Now showing items 1-20 of 4831

    • Temperature transcends partner specificity in the symbiosis establishment of a cnidarian

      Herrera Sarrias, Marcela; Klein, Shannon; Campana, Sara; Chen, Jit Ern; Prasanna, Arun; Duarte, Carlos M.; Aranda, Manuel (The ISME Journal, Springer Science and Business Media LLC, 2020-09-15) [Article]
      Abstract Coral reef research has predominantly focused on the effect of temperature on the breakdown of coral-dinoflagellate symbioses. However, less is known about how increasing temperature affects the establishment of new coral-dinoflagellate associations. Inter-partner specificity and environment-dependent colonization are two constraints proposed to limit the acquisition of more heat tolerant symbionts. Here, we investigated the symbiotic dynamics of various photosymbionts in different host genotypes under “optimal” and elevated temperature conditions. To do this, we inoculated symbiont-free polyps of the sea anemone Exaiptasia pallida originating from Hawaii (H2), North Carolina (CC7), and the Red Sea (RS) with the same mixture of native symbiont strains (Breviolum minutum, Symbiodinium linucheae, S. microadriaticum, and a Breviolum type from the Red Sea) at 25 and 32 °C, and assessed their ITS2 composition, colonization rates, and PSII photochemical efficiency (Fv/Fm). Symbiont communities across thermal conditions differed significantly for all hosts, suggesting that temperature rather than partner specificity had a stronger effect on symbiosis establishment. Overall, we detected higher abundances of more heat resistant Symbiodiniaceae types in the 32 °C treatments. Our data further showed that PSII photophysiology under elevated temperature improved with thermal pre-exposure (i.e., higher Fv/Fm), yet, this effect depended on host genotype and was influenced by active feeding as photochemical efficiency dropped in response to food deprivation. These findings highlight the role of temperature and partner fidelity in the establishment and performance of symbiosis and demonstrate the importance of heterotrophy for symbiotic cnidarians to endure and recover from stress.
    • The World Coral Conservatory: A Noah's ark for corals to support survival of reef ecosystems

      Zoccola, Didier; Ounais, Nadia; Barthelemy, Dominique; Calcagno, Robert; Gaill, Françoise; Henard, Stephane; Hoegh-Guldberg, Ove; Janse, Max; Jaubert, Jean; Putnam, Hollie; Salvat, Bernard; Voolstra, Christian R.; Allemand, Denis (PLOS Biology, Public Library of Science (PLoS), 2020-09-14) [Article]
      Global change causes widespread decline of coral reefs. In order to counter the anticipated disappearance of coral reefs by the end of this century, many initiatives are emerging, including creation of marine protected areas (MPAs), reef restoration projects, and assisted evolution initiatives. Such efforts, although critically important, are locally constrained. We propose to build a “Noah’s Ark” biological repository for corals that taps into the network of the world’s public aquaria and coral reef scientists. Public aquaria will serve not only as a reservoir for the purpose of conservation, restoration, and research of reef-building corals but also as a laboratory for the implementation of operations for the selection of stress-resilient and resistant genotypes. The proposed project will provide a global dimension to coral reef education and protection as a result of the involvement of a network of public and private aquaria.
    • Arginine citrullination of proteins as a specific response mechanism in Arabidopsis thaliana

      Marondedze, Claudius; Elia, Giuliano; Thomas, Ludivine; Wong, Aloysius; Gehring, Christoph A (Cold Spring Harbor Laboratory, 2020-09-13) [Preprint]
      Arginine citrullination, also referred to as arginine deimination, is a post-translational modification involved in an increasing number of physiological processes in animals, including histone modifications and transcriptional regulation, and in severe diseases such as rheumatoid arthritis and neurodegenerative conditions. It occurs when arginine side chains are deiminated and converted into side chains of the amino acid citrulline, a process catalysed by a family of Ca2+-dependent peptidyl arginine deiminases (PADs). PADs have been discovered in several mammalian species and in other vertebrates, like birds and fish, but have not been observed in bacteria, lower eukaryotes or higher plants. Here we show, firstly, that the Arabidopsis thaliana proteome does contain citrullinated proteins; secondly and importantly, that the citrullination signature changes in response to cold stress. Among the citrullinated proteins are DNA- or RNA-binding proteins thus implying a role for it the control of the transcriptional programming in plant cells. Thirdly, through sequence and structural analysis, we identify one arabidopsis protein, currently annotated as agmatine deiminase (At5g08170), as a candidate protein arginine deiminase. Finally, we show biochemical evidence that AT5G08170 can citrullinate peptides from LHP1-interacting factor 2 (AT4G00830) an RNA-binding protein that has been identified as citrullinated in cell suspension cultures of Arabidopsis thaliana roots. In addition, we show that, in vitro, agmatine deiminase can undergo auto-citrullination. In conclusion, our work established the presence of protein arginine citrullination in higher plants and assigns it a role in post-translational modifications during abiotic stress responses.
    • Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics

      Kharchenko, Vladlena; Nowakowski, Michal; Jaremko, Mariusz; Ejchart, Andrzej; Jaremko, Lukasz (Journal of Biomolecular NMR, Springer Science and Business Media LLC, 2020-09-12) [Article]
      Abstract Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.
    • Characterizing a strong pan-muscular promoter (Pmlc-1) as a fluorescent co-injection marker to select for single-copy insertions.

      El Mouridi, Sonia; Peng, Yuli; Frøkjær-Jensen, Christian (microPublication biology, 2020-09-10) [Article]
      Fluorescent markers are useful for identifying transgenic C. elegans after injection. In some cases, fluorophores are used to identify transgenics and to propagate animals with extra-chromosomal or integrated arrays (e.g., sur-5
    • Rapid Evolution of Plastic-degrading Enzymes Prevalent in the Global Ocean

      Alam, Intikhab; Gasol, Josep M; Arold, Stefan T.; Gojobori, Takashi; Kamau, Allan A; Aalismail, Nojood; Martin, Cecilia; Momin, Afaque Ahmad Imtiyaz; Acinas, Silvia G; Guzmán-Vega, Francisco J.; Agusti, Susana R; Jamil, Tahira; Duarte, Carlos M. (Cold Spring Harbor Laboratory, 2020-09-09) [Preprint]
      Estimates of marine plastic stocks, a major threat to marine life, are far lower than expected from exponentially-increasing litter inputs, suggesting important loss factors. These may involve microbial degradation, as the plastic-degrading polyethylene terephthalate enzyme (PETase) has been reported in marine microbial communities. An assessment of 416 metagenomes of planktonic communities across the global ocean identifies 68 oceanic PETase variants (oPETase) that evolved from ancestral enzymes degrading polycyclic aromatic hydrocarbons. Nearly 20 oPETases have predicted efficiencies comparable to those of laboratory-optimized PETases, suggesting strong selective pressures directing the evolution of these enzymes. We found oPETases in 90.1% of samples across all oceans and depths, particularly abundant at 1,000 m depth, with a strong dominance of Pseudomonadales containing putative highly-efficient oPETase variants in the dark ocean. Enzymatic degradation may be removing plastic from the marine environment while providing a carbon source for bathypelagic microbial communities.
    • Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli.

      Abdel-Haleem, Alyaa M.; Ravikumar, Vaishnavi; Ji, Boyang; Mineta, Katsuhiko; Gao, Xin; Nielsen, J.; Gojobori, Takashi; Mijakovic, Ivan (mSystems, American Society for Microbiology, 2020-09-09) [Article]
      Gene essentiality is altered during polymicrobial infections. Nevertheless, most studies rely on single-species infections to assess pathogen gene essentiality. Here, we use genome-scale metabolic models (GEMs) to explore the effect of coinfection of the diarrheagenic pathogen Vibrio cholerae with another enteric pathogen, enterotoxigenic Escherichia coli (ETEC). Model predictions showed that V. cholerae metabolic capabilities were increased due to ample cross-feeding opportunities enabled by ETEC. This is in line with increased severity of cholera symptoms known to occur in patients with dual infections by the two pathogens. In vitro coculture systems confirmed that V. cholerae growth is enhanced in cocultures relative to single cultures. Further, expression levels of several V. cholerae metabolic genes were significantly perturbed as shown by dual RNA sequencing (RNAseq) analysis of its cocultures with different ETEC strains. A decrease in ETEC growth was also observed, probably mediated by nonmetabolic factors. Single gene essentiality analysis predicted conditionally independent genes that are essential for the pathogen's growth in both single-infection and coinfection scenarios. Our results reveal growth differences that are of relevance to drug targeting and efficiency in polymicrobial infections.IMPORTANCE Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single infections and coinfections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae in single infections and coinfections with enterotoxigenic E. coli (ETEC), which cooccur in a large fraction of diarrheagenic patients. Coinfection model predictions showed that V. cholerae growth capabilities are enhanced in the presence of ETEC relative to V. cholerae single infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, cocultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in coculture relative to V. cholerae single cultures while ETEC growth was suppressed. Dual RNAseq analysis of the cocultures also confirmed that the transcriptome of V. cholerae was distinct during coinfection compared to single-infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knockout simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single infections and coinfections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single infections and coinfections; thus, designing inhibitors against those targets would provide a broader spectrum of coverage against cholera infections.
    • Using Eukaryotic Expression Systems to Generate Human α1,3 Fucosyltransferases that Effectively Create Selectin-binding Glycans on Stem Cells

      Al-Amoodi, Asma S.; Sakashita, Kosuke; Ali, Amal J.; Zhou, Ruoyu; Lee, Jae Man; Tehseen, Muhammad; Li, Mo; Izpisua Belmonte, Juan Carlos; Kusakabe, Takahiro; Merzaban, Jasmeen (Biochemistry, American Chemical Society (ACS), 2020-09-09) [Article]
      Recruitment of circulating cells towards target sites is primarily dependent on selectin/ligand adhesive interactions.Glycosyltransferases are involved in the creation of selectin ligands on proteins and lipids. α1,3-fucosylation is imperative for the creation of selectin ligands and a number of fucosyltransferases (FTs) are able to modify terminal lactosamines on cells to create these ligands. One FT, fucosyltransferase VI (FTVI) adds a fucose in an α1,3 configuration to N-acetylglucosamine to generate sialyl Lewis X (sLex) epitopes on proteins of live cells and enhances their ability to bind E-selectin. Although a number of recombinant human FTVIs have been purified, apart from limited commercial enzymes, they were not characterized for their activity on live cells. Here we focused on establishing a robust method to produce FTVI that is active on living cells (hematopoietic cells and mesenchymal stromal cells). To this end, we used two expression systems, Bombyx mori (silkworm) and Pichia pastoris (yeast), to produce significant amounts of N-terminally tagged FTVI and demonstrated that these enzymes have superior activity when compared to currently available commercial enzymes that are produced from various expression systems. Overall, we outline a scheme to attain large amounts of highly active FTVI that can be used for the applications of FTVI in enhancing the engraftment of cells lacking the sLex epitopes.
    • Plasmodium vinckei genomes provide insights into the pan-genome and evolution of rodent malaria parasites

      Ramaprasad, Abhinay; Klaus, Severina; Culleton, Richard; Pain, Arnab; Pain, Arnab (Cold Spring Harbor Laboratory, 2020-09-08) [Preprint]
      Background Rodent malaria parasites (RMPs) serve as tractable tools to study malaria parasite biology and host-parasite-vector interactions. Plasmodium vinckei is the most geographically widespread of the four RMP species with isolates collected in five countries in sub-Saharan Central Africa between 1940s and 1970s. Several P. vinckei isolates are available but are relatively less characterized compared to other RMPs thus hampering its exploitation as rodent malaria models. We have generated a comprehensive resource for P. vinckei comprising of high-quality reference genomes, genotypes, gene expression profiles and growth phenotypes for ten P. vinckei isolates. This also allows for a comprehensive pan-genome analysis of the reference-quality genomes of RMPs. Results Plasmodium vinckei isolates display a large degree of phenotypic and genotypic diversity and potentially constitute a valuable resource to study parasite virulence and immunogenicity. The P. vinckei subspecies have diverged widely from their common ancestor and have undergone genomic structural variations. The subspecies from Katanga, P. v. vinckei, is unique among the P. vinckei isolates with a smaller genome size and a reduced multigene family repertoire. P. v. vinckei infections provide good schizont yields and is amenable to genetic manipulation, making it an ideal vinckei group parasite for reverse genetics. Comparing P. vinckei genotypes reveal region-specific selection pressures particularly on genes involved in mosquito transmission. RMP multigene family expansions observed in P. chabaudi and P. vinckei have occurred in their common ancestor prior to speciation. The erythrocyte membrane antigen 1 (ema1) and fam-c families have considerably expanded among the lowland forests-dwelling P. vinckei parasites with, however, most of the ema1 genes pseudogenised. Genetic crosses can be established in P. vinckei but are limited at present by low transmission success under the experimental conditions tested in this study. Conclusions We observe significant diversity among P. vinckei isolates making them particularly useful for the identification of genotype-phenotype relationships. Inclusion of P. vinckei genomes provide new insights into the evolution of RMPs and their multigene families. Plasmodium vinckei parasites are amenable to experimental genetic crosses and genetic manipulation, making them suitable for classical and functional genetics to study Plasmodium biology.
    • Effect of phosphate availability on biofilm formation in cooling towers.

      Pinel, Ingrid S M; Kim, Lan Hee; Proença Borges, Vitor R; Farhat, Nadia M; Witkamp, Geert Jan; van Loosdrecht, Mark C M; Vrouwenvelder, Johannes S. (Biofouling, Informa UK Limited, 2020-09-05) [Article]
      Phosphate limitation has been suggested as a preventive method against biofilms. P-limited feed water was studied as a preventive strategy against biofouling in cooling towers (CTs). Three pilot-scale open recirculating CTs were operated in parallel for five weeks. RO permeate was fed to the CTs (1) without supplementation (reference), (2) with supplementation by biodegradable carbon (P-limited) and (3) with supplementation of all nutrients (non-P-limited). The P-limited water contained ≤10 µg PO4 l-1. Investigating the CT-basins and coupons showed that P-limited water (1) did not prevent biofilm formation and (2) resulted in a higher volume of organic matter per unit of active biomass compared with the other CTs. Exposure to external conditions and cycle of concentration were likely factors that allowed a P concentration sufficient to cause extensive biofouling despite being the limiting compound. In conclusion, phosphate limitation in cooling water is not a suitable strategy for CT biofouling control.
    • Phenotypic and molecular spectrum of pyridoxamine-5'-phosphate oxidase (PNPO) deficiency: a scoping review of 87 cases of PNPO deficiency.

      Alghamdi, Malak; Bashiri, Fahad A; Abdelhakim, Marwa; Adly, Nouran; Jamjoom, Dima Z; Sumaily, Khalid M; Alghanem, Bandar; Arold, Stefan T. (Clinical genetics, Wiley, 2020-09-05) [Article]
      Pyridoxamine-5'-phosphate oxidase (PNPO) deficiency is an autosomal recessive PLP-vitamin-responsive epileptic encephalopathy. The emerging feature of PNPO deficiency is the occurrence of refractory seizures in the first year of life. Prematurity and fetal distress, combined with neonatal seizures, are other associated key characteristics. The phenotype results from a dependency of pyridoxal 5'-phosphate (PLP) which regulates several enzymes in the body. We present the phenotypic and genotypic spectrum of (PNPO) deficiency based on a literature review (2002 to 2020) of reports (n = 33) of patients with confirmed PNPO deficiency (n = 87). All patients who received PLP (n = 36) showed a clinical response, with a complete dramatic PLP response with seizure cessation observed in 61% of patients. In spite of effective seizure control with PLP, approximately 56% of patients affected with PLP-dependent epilepsy suffer developmental delay/intellectual disability. There is no diagnostic biomarker, and molecular testing required for diagnosis. However, we noted that cerebrospinal fluid (CSF) PLP was low in 81%, CSF glycine was high in 80% and urinary VLA was high in 91% of the cases. We observed only a weak correlation between the severity of PNPO protein disruption and disease outcomes, indicating the importance of other factors, including seizure onset and time of therapy initiation. We found that prematurity, the delay in initiation of PLP therapy and early onset of seizures correlate with a poor neurocognitive outcome. Given the amenability of PNPO to PLP therapy for seizure control, early diagnosis is essential. This article is protected by copyright. All rights reserved.
    • Does color matter? Molecular and ecological divergence in four sympatric color morphs of a coral reef fish

      Gaither, Michelle R.; Coker, Darren James; Greaves, Samuel; Sarigol, Fatih; Payet, Samuel D.; Chaidez, Veronica; Sinclair-Taylor, Tane H.; DiBattista, Joseph; Berumen, Michael L. (Ecology and Evolution, Wiley, 2020-09-04) [Article]
      Non-sex-linked color polymorphism is common in animals and can be maintained in populations via balancing selection or, when under diversifying selection, can promote divergence. Despite their potential importance in ecological interactions and the evolution of biodiversity, their function and the mechanisms by which these polymorphisms are maintained are still poorly understood. Here, we combine field observations with life history and molecular data to compare four sympatric color morphs of the coral reef fish Paracirrhites forsteri (family Cirrhitidae) in the central Red Sea. Our findings verify that the color morphs are not sex-limited, inhabit the same reefs, and do not show clear signs of avoidance or aggression among them. A barcoding approach based on 1,276 bp of mitochondrial DNA could not differentiate the color morphs. However, when 36,769 SNPs were considered, we found low but significant population structure. Focusing on 1,121 FST outliers, we recovered distinct population clusters that corresponded to shifts in allele frequencies with each color morph harboring unique alleles. Genetic divergence at these outlier loci is accompanied by differences in growth and marginal variation in microhabitat preference. Together, life history and molecular analysis suggest subtle divergence between the color morphs in this population, the causes for which remain elusive.
    • Potential feminization of Red Sea turtle hatchlings as indicated by in situ sand temperature profiles

      Tanabe, Lyndsey K.; Ellis, Joanne; Elsadek, Islam; Berumen, Michael L. (Conservation Science and Practice, Wiley, 2020-09-04) [Article]
      Climate change poses a serious threat to species that demonstrate temperature-dependent sex determination, including marine turtles. Increased temperatures can result in highly female-skewed sex ratios and decreased hatching success. The pivotal temperature that delineates hatchling sex ratios is commonly considered to be 29.2°C, but whether this threshold applies to turtles in the Red Sea region has not been tested in situ. For all species of marine turtles, there is a supposed thermal range of 25–33°C in which egg incubation is successful, with prolonged temperatures above 33°C resulting in morphological abnormalities and hatchling mortality. Sand temperature data were collected from May–September 2018 from the average nesting depth of hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas) at five study sites. We calculated the expected sex ratio based on a maximum likelihood model. The sand temperature profile at four of the sites exceeded the pivotal temperature (29.2°C) throughout the study duration, which suggests feminization of turtles could be occurring; however, the pivotal temperature in this region still needs to be empirically confirmed. The percentage of days with sand temperature exceeding the maximum thermal threshold between June 3, and September 16, 2018, was site-specific rather than determined by latitudinal temperature gradients, and ranged between 0 and 100% of days. Maximum temperature recordings were as high as 36.0 and 35.3°C at 30 and 50 cm depth, respectively. Nesting sites in the Red Sea region could already be exceeding the thermal limits and may be particularly vulnerable to rising temperatures. Sites with lower sand temperatures, such as Small Gobal Island, may represent priority areas for conservation efforts. Alternatively, local adaptation may be a reality under extremely warm conditions, thus, further research into the thermal tolerance of hatchlings in the region could provide insight on how they might adapt to future climate change.
    • Removal of Bacteria and Organic Carbon by an Integrated Ultrafiltration—Nanofiltration Desalination Pilot Plant

      Rehman, Zahid Ur; Khojah, Bayan; Leiknes, TorOve; Alsogair, Safiya; Alsomali, Mona (Membranes, MDPI AG, 2020-09-04) [Article]
      Fouling caused by organic matter and bacteria remains a significant challenge for the membrane-based desalination industry. Fouling decreases the permeate quality and membrane performance and also increases energy demands. Here, we quantified the amount of organic matter and bacteria at several stages along the water-treatment train of an integrated ultrafiltration–nanofiltration seawater treatment pilot plant. We quantified the organic matter, in terms of Total Organic Carbon (TOC) and Assimilable Organic Carbon (AOC), and evaluated its composition using Liquid Chromatography for Organic Carbon Detection (LC-OCD). The bacterial cells were counted using Bactiquant. We found that ultrafiltration (UF) was effective at removing bacterial cells (99.7%) but not TOC. By contrast, nanofiltration (NF) successfully removed both TOC (95%) and bacterial cells. However, the NF permeate showed higher amounts of AOC than seawater. LC-OCD analysis suggested that the AOC was mostly composed of low molecular weight neutral substances. Furthermore, we found that the cleaning of the UF membrane using chemically enhanced backwash reduced the amount of AOC released into the UF permeate. By implementing the cleaning-in-place of the NF membrane, the pressure drop was restored to the normal level. Our results show that the UF and NF membrane cleaning regimes investigated in this study improved membrane performance. However, AOC remained the hardest-to-treat fraction of organic carbon. AOC should, therefore, be monitored closely and regularly to mitigate biofouling in downstream processes.
    • Conceptual design of a dynamic turbospacer for efficient low pressure membrane filtration

      Ali, Syed Muztuza; Qamar, Adnan; Phuntsho, Sherub; Ghaffour, NorEddine; Vrouwenvelder, Johannes S.; Shon, Ho Kyong (Desalination, Elsevier BV, 2020-09-03) [Article]
      This study presented a conceptual design of a novel dynamic turbospacer to enhance the performance of a low pressure membrane filtration process. It consists of ladder type filaments and a series of microturbine networks within the filament cells. The rotation of the turbines leads to the formation of turbulence in the feed channel that prevents foulants accumulation. Direct numerical simulation (DNS) was conducted to characterize the fluid flow behaviors of the feed channel for the proposed turbospacer and compared with a standard symmetric non-woven feed spacer. Further, their performances were investigated for a low pressure ultrafiltration (UF) process in a lab-scale experimental setup using 2.8 mm thick 3D printed prototypes of the turbospacer and the standard spacer. Experiments for the proof of this concept were conducted at 173 mL/min and 250 mL/min feed solution inlet velocity when Reynolds number of the flow is 160 and 230 respectively. Substantial reductions in fouling effects using the turbospacer was confirmed by the in-situ Optical Coherence Tomography (OCT) scans of the fouling cake layer accumulated over the membrane during the filtration of seawater with high fouling potential. The proposed turbospacer also lowered the average pressure drop by 4 times and enhanced the specific permeate flux by more than 3 times at 173 mL/min inlet flowratre. At the same operating condition, the specific energy consumption for the turbospacer was found about 2.5 folds lower than the standard spacer.
    • Exostosin-1 Glycosyltransferase Regulates Endoplasmic Reticulum Architecture and Dynamics

      Kerselidou, Despoina; Dohai, Bushra Saeed; Nelson, David R; Daakour, Sarah; De Cock, Nicolas; Kim, Dae-Kyum; Olivet, Julien; El Assal, Diana C; Jaiswal, Ashish; Saha, Deeya; Pain, Charlotte; Matthijssens, Filip; Lemaitre, Pierre; Herfs, Michael; Chapuis, Julien; Ghesquiere, Bart; Vertommen, Didier; Kriechbaumer, Verena; Knoops, Kevin; Lopez-Iglesias, Carmen; van Zandvoort, Marc; Lambert, Jean-Charles; Hanson, Julien; Desmet, Christophe; Thiry, Marc; Lauersen, Kyle J.; Vidal, Marc; Van Vlierberghe, Pieter; Dequiedt, Franck; Salehi-Ashtiani, Kourosh; Twizere, Jean-Claude (Cold Spring Harbor Laboratory, 2020-09-03) [Preprint]
      The endoplasmic reticulum (ER) is a central eukaryotic organelle with a tubular network made of hairpin proteins linked by hydrolysis of GTP nucleotides. Among post-translational modifications initiated at the ER level, glycosylation is the most common reaction. However, our understanding of the impact of glycosylation on ER structure remains unclear. Here, we show that Exostosin-1 (EXT1) glycosyltransferase, an enzyme involved in N-glycosylation, is a key regulator of ER morphology and dynamics. We have integrated multi-omics data and super-resolution imaging to characterize the broad effect of EXT1 inactivation, including ER shape-dynamics-function relationships in mammalian cells. We have observed that, inactivating EXT1 induces cell enlargement and enhances metabolic switches such as protein secretion. In particular, suppressing EXT1 in mouse thymocytes causes developmental dysfunctions associated to ER network extension. Our findings suggest that EXT1 drives glycosylation reactions involving ER structural proteins and high-energy nucleotide sugars, which might also apply to other organelles.
    • Antibacterial rGO-CuO-Ag film with contact- and release-based inactivation properties.

      Alayande, Abayomi Babatunde; Kim, Chang-Min; Vrouwenvelder, Johannes S.; Kim, In S (Environmental research, Elsevier BV, 2020-09-02) [Article]
      To reduce the high operational costs of water treatment because of membrane biofouling, next-generation materials are being developed to counteract microbial growth. These modern anti-biofouling strategies are based on new membrane materials or membrane surface modifications. In this study, antimicrobial films comprising rGO, rGO-CuO, rGO-Ag, and rGO-CuO-Ag were synthesized, evaluated, and tested for potential biofouling control using Pseudomonas aeruginosa PAO1 as the model bacterium. The combined rGO-CuO-Ag film displayed enhanced reduction (10-log reduction) in biofouling in comparison to the rGO film (control), followed by the rGO-Ag film (8-log reduction) and rGO-CuO film (0-log reduction). This demonstrated that the use of mixed antimicrobial agents is more effective in reducing biofouling than that of a single agent. The rGO-Cu-Ag film exhibited consistent, controlled, and moderate release of silver (Ag) ions. The release of Ag ions produced a long-lasting antimicrobial effect. These results underscore the potential applications of combined antimicrobial surface-based agents in practice and further research.
    • Intentional partial beaching in a coral reef fish: a newly recorded hunting behaviour for titan triggerfish, Balistoides viridescens.

      Tietbohl, Matthew; Hardenstine, Royale; Tanabe, Lyndsey K; Hulver, Ann Marie; Berumen, Michael L. (Journal of fish biology, Wiley, 2020-09-01) [Article]
      Coral reef fishes use a multitude of diverse feeding behaviours to increase their ability to successfully capture a wide range of prey. Here, we report a novel hunting behaviour in a coral reef fish, the titan triggerfish, Balistoides viridescens, where an individual was seen partially beaching itself while attempting to catch a Red Sea ghost crab, Ocypode saratan. This is the first report of this behaviour in the order Tetraodontiformes, and represents an astonishing capability for this species to exploit food resources outside their typical assumed ecological niche.
    • Induction of Salt Tolerance by Enterobacter sp. SA187 in the Model Organism Arabidopsis thaliana

      Alzubaidy, Hanin S. (2020-09) [Dissertation]
      Advisor: Hirt, Heribert
      Committee members: Blilou, Ikram; Aranda, Manuel; deZelicourt, Axel; Krasensky-Wrzaczek, Julia
      Arid and semi-arid regions, mostly found in developing countries with exponentially increasing populations, are in chronic lack of water thereby severely limiting agricultural production. Irrigation with saline water, which is available in large quantities, could be an obvious solution, but current crops are all salt sensitive. Although major efforts are underway to breed salt tolerant crops, no breakthrough results have yet been obtained. One alternative could rely on plant-interacting microbiota communities. Indeed, rhizophere and endosphere microbial communities are distinct from those of the surrounding soils, and these specific communities contribute to plant growth and health by increasing nutrient availability or plant resistance towards abiotic and biotic stresses. Here we show that plant microbe interactions induce plant tolerance to multiple stresses. From a collection of strains isolated from the desert plant Indigofera argentea, we could identify at least four different strategies to induce salt stress tolerance in Arabidopsis thaliana. A deep analysis of Enterobacter sp. SA187 showed that it induces Arabidopsis tolerance to salinity through activation of the ethylene signaling pathway. Interestingly, although SA187 does not produce ethylene as such, the association of SA187 with plants induces the expression of the methionine salvage pathway in SA187 resulting in the conversion of bacterially produced 2-keto-4-methylthiobutyric acid (KMBA) to ethylene. In addition, a metabolic network characterization of both SA187 and Arabidopsis in their free-living and endophytic state revealed that the sulfur metabolic pathways are strongly upregulated in both organisms. Furthermore, plant genetic experiments verified the essential role of the sulfur metabolism and ethylene signaling in plant salt stress tolerance. Our findings demonstrate how successful plant microbes of a given community can help other plants to enhance tolerance to abiotic stress, and reveal a part of the complex molecular communication process during beneficial plant-microbe interaction.
    • Environmental DNA identifies marine macrophyte contributions to Blue Carbon sediments

      Ortega, Alejandra; Geraldi, Nathan; Duarte, Carlos M. (Limnology and Oceanography, Wiley, 2020-08-31) [Article]
      Estimation of marine macrophyte contribution to coastal sediments is key to understand carbon sequestration dynamics. Nevertheless, identification of macrophyte carbon is challenging. We propose environmental DNA (eDNA) metabarcoding as a new approach for identification of sediment contributors, and compared this approach against stable isotopes—the traditional approach. eDNA metabarcoding allowed high-resolution identification of 48 macroalgae, seagrasses, and mangroves from coastal habitats. The relative eDNA contributions of macrophytes were similar to their contributions of organic carbon based on stable isotopes; however, isotopes were unreliable for taxonomical discrimination among macrophyte sources. Additionally, we experimentally found that eDNA abundance in the sediment correlates with both the DNA (84%, R2 = 0.71, p = 0.001) and the organic carbon content (76%, R2 = 0.58, p = 0.006) per macrophyte lineage. These results demonstrate the unparallel resolution of eDNA as a method for estimation of the organic carbon contribution of marine macrophytes to blue carbon stocks.