfunction and develop novel therapeutic targets.
  • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

    Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
    In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
  • Elucidating the Role of Virulence Traits in the Survival of Pathogenic E. coli PI-7 Following Disinfection

    Sivakumar, Krishnakumar; Lehmann, Robert; Rachmadi, Andri Taruna; Augsburger, Nicolas; Zaouri, Noor A.; Tegner, Jesper; Hong, Pei-Ying (Frontiers in bioengineering and biotechnology, Frontiers Media SA, 2021-01-08) [Article]
    Reuse and discharge of treated wastewater can result in dissemination of microorganisms into the environment. Deployment of disinfection strategies is typically proposed as a last stage remediation effort to further inactivate viable microorganisms. In this study, we hypothesize that virulence traits, including biofilm formation, motility, siderophore, and curli production along with the capability to internalize into mammalian cells play a role in survival against disinfectants. Pathogenic E. coli PI-7 strain was used as a model bacterium that was exposed to diverse disinfection strategies such as chlorination, UV and solar irradiation. To this end, we used a random transposon mutagenesis library screening approach to generate 14 mutants that exhibited varying levels of virulence traits. In these 14 isolated mutants, we observed that an increase in virulence traits such as biofilm formation, motility, curli production, and internalization capability, increased the inactivation half-lives of mutants compared to wild-type E. coli PI-7. In addition, oxidative stress response and EPS production contributed to lengthening the lag phase duration (defined as the time required for exposure to disinfectant prior to decay). However, traits related to siderophore production did not help with survival against the tested disinfection strategies. Taken together, the findings suggested that selected virulence traits facilitate survival of pathogenic E. coli PI-7, which in turn could account for the selective enrichment of pathogens over the nonpathogenic ones after wastewater treatment. Further, the study also reflected on the effectiveness of UV as a more viable disinfection strategy for inactivation of pathogens.
  • Molecular basis for the adaptive evolution of environment sensing by H-NS proteins

    Zhao, Xiaochuan; Shahul Hameed, Umar Farook; Kharchenko, Vladlena; Liao, Chenyi; Huser, Franceline; Remington, Jacob M; Radhakrishnan, Anand K; Jaremko, Mariusz; Jaremko, Lukasz; Arold, Stefan T.; Li, Jianing (eLife, eLife Sciences Publications, Ltd, 2021-01-07) [Article]
    The DNA-binding protein H-NS is a pleiotropic gene regulator in gram-negative bacteria. Through its capacity to sense temperature and other environmental factors, H-NS allows pathogens like Salmonella to adapt their gene expression to their presence inside or outside warm-blooded hosts. To investigate how this sensing mechanism may have evolved to fit different bacterial lifestyles, we compared H-NS orthologs from bacteria that infect humans, plants, and insects, and from bacteria that live on a deep-sea hypothermal vent. The combination of biophysical characterization, high-resolution proton-less NMR spectroscopy and molecular simulations revealed, at an atomistic level, how the same general mechanism was adapted to specific habitats and lifestyles. In particular, we demonstrate how environment-sensing characteristics arise from specifically positioned intra- or intermolecular electrostatic interactions. Our integrative approach clarified the exact modus operandi for H-NS–mediated environmental sensing and suggests that this sensing mechanism resulted from the exaptation of an ancestral protein feature.
  • Hole-Type Spacers for More Stable Shale Gas-Produced Water Treatment by Forward Osmosis

    Alqattan, Jawad; Kim, Youngjin; Kerdi, Sarah; Qamar, Adnan; Ghaffour, NorEddine (Membranes, MDPI AG, 2021-01-03) [Article]
    An appropriate spacer design helps in minimizing membrane fouling which remains the major obstacle in forward osmosis (FO) systems. In the present study, the performance of a hole-type spacer (having holes at the filament intersections) was evaluated in a FO system and compared to a standard spacer design (without holes). The hole-type spacer exhibited slightly higher water flux and reverse solute flux (RSF) when Milli-Q water was used as feed solution and varied sodium chloride concentrations as draw solution. During shale gas produced water treatment, a severe flux decline was observed for both spacer designs due to the formation of barium sulfate scaling. SEM imaging revealed that the high shear force induced by the creation of holes led to the formation of scales on the entire membrane surface, causing a slightly higher flux decline than the standard spacer. Simultaneously, the presence of holes aided to mitigate the accumulation of foulants on spacer surface, resulting in no increase in pressure drop. Furthermore, a full cleaning efficiency was achieved by hole-type spacer attributed to the micro-jets effect induced by the holes, which aided to destroy the foulants and then sweep them away from the membrane surface.
  • Assembly of Two CCDD Rice Genomes, Oryza grandiglumis and Oryza latifolia, and the Study of Their Evolutionary Changes

    Alsantely, Aseel O. (2021-01) [Thesis]
    Advisor: Wing, Rod Anthony
    Committee members: Gojobori, Takashi; Zuccolo, Andrea
    Every day more than half of the world consumes rice as a primary dietary resource. Thus, rice is one of the most important food crops in the world. Rice and its wild relatives are part of the genus Oryza. Studying the genome structure, function, and evolution of Oryza species in a comparative genomics framework is a useful approach to provide a wealth of knowledge that can significantly improve valuable agronomic traits. The Oryza genus includes 27 species, with 11 different genome types as identified by genetic and cytogenetic analyses. Six genome types, including that of domesticated rice - O. sativa and O. glaberrima, are diploid, and the remaining 5 are tetraploids. Three of the tetraploid species contain the CCDD genome types (O. grandiglumis, O. latifolia, and O. alta), which arose less than 2 million years ago. Polyploidization is one of the major contributors to evolutionary divergence and can thereby lead to adaptation to new environmental niches. An important first step in the characterization of the polyploid Oryza species is the generation of a high-quality reference genome sequence. Unfortunately, up until recently, the generation of such an important and fundamental resource from polyploid species has been challenging, primarily due to their genome complexity and repetitive sequence content. In this project, I assembled two high-quality genomes assemblies for O. grandiglumis and O. latifolia using PacBio long-read sequencing technology and an assembly pipeline that employed 3 genome assemblers (i.e., Canu/2.0, Mecat2, and Flye/2.5) and multiple rounds of sequence polishing with 5 both Arrow and Pilon/1.23. After the primary assembly, sequence contigs were arranged into pseudomolecules, and homeologous chromosomes were assigned to their respective genome types (i.e., CC or DD). Finally, the assemblies were extensively edited manually to close as many gaps as possible. Both assemblies were then analyzed for transposable element and structural variant content between species and homoeologous chromosomes. This enabled us to study the evolutionary divergence of those two genomes, and to explore the possibility of neo-domesticating either species in future research for my PhD dissertation.
  • Noble metal nanowire arrays as an ethanol oxidation electrocatalyst

    Lam, Zhenhui; Liu, Cuicui; Su, Dongmeng; Tao, Hua Bing; Wang, Hsin Yi; Chen, Jiazang; Xu, Weichang; Zhang, Liping; Zhu, Yihan; Liu, L. M.; Han, Yu; Chen, Hongyu; Liu, Bin (Nanoscale Advances, Royal Society of Chemistry (RSC), 2021) [Article]
    Vertically aligned noble metal nanowire arrays were grown on conductive electrodes based on a solution growth method. They show significant improvement of electrocatalytic activity in ethanol oxidation, from a re-deposited sample of the same detached nanowires. The unusual morphology provides open diffusion channels and direct charge transport pathways, in addition to the high electrochemically active surface from the ultrathin nanowires. Our best nanowire arrays exhibited much enhanced electrocatalytic activity, achieving a 38.0 fold increase in specific activity over that of commercial catalysts for ethanol electrooxidation. The structural design provides a new direction to enhance the electrocatalytic activity and reduce the size of electrodes for miniaturization of portable electrochemical devices.
  • Engineered Microgels—Their Manufacturing and Biomedical Applications

    Alzanbaki, Hamzah; Moretti, Manola; Hauser, Charlotte (Micromachines, MDPI AG, 2021-01-01) [Article]
    Microgels are hydrogel particles with diameters in the micrometer scale that can be fabricated in different shapes and sizes. Microgels are increasingly used for biomedical applications and for biofabrication due to their interesting features, such as injectability, modularity, porosity and tunability in respect to size, shape and mechanical properties. Fabrication methods of microgels are divided into two categories, following a top-down or bottom-up approach. Each approach has its own advantages and disadvantages and requires certain sets of materials and equipments. In this review, we discuss fabrication methods of both top-down and bottom-up approaches and point to their advantages as well as their limitations, with more focus on the bottom-up approaches. In addition, the use of microgels for a variety of biomedical applications will be discussed, including microgels for the delivery of therapeutic agents and microgels as cell carriers for the fabrication of 3D bioprinted cell-laden constructs. Microgels made from well-defined synthetic materials with a focus on rationally designed ultrashort peptides are also discussed, because they have been demonstrated to serve as an attractive alternative to much less defined naturally derived materials. Here, we will emphasize the potential and properties of ultrashort self-assembling peptides related to microgels.
  • Imaging of organic signals in individual fossil diatom frustules with nanoSIMS and Raman spectroscopy

    Akse, Shaun P.; Das, Gobind; Agusti, Susana; Pichevin, Laetitia; Polerecky, Lubos; Middelburg, Jack J. (Marine Chemistry, Elsevier BV, 2021-01) [Article]
    The organic matter occluded in the silica of fossil diatom frustules is thought to be protected from diagenesis and used for paleoceanographic reconstructions. However, the location of the organic matter within the frustule has hitherto not been identified. Here, we combined high spatial resolution imaging by nanoSIMS and Raman micro-spectroscopy to identify where the organic material is retained in cleaned fossil diatom frustules. NanoSIMS imaging revealed that organic signals were present throughout the frustule but in higher concentrations at the pore walls. Raman measurements confirmed the heterogenous presence of organics but could not, because of lower spatial resolution, resolve the spatial patterns observed by nanoSIMS.
  • Combining Nadir, Oblique, and Façade Imagery Enhances Reconstruction of Rock Formations Using Unmanned Aerial Vehicles

    Tu, Yu-Hsuan; Johansen, Kasper; Aragon Solorio, Bruno Jose Luis; Stutsel, Bonny M.; Angel, Yoseline; Camargo, Omar A. López; Al-Mashharawi, Samir K. M.; Jiang, Jiale; Ziliani, Matteo G.; McCabe, Matthew (IEEE Transactions on Geoscience and Remote Sensing, IEEE, 2021) [Article]
    Developments in computer vision, such as structure from motion and multiview stereo reconstruction, have enabled a range of photogrammetric applications using unmanned aerial vehicles (UAV)-based imagery. However, some specific cases still present reconstruction challenges, including survey areas composed of steep, overhanging, or vertical rock formations. Here, the suitability and geometric accuracy of four UAV-based image acquisition and data processing scenarios for topographic surveying applications in complex terrain are assessed and compared. The specific cases include the use of: 1) nadir imagery; 2) nadir and oblique imagery; 3) nadir and façade imagery; and 4) nadir, oblique, and façade imagery to reconstruct a topographically complex natural surface. Results illustrate that including oblique and façade imagery to supplement the more traditional nadir collections significantly improves the geometric accuracy of point cloud data reconstruction by approximately 35% when assessed against terrestrial laser scanning data of near-vertical rock walls. Most points (99.41%) had distance errors of less than 50 cm between the point clouds derived from the nadir imagery and nadir-oblique-façade imagery. Apart from delivering enhanced spatial resolution in façade details, the geometric accuracy improvements achieved from integrating nadir, oblique, and façade imagery provide value for a range of applications, including geotechnical and geohazard investigations. Such gains are particularly relevant for studies assessing rock integrity and stability, and engineering design, planning, and construction, where information on the position of rock cracks, joints, faults, shears, and bedding planes may be required.
  • Arabidopsis Plant Natriuretic Peptide Is a Novel Interactor of Rubisco Activase

    Turek, Ilona; Gehring, Christoph A; Irving, H R (Life, MDPI AG, 2020-12-31) [Article]
    Plant natriuretic peptides (PNPs) are a group of systemically acting peptidic hormones affecting solute and solvent homeostasis and responses to biotrophic pathogens. Although an increasing body of evidence suggests PNPs modulate plant responses to biotic and abiotic stress, which could lead to their potential biotechnological application by conferring increased stress tolerance to plants, the exact mode of PNPs action is still elusive. In order to gain insight into PNP-dependent signalling, we set out to identify interactors of PNP present in the model plant Arabidopsis thaliana, termed AtPNP-A. Here, we report identification of rubisco activase (RCA), a central regulator of photosynthesis converting Rubisco catalytic sites from a closed to an open conformation, as an interactor of AtPNP-A through affinity isolation followed by mass spectrometric identification. Surface plasmon resonance (SPR) analyses reveals that the full-length recombinant AtPNP-A and the biologically active fragment of AtPNP-A bind specifically to RCA, whereas a biologically inactive scrambled peptide fails to bind. These results are considered in the light of known functions of PNPs, PNP-like proteins, and RCA in biotic and abiotic stress responses.
  • Carotenoid Biofortification of Crops in the CRISPR Era

    Zheng, Xiongjie; Kuijer, Hendrik N.J.; Al-Babili, Salim (Trends in Biotechnology, Elsevier BV, 2020-12-29) [Article]
    Carotenoids are micronutrients important for human health. The continuous improvements in clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing techniques make rapid, DNA/transgene-free and targeted multiplex genetic modification a reality, thus promising to accelerate the breeding and generation of ‘golden’ staple crops. We discuss here the progress and future prospects of CRISPR/Cas9 applications for carotenoid biofortification.
  • Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes

    Bi, Chongwei; Wang, Lin; Fan, Yong; Ramos Mandujano, Gerardo; Yuan, Baolei; Zhou, Xuan; Wang, Jincheng; Shao, Yanjiao; Zhang, Pu-Yao; Huang, Yanyi; Yu, Yang; Izpisua Belmonte, Juan Carlos; Li, Mo (Cold Spring Harbor Laboratory, 2020-12-29) [Preprint]
    The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individual Mitochondrial Genome sequencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant detection, complete haplotyping, and unbiased evaluation of heteroplasmy levels, all at the individual mtDNA molecule level. iMiGseq uncovers unappreciated levels of heteroplasmic variants in single healthy human oocytes well below the current 1% detection limit, of which numerous variants are detrimental and could contribute to late-onset mitochondrial disease and cancer. Extreme mtDNA heterogeneity among oocytes of the same mouse female, and a strong selection against deleterious mutations in human oocytes are observed. iMiGseq could comprehensively characterize and haplotype single-nucleotide and structural variants of mtDNA and their genetic linkage in NARP/Leigh syndrome patient-derived cells. Therefore, iMiGseq could not only elucidate the mitochondrial etiology of diseases, but also help diagnose and prevent mitochondrial diseases with unprecedented precision.
  • The gap-free rice genomes provide insights for centromere structure and function exploration and graph-based pan-genome construction

    Song, Jia-Ming; Xie, Wen-Zhao; Wang, Shuo; Guo, Yi-Xiong; Poland, Jesse; Koo, Dal-Hoe; Kudrna, Dave; Long, Evan; Huang, Yicheng; Feng, Jia-Wu; Zhang, Wenhui; Lee, Seunghee; Talag, Jayson; Zhou, Run; Zhu, Xi-Tong; Yuan, Daojun; Udall, Joshua; Xie, Weibo; Wing, Rod Anthony; Zhang, Qifa; Zhang, Jianwei; Chen, Ling-Ling (Cold Spring Harbor Laboratory, 2020-12-25) [Preprint]
    Asia rice (Oryza sativa) is divided into two subgroups, indica/xian and japonica/geng, the former has greater intraspecific diversity than the latter. Here, for the first time, we report the assemblies and analyses of two gap-free xian rice varieties Zhenshan 97 (ZS97) and Minghui 63 (MH63). Genomic sequences of these elite hybrid parents express extensive difference as the foundation for studying heterosis. Furthermore, the gap-free rice genomes provide global insights to investigate the structure and function of centromeres in different chromosomes. All the rice centromeric regions share conserved centromere-specific satellite motifs but with different copy numbers and structures. Importantly, we show that there are >1,500 genes in centromere regions and ~16% of them are actively expressed. Based on MH63 gap-free reference genome, a graph-based rice pan-genome (Os-GPG) was constructed containing presence/absence variations of 79 rice varieties. Compared with the other rice varieties, MH63 contained the largest number of resistance genes. The acquisition of ZS97 and MH63 gap-free genomes and graph-based pan-genome of rice lays a solid foundation for the study of genome structure and function in plants.
  • Performance of Commercially Available Rapid Serological Assays for the Detection of SARS-CoV-2 Antibodies.

    Hashem, Anwar M; Alhabbab, Rowa Y; Algaissi, Abdullah; Alfaleh, Mohamed A; Hala, Sharif; Abujamel, Turki S; ElAssouli, M-Zaki; AL-Somali, Afrah A; Alofi, Fadwa S; Khogeer, Asim A; Alkayyal, Almohanad A; Mahmoud, Ahmad Bakur; Almontashiri, Naif A M; Pain, Arnab (Pathogens (Basel, Switzerland), MDPI AG, 2020-12-23) [Article]
    The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread globally. Although several rapid commercial serological assays have been developed, little is known about their performance and accuracy in detecting SARS-CoV-2-specific antibodies in COVID-19 patient samples. Here, we have evaluated the performance of seven commercially available rapid lateral flow immunoassays (LFIA) obtained from different manufacturers, and compared them to in-house developed and validated ELISA assays for the detection of SARS-CoV-2-specific IgM and IgG antibodies in RT-PCR-confirmed COVID-19 patients. While all evaluated LFIA assays showed high specificity, our data showed a significant variation in sensitivity of these assays, which ranged from 0% to 54% for samples collected early during infection (3-7 days post symptoms onset) and from 54% to 88% for samples collected at later time points during infection (8-27 days post symptoms onset). Therefore, we recommend prior evaluation and validation of these assays before being routinely used to detect IgM and IgG in COVID-19 patients. Moreover, our findings suggest the use of LFIA assays in combination with other standard methods, and not as an alternative.
  • Imprint of Climate Change on Pan-Arctic Marine Vegetation

    Krause-Jensen, Dorte; Archambault, Philippe; Assis, Jorge; Bartsch, Inka; Bischof, Kai; Filbee-Dexter, Karen; Dunton, Kenneth H.; Maximova, Olga; Ragnarsdóttir, Sunna Björk; Sejr, Mikael K.; Simakova, Uliana; Spiridonov, Vassily; Wegeberg, Susse; Winding, Mie H.S.; Duarte, Carlos M. (Frontiers in Marine Science, Frontiers Media SA, 2020-12-23) [Article]
    The Arctic climate is changing rapidly. The warming and resultant longer open water periods suggest a potential for expansion of marine vegetation along the vast Arctic coastline. We compiled and reviewed the scattered time series on Arctic marine vegetation and explored trends for macroalgae and eelgrass (Zostera marina). We identified a total of 38 sites, distributed between Arctic coastal regions in Alaska, Canada, Greenland, Iceland, Norway/Svalbard, and Russia, having time series extending into the 21st Century. The majority of these exhibited increase in abundance, productivity or species richness, and/or expansion of geographical distribution limits, several time series showed no significant trend. Only four time series displayed a negative trend, largely due to urchin grazing or increased turbidity. Overall, the observations support with medium confidence (i.e., 5–8 in 10 chance of being correct, adopting the IPCC confidence scale) the prediction that macrophytes are expanding in the Arctic. Species distribution modeling was challenged by limited observations and lack of information on substrate, but suggested a current (2000–2017) potential pan-Arctic macroalgal distribution area of 820.000 km2 (145.000 km2 intertidal, 675.000 km2 subtidal), representing an increase of about 30% for subtidal- and 6% for intertidal macroalgae since 1940–1950, and associated polar migration rates averaging 18–23 km decade–1. Adjusting the potential macroalgal distribution area by the fraction of shores represented by cliffs halves the estimate (412,634 km2). Warming and reduced sea ice cover along the Arctic coastlines are expected to stimulate further expansion of marine vegetation from boreal latitudes. The changes likely affect the functioning of coastal Arctic ecosystems because of the vegetation’s roles as habitat, and for carbon and nutrient cycling and storage. We encourage a pan-Arctic science- and management agenda to incorporate marine vegetation into a coherent understanding of Arctic changes by quantifying distribution and status beyond the scattered studies now available to develop sustainable management strategies for these important ecosystems.

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