bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and comparative genomics of R997, the first SXT/R391 integrative and conjugative element (ICE) of the Indian Sub-Continent
Authors: Ryan Michael P. , Armshaw Patricia , O’Halloran John A. , Pembroke J. Tony 
Published: August 2017

AbstractThe aim of this study was to analyse R997, the first integrative and conjugative element (ICE) isolated from the Indian Sub-Continent, and to determine its relationship to the SXT/R391 family of ICEs. WGS of Escherichia coli isolate AB1157 (which contains R997) was performed using Illumina sequencing technology. R997 context was assessed by de novo assembly, gene prediction and annotation tools, and compared to other SXT/R391 ICEs. R997 has a size of 85 Kb and harbours 85 ORFs. Within one of the variable regions a HMS-1 β-lactamase resistance gene is located. The Hotspot regions of the element contains restriction digestion systems and insertion sequences. R997 is very closely related to the SXT-like elements from widely dispersed geographic areas. The sequencing of R997 increases the knowledge of the earliest isolated SXT/R391 elements and may provide insight on the emergence of these elements on the Indian sub-continent.
Effects of catalase on chloroplast arrangement in Opuntia streptacantha chlorenchyma cells under salt stress
Authors: Arias-Moreno Diana Marcela , Jiménez-Bremont Juan Francisco , Maruri-López Israel , Delgado-Sánchez Pablo 
Published: August 2017

AbstractIn arid and semiarid regions, low precipitation rates lead to soil salinity problems, which may limit plant establishment, growth, and survival. Herein, we investigated the NaCl stress effect on chlorophyll fluorescence, photosynthetic-pigments, movement and chloroplasts ultrastructure in chlorenchyma cells of Opuntia streptacantha cladodes. Cladodes segments were exposed to salt stress at 0, 100, 200, and 300 mM NaCl for 8, 16, and 24 h. The results showed that salt stress reduced chlorophyll content, F
v
/F
m
, ΦPSII, and qP values. Under the highest salt stress treatments, the chloroplasts were densely clumped toward the cell center and thylakoid membranes were notably affected. We analyzed the effect of exogenous catalase in salt-stressed cladode segments during 8, 16, and 24 h. The catalase application to salt-stressed cladodes counteracted the NaCl adverse effects, increasing the chlorophyll fluorescence parameters, photosynthetic-pigments, and avoided chloroplast clustering. Our results indicate that salt stress triggered the chloroplast clumping and affected the photosynthesis in O. streptacantha chlorenchyma cells. The exogenous catalase reverted the H2O2 accumulation and clustering of chloroplast, which led to an improvement of the photosynthetic efficiency. These data suggest that H2O2 detoxification by catalase is important to protect the chloroplast, thus conserving the photosynthetic activity in O. streptacantha under stress.
Identification and Functional Characterization of Tomato CircRNAs Derived from Genes Involved in Fruit Pigment Accumulation
Authors: Tan Jinjuan , Zhou Zhongjing , Niu Yujie , Sun Xiaoyong , Deng Zhiping 
Published: August 2017

AbstractCircRNAs, a class of widespread circular RNAs produced from precursor mRNA back-splicing, have been implicated in regulation of gene expression in eukaryotes, but their biological functions in plants have not yet been elucidated. By deep sequencing of rRNA-removed and RNase R-digested RNA samples we have identified several thousands of putative back-splicing sites in tomato fruit (Solanum lycopersicum) and show that the abundance of some of these circRNAs derived from fruit pigment biosynthesis genes are regulated by fruit ripening. Herein, we overexpressed a circRNA derived from Phytoene Synthase 1 (PSY1) in tomato ‘Ailsa Craig’ and microTom. The PSY1 mRNA abundance, the lycopene and β-carotene accumulation were decreased significantly in the transgenic tomato fruits, likely due to the continuous highly expressed circRNAs and/or the low abundant linear RNAs generated from the overexpression vector. Besides, overexpression of a circRNA derived from Phytoene Desaturase (PDS) showed similar results. Our results provide biological insights into plant circRNAs.
A new mathematical model and experimental validation on foamy-oil flow in developing heavy oil reservoirs
Authors: Liu Pengcheng , Mu Zhenbao , Li Wenhui , Wu Yongbin , Li Xiuluan 
Published: August 2017

AbstractTo model foamy-oil flow in the development of heavy oil reservoirs, three depletion experiments were conducted with foamy oil treated as a pseudo-single-phase flow. In this pseudo single phase, dispersed bubbles are viewed as a part of the oil, and the redefined effective permeability varies with the changes of pressure depletion rate, oil viscosity, and gas saturation. A mathematical expression for the effective permeability was developed based on experiments, where the viscosity of foamy oil is assumed to be approximately equal to the saturated oil under equivalent conditions. The compressibility coefficient of foamy oil is treated as a volume-weighted compressibility coefficient of that of oil and gas phases. A new mathematical model for foamy-oil flow was proposed with consideration of foamy-oil supersaturation. To validate the mathematical model, the oil recovery and the production gas-oil ratio (GOR) calculated by the new model, conventional black oil model, supersaturation model and pseudo-bubble-point (PBP) model were all compared with those of the experimental data. The new model provided a substantially improved fit to the experimental data compared with the rest three models, which verifies the suitability of the mathematical model presented for simulating foamy-oil flow in the development of heavy oil reservoirs.
Cytochrome P450/ABC transporter inhibition simultaneously enhances ivermectin pharmacokinetics in the mammal host and pharmacodynamics in Anopheles gambiae
Authors: Chaccour Carlos J. , Hammann Felix , Alustiza Marta , Castejon Sandra , Tarimo Brian B. , Abizanda Gloria , Irigoyen Barrio Ángel , Martí Soler Helena , Moncada Rafael , Bilbao José Ignacio , Aldaz Azucena , Maia Marta , Del Pozo José Luis 
Published: August 2017

AbstractMass administration of endectocides, drugs that kill blood-feeding arthropods, has been proposed as a complementary strategy to reduce malaria transmission. Ivermectin is one of the leading candidates given its excellent safety profile. Here we provide proof that the effect of ivermectin can be boosted at two different levels by drugs inhibiting the cytochrome or ABC transporter in the mammal host and the target mosquitoes. Using a mini-pig model, we show that drug-mediated cytochrome P450/ABC transporter inhibition results in a 3-fold increase in the time ivermectin remains above mosquito-killing concentrations. In contrast, P450/ABC transporter induction with rifampicin markedly impaired ivermectin absorption. The same ketoconazole-mediated cytochrome/ABC transporter inhibition also occurs outside the mammal host and enhances the mortality of Anopheles gambiae. This was proven by using the samples from the mini-pig experiments to conduct an ex-vivo synergistic bioassay by membrane-feeding Anopheles mosquitoes. Inhibiting the same cytochrome/xenobiotic pump complex in two different organisms to simultaneously boost the pharmacokinetic and pharmacodynamic activity of a drug is a novel concept that could be applied to other systems. Although the lack of a dose-response effect in the synergistic bioassay warrants further exploration, our study may have broad implications for the control of parasitic and vector-borne diseases.
Platinum Nanoparticle-embedded Porous Diamond Spherical Particles as an Active and Stable Heterogeneous Catalyst
Authors: Kondo Takeshi , Morimura Takuji , Tsujimoto Tatsumi , Aikawa Tatsuo , Yuasa Makoto 
Published: August 2017

AbstractPlatinum nanoparticle-embedded porous diamond spherical particles (PtNP@PDSPs), as an active and stable catalyst, were fabricated by spray-drying of an aqueous slurry containing nanodiamond (ND) particles, platinum nanoparticles (PtNP), and polyethylene glycol (PEG) to form ND/PtNP/PEG composite spherical particles, followed by removal of PEG and a short-time diamond growth on the surface. The average diameter of the PtNP@PDSPs can be controlled in the range of 1–5 μm according to the spray-drying conditions. The Brunauer-Emmett-Teller (BET) surface area and average pore diameter of the PtNP@PDSPs were estimated to be ca. 170–300 m2 g−1 and ca. 4–13 nm, respectively. When ND with the size of 20–30 nm was used, the size of PtNP in the PtNP@PDSP was almost unchanged at 5–6 nm even after high temperature processes and reuse test for catalytic reaction, showing stable supporting. The catalytic activity of the PtNP@PDSPs for the dehydrogenation of cyclohexane was higher than that for a Pt/C catalyst, which is attributed to the stable PtNP support by the three-dimensional packing of ND and efficient mass transfer via the interconnected through-hole pores in the PDSPs.
RpoS-independent evolution reveals the importance of attenuated cAMP/CRP regulation in high hydrostatic pressure resistance acquisition in E. coli
Authors: Gayán Elisa , Cambré Alexander , Michiels Chris W. , Aertsen Abram 
Published: August 2017

AbstractHigh hydrostatic pressure (HHP) processing is an attractive non-thermal alternative to food pasteurization. Nevertheless, the large inter- and intra-species variations in HHP resistance among foodborne pathogens and the ease by which they can acquire extreme resistance are an issue of increasing concern. Since RpoS activity has been considered as a central determinant in the HHP resistance of E. coli and its pathovars, this study probed for the potential of an E. coli MG1655 ΔrpoS mutant to acquire HHP resistance by directed evolution. Despite the higher initial HHP sensitivity of the ΔrpoS mutant compared to the wild-type strain, evolved lineages of the former readily managed to restore or even succeed wild-type levels of resistance. A number of these ΔrpoS derivatives were affected in cAMP/CRP regulation, and this could be causally related to their HHP resistance. Subsequent inspection revealed that some of previously isolated HHP-resistant mutants derived from the wild-type strain also incurred a causal decrease in cAMP/CRP regulation. cAMP/CRP attenuated HHP-resistant mutants also exhibited higher resistance to fosfomycin, a preferred treatment for STEC infections. As such, this study reveals attenuation of cAMP/CRP regulation as a relevant and RpoS-independent evolutionary route towards HHP resistance in E. coli that coincides with fosfomycin resistance.
Cell damage produced by magnetic fluid hyperthermia on microglial BV2 cells
Authors: Calatayud M. Pilar , Soler Elisa , Torres Teobaldo E. , Campos-Gonzalez Enrique , Junquera Concepción , Ibarra M. Ricardo , Goya Gerardo F. 
Published: August 2017

AbstractWe present evidence on the effects of exogenous heating by water bath (WB) and magnetic hyperthermia (MHT) on a glial micro-tumor phantom. To this, magnetic nanoparticles (MNPs) of 30–40 nm were designed to obtain particle sizes for maximum heating efficiency. The specific power absorption (SPA) values (f = 560 kHz, H = 23.9 kA/m) for as prepared colloids (533–605 W/g) dropped to 98–279 W/g in culture medium. The analysis of the intracellular MNPs distribution showed vesicle-trapped MNPs agglomerates spread along the cytoplasm, as well as large (~0.5–0.9 μm) clusters attached to the cell membrane. Immediately after WB and MHT (T = 46 °C for 30 min) the cell viability was ≈70% and, after 4.5 h, decreased to 20–25%, demonstrating that metabolic processes are involved in cell killing. The analysis of the cell structures after MHT revealed a significant damage of the cell membrane that is correlated to the location of MNPs clusters, while local cell damage were less noticeable after WB without MNPs. In spite of the similar thermal effects of WB and MHT on the cell viability, our results suggest that there is an additional mechanism of cell damage related to the presence of MNPs at the intracellular space.
Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
Authors: Sharma Bhaskar , Bhatt Tarun Kumar 
Published: August 2017

AbstractThe ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme. We have utilized in-silico methods to analyze E2 enzymes in Solanum lycopersicum and 59 genes were identified with UBC family domains. The physio-chemical properties, chromosomal localization, structural organization, gene duplication, promoter analysis, gene ontology and conserved motifs were investigated along with phylogenetic analysis of tomato E2 genes exploring evolutionary relations. The gene expression analysis of RNA sequencing data revealed expression profile of tomato E2 genes in seedling, root, leaf, seed, fruit, and flower tissues. Our study aid in the understanding of distribution, expansion, evolutionary relation and probable participation in plant biological processes of tomato E2 enzymes that will facilitate strong base for future research on ubiquitin-mediated regulations in tomato and other plant systems.
YebC, a putative transcriptional factor involved in the regulation of the proteolytic system of Lactobacillus
Authors: Brown Lucía , Villegas Josefina M. , Elean Mariano , Fadda Silvina , Mozzi Fernanda , Saavedra Lucila , Hebert Elvira M. 
Published: August 2017

AbstractThe proteolytic system of Lactobacillus plays an essential role in bacterial growth, contributes to the flavor development of fermented products, and can release bioactive health-beneficial peptides during milk fermentation. In this work, a genomic analysis of all genes involved in the proteolytic system of L. delbrueckii subsp. lactis CRL 581 was performed. Genes encoding the cell envelope-associated proteinase, two peptide transport systems, and sixteen peptidases were identified. The influence of the peptide supply on the transcription of 23 genes involved in the proteolytic system of L. delbrueckii subsp. lactis was examined after cell growth in a chemically defined medium (CDM) and CDM supplemented with Casitone. prtL, oppA1, optS, optA genes as well as oppDFBC and optBCDF operons were the most highly expressed genes in CDM; their expression being repressed 6- to 115-fold by the addition of peptides. The transcriptional analysis was confirmed by proteomics; the up-regulation of the PrtL, PepG, OppD and OptF proteins in the absence of peptides was observed while the DNA-binding protein YebC was up-regulated by peptides. Binding of YebC to the promoter region of prtL, oppA1, and optS, demonstrated by electrophoretic mobility shift assays, showed that YebC acts as a transcriptional repressor of key proteolytic genes.
Increasing spring temperatures favor oak seed production in temperate areas
Authors: Caignard Thomas , Kremer Antoine , Firmat Cyril , Nicolas Manuel , Venner Samuel , Delzon Sylvain 
Published: August 2017

AbstractThe changes in reproductive phenology (i.e. timing of flowering and fruiting) observed in recent decades demonstrate that tree reproduction has already been altered by climate change. However, understanding the impact of these changes in reproductive success and fitness remains a major challenge for ecologists. We describe here a previously unreported phenomenon: a significant increase in the reproductive effort (seed production) of temperate oaks with increasing spring temperature, observed over the last decade. In contrast, no relationship was found between seed production and precipitation. This sensitivity of seed production to temperature was confirmed by a “space-for-time” substitution based on elevation gradients. Our findings suggest that global warming may enhance oak reproductive effort in temperate ecosystems. Nevertheless, while fitness can be enhanced by higher levels of seed production, it also depends on the frequency and synchronization of mast seeding production, which may also be influenced by climate change.
Identification of boric acid as a novel chemoattractant and elucidation of its chemoreceptor in Ralstonia pseudosolanacearum Ps29
Authors: Hida Akiko , Oku Shota , Nakashimada Yutaka , Tajima Takahisa , Kato Junichi 
Published: August 2017

AbstractChemotaxis enables bacteria to move toward more favorable environmental conditions. We observed chemotaxis toward boric acid by Ralstonia pseudosolanacearum Ps29. At higher concentrations, the chemotactic response of R. pseudosolanacearum toward boric acid was comparable to or higher than that toward L-malate, indicating that boric acid is a strong attractant for R. pseudosolanacearum. Chemotaxis assays under different pH conditions suggested that R. pseudosolanacearum recognizes B(OH)3 (or B(OH3) + B(OH)4−) but not B(OH)4− alone. Our previous study revealed that R. pseudosolanacearum Ps29 harbors homologs of all 22R. pseudosolanacearum GMI1000 mcp genes. Screening of 22 mcp single-deletion mutants identified the RS_RS17100 homolog as the boric acid chemoreceptor, which was designated McpB. The McpB ligand-binding domain (LBD) was purified in order to characterize its binding to boric acid. Using isothermal titration calorimetry, we demonstrated that boric acid binds directly to the McpB LBD with a K
D
(dissociation constant) of 5.4 µM. Analytical ultracentrifugation studies revealed that the McpB LBD is present as a dimer that recognizes one boric acid molecule.
Exploring the Sorption Mechanism of Ni(II) on Illite: Batch Sorption, Modelling, EXAFS and Extraction Investigations
Authors: Zhao Xiaolan , Qiang Shirong , Wu Hanyu , Yang Yunbo , Shao Dadong , Fang Linchuan , Liang Jianjun , Li Ping , Fan Qiaohui 
Published: August 2017

AbstractThe sorption mechanism of nickel (Ni) at the illite/water interface was investigated using batch, sorption modelling, extended X-ray absorption fine structure (EXAFS), and extraction approaches. The results showed that Ni(II) sorption on illite was strongly dependent on pH, contact time, temperature, and initial Ni(II) concentration. At a low initial Ni(II) concentration, the ion exchange species of ≡X2Ni° and the inner-sphere complexes including ≡SsONi+, ≡SwONi+ and ≡SwONiOH° species are observed on the sorption edges of Ni(II) on illite. As the initial Ni(II) concentration increased to 1.7 × 10−3 mol/L, precipitates including surface-induced precipitation of s-Ni(OH)2 and amorphous Ni(OH)2 became more significant, especially under neutral to alkaline conditions. EXAFS analysis confirmed that Ni-Al layered double hydroxide (LDH) can gradually form with an increase in the contact time. At pH 7.0, α-Ni(OH)2 was produced in the initial stage and then transformed to the more stable form of Ni-Al LDH with increasing contact time because of the increased Al3+ dissolution. With an increase in temperatures, α-Ni(OH)2 phase on illite transformed to Ni-Al LDH phase, indicating a lower thermodynamic stability compared to Ni-Al LDH phase. These results are important to understand the geochemical behaviors to effectively remediate soil contaminated with Ni(II).
Carbon nanotube/Co3O4 nanocomposites selectively coated by polyaniline for high performance air electrodes
Authors: Kim Jin Young , Park Yong Joon 
Published: August 2017

AbstractWe herein report the preparation of carbon nanotube (CNT)/Co3O4 nanocomposites selectively coated with polyaniline (PANI) via an electropolymerization method, for use as an effective electrode material for Li-air (Li-O2) batteries. The Co3O4 catalyst attached to the CNTs facilitated the dissociation of reaction products and reduced the overpotential of the cells. As the carbon surface activates the side reactions, the PANI coating on the carbon surface of the electrode suppressed the side reaction at the electrode/Li2O2 and electrode/electrolyte interfaces, thus enhancing the cycle performance of the electrode. In addition, the catalytic activity of Co3O4 on the CNT/Co3O4 nanocomposites remained unaffected, as the Co3O4 surface was not covered with a PANI layer due to the nature of the electropolymerization method. Overall, the synergic effect of the PANI layer and the Co3O4 catalyst leads to a superior cyclic performance and a low overpotential for the electrode based on selectively PANI-coated CNT/Co3O4 nanocomposites.
The possible molecular mechanisms of bisphenol A action on porcine early embryonic development
Authors: Guo Jing , Zhao Ming-Hui , Shin Kyung-Tae , Niu Ying-Jie , Ahn Yong-Dae , Kim Nam-Hyung , Cui Xiang-Shun 
Published: August 2017

AbstractBisphenol A (BPA) is an environmental contaminant widely used in the plastic industry. BPA has been demonstrated to be an endocrine disruptor and has an adverse effect on the embryonic development of mammals. However, the mechanism of action of BPA is limited. In this study, we investigated the role and mechanism of BPA in porcine embryonic development. First, the parthenotes were treated with different concentrations of BPA. We found that blastocyst formation was impaired and the parthenotes were arrested at the 4-cell stage after treatment with 100 μm BPA. Second, ROS increased following the addition of BPA, which further caused mitochondrial damage, and cytochrome c was released from the mitochondria to induce apoptosis. The adaptive response was demonstrated through LC3 immunofluorescence staining and by assessing autophagy-related gene expression. In addition, BPA caused DNA damage through the p53-p21 signaling pathway. Thus, our results indicate that BPA displays an adverse effect on porcine early embryonic development through mitochondrial and DNA damage.
Seismic waveform tomography with shot-encoding using a restarted L-BFGS algorithm
Authors: Rao Ying , Wang Yanghua 
Published: August 2017

AbstractIn seismic waveform tomography, or full-waveform inversion (FWI), one effective strategy used to reduce the computational cost is shot-encoding, which encodes all shots randomly and sums them into one super shot to significantly reduce the number of wavefield simulations in the inversion. However, this process will induce instability in the iterative inversion regardless of whether it uses a robust limited-memory BFGS (L-BFGS) algorithm. The restarted L-BFGS algorithm proposed here is both stable and efficient. This breakthrough ensures, for the first time, the applicability of advanced FWI methods to three-dimensional seismic field data. In a standard L-BFGS algorithm, if the shot-encoding remains unchanged, it will generate a crosstalk effect between different shots. This crosstalk effect can only be suppressed by employing sufficient randomness in the shot-encoding. Therefore, the implementation of the L-BFGS algorithm is restarted at every segment. Each segment consists of a number of iterations; the first few iterations use an invariant encoding, while the remainder use random re-coding. This restarted L-BFGS algorithm balances the computational efficiency of shot-encoding, the convergence stability of the L-BFGS algorithm, and the inversion quality characteristic of random encoding in FWI.