Recent Submissions

  • Species delineation and hybrid identification using diagnostic nuclear markers for Plectropomus leopardus and Plectropomus maculatus

    He, Song; Harrison, Hugo B.; Berumen, Michael L. (Elsevier BV, 2018-06-01)
    Diagnostic molecular markers are an essential tool in the study of species’ ecology and evolution, particularly in closely related and sympatric species. Furthermore, the increasing awareness of wild-hybrids has led to a renewed interest in rapid diagnostic assays. Here, we test the ability of two mitochondrial (Cytb and COI) and two nuclear markers (ETS2 and TMO-4c4) to confidently discriminate purebred P. leopardus and P. maculatus and their first-generation hybrids. A sample of 48 purebred individuals and 91 interspecific hybrids were used in this study and their delineation confirmed using a set of microsatellite markers. Our results indicate mitochondrial markers could not distinguish even between species but both nuclear markers confidently identified species and first-generation hybrids. However, later-generation hybrids could not always be confidently identified due to on-going introgression between species. Our findings provide a robust tool to distinguish purebred individuals and interspecific hybrids in a pair of species with an unexpectedly high incidence of hybridization. The quick species discrimination abilities provided by these diagnostic markers are important for stock assessment and recruitment studies of these important fishery species.
  • Bacterial polyextremotolerant bioemulsifiers from arid soils improve water retention capacity and humidity uptake in sandy soil

    Raddadi, Noura; Giacomucci, Lucia; Marasco, Ramona; Daffonchio, Daniele; Cherif, Ameur; Fava, Fabio (Springer Nature, 2018-05-31)
    Water stress is a critical issue for plant growth in arid sandy soils. Here, we aimed to select bacteria producing polyextremotolerant surface-active compounds capable of improving water retention and humidity uptake in sandy soils.From Tunisian desert and saline systems, we selected eleven isolates able to highly emulsify different organic solvents. The bioemulsifying activities were stable with 30% NaCl, at 4 and 120 °C and in a pH range 4-12. Applications to a sandy soil of the partially purified surface-active compounds improved soil water retention up to 314.3% compared to untreated soil. Similarly, after 36 h of incubation, the humidity uptake rate of treated sandy soil was up to 607.7% higher than untreated controls.Overall, results revealed that polyextremotolerant bioemulsifiers of bacteria from arid and desert soils represent potential sources to develop new natural soil-wetting agents for improving water retention in arid soils.
  • The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and apoplastic immunity

    Abulfaraj, Aala A.; Mariappan, Kiruthiga; Bigeard, Jean; Manickam, Prabhu; Blilou, Ikram; Guo, Xiujie; Al-Babili, Salim; Pflieger, Delphine; Hirt, Heribert; Rayapuram, Naganand (Life Science Alliance, LLC, 2018-05-31)
    Mammalian Ras-GTPase–activating protein SH3-domain–binding proteins (G3BPs) are a highly conserved family of RNA-binding proteins that link kinase receptor-mediated signaling to RNA metabolism. Mammalian G3BP1 is a multifunctional protein that functions in viral immunity. Here, we show that the Arabidopsis thaliana homolog of human G3BP1 negatively regulates plant immunity. Arabidopsis g3bp1 mutants showed enhanced resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Pathogen resistance was mediated in Atg3bp1 mutants by altered stomatal and apoplastic immunity. Atg3bp1 mutants restricted pathogen entry into stomates showing insensitivity to bacterial coronatine–mediated stomatal reopening. AtG3BP1 was identified as a negative regulator of defense responses, which correlated with moderate up-regulation of salicylic acid biosynthesis and signaling without growth penalty.
  • Towards informed metrics for examining the role of human-induced animal responses in tag studies on wild animals

    Wilson, Rory P.; Holton, Mark; Wilson, Vianney L.; Gunner, Richard; Tysse, Brenda; Wilson, Gwendoline I; Quintana, Flavio; Duarte, Carlos M.; Scantlebury, D. Michael (Wiley, 2018-05-31)
    Two prime issues can detrimentally affect animals that have been equipped with tags; (i) the effect of the capture and restraint process and (ii) the effect of the tag itself. This work examines some of the issues surrounding quantification of tag effects on wild animals for both restrained and free-living animals. A new method to quantify stress effects based on monitoring ventilation rates in relation to activity is suggested for restrained animals which may help improve the practice of handling animals. It is also suggested that various metrics, many derived from accelerometers, can be examined in tagged wild animals to examine the change in behaviours over time with a view to having a better understanding of welfare issues, assuring the quality of recorded data and informing best practice. This article is protected by copyright. All rights reserved.
  • Chick chorioallantoic membrane assay as an in vivo model to study the effect of nanoparticle-based anticancer drugs in ovarian cancer

    Vu, Binh Thanh; Shahin, Sophia Allaf; Croissant, Jonas G.; Fatieiev, Yevhen; Matsumoto, Kotaro; Le-Hoang Doan, Tan; Yik, Tammy; Simargi, Shirleen; Conteras, Altagracia; Ratliff, Laura; Jimenez, Chiara Mauriello; Raehm, Laurence; Khashab, Niveen M.; Durand, Jean-Olivier; Glackin, Carlotta; Tamanoi, Fuyuhiko (Springer Nature, 2018-05-29)
    New therapy development is critically needed for ovarian cancer. We used the chicken egg CAM assay to evaluate efficacy of anticancer drug delivery using recently developed biodegradable PMO (periodic mesoporous organosilica) nanoparticles. Human ovarian cancer cells were transplanted onto the CAM membrane of fertilized eggs, resulting in rapid tumor formation. The tumor closely resembles cancer patient tumor and contains extracellular matrix as well as stromal cells and extensive vasculature. PMO nanoparticles loaded with doxorubicin were injected intravenously into the chicken egg resulting in elimination of the tumor. No significant damage to various organs in the chicken embryo occurred. In contrast, injection of free doxorubicin caused widespread organ damage, even when less amount was administered. The lack of toxic effect of nanoparticle loaded doxorubicin was associated with specific delivery of doxorubicin to the tumor. Furthermore, we observed excellent tumor accumulation of the nanoparticles. Lastly, a tumor could be established in the egg using tumor samples from ovarian cancer patients and that our nanoparticles were effective in eliminating the tumor. These results point to the remarkable efficacy of our nanoparticle based drug delivery system and suggests the value of the chicken egg tumor model for testing novel therapies for ovarian cancer.
  • Genetic Determinants Associated With in Vivo Survival of Burkholderia cenocepacia in the Caenorhabditis elegans Model

    Wong, Yee-Chin; Abd El Ghany, Moataz; Ghazzali, Raeece N. M.; Yap, Soon-Joo; Hoh, Chee-Choong; Pain, Arnab; Nathan, Sheila (Frontiers Media SA, 2018-05-29)
    A Burkholderia cenocepacia infection usually leads to reduced survival and fatal cepacia syndrome in cystic fibrosis patients. The identification of B. cenocepacia essential genes for in vivo survival is key to designing new anti-infectives therapies. We used the Transposon-Directed Insertion Sequencing (TraDIS) approach to identify genes required for B. cenocepacia survival in the model infection host, Caenorhabditis elegans. A B. cenocepacia J2315 transposon pool of ∼500,000 mutants was used to infect C. elegans. We identified 178 genes as crucial for B. cenocepacia survival in the infected nematode. The majority of these genes code for proteins of unknown function, many of which are encoded by the genomic island BcenGI13, while other gene products are involved in nutrient acquisition, general stress responses and LPS O-antigen biosynthesis. Deletion of the glycosyltransferase gene wbxB and a histone-like nucleoid structuring (H-NS) protein-encoding gene (BCAL0154) reduced bacterial accumulation and attenuated virulence in C. elegans. Further analysis using quantitative RT-PCR indicated that BCAL0154 modulates B. cenocepacia pathogenesis via transcriptional regulation of motility-associated genes including fliC, fliG, flhD, and cheB1. This screen has successfully identified genes required for B. cenocepacia survival within the host-associated environment, many of which are potential targets for developing new antimicrobials.
  • Candidate enzymes for saffron crocin biosynthesis are localized in multiple cellular compartments

    Demurtas, Olivia Costantina; Frusciante, Sarah; Ferrante, Paola; Diretto, Gianfranco; Azad, Noraddin Hosseinpour; Pietrella, Marco; Aprea, Giuseppe; Taddei, Anna Rita; Romano, Elena; Mi, Jianing; Al-Babili, Salim; Frigerio, Lorenzo; Giuliano, Giovanni (American Society of Plant Biologists (ASPB), 2018-05-29)
    Saffron is composed of the dried stigmas of Crocus sativus and is the most expensive spice on Earth. Its red color is due to the apocarotenoid glycosides, crocins, which accumulate in the vacuole and reach up to 10% of the stigma dry weight. We have previously characterized the first dedicated enzyme in crocin biosynthesis, CsCCD2, which cleaves zeaxanthin to yield crocetin dialdehyde. In this work, we identified six putative aldehyde dehydrogenase (ALDH) transcripts expressed in saffron stigmas. When expressed in E. coli, only one of corresponding proteins (CsALDH3I1), was able to convert crocetin dialdehyde into the crocin precursor, crocetin. CsALDH3I1 carries a C-terminal hydrophobic domain, similar to that of a Neurospora membrane-associated apocarotenoid dehydrogenase, YLO-1. We also characterized a UDP-glycosyltransferase enzyme, CsUGT74AD1, able to convert crocetin to crocins 1 and 2'. In vitro assays showed high specificity of CsALDH3I1 for crocetin dialdehyde and long chain apocarotenals, and of CsUGT74AD1 for crocetin. Upon extract fractionation, the CsCCD2, CsALDH3I1 and CsUGT74AD1 enzymes partitioned in the insoluble fraction, suggesting that they are associated to membranes or to large insoluble complexes. Immunogold labeling of saffron stigmas and confocal microscopy of fusions to Green Fluorescent Protein expressed in N. benthamiana leaves revealed that CsCCD2 localizes to plastids, CsALDH3I1 to the endoplasmic reticulum (ER) and CsUGT74AD1 to the cytoplasm, in association with cytoskeletal-like structures. Based on our and on literature data, we propose that the ER and cytoplasm function as
  • Positivity-preserving CE/SE schemes for solving the compressible Euler and Navier–Stokes equations on hybrid unstructured meshes

    Shen, Hua; Parsani, Matteo (Elsevier BV, 2018-05-28)
    We construct positivity-preserving space–time conservation element and solution element (CE/SE) schemes for solving the compressible Euler and Navier–Stokes equations on hybrid unstructured meshes consisting of triangular and rectangular elements. The schemes use an a posteriori limiter to prevent negative densities and pressures based on the premise of preserving optimal accuracy. The limiter enforces a constraint for spatial derivatives and does not change the conservative property of CE/SE schemes. Several numerical examples suggest that the proposed schemes preserve accuracy for smooth flows and strictly preserve positivity of densities and pressures for the problems involving near vacuum and very strong discontinuities.
  • Flashed-feed VMD configuration as a novel method for eliminating temperature polarization effect and enhancing water vapor flux

    Alsaadi, Ahmad Salem; Alpatova, Alla; Lee, Jung Gil; Francis, Lijo; Ghaffour, NorEddine (Elsevier BV, 2018-05-28)
    The coupling of heat and mass transfer in membrane distillation (MD) process makes enhancing water vapor flux and determining MD membrane mass transfer coefficient (MTC) fairly challenging due to the development of temperature gradient near the membrane surface, referred to as temperature polarization (TP). As a result, the change in feed temperature at the membrane surface will be difficult to measure accurately. In this paper, the effect of TP was decoupled from the membrane MTC by preventing the liquid feed stream from contacting the membrane surface through the use of a novel custom-made vacuum MD (VMD) module design. Results showed that a temperature difference of 10°C between the feed bulk and feed temperatures at the membrane surface/interface is estimated to take place in the typical VMD configuration, while the proposed flashed-feed VMD configuration eliminates TP effect and gives a flux 3.5-fold higher (200kg/m2.hr) under similar operating conditions. Therefore, it can be concluded that heat transfer coefficient is considered to be the main factor controlling resistance of water vapor flux in the typical VMD configuration. The measured MTC of the tested commercial membrane was found to be more accurate and the highest among all reported MTCs in the MD literature (2.44×10−6kg/m2.s.Pa). Additionally, a transmembrane temperature difference of 5°C and 10°C in the novel configuration can produce water vapor fluxes of about 9kg/m2.hr and 40kg/m2.hr, respectively, at a feed temperature of 70°C, which is very attractive for scaling-up the process.
  • Efficient Photon Recycling and Radiation Trapping in Cesium Lead Halide Perovskite Waveguides

    Dursun, Ibrahim; Zheng, Yangzi; Guo, Tianle; de Bastiani, Michele; Turedi, Bekir; Sinatra, Lutfan; Haque, Mohammed; Sun, Bin; Zhumekenov, Ayan A.; Saidaminov, Makhsud I.; Garcia de Arquer, F. Pelayo; Sargent, Edward H.; Wu, Tao; Gartstein, Yuri N; Bakr, Osman; Mohammed, Omar F.; Malko, Anton V. (American Chemical Society (ACS), 2018-05-26)
    Cesium lead halide perovskite materials have attracted considerable attention for potential applications in lasers, light emitting diodes and photodetectors. Here, we provide the experimental and theoretical evidence for photon recycling in CsPbBr3 perovskite microwires. Using two-photon excitation, we recorded photoluminescence (PL) lifetimes and emission spectra as a function of the lateral distance between PL excitation and collection positions along the microwire, with separations exceeding 100 µm. At longer separations, the PL spectrum develops a red-shifted emission peak accompanied by an appearance of well-resolved rise times in the PL kinetics. We developed quantitative modeling that accounts for bimolecular recombination and photon recycling within the microwire waveguide and is sufficient to account for the observed decay modifications. It relies on a high radiative efficiency in CsPbBr3 perovskite microwires and provides crucial information about the potential impact of photon recycling and waveguide trapping on optoelectronic properties of cesium lead halide perovskite materials.
  • SiC-C Composite as A Highly Stable and Easily Regenerable Photothermal Material for Practical Water Evaporation

    Shi, Le; Shi, Yusuf; Li, Renyuan; Chang, Jian; Zaouri, Noor A.; Ahmed, Elaf Ali; Jin, Yong; Zhang, Chenlin; Zhuo, Sifei; Wang, Peng (American Chemical Society (ACS), 2018-05-26)
    Solar-driven water distillation by photothermal materials is emerging as a promising way of renewable energy-driven clean water production. In designing photothermal materials, light absorption, photo-to-thermal conversion efficiency, and ability to localize thermal energy at the water-air interface are three important considerations. However, one additional consideration, regenerability, has so far slipped out of the photothermal material designs at status quo. This work reveals that there is a fouling layer formed during photothermal evaporation of real seawater (Red Sea water) and domestic wastewater, which once formed, would be difficult to remove. Herein, we synthesize a SiC-C composite monolith as an effective photothermal material where carbon acts as photothermal component and SiC serves as a heat conductor and strong structural support. The high mechanical strength of the monolithic composite makes it able to withstand repeatedly high strength physical cleaning by brush scrubbing and sonication and the anti-carbon-loss mechanism generates zero carbon loss during the physical cleaning. In the case of the domestic wastewater evaporation, the bio- and organic foulants on the SiC-C composite monolith can be totally removed by annealing at 1000 oC in N2 atmosphere. We believe that the SiC-C composite monoliths are promising photothermal materials in practical solar-driven water evaporation applications thanks to their highly stable and easily regenerable properties and therefore more research efforts are warranted to further improve their performances.
  • Quantification of Ionic Diffusion in Lead Halide Perovskite Single Crystals

    Peng, Wei; Aranda, Clara; Bakr, Osman; Garcia-Belmonte, Germà; Bisquert, Juan; Guerrero, Antonio (American Chemical Society (ACS), 2018-05-25)
    Lead halide perovskites are mixed electronic/ionic semiconductors that have recently revolutionized the photovoltaics field. The physical characterization of the ionic conductivity has been rather elusive due to the highly intermixing of ionic and electronic current. In this work the synthesis of low defect density monocrystalline MAPbBr3 (MA=Methyl ammonium) solar cells free of hole transport layer (HTL) suppresses the effect of electronic current. Impedance spectroscopy reveals the characteristic signature of ionic diffusion (the Warburg element and transmission line equivalent circuit) and ion accumulation at the MAPbBr3/Au interface. Diffusion coefficients are calculated based on a good correlation between thickness of MAPbBr3 and characteristic diffusion transition frequency. In addition, reactive external interfaces are studied by comparison of polycrystalline MAPbBr3 devices prepared either with or without a HTL. The low frequency response in IS measurements is correlated with the chemical reactivity of moving ions with the external interfaces and diffusion into the HTL.
  • PTK2B/Pyk2 overexpression improves a mouse model of Alzheimer's disease

    Giralt, Albert; de Pins, Benoît; Cifuentes-Díaz, Carmen; López-Molina, Laura; Farah, Amel Thamila; Tible, Marion; Deramecourt, Vincent; Arold, Stefan T.; Ginés, Silvia; Hugon, Jacques; Girault, Jean-Antoine (Elsevier BV, 2018-05-24)
    Pyk2 is a Ca2+-activated non-receptor tyrosine kinase enriched in forebrain neurons and involved in synaptic regulation. Human genetic studies associated PTK2B, the gene coding Pyk2, with risk for Alzheimer's disease (AD). We previously showed that Pyk2 is important for hippocampal function, plasticity, and spine structure. However, its potential role in AD is unknown. To address this question we used human brain samples and 5XFAD mice, an amyloid mouse model of AD expressing mutated human amyloid precursor protein and presenilin1. In the hippocampus of 5XFAD mice and in human AD patients' cortex and hippocampus, Pyk2 total levels were normal. However, Pyk2 Tyr-402 phosphorylation levels, reflecting its autophosphorylation-dependent activity, were reduced in 5XFAD mice at 8 months of age but at 3 months. We crossed these mice with Pyk2−/− mice to generate 5XFAD animals devoid of Pyk2. At 8 months the phenotype of 5XFAD x Pyk2−/− double mutant mice was not different from that of 5XFAD. In contrast, overexpression of Pyk2 in the hippocampus of 5XFAD mice, using adeno-associated virus, rescued autophosphorylated Pyk2 levels and improved synaptic markers and performance in several behavioral tasks. Both Pyk2−/− and 5XFAD mice showed an increase of potentially neurotoxic Src cleavage product, which was rescued by Pyk2 overexpression. Manipulating Pyk2 levels had only minor effects on Aβ plaques, which were slightly decreased in hippocampus CA3 region of double mutant mice and increased following overexpression. Our results show that Pyk2 is not essential for the pathogenic effect of human amyloidogenic mutations in the 5XFAD mouse model. However, the slight decrease in plaque number observed in these mice in the absence of Pyk2 and their increase following Pyk2 overexpression suggest a contribution of this kinase in plaque formation. Importantly, a decreased function of Pyk2 was observed in 5XFAD mice, indicated by its decreased autophosphorylation and associated Src alterations. Overcoming this deficit by Pyk2 overexpression improved the behavioral and molecular phenotype of 5XFAD mice. Thus, our results in a mouse model of AD suggest that Pyk2 impairment may play a role in the symptoms of the disease.
  • Field data provide estimates of effective permeability, fracture spacing, well drainage area and incremental production in gas shales

    Eftekhari, Behzad; Marder, M.; Patzek, Tadeusz (Elsevier BV, 2018-05-23)
    About half of US natural gas comes from gas shales. It is valuable to study field production well by well. We present a field data-driven solution for long-term shale gas production from a horizontal, hydrofractured well far from other wells and reservoir boundaries. Our approach is a hybrid between an unstructured big-data approach and physics-based models. We extend a previous two-parameter scaling theory of shale gas production by adding a third parameter that incorporates gas inflow from the external unstimulated reservoir. This allows us to estimate for the first time the effective permeability of the unstimulated shale and the spacing of fractures in the stimulated region. From an analysis of wells in the Barnett shale, we find that on average stimulation fractures are spaced every 20 m, and the effective permeability of the unstimulated region is 100 nanodarcy. We estimate that over 30 years on production the Barnett wells will produce on average about 20% more gas because of inflow from the outside of the stimulated volume. There is a clear tradeoff between production rate and ultimate recovery in shale gas development. In particular, our work has strong implications for well spacing in infill drilling programs.
  • An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region

    Hume, Benjamin C.C.; Ziegler, Maren; Poulain, Julie; Pochon, Xavier; Romac, Sarah; Boissin, Emilie; de Vargas, Colomban; Planes, Serge; Wincker, Patrick; Voolstra, Christian R. (PeerJ, 2018-05-23)
    The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol’s ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.
  • Intra-pulse laser absorption sensor with cavity enhancement for oxidation experiments in a rapid compression machine

    Nasir, Ehson Fawad; Farooq, Aamir (The Optical Society, 2018-05-23)
    A sensor based on a mid-IR pulsed quantum cascade laser (QCL) and off-axis cavity enhanced absorption spectroscopy (OA-CEAS) has been developed for highly sensitive concentration measurements of carbon monoxide (CO) in a rapid compression machine. The duty cycle and the pulse repetition rate of the laser were optimized for increased tuning range, high chirp rate, and small line width to achieve effective laser-cavity coupling. This enabled spectrally resolved CO line-shape measurements at high pressures (P ~10 bar). A gain factor of 133 and a time resolution of 10 μs were demonstrated. CO concentration-time profiles during the oxidation of highly dilute n-octane/air mixtures were recorded, illustrating new opportunities in RCM experiments for chemical kinetics.
  • In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

    Othoum, Ghofran K; Bougouffa, Salim; Razali, Rozaimi; Bokhari, Ameerah; Alamoudi, Soha; Antunes, André; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T.; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Lafi, Feras Fawzi; Essack, Magbubah (Springer Nature, 2018-05-22)
    BackgroundThe increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions.ResultsWe report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species.ConclusionsB. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.
  • Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+ -pumping pyrophosphatase in pepper plants

    Vigani, Gianpiero; Rolli, Eleonora; Marasco, Ramona; Dell'Orto, Marta; Michoud, Gregoire; Soussi, Asma; Raddadi, Noura; Borin, Sara; Sorlini, Claudia; Zocchi, Graziano; Daffonchio, Daniele (Wiley, 2018-05-22)
    It has been previously shown that the transgenic overexpression of the plant root vacuolar proton pumps H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase) confer tolerance to drought. Since plant-root endophytic bacteria can also promote drought tolerance, we hypothesize that such promotion can be associated to the enhancement of the host vacuolar proton pumps expression and activity. To test this hypothesis, we selected two endophytic bacteria endowed with an array of in vitro plant growth promoting traits. Their genome sequences confirmed the presence of traits previously shown to confer drought resistance to plants, such as the synthesis of nitric oxide and of organic volatile organic compounds. We used the two strains on pepper (Capsicuum annuum L.) because of its high sensitivity to drought. Under drought conditions, both strains stimulated a larger root system and enhanced the leaves' photosynthetic activity. By testing the expression and activity of the vacuolar proton pumps, H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase), we found that bacterial colonization enhanced V-PPase only. We conclude that the enhanced expression and activity of V-PPase can be favoured by the colonization of drought-tolerance-inducing bacterial endophytes. This article is protected by copyright. All rights reserved.
  • Application of Semiempirical Methods to Transition Metal Complexes: Fast Results but Hard-to-Predict Accuracy.

    Minenkov, Yury; Sharapa, Dmitry I.; Cavallo, Luigi (American Chemical Society (ACS), 2018-05-22)
    A series of semiempirical PM6* and PM7 methods has been tested in reproducing of relative conformational energies of 27 realistic-size complexes of 16 different transition metals (TMs). An analysis of relative energies derived from single-point energy evaluations on density functional theory (DFT) optimized conformers revealed pronounced deviations between semiempirical and DFT methods indicating fundamental difference in potential energy surfaces (PES). To identify the origin of the deviation, we compared fully optimized PM7 and respective DFT conformers. For many complexes, differences in PM7 and DFT conformational energies have been confirmed often manifesting themselves in false coordination of some atoms (H, O) to TMs and chemical transformations/distortion of coordination center geometry in PM7 structures. Despite geometry optimization with fixed coordination center geometry leads to some improvements in conformational energies, the resulting accuracy is still too low to recommend explored semiempirical methods for out-of-the-box conformational search/sampling: careful testing is always needed.
  • Analysis of the current–voltage curves and saturation currents in burner-stabilised premixed flames with detailed ion chemistry and transport models

    Belhi, Memdouh; Han, Jie; Casey, Tiernan A.; Chen, Jyh-Yuan; Im, Hong G.; Sarathy, S. Mani; Bisetti, Fabrizio (Informa UK Limited, 2018-05-22)
    Current-voltage, or i–V, curves are used in combustion to characterise the ionic structure of flames. The objective of this paper is to develop a detailed modelling framework for the quantitative prediction of the i–V curves in methane/air flames. Ion and electron transport coefficients were described using methods appropriate for charged species interactions. An ionic reaction mechanism involving cations, anions and free electrons was used, together with up-to-date rate coefficients and thermodynamic data. Because of the important role of neutral species in the ion production process, its prediction by the detailed AramcoMech 1.4 mechanism was optimised by using available experimental measurements. Model predictions were evaluated by comparing to i–V curves measured in atmospheric-pressure, premixed, burner-stabilised flames. A detailed evaluation of the reliability of ion kinetic and transport parameters adopted was performed. The model provides good quantitative agreement with experimental data for various conditions.

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