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  • 3D -printed high-NA catadioptric thin lens for suppression of XPM background in Stimulated Raman Scattering microscopy

    Bertoncini, Andrea; Laptenok, Siarhei; Genchi, Luca; Rajamanickam, Vijayakumar Palanisamy; Liberale, Carlo (Journal of Biophotonics, Wiley, 2020-07-13) [Article]
    Stimulated Raman Scattering (SRS) is a fast chemical imaging technique with remarkable bio-science applications. Cross Phase Modulation (XPM) is a ubiquitous non-linear phenomenon that can create spurious background signals that render difficult a high-contrast imaging in SRS measurements. The XPM-induced signal is usually suppressed using high Numerical Aperture (NA) microscope objectives or condensers to collect the transmitted excitation beam. However, these high-NA optics feature short working distances, hence they are not compatible with stage-top incubators, that are necessary to perform live-cell time-lapse experiments in controlled environments. Here,we showa 3D printed high-NAcompact catadioptric lens that fits inside stage-top incubators and allows the collection of XPM-free SRS signals. The lens delivers SRS images and spectra with a quality comparable to a signal collection with a high-NA microscope objective. We also demonstrate the compatibility of the 3D printed lens with other non-linear microscopies usually associated with SRS in multimodal microscopes.
  • Simplified detection of polyhistidine-tagged proteins in gels and membranes using a UV-excitable dye and a multiple chelator head pair

    Raducanu, Vlad-Stefan; Isaioglou, Ioannis; Raducanu, Daniela-Violeta; Merzaban, Jasmeen; Hamdan, Samir (Journal of Biological Chemistry, American Society for Biochemistry & Molecular Biology (ASBMB), 2020-07-09) [Article]
    <jats:p>The polyhistidine tag (His-tag) is one of the most popular protein tags used in the life sciences. Traditionally, the detection of His-tagged proteins relies on immunoblotting with anti-His antibodies. This approach is laborious for certain applications such as protein purification, where time and simplicity are critical. The His-tag can also be directly detected by metal ion–loaded N-nitrilotriacetic acid–based chelator heads conjugated to fluorophores, which is a convenient alternative method to immunoblotting. Typically, such chelator heads are conjugated to either green or red fluorophores, the detection of which requires specialized excitation sources and detection systems. Here, we demonstrate that post-run staining is ideal for His-tag detection by metal ion–loaded and fluorescently labeled chelator heads in PAGE and blot membranes. Additionally, by comparing the performances of different chelator heads, we show how differences in microscopic affinity constants translate to macroscopic differences in the detection limits in environments with limited diffusion, such as PAGE. On the basis of these results, we devise a simple approach, called UVHis-PAGE, that uses metal ion–loaded and fluorescently labeled chelator heads to detect His-tagged proteins in PAGE and blot membranes. Our method uses a UV transilluminator as an excitation source, and the results can be visually inspected by the naked eye.</jats:p>
  • NIR multiphoton ablation of cancer cells, fluorescence quenching and cellular uptake of dansyl-glutathione-coated gold nanoparticles

    Buonerba, Antonio; Lapenta, Rosita; Donniacuo, Anna; Licasale, Magda; Vezzoli, Elena; Milione, Stefano; Capacchione, Carmine; Tecce, Mario Felice; Falqui, Andrea; Piacentini, Roberto; Grassi, Claudio; Grassi, Alfonso (Scientific Reports, Springer Science and Business Media LLC, 2020-07-09) [Article]
    Theranostics based on two-photon excitation of therapeutics in the NIR region is an emerging and powerful tool in cancer therapy since this radiation deeply penetrates healthy biological tissues and produces selective cell death. Aggregates of gold nanoparticles coated with glutathione corona functionalized with the dansyl chromophore (a-DG-AuNPs) were synthesized and found efficient nanodevice for applications in photothermal therapy (PTT). Actually the nanoparticle aggregation enhances the quenching of radiative excitation and the consequent conversion into heat. The a-DG-AuNPs are readily internalized in Hep G2 where the chromophore acts as both antenna and transducer of the NIR radiation under two-photons excitation, determining efficient cell ablation via photothermal effect.
  • Physical and economical evaluation of laboratory-scale membrane bioreactor by long-term relative cost–benefit analysis

    Ayub, Mariam; Saeed, Nadeeha; Chung, Shinho; Nawaz, Muhammad Saqib; Ghaffour, NorEddine (Journal of Water Reuse and Desalination, IWA Publishing, 2020-07-08) [Article]
    Two laboratory-scale single-stage submerged membrane bioreactors (MBRs) were operated in parallel to examine the effect of different flux conditions and several fouling mitigation methods. After control operation (filtration only), three fouling control methods (relaxation, standard backwash and chemical backwash) at 27 LMH flux and four different flux conditions (54, 36, 27 and 18 LMH) with standard backwash were applied. Physical performance of MBRs was evaluated based on the operational duration to reach maximum transmembrane pressure and the volume of permeate produced during the operational duration. Then relative cost–benefit analysis was carried out. Results showed that the combination of chemical backwash and standard backwash was the most effective for fouling mitigation in terms of physical improvement of MBR performance. However, the combination proved less economical (400% + α relative cost) than standard backwash alone (343% relative cost), because of the additional cost for pumps and chemical. It also showed that lower flux (18 LMH) is desirable as it showed better physical performance (1,770% improvement as compared to the highest flux, 54 LMH) and proved more economical than higher flux configuration. Therefore, it is concluded that the operation with standard backwash at the lowest possible flux is the best combination to improve MBR performance as well as long-term cost–benefit.
  • Natal philopatry increases relatedness within groups of coral reef cardinalfish

    Rueger, Theresa; Harrison, Hugo B.; Buston, Peter M.; Gardiner, Naomi M.; Berumen, Michael L.; Jones, G. P. (Proceedings of the Royal Society B: Biological Sciences, The Royal Society, 2020-07-08) [Article]
    A central issue in evolutionary ecology is how patterns of dispersal influence patterns of relatedness in populations. In terrestrial organisms, limited dispersal of offspring leads to groups of related individuals. By contrast, for most marine organisms, larval dispersal in open waters is thought to minimize kin associations within populations. However, recent molecular evidence and theoretical approaches have shown that limited dispersal, sibling cohesion and/or differential reproductive success can lead to kin association and elevated relatedness. Here, we tested the hypothesis that limited dispersal explains small-scale patterns of relatedness in the pajama cardinalfish Sphaeramia nematoptera. We used 19 microsatellite markers to assess parentage of 233 juveniles and pairwise relatedness among 527 individuals from 41 groups in Kimbe Bay, Papua New Guinea. Our findings support three predictions of the limited dispersal hypothesis: (i) elevated relatedness within groups, compared with among groups and elevated relatedness within reefs compared with among reefs; (ii) a weak negative correlation of relatedness with distance; (iii) more juveniles than would be expected by chance in the same group and the same reef as their parents. We provide the first example for natal philopatry at the group level causing small-scale patterns of genetic relatedness in a marine fish.
  • Seagrass losses since mid-20th century fuelled CO 2 emissions from soil carbon stocks

    Salinas, Cristian; Duarte, Carlos M.; Lavery, P. S.; Masqué, Pere; Arias-Ortiz, Ariane; Leon, Javier X.; Callaghan, David; Kendrick, G. A.; Serrano, Oscar (Global Change Biology, Wiley, 2020-07-07) [Article]
    Seagrass meadows store globally significant organic carbon (Corg) stocks which, if disturbed, can lead to CO2 emissions, contributing to climate change. Eutrophication and thermal stress continue to be a major cause of seagrass decline worldwide, but the associated CO2 emissions remain poorly understood. This study presents comprehensive estimates of seagrass soil Corg erosion following eutrophication-driven seagrass loss in Cockburn Sound (23 km2 between 1960s and 1990s) and identifies the main drivers. We estimate that shallow seagrass meadows (<5 m depth) had significantly higher Corg stocks in 50 cm thick soils (4.5 ± 0.7 kg Corg/m2) than previously vegetated counterparts (0.5 ± 0.1 kg Corg/m2). In deeper areas (>5 m), however, soil Corg stocks in seagrass and bare but previously vegetated areas were not significantly different (2.6 ± 0.3 and 3.0 ± 0.6 kg Corg/m2, respectively). The soil Corg sequestration capacity prevailed in shallow and deep vegetated areas (55 ± 11 and 21 ± 7 g Corg m−2 year−1, respectively), but was lost in bare areas. We identified that seagrass canopy loss alone does not necessarily drive changes in soil Corg but, when combined with high hydrodynamic energy, significant erosion occurred. Our estimates point at ~0.20 m/s as the critical shear velocity threshold causing soil Corg erosion. We estimate, from field studies and satellite imagery, that soil Corg erosion (within the top 50 cm) following seagrass loss likely resulted in cumulative emissions of 0.06–0.14 Tg CO2-eq over the last 40 years in Cockburn Sound. We estimated that indirect impacts (i.e. eutrophication, thermal stress and light stress) causing the loss of ~161,150 ha of seagrasses in Australia, likely resulted in the release of 11–21 Tg CO2-eq since the 1950s, increasing cumulative CO2 emissions from land-use change in Australia by 1.1%–2.3% per annum. The patterns described serve as a baseline to estimate potential CO2 emissions following disturbance of seagrass meadows.
  • SARS-CoV-2 infections and COVID-19 mortalities strongly correlate with ACE1 I/D genotype.

    Yamamoto, Naoki; Ariumi, Yasuo; Nishida, Nao; Yamamoto, Rain; Bauer, Georg; Gojobori, Takashi; Shimotohno, Kunitada; Mizokami, Masashi (Gene, Elsevier BV, 2020-07-07) [Article]
    Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). The relentless spread and pathogenicity of the virus have become a global public health emergency. One of the striking features of this pandemic is the pronounced impact on specific regions and ethnic groups. In particular, compared with East Asia, where the virus first emerged, SARS-CoV-2 has caused high rates of morbidity and mortality in Europe. This has not been experienced in past global viral infections, such as influenza, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and is unique to SARS-CoV-2. For this reason, we investigated the involvement of genetic factors associated with SARS-CoV-2 infection with a focus on angiotensin-converting enzyme (ACE)-related genes, because ACE2 is a receptor for SARS-CoV-2. We found that the ACE1 II genotype frequency in a population was significantly negatively correlated with the number of SARS-CoV-2 cases. Similarly, the ACE1 II genotype was negatively correlated with the number of deaths due to SARS-CoV-2 infection. These data suggest that the ACE1 II genotype may influence the prevalence and clinical outcome of COVID-19 and serve as a predictive marker for COVID-19 risk and severity.
  • Expression of a carotenogenic gene allows faster biomass production by redesigning plant architecture and improving photosynthetic efficiency in tobacco.

    Moreno, Juan C; Mi, Jianing; Agrawal, Shreya; Kössler, Stella; Turečková, Veronika; Tarkowská, Danuše; Thiele, Wolfram; Al-Babili, Salim; Bock, Ralph; Schöttler, Mark Aurel (The Plant journal : for cell and molecular biology, Wiley, 2020-07-06) [Article]
    Because carotenoids act as accessory pigments in photosynthesis, play a key photoprotective role, and are of major nutritional importance, carotenogenesis has been a target for crop improvement. Although carotenoids are important precursors of phytohormones, previous genetic manipulations reported little if any effects on biomass production and plant development, but resulted in specific modifications in carotenoid content. Unexpectedly, the expression of the carrot lycopene b-cyclase (DcLCYB1) in Nicotiana tabacum cv. Xanthi not only resulted in increased carotenoid accumulation, but also in altered plant architecture characterized by longer internodes, faster plant growth, early flowering and increased biomass. Here, we have challenged these transformants with a range of growth conditions to determine the robustness of their phenotype and analyze the underlying mechanisms. Transgenic DcLCYB1 lines showed increased transcript levels of key genes involved in carotenoid, chlorophyll, gibberellin (GA) and abscisic acid (ABA) biosynthesis, but also in photosynthesis-related genes. Accordingly, their carotenoid, chlorophyll, ABA and GA contents were increased. Hormone application and inhibitor experiments confirmed the key role of altered GA/ABA contents in the growth phenotype. Because the longer internodes reduce shading of mature leaves, induction of leaf senescence was delayed, and mature leaves maintained a high photosynthetic capacity. This increased total plant assimilation, as reflected in higher plant yields under both fully-controlled constant and fluctuating light, and in non-controlled conditions. Furthermore, our data is a warning that engineering of isoprenoid metabolism can cause complex changes in phytohormone homeostasis and therefore plant development, which have not been sufficiently considered in previous studies.
  • Unfamiliar partnerships limit cnidarian holobiont acclimation to warming

    Herrera Sarrias, Marcela; Klein, Shannon; Schmidt-Roach, Sebastian; Campana, Sara; Cziesielski, Maha Joana; Chen, Jit Ern; Duarte, Carlos M.; Aranda, Manuel (Global Change Biology, Wiley, 2020-07-06) [Article]
    Enhancing the resilience of corals to rising temperatures is now a matter of urgency, leading to growing efforts to explore the use of heat tolerant symbiont species to improve their thermal resilience. The notion that adaptive traits can be retained by transferring the symbionts alone, however, challenges the holobiont concept, a fundamental paradigm in coral research. Holobiont traits are products of a specific community (holobiont) and all its co-evolutionary and local adaptations, which might limit the retention or transference of holobiont traits by exchanging only one partner. Here, we evaluate how interchanging partners affect the short- and long-term performance of holobionts under heat stress using clonal lineages of the cnidarian model system Aiptasia (host and Symbiodiniaceae strains) originating from distinct thermal environments. Our results show that holobionts from more thermally variable environments have higher plasticity to heat stress, but this resilience could not be transferred to other host genotypes through the exchange of symbionts. Importantly, our findings highlight the role of the host in determining holobiont productivity in response to thermal stress and indicate that local adaptations of holobionts will likely limit the efficacy of interchanging unfamiliar compartments to enhance thermal tolerance.
  • Biofouling control by phosphorus limitation strongly depends on the assimilable organic carbon concentration.

    Javier, Luisa; Farhat, Nadia M; Desmond, Peter; Linares, Rodrigo Valladares; Bucs,Szilard; Kruithof, Joop C; Vrouwenvelder, Johannes S. (Water research, Elsevier BV, 2020-07-05) [Article]
    Nutrient limitation is a biofouling control strategy in reverse osmosis (RO) membrane systems. In seawater, the assimilable organic carbon content available for bacterial growth ranges from about 50 to 400 μg C·L-1, while the phosphorus concentration ranges from 3 to 11 μg P·L-1. Several studies monitored biofouling development, limiting either carbon or phosphorus. The effect of carbon to phosphorus ratio and the restriction of both nutrients on membrane system performance have not yet been investigated. This study examines the impact of reduced phosphorus concentration (from 25 μg P·L-1 and 3 μg P·L-1, to a low concentration of ≤0.3 μg P·L-1), combined with two different carbon concentrations (250 C L-1 and 30 μg C·L-1), on biofilm development in an RO system. Feed channel pressure drop was measured to determine the effect of the developed biofilm on system performance. The morphology of the accumulated biomass for both carbon concentrations was characterized by optical coherence tomography (OCT) and the biomass amount and composition was quantified by measuring total organic carbon (TOC), adenosine triphosphate (ATP), total cell counts (TCC), and extracellular polymeric substances (EPS) concentration for the developed biofilms under phosphorus restricted (P-restricted) and dosed (P-dosed) conditions. For both carbon concentrations, P-restricted conditions (≤0.3 μg P·L-1) limited bacterial growth (lower values of ATP, TCC). A faster pressure drop increase was observed for P-restricted conditions compared to P-dosed conditions when 250 μg C·L-1 was dosed. This faster pressure drop increase can be explained by a higher area covered by biofilm in the flow channel and a higher amount of produced EPS. Conversely, a slower pressure drop increase was observed for P-restricted conditions compared to P-dosed conditions when 30 μg C·L-1 was dosed. Results of this study demonstrate that P-limitation delayed biofilm formation effectively when combined with low assimilable organic carbon concentration and thereby, lengthening the overall membrane system performance.
  • Effect of organic micropollutants on biofouling in a forward osmosis process integrating seawater desalination and wastewater reclamation

    Kim,Youngjin; Kim, Lan Hee; Vrouwenvelder, Johannes S.; Ghaffour, NorEddine (Journal of Hazardous Materials, Elsevier BV, 2020-07-04) [Article]
    This study systematically investigated the effect of organic micropollutants (OMPs) on biofouling in forward osmosis (FO) integrating wastewater treatment and seawater dilution. Synthetic seawater (0.6 M sodium chloride) was used as a draw solution and synthetic municipal wastewater as a feed solution. To evaluate the impact of OMPs in a replicate parallel study, wastewater was supplemented with a mixture of 7 OMPs (OMPs-feed) and without OMPs (control) during 8 batch filtration cycles with feed and draw solution replacement after each filtration. The FO performance (water flux), development and microbial composition properties of biofilm layers on the wastewater side of the FO membrane were studied. Compared to the control without OMPs, the FO fed with OMPs containing wastewater showed (i) initially the same water flux and flux decline during the first filtration cycle, (ii) with increasing filtration cycle a lower flux decline and (iii) lower concentrations for the total cells, ATP, EPS carbohydrates and proteins in biofilm layers, and (iv) a lower diversity of the biofilm microbial community composition (indicating selective pressure) and (v) increasing rejection of 6 of the 7 OMPs. In essence, biofouling on the FO membrane showed (i) a lower flux decline in the presence of OMPs in the feed water and (ii) a higher OMPs rejection, both illustrating better membrane performance. This study has a significant implication for optimizing osmotic dilution in terms of FO operation and OMPs rejection.
  • Deracemization and Stereoinversion of Alcohols Using Two Mutants of Secondary Alcohol Dehydrogenase from Thermoanaerobacter pseudoethanolicus

    Nafiu, Sodiq A.; Takahashi, Masateru; Takahashi, Etsuko; Hamdan, Samir; Musa, Musa M. (European Journal of Organic Chemistry, Wiley, 2020-07-03) [Article]
    We developed a one-pot two-step deracemization approach for alcohols using two mutants of Thermoanaerobacter pseudoethanolicus secondary alcohol dehydrogenase ( Te SADH). This approach relies on consecutive non-stereospecific oxidation of alcohols and stereoselective reduction of their prochiral ketones using two mutants of Te SADH with poor and good stereoselectivities, respectively. More specifically, W110G Te SADH enables a non-stereospecific oxidation of alcohol racemates to their corresponding prochiral ketones, followed by W110V Te SADH-catalyzed stereoselective reduction of the resultant ketone intermediates to enantiopure ( S )-configured alcohols in up to >99% enantiomeric excess. A heat treatment after the oxidation step was required to avoid the interference of the marginally stereoselective W110G Te SADH in the reduction step; this heat treatment was eliminated by using sol-gel encapsulated W110G Te SADH in the oxidation step. Moreover, this bi-enzymatic approach was implemented in the stereoinversion of ( R )-configured alcohols, and ( S )-configured alcohols with up to >99% enantiomeric excess were obtained by this Mitsunobu-like stereoinversion reaction.
  • Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1.

    Tauber, Maria; Kreuz, Sarah; Lemak, Alexander; Mandal, Papita; Yerkesh, Zhadyra; Veluchamy, Alaguraj; Al-Gashgari, Bothayna; Aljahani, Abrar; Cortés-Medina, Lorena V; Azhibek, Dulat; Fan, Lixin; Ong, Michelle S; Duan, Shili; Houliston, Scott; Arrowsmith, Cheryl H; Fischle, Wolfgang (Nucleic acids research, Oxford University Press (OUP), 2020-07-02) [Article]
    UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.
  • High rates of carbon and dinitrogen fixation suggest a critical role of benthic pioneer communities in the energy and nutrient dynamics of coral reefs

    Roth, Florian; Karcher, Denis B.; Rädecker, Nils; Hohn, Sönke; Carvalho, Susana; Thomson, Timothy; Saalmann, Franziska; Voolstra, Christian R.; Kürten, Benjamin; Struck, Ulrich; Jones, Burton; Wild, Christian (Functional Ecology, Wiley, 2020-07-02) [Article]
    1. Following coral mortality in tropical reefs, pioneer communities dominated by filamentous and crustose algae efficiently colonize substrates previously occupied by coral tissue. This phenomenon is particularly common after mass coral mortality following prolonged bleaching events associated with marine heatwaves. 2. Pioneer communities play an important role for the biological succession and reorganization of reefs after disturbance. However, their significance for critical ecosystem functions previously mediated by corals, such as the efficient cycling of carbon (C) and nitrogen (N) within the reef, remains uncertain. 3. We used 96 carbonate tiles to simulate the occurrence of bare substrates after disturbance in a coral reef of the central Red Sea. We measured rates of C and dinitrogen (N2) fixation of pioneer communities on these tiles monthly over an entire year. Coupled with elemental and stable isotope analyses, these measurements provide insights into macronutrient acquisition, export, and the influence of seasonality. 4. Pioneer communities exhibited high rates of C and N2 fixation within 4 – 8 weeks after the introduction of experimental bare substrates. Ranging from 13 to 25 μmol C cm−2 d−1 and 8 to 54 nmol N cm−2 d−1, respectively, C and N2 fixation rates were comparable to reported values for established Red Sea coral reefs. This similarity indicates that pioneer communities may quickly compensate for the loss of benthic productivity by corals. Notably, between 40 and 85% of fixed organic C was exported into the environment, constituting a vital source of energy for the coral reef food web. 5. Our findings suggest that benthic pioneer communities may play a crucial, yet overlooked role in the C and N dynamics of oligotrophic coral reefs by contributing to the input of new C and N after coral mortality. While not substituting other critical ecosystem functions provided by corals (e.g. structural habitat complexity and coastal protection), pioneer communities likely contribute to maintaining coral reef nutrient cycling through the accumulation of biomass and import of macronutrients following coral loss.
  • DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques.

    Thafar, Maha A.; Olayan, Rawan S.; Ashoor, Haitham; Albaradei, Somayah; Bajic, Vladimir B.; Gao, Xin; Gojobori, Takashi; Essack, Magbubah (Journal of Cheminformatics, Springer Science and Business Media LLC, 2020-07-02) [Article]
    In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. However, developing such computational methods is not an easy task, but is much needed, as current methods that predict potential drug–target interactions suffer from high false-positive rates. Here we introduce DTiGEMS+, a computational method that predicts Drug–Target interactions using Graph Embedding, graph Mining, and Similarity-based techniques. DTiGEMS+ combines similarity-based as well as feature-based approaches, and models the identification of novel drug–target interactions as a link prediction problem in a heterogeneous network. DTiGEMS+ constructs the heterogeneous network by augmenting the known drug–target interactions graph with two other complementary graphs namely: drug–drug similarity, target–target similarity. DTiGEMS+ combines different computational techniques to provide the final drug target prediction, these techniques include graph embeddings, graph mining, and machine learning. DTiGEMS+ integrates multiple drug–drug similarities and target–target similarities into the final heterogeneous graph construction after applying a similarity selection procedure as well as a similarity fusion algorithm. Using four benchmark datasets, we show DTiGEMS+ substantially improves prediction performance compared to other state-of-the-art in silico methods developed to predict of drug-target interactions by achieving the highest average AUPR across all datasets (0.92), which reduces the error rate by 33.3% relative to the second-best performing model in the state-of-the-art methods comparison.
  • Cell-by-cell estimation of PAH sorption and subsequent toxicity in marine phytoplankton

    Kottuparambil, Sreejith; Agusti, Susana (Chemosphere, Elsevier BV, 2020-07-01) [Article]
    Polycyclic Aromatic Hydrocarbons (PAHs) have elicited increasing concern due to their ubiquitous occurrence in coastal marine environments and resultant toxicity in organisms. Due to their lipophilic nature, PAHs tend to accumulate in phytoplankton cells and thus subsequently transfer to other compartments of the marine ecosystem. The intrinsic fluorescence properties of PAHs in the ultraviolet (UV)/blue spectral range have recently been exploited to investigate their uptake modes, localization, and aggregation in various biological tissues. Here, we quantitatively evaluate the sorption of two model PAHs (phenanthrene and pyrene) in three marine phytoplankton species (Chaetoceros tenuissimus, Thalassiosira sp. and Proteomonas sp.) using a combined approach of UV excitation flow cytometry and fluorescence microscopy. Over a 48-h exposure to a gradient of PAHs, Thalassiosira sp. showed the highest proportion of PAH-sorbed cells (29% and 97% of total abundance for phenanthrene and pyrene, respectively), which may be attributed to its relatively high total lipid content (33.87 percent dry weight). Moreover, cell-specific pulse amplitude modulation (PAM) microscope fluorometry revealed that PAH sorption significantly reduced the photosynthetic quantum efficiency (Fv/Fm) of individual phytoplankton cells. We describe a rapid and precise hybrid method for the detection of sorption of PAHs on phytoplankton cells. Our results emphasize the ecologically relevant sub-lethal effects of PAHs in phytoplankton at the cellular level, even at concentrations where no growth inhibition was apparent. This work is the first study to address the cell-specific impacts of fluorescent toxicants in a more relevant toxicant-sorbed subpopulation; these cell-specific impacts have to date been unidentified in traditional population-based phytoplankton toxicity assays.
  • A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples

    Ramos Mandujano, Gerardo; Salunke, Rahul; Mfarrej, Sara; Rachmadi, Andri Taruna; Hala, Sharif; Xu, Jinna; Alofi, Fadwa S; Khogeer, Asim; Hashem, Anwar M; Almontashiri, Naif AM; Alsomali, Afrah; Hamdan, Samir; Hong, Pei-Ying; Pain, Arnab; Li, Mo (Cold Spring Harbor Laboratory, 2020-06-29) [Preprint]
    <jats:p>Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magnetic- nanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics.</jats:p>
  • Patterns, drivers, and ecological implications of upwelling in coral reef habitats of the southern Red Sea

    De Carlo, Thomas Mario; Carvalho, Susana; Gajdzik, Laura; Hardenstine, Royale; Tanabe, Lyndsey K; Villalobos, Rodrigo; Berumen, Michael L. (Wiley, 2020-06-28) [Preprint]
    Coral reef ecosystems are highly sensitive to thermal anomalies, making them vulnerable to ongoing global warming. Yet, a variety of cooling mechanisms, such as upwelling, offer some respite to certain reefs. The Farasan Banks in the southern Red Sea is home to hundreds of coral reefs covering 16,000 km and experiences among the highest water temperatures of any coral-reef region despite exposure to summertime upwelling. We deployed an array of temperature loggers on coral reefs in the Farasan Banks, enabling us to evaluate the skill of satellite-based sea surface temperature (SST) products for capturing patterns of upwelling. Additionally, we used remote sensing products to investigate the physical drivers of upwelling, and to better understand how upwelling modulates summertime heat stress on coral communities. Our results show that various satellite SST products underestimate reef-water temperatures but differ in their ability to capture the spatial and temporal dynamics of upwelling. Monsoon winds from June to September drive the upwelling in the southern Red Sea via Ekman transport of surface waters off the shelf, and this process is ultimately controlled by the southwest Indian monsoon in the Arabian Sea. Further, the timing of the cessation of monsoon winds regulates the maximum water temperatures that are reached in September and October. In addition to describing the patterns and mechanisms of upwelling, our study sheds light on the broad ecological implications of this upwelling system, including modulation of coral bleaching events and effects on biodiversity, sea turtle reproduction, fish pelagic larval duration, and planktivore populations.
  • Additive impacts of deoxygenation and acidification threaten marine biota.

    Steckbauer, Alexandra; Klein, Shannon; Duarte, Carlos M. (Global change biology, Wiley, 2020-06-26) [Article]
    Deoxygenation in coastal and open-ocean ecosystems rarely exists in isolation but occurs concomitantly with acidification. Here, we first combine meta-data of experimental assessments from across the globe to investigate the potential interactive impacts of deoxygenation and acidification on a broad range of marine taxa. We then characterize the differing degrees of deoxygenation and acidification tested in our dataset using a ratio between the partial pressure of oxygen and carbon dioxide (pO2 /pCO2 ) to assess how biological processes change under an extensive, yet diverse range of pO2 and pCO2 conditions. The dataset comprised 375 experimental comparisons and revealed predominantly additive but variable effects (91.7%-additive, 6.0%-synergistic, 2.3%-antagonistic) of the dual stressors, yielding negative impacts across almost all responses examined. Our data indicates that the pO2 /pCO2 -ratio offers a simplified metric to characterize the extremity of the concurrent stressors and shows that more severe impacts occurred when ratios represented more extreme deoxygenation and acidification conditions. Importantly, our analysis highlights the need to assess the concurrent impacts of deoxygenation and acidification on marine taxa and that assessments considering the impact of O2 depletion alone will likely underestimate the impacts of deoxygenation events and their ecosystem-wide consequences.
  • Flow field in fouling spiral wound reverse osmosis membrane modules using MRI velocimetry

    Bristow, Nicholas W.; Vogt, Sarah J.; O'Neill, Keelan T.; Vrouwenvelder, Johannes S.; Johns, Michael L.; Fridjonsson, Einar O. (Desalination, Elsevier BV, 2020-06-26) [Article]
    Magnetic Resonance Imaging (MRI) velocimetry was applied to study non-invasively the water flow field inside a spiral-wound desalination membrane module (diameter: 2.5 in.; length: 18.5 in.), located in a pressure vessel, at typical practice operational conditions as a function of alginate fouling, simulating extracellular polymeric substances (EPS). Cross-sectional velocity images were acquired at an in-plane spatial resolution of 0.137 mm at multiple locations along the length of the reverse osmosis module and were acquired as a function of alginate concentration. At a total system alginate concentration of 3.25 mg/l, significant changes in the cross-sectional velocity map were observed near the module inlet due to alginate fouling, with limited changes observed in the middle and outlet regions of the module. When the total system alginate concentration was increased to 75 mg/l, it caused the module brine seal to fail resulting in significant local water flow by-passing the membrane module. This was clearly discernible in this opaque membrane system using MRI and resulting in dramatic changes in fluid velocity distribution through the membrane module. These observations of significant flow field heterogeneity as fouling develops are consistent with ‘irreversible’ fouling effects noted frequently in practice by the water treatment industry.

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