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Sample records for 2-go kontura vvehr-1000

  1. Highly recoverable TiO2-GO nanocomposites for stormwater disinfection.

    PubMed

    Wang, Gen; Feng, Wenjun; Zeng, Xiangkang; Wang, Zhouyou; Feng, Chuanping; McCarthy, David T; Deletic, Ana; Zhang, Xiwang

    2016-05-01

    A highly recoverable titanium dioxide-graphene oxide (TiO2-GO) composite was developed by a facile method of ultrasonic treatment of GO nanosheets and TiO2 nanoparticles, which should overcome the separation problem of nanosized TiO2 from treated water. Separability of the prepared samples was systematically investigated by gravity settling experiments. The samples' photocatalytic activity for stormwater disinfection was also studied under the irradiation of a solar simulator. The results demonstrated that TiO2-GO showed high efficient separability due to its accelerated settling behaviour. Zeta-potential analysis showed that the accelerated sedimentation of the catalyst was attributed to the aggregation of TiO2-GO resulting from the electrostatic attraction between TiO2 and GO. The TiO2-GO composite with a mass ratio of 100:2 (TiO2-2%GO) achieved both higher separability and good photocatalytic activity for stormwater disinfection. Its suspension became clear (turbidity < 50 NTU) after 8 h of sedimentation, while 99.5% of E.coli were deactivated in 90 min. The TiO2-GO composite exhibited excellent durability; no apparent change in the separability of TiO2-2%GO was observed after 10 treatment cycles (15 h in total), while only slight decrease in the photocatalytic activity was noted. In conclusion, the developed TiO2-GO composite showed promising results for stormwater disinfection.

  2. Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics

    PubMed Central

    Conesa, Ana; Götz, Stefan

    2008-01-01

    Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use. PMID:18483572

  3. High-throughput functional annotation and data mining with the Blast2GO suite

    PubMed Central

    Götz, Stefan; García-Gómez, Juan Miguel; Terol, Javier; Williams, Tim D.; Nagaraj, Shivashankar H.; Nueda, María José; Robles, Montserrat; Talón, Manuel; Dopazo, Joaquín; Conesa, Ana

    2008-01-01

    Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data. PMID:18445632

  4. Environmental estrogen Bisphenol A adsorption/oxidation on Graphene oxide/MnO2 (GO/MnO2) nanocomposite

    NASA Astrophysics Data System (ADS)

    Bele, Sotiria I.; Deliyanni, Eleni A.

    2015-04-01

    The environmental fate and decontamination of Bisphenol A (BPA), an environmental estrogen that is used as a monomer in plastic industry, are of emerging concern. This study focused on the kinetics, influencing factors and pathways of its adsorption and oxidative decomposition by MnO2. Additionally, Graphene oxide/MnO2 (GO/MnO2) nanocomposite was prepared and tested as a kind of adsorbent and/or catalysts for oxidative decomposition of Bisphenol A (BPA). A suspension of graphene oxide/manganese sulfate (GO/MnSO4) produced by the modified Hummers method was in situ transformed into GO/MnO2 nanocomposite in combination with KMnO4. It is found that MnO2 nanoparticles are uniformly distributed in the structure of GO. The surface chemistry and the porous texture of the prepared nanocomposite were characterized by thermal analysis (DTA), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscope (SEM) and Nitrogen adsorption (BET). The nanocomposite presented superior catalytic activities, much higher than that of the bare MnO2 for the decomposition of BPA in the presence of H2O2. The high activity of GO/MnO2 nanocomposite for the decomposition of BPA could be related to the synergistic effect of GO and MnO2 with the assistance of H2O2 according to the adsorption-oxidation-desorption mechanism.

  5. A chemiluminescence biosensor based on the adsorption recognition function between Fe3O4@SiO2@GO polymers and DNA for ultrasensitive detection of DNA.

    PubMed

    Sun, Yuanling; Li, Jianbo; Wang, Yanhui; Ding, Chaofan; Lin, Yanna; Sun, Weiyan; Luo, Chuannan

    2017-05-05

    In this work, a chemiluminescence (CL) biosensor was prepared for ultrasensitive determination of deoxyribonucleic acid (DNA) based on the adsorption recognition function between core-shell Fe3O4@SiO2 - graphene oxide (Fe3O4@SiO2@GO) polymers and DNA. The Fe3O4@SiO2@GO polymers were composed by GO and magnetite nanoparticles. And the core-shell polymers were confirmed by Scanning Electron Microscope (SEM), X-Ray Powder Diffraction (XRD) and Fourier Transform Infrared (FTIR). Then Fe3O4@SiO2@GO was modified by DNA. Based on the principle of complementary base, Fe3O4@SiO2@GO-DNA was introduced to the CL system and the selectivity, sensitivity of DNA detection was significantly improved. The adsorption properties of Fe3O4@SiO2@GO to DNA were researched through the adsorption equilibrium, adsorption kinetic and thermodynamics. Under optimized CL conditions, DNA could be assayed with the linear concentration range of 5.0×10(-12)-2.5×10(-11)mol/L. The detection limit was 1.7×10(-12)mol/L (3δ) and the relative standard deviation (RSD) was 3.1%. The biosensor was finally used for the determination of DNA in laboratory samples and recoveries ranged from 99% to 103%. The satisfactory results revealed the potential application of Fe3O4@SiO2@GO-DNA-CL biosensor in the diagnosis and the treatment of human genetic diseases.

  6. Heterogeneous UV/Fenton degradation of bisphenol A catalyzed by synergistic effects of FeCo2O4/TiO2/GO.

    PubMed

    Bai, Xue; Lyu, Lingling; Ma, Wenqiang; Ye, Zhengfang

    2016-11-01

    A new method for bisphenol A (BPA) degradation in aqueous solution was developed. The characteristics of BPA degradation in a heterogeneous ultraviolet (UV)/Fenton reaction catalyzed by FeCo2O4/TiO2/graphite oxide (GO) were studied. The properties of the synthesized catalysts were characterized using scanning electron microscopy, X-ray diffraction, and vibrating sample magnetometry. FeCo2O4 and TiO2 were grown as spherical shape, rough surface, and relatively uniform on the surface of GO (FeCo2O4/TiO2/GO). Batch tests were conducted to evaluate the effects of the initial pH, FeCo2O4/TiO2/GO dosage, and H2O2 concentration on BPA degradation. In a system with 0.5 g L(-1) of FeCo2O4/TiO2/GO and 10 mmol L(-1) of H2O2, approximately 90 % of BPA (20 mg L(-1)) was degraded within 240 min of UV irradiation at pH 6.0. The reused FeCo2O4/TiO2/GO catalyst retained its activity after three cycles, which indicates that it is stable and reusable. The heterogeneous UV/Fenton reaction catalyzed by FeCo2O4/TiO2/GO is a promising advanced oxidation technology for treating wastewater that contains BPA.

  7. Numerical and experimental study on shear coaxial injectors with hot hydrogen-rich gas/oxygen-rich gas and GH2/GO2

    NASA Astrophysics Data System (ADS)

    Jin, Ping; Li, Mao; Cai, Guo-Biao

    2013-04-01

    The influences of the shear coaxial injector parameters on the combustion performance and the heat load of a combustor are studied numerically and experimentally. The injector parameters, including the ratio of the oxidizer pressure drop to the combustor pressure (DP), the velocity ratio of fuel to oxidizer (RV), the thickness (WO), and the recess (HO) of the oxidizer injector post tip, the temperature of the hydrogen-rich gas (TH) and the oxygen-rich gas (TO), are integrated by the orthogonal experimental design method to investigate the performance of the shear coaxial injector. The gaseous hydrogen/oxygen at ambient temperature (GH2/GO2), and the hot hydrogen-rich gas/oxygen-rich gas are used here. The length of the combustion (LC), the average temperatures of the combustor wall (TW), and the faceplate (TF) are selected as the indicators. The tendencies of the influences of injector parameters on the combustion performance and the heat load of the combustor for the GH2/GO2 case are similar to those in the hot propellants case. However, the combustion performance in the hot propellant case is better than that in the GH2/GO2 case, and the heat load of the combustor is also larger than that in the latter case.

  8. A novel fabrication of a high performance SiO2-graphene oxide (GO) nanohybrids: Characterization of thermal properties of epoxy nanocomposites filled with SiO2-GO nanohybrids.

    PubMed

    Haeri, S Z; Ramezanzadeh, B; Asghari, M

    2017-05-01

    In this study it has been aimed to enhance the thermal resistance of epoxy coating through incorporation of SiO2-GO nanohybrids. SiO2-GO nanohybrids were synthesized through one-step sol-gel route using a mixture of Tetraethylorthosilane (TEOS) and 3-Aminopropyl triethoxysilane (APTES) silanes. The SiO2-GO nanohybrids were prepared at various hydrolysis times of 24, 48 and 72h. Then 0.2wt.% of GO and SiO2-GO nanohybrids were separately incorporated into the epoxy coating. Results revealed that amino functionalized SiO2 nanoparticles with particle size around 20-30nm successfully synthesized on the basal plane of GO. Results showed significant improvement of dispersion and interfacial interactions between nanohybrids and epoxy composite arising from covalent bonding between the SiO2-GO and the epoxy matrix. It was found that the thermal resistance of SiO2-GO nanohybrids and SiO2-GO/Epoxy nanocomposite was noticeably higher than GO and epoxy matrix, respectively.

  9. Synthesis of novel ZrO2&GO@TiO2 nanocomposite as an efficient photoanode in dye-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Mohamed, Ibrahim M. A.; Dao, Van-Duong; Yasin, Ahmed S.; Yassin, Mohamed A.; Barakat, Nasser A. M.; Choi, Ho-Suk

    2017-02-01

    Due to the physicochemical and photo-electro properties, TiO2 nanostructures still being the outstanding photoanode materials in the dye-sensitized solar cells (DSCs). However, it is well known that a low dye-loading and charge recombination constrain the limitation of large-scale application. This work introduces the synthesis of ZrO2&GO@TiO2 nanofibers (NFs) by facile two steps using electrospinning and hydrothermal treatment. Furthermore, the developed materials are applied as an efficient photoanode of DSCs. The synthesized NFs are described in terms of morphology, crystallography and chemistry via FESEM, TEM, XRD, Raman spectra and EDX analysis. As the results, the Ti, Zr, O and C elements are uniformly distributed in the synthesized sample. The percentages of the atomic elements are 10.77, 57.69, 1.45 and 30.09 for C, O, Zr and Ti, respectively. The synthesized composite shows only anatase with crystal size of 25.86 nm and cell volume of 142.39 Å3. The developed material is employed as working electrode of DSCs. The J-V characteristic showed 5.09% efficiency for device using the synthesized material, which is higher than those of cells assembled with TiO2 NFs and ZrO2@TiO2 NFs photoanodes. The obtained result is explained by enhanced dye-loading (1.055 × 1017 molecule/cm2) and improved charge transfer resistance (Rct = 9.18 Ω) of the photoanode substrate. Hence, the presented nanocomposite can be an efficient photoanode towards technology of DSC.

  10. Extremely stable all solution processed organic tandem solar cells with TiO2/GO recombination layer under continuous light illumination.

    PubMed

    Yusoff, Abd Rashid bin Mohd; Jose da Silva, Wilson; Kim, Hyeong Pil; Jang, Jin

    2013-11-21

    One approach to harvest a wide solar spectral solar energy is to stack two solar cells with different absorption characteristics in a tandem cell architecture. Herein, solution processed tandem solar cells, with highly transparent titanium oxide (TiO2) and graphene oxide (GO) as an efficient recombination layer, were designed, fabricated and characterized. We have adopted poly[(4,4'-bis(3-ethylhexyl)dithieno[3,2-b:''3'-d]silole)-2,6-diyl-alt-(2,5-(3-(2-ethylhexyl)thiophen-2-yl)thiazolo[5,4-d]thiazole]:indene-C60 bisadduct (PSEHTT:ICBA) and poly[(4,4'-bis(2-ethylhexyl)dithieno[3,2-b:2',3'-d]silole)-2,6-diyl-alt-(2,1,3-benzothiadiazole)-4,7-diyl]:[6,6]-phenyl-C70 butyric acid methyl ester (PSBTBT:PC70BM) as the active layers for the front and rear cells, respectively. The TiO2/GO serves as an electron and hole collecting and recombination layer. The tandem solar cells showed a high open circuit voltage (VOC) 1.62 V, a moderate short circuit current density (JSC) 8.23 mA cm(-2), fill factor (FF) 62.98%, leading to the power conversion efficiency of 8.40%. The obtained VOC value of tandem solar cells is ideal for the summation of VOCs attained from front and rear cells and it is evident that our tandem solar cells are well connected in series. Moreover, this tandem cell exhibits a 20% drop in conversion efficiency under continuous AM illumination for 2880 h.

  11. Structure and dynamics of liquid CS2: Going from ambient to elevated pressure conditions

    NASA Astrophysics Data System (ADS)

    Skarmoutsos, Ioannis; Mossa, Stefano; Samios, Jannis

    2016-10-01

    Molecular dynamics simulation studies were performed to investigate the structural and dynamic properties of liquid carbon disulfide (CS2) from ambient to elevated pressure conditions. The results obtained have revealed structural changes at high pressures, which are related to the more dense packing of the molecules inside the first solvation shell. The calculated neutron and X-ray structure factors have been compared with available experimental diffraction data, also revealing the pressure effects on the short-range structure of the liquid. The pressure effects on the translational, reorientational, and residence dynamics are very strong, revealing a significant slowing down when going from ambient pressure to 1.2 GPa. The translational dynamics of the linear CS2 molecules have been found to be more anisotropic at elevated pressures, where cage effects and librational motions are reflected on the shape of the calculated time correlation functions and their corresponding spectral densities.

  12. Separated Oscillatory Field Measurement of Hydrogen DOUBLET-2S(1/2) Going to DOUBLET-2P (3/2) Fine Structure Interval

    NASA Astrophysics Data System (ADS)

    Hagley, Edward Walter

    The 2^2P_{3/2} >=ts 2^2S_{1/2} interval in hydrogen has been measured using a fast atomic beam and a separated oscillatory field technique. Measurements were made at a beam energy of 96.5 keV using standard X -band waveguides as interaction regions. The signals obtained were extremely reproducible, and the experimental signal to noise ratio was very high. The final experimental value for the 2 ^2P_{3/2}>=ts 2^2S _{1/2} transition in hydrogen is upsilon(2^2P_{3/2 }>=ts 2^2S_{1/2})=9911.200(12) {MHz}.Subtracting this value from the well known fine structure interval in hydrogen yields a prediction for the n=2 Lamb shift. The inferred n=2 Lamb shift interval in hydrogen is{cal L}(Experiment)=1057.844(12) {MHz }.This result agrees better with theoretical calculations assuming the smaller of the two discrepant proton radii in the literature. The theoretical prediction of this Lamb shift assuming the smaller proton radius is {cal L}(Theory)=1057.859(8) {MHz},which is in good agreement with the results of this experiment. This experimental result predicts the higher order electron self energy remainder to beDelta G_sp{SE}{EXP.}(Zalpha)= -25.02 +/- 1.67 +/- 0.57,where the first uncertainty is due to this experimental uncertainty, and the second is due to the uncertainty in the proton radius itself. This value was calculated using the smaller proton radius.

  13. Whey protein lowers blood pressure and improves endothelial function and lipid biomarkers in adults with prehypertension and mild hypertension: results from the chronic Whey2Go randomized controlled trial12

    PubMed Central

    Givens, D Ian

    2016-01-01

    Background: Cardiovascular diseases (CVDs) are the greatest cause of death globally, and their reduction is a key public-health target. High blood pressure (BP) affects 1 in 3 people in the United Kingdom, and previous studies have shown that milk consumption is associated with lower BP. Objective: We investigated whether intact milk proteins lower 24-h ambulatory blood pressure (AMBP) and other risk markers of CVD. Design: The trial was a double-blinded, randomized, 3-way–crossover, controlled intervention study. Forty-two participants were randomly assigned to consume 2 × 28 g whey protein/d, 2 × 28 g Ca caseinate/d, or 2 × 27 g maltodextrin (control)/d for 8 wk separated by a 4-wk washout. The effects of these interventions were examined with the use of a linear mixed-model ANOVA. Results: Thirty-eight participants completed the study. Significant reductions in 24-h BP [for systolic blood pressure (SBP): −3.9 mm Hg; for diastolic blood pressure (DBP): −2.5 mm Hg; P = 0.050 for both)] were observed after whey-protein consumption compared with control intake. After whey-protein supplementation compared with control intake, peripheral and central systolic pressures [−5.7 mm Hg (P = 0.007) and −5.4 mm Hg (P = 0.012), respectively] and mean pressures [−3.7 mm Hg (P = 0.025) and −4.0 mm Hg (P = 0.019), respectively] were also lowered. Flow-mediated dilation (FMD) increased significantly after both whey-protein and calcium-caseinate intakes compared with control intake [1.31% (P < 0.001) and 0.83% (P = 0.003), respectively]. Although both whey protein and calcium caseinate significantly lowered total cholesterol [−0.26 mmol/L (P = 0.013) and −0.20 mmol/L (P = 0.042), respectively], only whey protein decreased triacylglycerol (−0.23 mmol/L; P = 0.025) compared with the effect of the control. Soluble intercellular adhesion molecule 1 and soluble vascular cell adhesion molecule 1 were reduced after whey protein consumption (P = 0.011) and after calcium-caseinate consumption (P = 0.039), respectively, compared with after control intake. Conclusions: The consumption of unhydrolyzed milk proteins (56 g/d) for 8 wk improved vascular reactivity, biomarkers of endothelial function, and lipid risk factors. Whey-protein supplementation also lowered 24-h ambulatory SBP and DBP. These results may have important implications for public health. This trial was registered at clinicaltrials.gov as NCT02090842. PMID:27797709

  14. When Networks Build a Platform Students Step up. Lumina Foundation Lesson. Spring 2010

    ERIC Educational Resources Information Center

    Brennan, Patricia L.

    2010-01-01

    For the people behind the Lumina Foundation for Education, the term "network" has particular meaning. In fact, largely as a result of their work in a national college awareness and action campaign called KnowHow2GO, they have come to define networks in a specific way--and they ask their KnowHow2GO grantees and partners to form networks…

  15. A green and facile route for constructing flower-shaped TiO2 nanocrystals assembled on graphene oxide sheets for enhanced photocatalytic activity.

    PubMed

    Cai, Chang-Jun; Xu, Mao-Wen; Bao, Shu-Juan; Ji, Chen-Chen; Lu, Zhen-Jiang; Jia, Dian-Zeng

    2013-07-12

    We have demonstrated an environmentally friendly in situ assembly method for the preparation of novel three-dimensional TiO2/graphene oxide (TiO2/GO) nanostructures with favorable flower-shaped architectures. Very little information on such a morphology of TiO2/GO nanostructures is available in the literature. The as-synthesized sample was characterized by x-ray diffraction, scanning electron microscopy, transmission electron microscopy, N2 adsorption-desorption measurements and Raman spectroscopy. Also the TiO2/GO composites exhibited enhanced photocatalytic properties.

  16. In situ loading ultra-small Cu2O nanoparticles on 2D hierarchical TiO2-graphene oxide dual-nanosheets: Towards reducing fire hazards of unsaturated polyester resin.

    PubMed

    Wang, Dong; Kan, Yongchun; Yu, Xiaojuan; Liu, Jiajia; Song, Lei; Hu, Yuan

    2016-12-15

    Fire hazards have seriously hindered the commercial application of unsaturated polyester resin (UPR), and polymer inorganic nanosheet nanocomposites hold great promise in improving their flame-retardant properties. Herein, the hierarchical structured Cu2OTiO2GO nanosheets were synthesized and characterized by XRD, Raman, TEM and XPS. Then Cu2OTiO2GO nanosheets were incorporated into UPR matrix to obtain flame-retardant UPR nanocomposite. Incorporation of 2wt% Cu2OTiO2GO nanosheets into UPR matrix resulted in an obvious reduction in PHRR and THR by 29.7 and 19.1%. TG-IR-MS results revealed that toxic pyrolysis gas such as benzene, CO and aromatic compounds greatly were decreased. In addition, RIIR spectra demonstrated the limited influence of Cu2OTiO2GO nanosheets on thermal degradation of UPR matrix, and SEM images of char residues showed that Cu2OTiO2GO nanosheets could improve their compactness. Based on the analysis of gaseous and condensed phase, a plausible flame-retardant mechanism was hypothesized to elaborate how Cu2OTiO2GO nanosheets work inside the flaming UPR nanocomposite. This innovative idea may be expanded to other polymer system and open a new door to develop polymeric nanocomposites with high performance.

  17. Simultaneous determination of epinephrine and dopamine by electrochemical reduction on the hybrid material SiO₂/graphene oxide decorated with Ag nanoparticles.

    PubMed

    Cincotto, Fernando H; Canevari, Thiago C; Campos, Anderson M; Landers, Richard; Machado, Sérgio A S

    2014-09-21

    This paper describes the synthesis, characterization and applications of a new hybrid material composed of mesoporous silica (SiO2) modified with graphene oxide (GO), SiO2/GO, obtained by the sol-gel process using HF as the catalyst. The hybrid material, SiO2/GO, was decorated with silver nanoparticles (AgNPs) with a size of less than 20 nanometres, prepared directly on the surface of the material using N,N-dimethylformamide (DMF) as the reducing agent. The resulting material was designated as AgNP/SiO2/GO. The Ag/SiO2/GO material was characterized by X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) and high-resolution transmission electron microscopy (HR-TEM). A glassy carbon electrode modified with AgNP/SiO2/GO was used in the development of a sensitive electrochemical sensor for the simultaneous determination of epinephrine and dopamine employing electrocatalytic reduction using squarewave voltammetry. Well-defined and separate reduction peaks were observed in PBS buffer at pH 7. No significant interference was seen for primarily biological interferents such as uric acid and ascorbic acid in the detection of dopamine and epinephrine. Our study demonstrated that the resultant AgNP/SiO2/GO-modified electrode is highly sensitive for the simultaneous determination of dopamine and epinephrine, with the limits of detection being 0.26 and 0.27 μmol L(-1), respectively. The AgNP/SiO2/GO-modified electrode is highly selective and can be used to detect dopamine and epinephrine in a human urine sample.

  18. Continuous release of bone morphogenetic protein-2 through nano-graphene oxide-based delivery influences the activation of the NF-κB signal transduction pathway

    PubMed Central

    Zhong, Cheng; Feng, Jun; Lin, Xiangjin; Bao, Qi

    2017-01-01

    Graphene oxide (GO) has been used as a delivery vehicle for small molecule drugs and nucleotides. To further investigate GO as a smart biomaterial for the controlled release of cargo molecules, we hypothesized that GO may be an appropriate delivery vehicle because it releases bone morphogenetic protein 2 (BMP2). GO characterization indicated that the size distribution of the GO flakes ranged from 81.1 nm to 45,749.7 nm, with an approximate thickness of 2 nm. After BMP2 adsorption onto GO, Fourier-transformed infrared spectroscopy (FTIR) and thermal gravimetric analysis were performed. Compared to GO, BMP2-GO did not induce significant changes in the characteristics of the materials. GO continuously released BMP2 for at least 40 days. Bone marrow stem cells (BMSCs) and chondrocytes were treated with BMP2-GO in interleukin-1 media and assessed in terms of cell viability, flow cytometric characterization, and expression of particular mRNA. Compared to GO, BMP2-GO did not induce any significant changes in biocompatibility. We treated osteoarthritic rats with BMP2 and BMP2-GO, which showed significant differences in Osteoarthritis Research Society International (OARSI) scores (P<0.05). Quantitative assessment revealed significant differences compared to that using BMP2 and BMP2-GO (P<0.05). These findings indicate that GO may be potentially used to control the release of carrier materials. The combination of BMP2 and GO slowed the progression of NF-κB-activated degenerative changes in osteoarthritis. Therefore, we infer that our BMP2-GO strategy could alleviate the NF-κB pathway by inducing continuous BMP2 release. PMID:28243085

  19. Continuous release of bone morphogenetic protein-2 through nano-graphene oxide-based delivery influences the activation of the NF-κB signal transduction pathway.

    PubMed

    Zhong, Cheng; Feng, Jun; Lin, Xiangjin; Bao, Qi

    2017-01-01

    Graphene oxide (GO) has been used as a delivery vehicle for small molecule drugs and nucleotides. To further investigate GO as a smart biomaterial for the controlled release of cargo molecules, we hypothesized that GO may be an appropriate delivery vehicle because it releases bone morphogenetic protein 2 (BMP2). GO characterization indicated that the size distribution of the GO flakes ranged from 81.1 nm to 45,749.7 nm, with an approximate thickness of 2 nm. After BMP2 adsorption onto GO, Fourier-transformed infrared spectroscopy (FTIR) and thermal gravimetric analysis were performed. Compared to GO, BMP2-GO did not induce significant changes in the characteristics of the materials. GO continuously released BMP2 for at least 40 days. Bone marrow stem cells (BMSCs) and chondrocytes were treated with BMP2-GO in interleukin-1 media and assessed in terms of cell viability, flow cytometric characterization, and expression of particular mRNA. Compared to GO, BMP2-GO did not induce any significant changes in biocompatibility. We treated osteoarthritic rats with BMP2 and BMP2-GO, which showed significant differences in Osteoarthritis Research Society International (OARSI) scores (P<0.05). Quantitative assessment revealed significant differences compared to that using BMP2 and BMP2-GO (P<0.05). These findings indicate that GO may be potentially used to control the release of carrier materials. The combination of BMP2 and GO slowed the progression of NF-κB-activated degenerative changes in osteoarthritis. Therefore, we infer that our BMP2-GO strategy could alleviate the NF-κB pathway by inducing continuous BMP2 release.

  20. Mentors and Models.

    ERIC Educational Resources Information Center

    Journal of Counseling and Development, 1988

    1988-01-01

    Contains five personal accounts: (1) "Critical Incidents Aren't Accidents" (Suzanne Lange); (2) "Going from Serious to Fun and Remaining Professional" (Mary Olona); (3) "The Personification of the Core Conditions" (B.S. Tillinghast, Jr.); (4) "A Personal Reaction to Carl Whitaker as a Teacher" (Katherine H. von Schmidt); and (5) "Jampy: Imaginary…

  1. The Best We Can Be.

    ERIC Educational Resources Information Center

    National Aeronautics and Space Administration, Washington, DC.

    This booklet describes the manned space flight record of the National Aeronautics and Space Administration (NASA). Sections include: (1) "The Early Days" (describing the Mercury and Gemini missions); (2) "Going to the Moon" (summarizing the Apollo missions); (3) "An Orbital Workshop" (discussing three manned skylab…

  2. Encouraging Students to Think Strategically when Learning to Solve Linear Equations

    ERIC Educational Resources Information Center

    Robson, Daphne; Abell, Walt; Boustead, Therese

    2012-01-01

    Students who are preparing to study science and engineering need to understand equation solving but adult students returning to study can find this difficult. In this paper, the design of an online resource, Equations2go, for helping students learn to solve linear equations is investigated. Students learning to solve equations need to consider…

  3. 26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... or business attributable to the expectancy of continued customer patronage. This expectancy may be due to the name or reputation of a trade or business or any other factor. (2) Going concern value... attaches to property by reason of its existence as an integral part of an ongoing business activity....

  4. Digital Geogames to Foster Local Biodiversity

    ERIC Educational Resources Information Center

    Schaal, Sonja; Schaal, Steffen; Lude, Armin

    2015-01-01

    The valuing of biodiversity is considered to be a first step towards its conservation. Therefore, the aim of the BioDiv2Go project is to combine sensuous experiences discovering biodiversity with mobile technology and a game-based learning approach. Following the competence model for environmental education (Roczen et al, 2014), Geogames (location…

  5. Latin America Curriculum. World Neighbors in the Classroom.

    ERIC Educational Resources Information Center

    World Neighbors, Inc., Oklahoma City, OK.

    This collection of lessons about the geography, languages, and social issues of several Latin American countries is intended for use with students in grades 6-12. The collection contains five lesson plans: (1) "Cold in the Tropics?" (Marilyn Kesler); (2) "Going beyond the Map: Comparing Geographic Characteristics and Related Social…

  6. Teachers Caught in the Action: Professional Development That Matters. The Series on School Reform.

    ERIC Educational Resources Information Center

    Lieberman, Ann, Ed.; Miller, Lynne, Ed.

    This collection of papers focuses on what is known and practiced in professional development. Part 1, "The Purposes of Professional Development," includes (1) "Educational Purposes and Teacher Development" (Maxine Greene); (2) "Going Public: The Imperative of Public Education in the 21st Century" (Carl D. Glickman and…

  7. International. [SITE 2002 Section].

    ERIC Educational Resources Information Center

    Willis, Dee Anna, Ed.

    This document contains the following papers on international issues from the SITE (Society for Information Technology & Teacher Education) 2002 conference: (1) "The Management of Technological Change within Faculties in International American Schools" (Martine Audeoud); (2) "Going Global: Using a Website Development Project To…

  8. Hole injection enhancement in organic light emitting devices using plasma treated graphene oxide

    NASA Astrophysics Data System (ADS)

    Jesuraj, P. Justin; Parameshwari, R.; Kanthasamy, K.; Koch, J.; Pfnür, H.; Jeganathan, K.

    2017-03-01

    The hole injection layer (HIL) with high work function (WF) is desirable to reduce the injection barrier between anode and hole transport layer in organic light emitting devices (OLED). Here, we report a novel approach to tune the WF of graphene oxide (GO) using oxygen and hydrogen plasma treatment and its hole injection properties in OLEDs. The mild exposure of oxygen plasma on GO (O2-GO) significantly reduces the injection barrier by increasing the WF of anode (4.98 eV) through expansion of Csbnd O bonds. In contrast, the hole injection barrier was drastically increased for hydrogen plasma treated GO (H2-GO) layers as the WF is lowered by the contraction of Csbnd O bond. By employing active O2-GO as HIL in OLEDs found to exhibit superior current efficiency of 4.2 cd/A as compared to 3.3 cd/A for pristine GO. Further, the high injection efficiency of O2-GO infused hole only device can be attributed to the improved energy level matching. Ultraviolet and X-ray photoelectron spectroscopy were used to correlate the WF of HIL infused anode towards the enhanced performance of OLEDs with their capricious content of Csbnd O in GO matrix.

  9. Rhetorical and Communication Theory: Abstracts of Doctoral Dissertations Published in "Dissertation Abstracts International," July through December 1984 (Vol. 45 Nos. 1 through 6).

    ERIC Educational Resources Information Center

    ERIC Clearinghouse on Reading and Communication Skills, Urbana, IL.

    This collection of abstracts is part of a continuing series providing information on recent doctoral dissertations. The 19 titles deal with the following topics: (1) cinema, culture, and the social formation; (2) going beyond historical-critical dualism in the analysis of theoretical discourse; (3) empathy in instrumental communication; (4) a…

  10. House Detective: Finding History in Your Home.

    ERIC Educational Resources Information Center

    National Museum of American History, Washington, DC.

    Every person's home has a story to tell and a place in history. Whether a person owns their house, rents it, or lives in an apartment, they can become a house detective and discover the history of the home. This brochure enumerates the following nine steps for investigation: (1) "Start at Home"; (2) "Go to the Courthouse"; (3)…

  11. A MnO2/Graphene Oxide/Multi-Walled Carbon Nanotubes-Sulfur Composite with Dual-Efficient Polysulfide Adsorption for Improving Lithium-Sulfur Batteries.

    PubMed

    Li, Yong; Ye, Daixin; Liu, Wen; Shi, Bin; Guo, Rui; Zhao, Hongbin; Pei, Haijuan; Xu, Jiaqiang; Xie, Jingying

    2016-10-12

    Lithium-sulfur batteries can potentially be used as a chemical power source because of their high energy density. However, the sulfur cathode has several shortcomings, including fast capacity attenuation, poor electrochemical activity, and low Coulombic efficiency. Herein, multi-walled carbon nanotubes (CNTs), graphene oxide (GO), and manganese dioxide are introduced to the sulfur cathode. A MnO2/GO/CNTs-S composite with a unique three-dimensional (3D) architecture was synthesized by a one-pot chemical method and heat treatment approach. In this structure, the innermost CNTs work as a conducting additive and backbone to form a conducting network. The MnO2/GO nanosheets anchored on the sidewalls of CNTs have a dual-efficient absorption capability for polysulfide intermediates as well as afford adequate space for sulfur loading. The outmost nanosized sulfur particles are well-distributed on the surface of the MnO2/GO nanosheets and provide a short transmission path for Li(+) and the electrons. The sulfur content in the MnO2/GO/CNTs-S composite is as high as 80 wt %, and the as-designed MnO2/GO/CNTs-S cathode displays excellent comprehensive performance. The initial specific capacities are up to 1500, 1300, 1150, 1048, and 960 mAh g(-1) at discharging rates of 0.05, 0.1, 0.2, 0.5, and 1 C, respectively. Moreover, the composite cathode shows a good cycle performance: the specific capacity remains at 963.5 mAh g(-1) at 0.2 C after 100 cycles when the area density of sulfur is 2.8 mg cm(-2).

  12. Synthesis of double-clickable functionalised graphene oxide for biological applications† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5cc05412e Click here for additional data file.

    PubMed Central

    Mei, Kuo-Ching; Rubio, Noelia; Costa, Pedro M.; Kafa, Houmam; Abbate, Vincenzo; Festy, Frederic; Bansal, Sukhvinder S.; Hider, Robert C.

    2015-01-01

    Azide- and alkyne-double functionalised graphene oxide (Click2 GO) was synthesised and characterised with attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), thermogravimetric analysis (TGA) and Raman spectroscopy. Fourteen-percentage increase in azide content was found, after pre-treatment of GO with meta-chloroperoxybenzoic acid (mCPBA), determined with elemental analysis. No effect on A549 cell viability was found, up to 100 μg mL–1 and 72 h of incubation, determined with the modified lactate dehydrogenase (mLDH) assay. Two sequential copper(i) catalysed azide–alkyne cycloaddition (CuAAC) reactions were performed to conjugate the propargyl-modified blood–brain barrier targeting peptide Angiopep-2, and a bis-azide polyethylene glycol (M W = 3500), to the Click2 GO. The final conjugate was characterised with ATR-FTIR and TGA. PMID:26295072

  13. Conjugated polymer/graphene oxide nanocomposite as thermistor

    NASA Astrophysics Data System (ADS)

    Joshi, Girish M.; Deshmukh, Kalim

    2015-06-01

    We demonstrated the synthesis and measurement of temperature dependent electrical resistivity of graphene oxide (GO) reinforced poly (3, 4 - ethylenedioxythiophene) - tetramethacrylate (PEDOTTMA)/Polymethylmethacrylate (PMMA) based nanocomposites. Negative temperature coefficient (NTC) was observed for 0.5, 1 % GO loading and the positive temperature coefficient (PTC) was observed for 1.5 and 2 % Go loading in the temperature (40 to 120 °C). The GO inducted nanocomposite perform as an excellent thermistor and suitable for electronic and sensor domain.

  14. Conjugated polymer/graphene oxide nanocomposite as thermistor

    SciTech Connect

    Joshi, Girish M. Deshmukh, Kalim

    2015-06-24

    We demonstrated the synthesis and measurement of temperature dependent electrical resistivity of graphene oxide (GO) reinforced poly (3, 4 - ethylenedioxythiophene) - tetramethacrylate (PEDOTTMA)/Polymethylmethacrylate (PMMA) based nanocomposites. Negative temperature coefficient (NTC) was observed for 0.5, 1 % GO loading and the positive temperature coefficient (PTC) was observed for 1.5 and 2 % Go loading in the temperature (40 to 120 °C). The GO inducted nanocomposite perform as an excellent thermistor and suitable for electronic and sensor domain.

  15. Application of Computational and Visualization Methods to Groundwater Modeling

    DTIC Science & Technology

    1994-09-01

    John B. Palmerton, Rock Me- chanics Branch, Soil and Rock Mechanics Division, GL, WES, performed the analysis of Cerrilios Dam in Puerto Rico discussed...two different grid sizes of the Cerrillos Dam in Puerto Rico seepage model were used (the Cerrillos Dam study was performed by Mr. John Palmerton, GL...in Table 2 go to zero for this square grid, making the formulation similar to a standard finite difference algorithm. Laboratory tesi problem Results

  16. Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

    PubMed

    Emmert, Steffen; Ueda, Takahiro; Zumsteg, Urs; Weber, Peter; Khan, Sikandar G; Oh, Kyu-Seon; Boyle, Jennifer; Laspe, Petra; Zachmann, Karolin; Boeckmann, Lars; Kuschal, Christiane; Bircher, Andreas; Kraemer, Kenneth H

    2009-01-01

    We examined the clinical, molecular and genetic features of a 16-year-old boy (XP2GO) with xeroderma pigmentosum (XP) and progressive neurological symptoms. The parents are not consanguineous. Increased sun sensitivity led to the diagnosis of XP at 2 years of age and a strict UV protection scheme was implemented. Besides recurrent conjunctivitis and bilateral pterygium, only mild freckling was present on his lips. He shows absent deep tendon reflexes, progressive sensorineural deafness and progressive mental retardation. MRI shows diffuse frontal cerebral atrophy and dilated ventricles. Symptoms of trichothiodystrophy (brittle hair with a tiger-tail banding pattern on polarized microscopy) or Cockayne syndrome (cachectic dwarfism, cataracts, pigmentary retinopathy and spasticity) were absent. XP2GO fibroblasts showed reduced post-UV cell survival (D(37) = 3.8 J/m(2)), reduced nucleotide excision repair, reduced expression of XPD mRNA and an undetectable level of XPD protein. Mutational analysis of the XPD gene in XP2GO revealed two different mutations: a common p.Arg683Trp amino acid change (c.2047C>T) known to be associated with XP and a novel frameshift mutation c.2009delG (p.Gly670Alafs*39). The latter mutation potentially behaves as a null allele. While not preventing neurological degeneration, early diagnosis and rigorous sun protection can result in minimal skin disease without cancer in XP patients.

  17. Graphene oxide-based microspheres for the dispersive solid-phase extraction of non-steroidal estrogens from water samples.

    PubMed

    Wen, Yingying; Niu, Zongliang; Ma, Yanling; Ma, Jiping; Chen, Lingxin

    2014-11-14

    A modified Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) method based on the dispersive solid-phase extraction (dSPE) combined with high performance liquid chromatography (HPLC) was developed for the determination of non-steroidal estrogens in water samples. In this study, graphene oxide-based silica microspheres (SiO2@GO) were used as dSPE material for the preconcentration of analytes. HPLC was used for the separation and detection. This was the first time that the synthesized SiO2@GO microspheres were used as stationary phases for the off-line preconcentration of the non-steroidal estrogens in dSPE. dSPE parameters, such as sample pH, volume and type of eluent were optimized. Application of the developed method to analyze spiked lake, reservoir and tap water samples resulted in good recoveries values ranging from 70 to 106% with relative standard deviation values lower than 7.0% in all cases. Limits of detection were in the range of 0.2-6.1 μg/L. The combined data obtained in this study recommended that the proposed method is very fast, simple, repeatable and accurate for the detection of non-steroidal estrogens. Furthermore, the SiO2@GO microspheres application could potentially be expanded to extract and pre-concentrate other compounds in various matrices.

  18. Influences of graphene oxide support on the electrochemical performances of graphene oxide-MnO2 nanocomposites

    PubMed Central

    2011-01-01

    MnO2 supported on graphene oxide (GO) made from different graphite materials has been synthesized and further investigated as electrode materials for supercapacitors. The structure and morphology of MnO2-GO nanocomposites are characterized by X-ray diffraction, X-ray photoemission spectroscopy, scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, and Nitrogen adsorption-desorption. As demonstrated, the GO fabricated from commercial expanded graphite (denoted as GO(1)) possesses more functional groups and larger interplane gap compared to the GO from commercial graphite powder (denoted as GO(2)). The surface area and functionalities of GO have significant effects on the morphology and electrochemical activity of MnO2, which lead to the fact that the loading amount of MnO2 on GO(1) is much higher than that on GO(2). Elemental analysis performed via inductively coupled plasma optical emission spectroscopy confirmed higher amounts of MnO2 loading on GO(1). As the electrode of supercapacitor, MnO2-GO(1) nanocomposites show larger capacitance (307.7 F g-1) and better electrochemical activity than MnO2-GO(2) possibly due to the high loading, good uniformity, and homogeneous distribution of MnO2 on GO(1) support. PMID:21951643

  19. Water and Carbon as Creators of Imbalances in Nature

    NASA Astrophysics Data System (ADS)

    Shlafman, L. M.; Kontar, V. A.

    2012-12-01

    Our studies are showing that the carbon and water are closely intertwined. There are many reasons to study the imbalance of water and carbon together. For example, in photosynthesis six molecules of water and six molecules of carbon dioxide have created one molecule of sugar and six molecules of oxygen. 6H2O + 6CO2 go C6H12O6 + 6O2 For water and carbon dioxide, regarding the point of view of the imbalance, this process is the creator of imbalance of the decreasing type. The concentration of water and carbon dioxide in the atmosphere will decrease. For oxygen this process is the creator of imbalance of the increasing type. The concentration of oxygen in the atmosphere will increase. Water and carbon dioxide can be created independently of each other. For example, water is obtained from combining two hydrogen atoms and one oxygen atom: 2 H2 + O2 go 2 H2O Carbon dioxide also is possible to create without water: Na2CO3 go Na2O + CO2 or CaCO3 go CaO + CO2 But it is very often the water and carbon dioxide made up simultaneously in one reaction. For example combustion of methane gives carbon dioxide and water: CH4 + 2 O2 go CO2 + 2 H2O Carbon dioxide can come up more complicated way. Initially created carbon monoxide and water 2 CH4 + 3 O2 go 2 CO + 4 H2O After then the carbon monoxide rapidly oxidized to carbon dioxide. The gasification of solid fuels is the reaction: C + H20 go CO + H2 In the next step carbon monoxide is oxidized to carbon dioxide, and hydrogen is oxidized to water. C3H8 + 5 O2 go 3 CO2 + 4 H2O By the incomplete combustion of propane will be produced some very interesting components: 2 C3H8 + 7 O2 go 8 H2O + 2 CO2 + 2 CO + 2 C It will be water, carbon dioxide, carbon monoxide and pure carbon. Carbon monoxide will oxidize to carbon dioxide. But the pure carbon will have a very serious going on. By the incomplete combustion of not only propane, but other hydrocarbons, will be produced and the pure carbon also. This "pure carbon" or "black carbon" plays a

  20. Graphene oxide nanosheets as an effective template for the synthesis of porous TiO2 film in dye-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Wang, Ping; He, Fenglong; Wang, Jin; Yu, Huogen; Zhao, Li

    2015-12-01

    Template method by using various organic components as the pore-forming agent is an effective strategy for the preparation of various porous inorganic materials. After high-temperature calcination in air, the organic components can be in situ decomposed into the gaseous CO2, resulting in the formation of porous structures in inorganic materials. In addition to the well-known organic components, it is highly required to develop new and simple carbon-containing template to prepare porous inorganic nanostructures. In this study, graphene oxide (GO) nanosheets were used as a new template for the preparation of porous TiO2 film photoelectrode, which can be applied in dye-sensitized solar cells (DSSCs). The porous TiO2 film was fabricated via a three-step method, including the initially homogeneous grafting of GO nanosheets on the TiO2 surface (TiO2-GO), the preparation of TiO2-GO film using blade method and final formation of porous structure after the in situ removal of GO by high-temperature calcination. The effect of GO content on photoelectric conversion performance of the as-fabricated DSSCs was investigated. It was found that the conversion efficiency of DSSC based on porous TiO2-GO (0.75%) film reached up to a maximum value (4.65%), which was much higher than that of DSSC based on nonporous TiO2 film (4.01%). The enhanced conversion efficiency can be attributed to the formation of more porous structures caused by the GO nanosheets after high-temperature calcination. This work may provide a new insight for preparing other porous structured materials.

  1. Phase Transitions and Free Boundaries

    DTIC Science & Technology

    1991-10-31

    described. The second approximation technique, finite-volume, will be employed on three, three-dimensional nonisother- mal flows: a sphere in linear shear...function is uo = r2 go( O ) (r and 0 are polar coordinates in the plane). The non-negative function go equals zero outside the interval [-6, 6], where 6 E...21 SEMINAR IN {Free Boundary Problems I Vincent Hall 570 11:15 am Wei-Ming Ni Spike layers in singular perturbation theory University of Minnesota

  2. EST analysis pipeline: use of distributed computing resources.

    PubMed

    González, Francisco Javier; Vizcaíno, Juan Antonio

    2011-01-01

    This chapter describes how a pipeline for the analysis of expressed sequence tag (EST) data can be -implemented, based on our previous experience generating ESTs from Trichoderma spp. We focus on key steps in the workflow, such as the processing of raw data from the sequencers, the clustering of ESTs, and the functional annotation of the sequences using BLAST, InterProScan, and BLAST2GO. Some of the steps require the use of intensive computing power. Since these resources are not available for small research groups or institutes without bioinformatics support, an alternative will be described: the use of distributed computing resources (local grids and Amazon EC2).

  3. FOURFIT-A Computer Code for Determining Equivalent Nuclear Yield and Peak Overpressure by a Fourier Spectrum Fit Method

    DTIC Science & Technology

    1984-05-25

    NBPTS equal to 2048. Each array must be at least large enough to accomodate this value. i3 7% 4 z 32 "- : -" ,-. - -.- ;-.°. :. .’ -,i...F5.2.5X..WI -,*F5.2) WR:TE(48. 113) IOPT.IFILT ICOUNT *0 NBPTS 2048 IF(IOPT.EO.3) GO TO 7 CALL EBREAD IF(IOPT.EO.2) GO TO 666 CALL FIT 7 ICOUINT - I CALL...UPON THE POSITIVE PHASE DURATION. DTB - DP/ NBPTS GO TO 15 5 ISTL(i) - IOHWITH FOURF ISTL(2) - iGHIT SPEICHE ISTL(3) - 1OHR-BRODE ISTL(4) - 10H ISTL(5

  4. Children's attitudes toward interaction with an unfamiliar peer with complex communication needs: comparing high- and low-technology devices.

    PubMed

    Dada, Shakila; Horn, Tenille; Samuels, Alecia; Schlosser, Ralf W

    2016-12-01

    This study examined the attitudes of children with typical development towards an unfamiliar peer with complex communication needs using augmentative and alternative communication (AAC) systems. Specifically, the study aimed to compare attitudes when the peer used mobile technology (i.e., iPad(©)(1) ) with an AAC-specific application (Proloquo2Go™ (2) ) versus a low-technology communication board. A within-group crossover design was utilized involving 78 children. Half of the participants (i.e., Group 1) viewed Video 1 of an unfamiliar peer with complex communication needs in a scripted communication interaction using an iPad with Proloquo2Go followed by Video 2 of the same interaction using a communication board. The other half of the participants (Group 2) viewed these videos in the reverse sequence. The Communication Aid/Device Attitudinal Questionnaire (CADAQ) was completed after watching each video. Results indicated that both groups were more positive towards Video 1 (iPad with Prologuo2Go) on certain dimensions of the CADAQ. The results are discussed and recommendations for future research provided.

  5. Functionalized Graphene Oxide as a Nanocarrier in a Multienzyme Labeling Amplification Strategy for Ultrasensitive Electrochemical Immunoassay of Phosphorylated p53 (S392)

    SciTech Connect

    Du, Dan; Wang, Limin; Shao, Yuyan; Wang, Jun; Engelhard, Mark H.; Lin, Yuehe

    2011-01-06

    P53 phosphorylation plays an important role in many biological processes and might be used as a potential biomarker in clinical diagnoses. We report a new electrochemical immunosensor for ultrasensitive detection of phosphorylated p53 at Ser392 (phospho-p53-392) based on graphene oxide (GO) as a nanocarrier in multienzymes amplification strategy. Greatly enhanced sensitivity was achieved by using the bioconjugates featuring horseradish peroxidase (HRP) and p53392 signal antibody (p53Ab2) linked to functionalized GO (HRP-p53Ab2-GO) at high ratio of HRP/p53Ab2. After a sandwich immunoreaction, the HRP-p53Ab2-GO captured onto the electrode surface produced an amplified electrocatalytic response by the reduction of enzymatically oxidized thionine in the presence of hydrogen peroxide. The increase of response current was proportional to the phospho-p53 concentration in the range of 0.02 to 2 nM with the detection limit of 0.01 nM, which was 10-fold lower than that of traditional sandwich electrochemical measurement for p53. The amplified immunoassay developed in this work shows acceptable stability and reproducibility and the assay results for phospho-p53 spiked in human plasma also show good recovery (92%~103.8%). This simple and low-cost immunosensor shows great promise for detection of other phosphorylated proteins and clinical applications.

  6. Graphene oxide-SiO2 nanocomposite as the adsorbent for extraction and preconcentration of plant hormones for HPLC analysis.

    PubMed

    Zhang, Xiaona; Niu, Jiahua; Zhang, Xiaoting; Xiao, Rui; Lu, Minghua; Cai, Zongwei

    2017-03-01

    In this research, a modified Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) method based on graphene oxide@SiO2(SiO2@GO) nanocomposite as adsorbent of dispersive solid-phase extraction (dSPE) combined with high performance liquid chromatography (HPLC) for the analysis of four plant hormones in different plants was established. The as-prepared SiO2@GO was characterized by scanning electron microscopy, transmission electron microscopy and infrared spectroscopy. The experimental conditions for dSPE, including the ratio of material to liquid, pH of sample, adsorption and desorption time, desorption temperature as well as desorption solution, were investigated. The detection limits for the analysis of indole-3-acetic acid, indole-3-butyric acid, 1-naphthylacetic acid and abscisic acid were achieved below 0.05μgmL(-1). The established method was applied to the analysis of the plant hormones in fruits, vegetables and other food samples. The obtained results indicated that the method was sensitive, accurate, convenient and quick, which provided an alternative analytical approach for plant hormones in complex matrices.

  7. TiO2-graphene oxide nanocomposite as advanced photocatalytic materials

    PubMed Central

    2013-01-01

    Background Graphene oxide composites with photocatalysts may exhibit better properties than pure photocatalysts via improvement of their textural and electronic properties. Results TiO2-Graphene Oxide (TiO2 - GO) nanocomposite was prepared by thermal hydrolysis of suspension with graphene oxide (GO) nanosheets and titania peroxo-complex. The characterization of graphene oxide nanosheets was provided by using an atomic force microscope and Raman spectroscopy. The prepared nanocomposites samples were characterized by Brunauer–Emmett–Teller surface area and Barrett–Joiner–Halenda porosity, X-ray Diffraction, Infrared Spectroscopy, Raman Spectroscopy and Transmission Electron Microscopy. UV/VIS diffuse reflectance spectroscopy was employed to estimate band-gap energies. From the TiO2 - GO samples, a 300 μm thin layer on a piece of glass 10×15 cm was created. The photocatalytic activity of the prepared layers was assessed from the kinetics of the photocatalytic degradation of butane in the gas phase. Conclusions The best photocatalytic activity under UV was observed for sample denoted TiGO_100 (k = 0.03012 h-1), while sample labeled TiGO_075 (k = 0.00774 h-1) demonstrated the best activity under visible light. PMID:23445868

  8. Fabrication of Fe3O4/SiO2 core/shell nanoparticles attached to graphene oxide and its use as an adsorbent.

    PubMed

    Yao, Yunjin; Miao, Shiding; Yu, Shaoming; Ma, Li Ping; Sun, Hongqi; Wang, Shaobin

    2012-08-01

    Amino-functionalized Fe(3)O(4)/SiO(2) core/shell nanoparticles were synthesized by reacting Fe(3)O(4) nanoparticles with tetraethyl orthosilicate and (3-aminopropyl) triethoxysilane to introduce amino groups on the surface. The amino groups on the Fe(3)O(4)/SiO(2) were reacted with the carboxylic groups of graphene oxide (GO) with the aid of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide and N-hydroxysuccinnimide to form Fe(3)O(4)/SiO(2)GO nanoparticles. The structural, surface, and magnetic characteristics of the material were investigated by scanning and transmission electron microscopy, energy-dispersive X-ray spectrometry, powder X-ray diffraction, Fourier transform infrared spectroscopy, and thermogravimetric analysis. Adsorption equilibrium and kinetics of methylene blue on the Fe(3)O(4)/SiO(2)GO were studied in a batch system. The maximum adsorption capacities were found to be 97.0, 102.6, and 111.1 mg g(-1) at 25, 45, and 60°C, respectively. A second-order kinetic equation could best describe the sorption kinetics. Thermodynamic parameters indicated that the adsorption of methylene blue onto the material was thermodynamically feasible and could occur spontaneously.

  9. Development of magnetic graphene oxide adsorbent for the removal and preconcentration of As(III) and As(V) species from environmental water samples.

    PubMed

    Rashidi Nodeh, Hamid; Wan Ibrahim, Wan Aini; Ali, Imran; Sanagi, Mohd Marsin

    2016-05-01

    New-generation adsorbent, Fe3O4@SiO2/GO, was developed by modification of graphene oxide (GO) with silica-coated (SiO2) magnetic nanoparticles (Fe3O4). The synthesized adsorbent was characterized using Fourier transform infrared spectroscopy, X-ray diffractometry, energy-dispersive X-ray spectroscopy, and field emission scanning electron microscopy. The developed adsorbent was used for the removal and simultaneous preconcentration of As(III) and As(V) from environmental waters prior to ICP-MS analysis. Fe3O4@SiO2/GO provided high adsorption capacities, i.e., 7.51 and 11.46 mg g(-1) for As(III) and As(V), respectively, at pH 4.0. Adsorption isotherm, kinetic, and thermodynamic were investigated for As(III) and As(V) adsorption. Preconcentration of As(III) and As(V) were studied using magnetic solid-phase extraction (MSPE) method at pH 9.0 as the adsorbent showed selective adsorption for As(III) only in pH range 7-10. MSPE using Fe3O4@SiO2/GO was developed with good linearities (0.05-2.0 ng mL(-1)) and high coefficient of determination (R (2) = 0.9992 and 0.9985) for As(III) and As(V), respectively. The limits of detection (LODs) (3× SD/m, n = 3) obtained were 7.9 pg mL(-1) for As(III) and 28.0 pg mL(-1) for As(V). The LOD obtained is 357-1265× lower than the WHO maximum permissible limit of 10.0 ng mL(-1). The developed MSPE method showed good relative recoveries (72.55-109.71 %) and good RSDs (0.1-4.3 %, n = 3) for spring water, lake, river, and tap water samples. The new-generation adsorbent can be used for the removal and simultaneous preconcentration of As(III) and As(V) from water samples successfully. The adsorbent removal for As(III) is better than As(V).

  10. The Buckling and Vibration of Composite Plates Using the Levy Method Considering Shear Deformation and Rotary Inertia.

    DTIC Science & Technology

    1987-12-01

    KAPA1(3), OMEGA ( 3 ),OMEGAl(3) REAL NU,n INTEGER type,bc,pp,sd DOUBLE PRECISION aa,thick,r,w,coeft4,coeft2,coeft0,e,f,g, *h,z,x,b,c,dpp,q,ALPHA,BETA...v3- omega ( 3 ) Y4-omnegal (1) v5inomegal (2) 95 v6-omegal (3) 990 a11=(dsinh(alpha*bb))/1.dlO a12=(dsinh(beta*bb) )/1.dlO a13=(dsinh(gamma*bb) )/1.dlO...v6=KAPA1 (3) v7=(vl-v3) /(v3-v2) - vB(v2-vl)/(v3-v2) go to 1020 1010 v1ODMEGA(1) v2ODMEGA(2) Al v3= OMEGA ( 3 ) v4=OMEGA1 (1) v5SOMEGA1 (2) v6=OMEGAI (3

  11. One-step amine modification of graphene oxide to get a green trifunctional metal-free catalyst

    NASA Astrophysics Data System (ADS)

    Yang, Anwei; Li, Jingjing; Zhang, Chen; Zhang, Wenqin; Ma, Ning

    2015-08-01

    Graphene oxide is modified by diethylenetriamine through a one-step route to prepare GO-NH(CH2)2NH(CH2)2NH2 (GO-DETA), which has primary and secondary amino groups and carboxyl groups. GO-DETA is characterized by Fourier transform-infrared spectrum (FT-IR), X-ray diffraction spectroscopy (XRD), thermo-gravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM). The catalytic performance of obtained GO-DETA is investigated in Knoevenagel condensation and Michael addition in water; the results show it can be used as an efficient and stable catalyst. In addition, it has other features, such as simple preparation, good recyclability and environmental friendliness.

  12. Integrated thruster assembly program

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The program is reported which has provided technology for a long life, high performing, integrated ACPS thruster assembly suitable for use in 100 typical flights of a space shuttle vehicle over a ten year period. The four integrated thruster assemblies (ITA) fabricated consisted of: propellant injector; a capacitive discharge, air gap torch type igniter assembly; fast response igniter and main propellant valves; and a combined regen-dump film cooled chamber. These flightweight 6672 N (1500 lb) thruster assemblies employed GH2/GO2 as propellants at a chamber pressure of 207 N/sq cm (300 psia). Test data were obtained on thrusted performance, thermal and hydraulic characteristics, dynamic response in pulsing, and cycle life. One thruster was fired in excess of 42,000 times.

  13. Strong interlayer coupling mediated giant two-photon absorption in MoS e2 /graphene oxide heterostructure: Quenching of exciton bands

    NASA Astrophysics Data System (ADS)

    Sharma, Rituraj; Aneesh, J.; Yadav, Rajesh Kumar; Sanda, Suresh; Barik, A. R.; Mishra, Ashish Kumar; Maji, Tuhin Kumar; Karmakar, Debjani; Adarsh, K. V.

    2016-04-01

    A complex few-layer MoS e2 /graphene oxide (GO) heterostructure with strong interlayer coupling was prepared by a facile hydrothermal method. In this strongly coupled heterostructure, we demonstrate a giant enhancement of two-photon absorption that is in stark contrast to the reverse saturable absorption of a weakly coupled MoS e2 /GO heterostructure and saturable absorption of isolated MoS e2 . Spectroscopic evidence of our study indicates that the optical signatures of isolated MoS e2 and GO domains are significantly modified in the heterostructure, displaying a direct coupling of both domains. Furthermore, our first-principles calculations indicate that strong interlayer coupling between the layers dramatically suppresses the MoS e2 excitonic bands. We envision that our findings provide a powerful tool to explore different optical functionalities as a function of interlayer coupling, which may be essential for the development of device technologies.

  14. High throughput CIGS solar cell fabrication via ultra-thin absorber layer with optical confinement and (Cd, CBD)-free heterojunction partner

    SciTech Connect

    Marsillac, Sylvain

    2015-11-30

    The main objective of this proposal was to use several pathways to reduce the production cost of Cu(In,Ga)Se2 (CIGS) PV modules and therefore the levelized cost of energy (LCOE) associated with this technology. Three high cost drivers were identified, nominally: 1) Materials cost and availability; 2) Large scale uniformity; 3) Improved throughput These three cost drivers were targeted using the following pathways: 1) Reducing the thickness of the CIGS layer while enhancing materials quality; 2) Developing and applying enhanced in-situ metrology via real time spectroscopic ellipsometry; 3) Looking into alternative heterojunction partner, back contact and anti-reflection (AR) coating Eleven main Tasks were then defined to achieve these goals (5 in Phase 1 and 6 in Phase 2), with 11 Milestones and 2 Go/No-go decision points at the end of Phase 1. The key results are summarized below

  15. Nanostructured Graphene-Titanium Dioxide Composites Synthesized by a Single-Step Aerosol Process for Photoreduction of Carbon Dioxide

    PubMed Central

    Wang, Wei-Ning; Jiang, Yi; Fortner, John D.; Biswas, Pratim

    2014-01-01

    Abstract Photocatalytic reduction of carbon dioxide (CO2) to hydrocarbons by using nanostructured materials activated by solar energy is a promising approach to recycling CO2 as a fuel feedstock. CO2 photoreduction, however, suffers from low efficiency mainly due to the inherent drawback of fast electron-hole recombination in photocatalysts. This work reports the synthesis of nanostructured composites of titania (TiO2) nanoparticles (NPs) encapsulated by reduced graphene oxide (rGO) nanosheets via an aerosol approach. The role of synthesis temperature and TiO2/GO ratio in CO2 photoreduction was investigated. As-prepared nanocomposites demonstrated enhanced CO2 conversion performance as compared with that of pristine TiO2 NPs due to the strong electron trapping capability of the rGO nanosheets. PMID:25053879

  16. Fabrication of graphene oxide decorated with Fe3O4@SiO2 for immobilization of cellulase

    NASA Astrophysics Data System (ADS)

    Li, Yue; Wang, Xiang-Yu; Jiang, Xiao-Ping; Ye, Jing-Jing; Zhang, Ye-Wang; Zhang, Xiao-Yun

    2015-01-01

    Fe3O4@SiO2-graphene oxide (GO) composites were successfully fabricated by chemical binding of functional Fe3O4@SiO2 and GO and applied to immobilization of cellulase via covalent attachment. The prepared composites were further characterized by transmission electron microscopy and Fourier transform infrared spectroscopy. Fe3O4 nanoparticles (NPs) were monodisperse spheres with a mean diameter of 17 ± 0.2 nm. The thickness of SiO2 layer was calculated as being 6.5 ± 0.2 nm. The size of Fe3O4@SiO2 NPs was 24 ± 0.3 nm, similar to that of Fe3O4@SiO2-NH2. Fe3O4@SiO2-GO composites were synthesized by linking of Fe3O4@SiO2-NH2 NPs to GO with the catalysis of EDC and NHS. The prepared composites were used for immobilization of cellulase. A high immobilization yield and efficiency of above 90 % were obtained after the optimization. The half-life of immobilized cellulase (722 min) was 3.34-fold higher than that of free enzyme (216 min) at 50 °C. Compared with the free cellulase, the optimal temperature of the immobilized enzyme was not changed; but the optimal pH was shifted from 5.0 to 4.0, and the thermal stability was enhanced. The immobilized cellulase could be easily separated and reused under magnetic field. These results strongly indicate that the cellulase immobilized onto the Fe3O4@SiO2-GO composite has potential applications in the production of bioethanol.

  17. Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray

    PubMed Central

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement. PMID:23110046

  18. Enhanced peroxidase-like activity of MoS2/graphene oxide hybrid with light irradiation for glucose detection.

    PubMed

    Peng, Jian; Weng, Jian

    2017-03-15

    Construction of novel enzyme-free mimetic is very important in improving the sensitivity of biosensor. Here, an intrinsic peroxidase-like activity of MoS2 and graphene oxide (MoS2/GO) hybrid is demonstrated and the hybrid is also used to detect glucose with high sensitivity. Firstly, the peroxidase-like activity of hydrid is compared with that of two components alone, the mixture of two components and horseradish peroxidase. The results show that the hydrid has highest catalytic activity and the Michaelis constant of this hybrid is 4.35 times lower and the maximal reaction velocity is 3.34 times higher than those of horseradish peroxidase, respectively. Electrochemical technologies are used to investigate the enhancing mechanism. The results show that the excellently catalytic performance could be attributed to the fast electron transfer on the surface of MoS2/GO and the synergistic interaction of two components. Secondly, the effect of visible light and near-infrared light on the peroxidase-like activity of hybrid is also investigated. The results show that the limit of detection for H2O2 can be reduced from 10nM to 2.5nM with visible light. Thirdly, the hybrid is further used to detect glucose in serum with and without light. The results show that the hybrid has high selectivity and sensitivity for glucose detection in serum and the limit of detection for glucose is reduced from 0.83μM to 65nM with visible light. Therefore, the hybrid may have a potential application in glucose detection in serum with high sensitivity and selectivity.

  19. Bis(trifluoromethanesulfonyl)imide-based ionic liquids grafted on graphene oxide-coated solid-phase microextraction fiber for extraction and enrichment of polycyclic aromatic hydrocarbons in potatoes and phthalate esters in food-wrap.

    PubMed

    Hou, Xiudan; Guo, Yong; Liang, Xiaojing; Wang, Xusheng; Wang, Lei; Wang, Licheng; Liu, Xia

    2016-06-01

    A class of novel, environmental friendly ionic liquids (ILs) were synthesized by on-fiber preparation strategy and modified on graphene oxide (GO)-coated stainless steel wire, which was used as a solid-phase microextraction (SPME) fiber for efficient enrichment of polycyclic aromatic hydrocarbons (PAHs) and phthalate esters (PAEs). Surface characteristic of the ILs and polymeric-ILs (PILs) fibers with the wave-structure were inspected by scanning electron microscope. The successfully synthesis of bis(trifluoromethanesulfonyl)imide (NTf2(-))-based ILs were also characterized by energy dispersive spectrometer analysis. Through the chromatograms of the proposed two ILs (1-aminoethyl-3-methylimidazolium bromide (C2NH2MIm(+)Br(-)), C2NH2MIm(+)NTf2(-)) and two PILs (polymeric 1-vinyl-3-hexylimidazolium bromide (poly(VHIm(+)Br(-))), poly(VHIm(+)NTf2(-)))-GO-coated fibers for the extraction of analytes, NTf2(-)-based PIL demonstrated higher extraction capacity for hydrophobic compounds than other as-prepared ILs. Analytical performances of the proposed fibers were investigated under the optimized extraction and desorption conditions coupled with gas chromatography (GC). Compared with the poly(VHIm(+)Br(-))-GO fiber, the poly(VHIm(+)NTf2(-))-GO SPME fiber brought wider linear ranges for analytes with correlation coefficient in the range of 0.9852-0.9989 and lower limits of detection ranging from 0.015-0.025μgL(-1). The obtained results indicated that the newly prepared PILs-GO coating was a feasible, selective and green microextraction medium, which could be suitable for extraction and determination of PAHs and PAEs in potatoes and food-wrap sample, respectively.

  20. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    PubMed

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  1. Removal of microcystin-LR and microcystin-RR by graphene oxide: adsorption and kinetic experiments.

    PubMed

    Pavagadhi, Shruti; Tang, Ai Ling Lena; Sathishkumar, Muthuswamy; Loh, Kian Ping; Balasubramanian, Rajasekhar

    2013-09-01

    Graphene oxide (GO) was employed in the present study for removal of two commonly occurring algal toxins, microcystin-LR (MC-LR) and microcystin-RR (MC-RR), from water. The adsorption performance of GO was compared to that of commercially available activated carbon. Further, adsorption experiments were conducted in the presence of other environmental pollutants to understand the matrix effects of contaminated water on the selective adsorption of MC-LR and MC-RR onto GO. The environmental pollutants addressed in this study included different anions (nitrate NO3-, nitrite NO2-, sulphate SO4(2-), chloride (Cl(-)), phosphate PO4(3-) and fluoride (F(-))) and cations (sodium (Na(+)), potassium (K(+)), magnesium (Mg(2+)) and calcium (Ca(2+))). GO showed very a high adsorption capacity of 1700 μg/g for removal of MC-LR and 1878 μg/g for MC-RR while the maximum adsorption capacity obtained with the commercial activated carbon was 1481.7 μg/g and 1034.1 μg/g for MC-LR and MC-RR, respectively. The sorption kinetic experiments revealed that more than 90% removal of both MC-LR/RR was achieved within 5 min for all the doses studied (500, 700 and 900 μg/L). GO could be reused as an adsorbent following ten cycles of adsorption/desorption with no significant loss in its adsorption capacity.

  2. DNA@Mn3(PO4)2 Nanoparticles Supported with Graphene Oxide as Photoelectrodes for Photoeletrocatalysis

    NASA Astrophysics Data System (ADS)

    Gao, Lixia; Xie, Jiale; Ma, Xiaoqing; Li, Man; Yu, Ling

    2017-01-01

    A novel deoxyribose nucleic acid (DNA)-based photoelectrode consisting of DNA@Mn3(PO4)2 nanoparticles on graphene oxide (GO) sheets was successfully fabricated for photoelectrocatalysis. DNA served as a soft template to guide the nucleation and growth of Mn3(PO4)2 nanoparticles in the synthesis of Mn3(PO4)2 nanoparticles. More importantly, the DNA also serves as semiconductor materials to adjust charge transport. Under UV light irradiation (180-420 nm, 15 mW/cm2), the photocurrent density of DNA@ Mn3(PO4)2/GO electrodes reached 9 μA/cm2 at 0.7 V bias (vs. SCE). An applied bias photon-to-current efficiency (ABPE) of 0.18% can be achieved, which was much higher than that of other control electrodes (<0.04%). In this DNA-based photoelectrode, well-matched energy levels can efficiently improve charge transfer and reduce the recombination of photogenerated electron-hole pairs.

  3. De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome.

    PubMed

    Harney, Ewan; Dubief, Bruno; Boudry, Pierre; Basuyaux, Olivier; Schilhabel, Markus B; Huchette, Sylvain; Paillard, Christine; Nunes, Flavia L D

    2016-08-01

    The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata.

  4. Synergistic effect of titanium dioxide nanocrystal/reduced graphene oxide hybrid on enhancement of microbial electrocatalysis

    NASA Astrophysics Data System (ADS)

    Zou, Long; Qiao, Yan; Wu, Xiao-Shuai; Ma, Cai-Xia; Li, Xin; Li, Chang Ming

    2015-02-01

    A small sized TiO2 nanocrystal (˜10 nm)/reduced graphene oxide (TiO2/rGO) hybrid is synthesized through a sol-gel process for hybrid TiO2/GO followed by solvothermal reduction of GO to rGO and is further used as a microbial fuel cell (MFC) anode. The strong synergistic effect from a large surface area produced by uniformly deposited TiO2 nanocrystals, good hydrophilicity of TiO2 nanocrystals and superior conductivity of rGO leads to significantly improved electrocatalysis. In particular, a direct electrochemistry is realized by generating endogenous flavins from a large amount of microbes grown on the highly biocompatible TiO2 nanocrystals to mediate fast electron transfer between microbes and conductive rGO for a high performance anode. The TiO2/rGO hybrid anode delivers a maximum power density of 3169 mW m-2 in Shewanella putrefaciens CN32 MFC, which is much large than that of the conventional carbon cloth anode and reported TiO2/carbon hybrid anode, thus offering great potential for practical applications of MFC. This work is for the first time to report that the synergistic effect from tailoring the physical structure to achieve small sized TiO2 nanocrystals while rationally designing chemistry to introduce highly conductive rGO and superior biocompatible TiO2 is able to significantly boost the MFC performance.

  5. Real-time spectroscopic monitoring of photocatalytic activity promoted by graphene in a microfluidic reactor

    NASA Astrophysics Data System (ADS)

    Li, Yifan; Lin, Beichen; Ge, Likai; Guo, Hongchen; Chen, Xinyi; Lu, Miao

    2016-06-01

    Photocatalytic microreactors have been utilized as rapid, versatile platforms for the characterization of photocatalysts. In this work, a photocatalytic microreactor integrated with absorption spectroscopy was proposed for the real-time monitoring of photocatalytic activity using different catalysts. The validity of this method was investigated by the rapid screening on the photocatalytic performance of a titanium oxide (TiO2)-decorated graphene oxide (GO) sheet for the degradation of methylene blue under monochromatic visible irradiation. The sampling interval time could be minimized to 10 s for achieving real-time detection. The best photocatalytic activity was observed for an optimized TiO2/GO weight mixing ratio of 7:11, with a reaction rate constant up to 0.067 min‑1. The addition of GO into TiO2 enhances photocatalytic activity and adsorption of MB molecules. The synthetic reaction rate constant was up to approximately 0.11 min‑1, which was also the highest among the catalysts. The microreactor exhibited good sensitivity and reproducibility without weakening the performance of the photocatalysts. Consequently, the photocatalytic microreactor is promising as a simple, portable, and rapid screening tool for new photocatalysts.

  6. Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms.

    PubMed

    Koepke, Tyson; Schaeffer, Scott; Harper, Artemus; Dicenta, Federico; Edwards, Mark; Henry, Robert J; Møller, Birger L; Meisel, Lee; Oraguzie, Nnadozie; Silva, Herman; Sánchez-Pérez, Raquel; Dhingra, Amit

    2013-09-01

    Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non-sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non-sense SNPs revealed several interesting results. First, non-sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non-sense SNP abundance in a genus being linked to specific GO terms.

  7. Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose.

    PubMed

    Williams, Tim D; Diab, Amer M; George, Stephen G; Godfrey, Rita E; Sabine, Victoria; Conesa, Ana; Minchin, Steven D; Watts, Phil C; Chipman, James K

    2006-10-15

    We have constructed a high density, 13 270-clone cDNA array for the sentinel fish species European flounder (Platichthys flesus), combining clones from suppressive subtractive hybridization and a liver cDNA library; DNA sequences of 5211 clones were determined. Fish were treated by single intraperitoneal injection with 50 micrograms cadmium chloride per kilogram body weight, a dose relevant to environmental exposures, and hepatic gene expression changes were determined at 1, 2, 4, 8, and 16 days postinjection in comparison to saline-treated controls. Gene expression responses were confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR). Blast2GO gene ontology analysis highlighted a general induction of the unfolded protein response, response to oxidative stress, protein synthesis, transport, and degradation pathways, while apoptosis, cell cycle, cytoskeleton, and cytokine genes were also affected. Transcript levels of cytochrome P450 1A (CYP1A) were repressed and vitellogenin altered, real-time PCR showed induction of metallothionein. We thus describe the establishment of a useful resource for ecotoxicogenomics and the determination of the temporal molecular responses to cadmium, a prototypical heavy metal pollutant.

  8. Three-dimensional conductive networks based on stacked SiO2@graphene frameworks for enhanced gas sensing.

    PubMed

    Huang, Da; Yang, Zhi; Li, Xiaolin; Zhang, Liling; Hu, Jing; Su, Yanjie; Hu, Nantao; Yin, Guilin; He, Dannong; Zhang, Yafei

    2017-01-07

    Graphene is an ideal candidate for gas sensing due to its excellent conductivity and large specific surface areas. However, it usually suffers from sheet stacking, which seriously debilitates its sensing performance. Herein, we demonstrate a three-dimensional conductive network based on stacked SiO2@graphene core-shell hybrid frameworks for enhanced gas sensing. SiO2 spheres are uniformly encapsulated by graphene oxide (GO) through an electrostatic self-assembly approach to form SiO2@GO core-shell hybrid frameworks, which are reduced through thermal annealing to establish three-dimensional (3D) conductive sensing networks. The SiO2 supported 3D conductive graphene frameworks reveal superior sensing performance to bare reduced graphene oxide (RGO) films, which can be attributed to their less agglomeration and larger surface area. The response value of the 3D framework based sensor for 50 ppm NH3 and 50 ppm NO2 increased 8 times and 5 times, respectively. Additionally, the sensing performance degradation caused by the stacking of the sensing materials is significantly suppressed because the graphene layers are separated by the SiO2 spheres. The sensing performance decays by 92% for the bare RGO films when the concentration of the sensing material increases 8 times, while there is only a decay of 25% for that of the SiO2@graphene core-shell hybrid frameworks. This work provides an insight into 3D frameworks of hybrid materials for effectively improving gas sensing performance.

  9. Functional Immunomics of the Squash Bug, Anasa tristis (De Geer) (Heteroptera: Coreidae)

    PubMed Central

    Shelby, Kent S.

    2013-01-01

    The Squash bug, Anasa tristis (De Geer), is a major piercing/sucking pest of cucurbits, causing extensive damage to plants and fruits, and transmitting phytopathogens. No genomic resources to facilitate field and laboratory studies of this pest were available; therefore the first de novo exome for this destructive pest was assembled. RNA was extracted from insects challenged with bacterial and fungal immunoelicitors, insects fed on different cucurbit species, and insects from all life stages from egg to adult. All treatments and replicates were separately barcoded for subsequent analyses, then pooled for sequencing in a single lane using the Illumina HiSeq2000 platform. Over 211 million 100-base tags generated in this manner were trimmed, filtered, and cleaned, then assembled into a de novo reference transcriptome using the Broad Institute Trinity assembly algorithm. The assembly was annotated using NCBIx NR, BLAST2GO, KEGG and other databases. Of the >130,000 total assemblies 37,327 were annotated identifying the sequences of candidate gene silencing targets from immune, endocrine, reproductive, cuticle, and other physiological systems. Expression profiling of the adult immune response was accomplished by aligning the 100-base tags from each biological replicate from each treatment and controls to the annotated reference assembly of the A. tristis transcriptome. PMID:26462532

  10. Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq.

    PubMed

    Guo, Hui; Ye, Chao-Xia; Wang, An-Li; Xian, Jian-An; Liao, Shao-An; Miao, Yu-Tao; Zhang, Sheng-Peng

    2013-12-01

    In the present study, transcriptome of nitrite-exposed Litopenaeus vannamei was performed using a newly developed high-throughput sequencing technology (Illumina RNA-seq). As many as 42,336 unigenes were generated with 561 bp of average length and 736 bp of unigene N50 after filtering and assembly. These unigenes from the de novo assembly were further annotated using BLAST and BLAST2GO softwares. A total of 23,532 unigenes were unambiguous alignments to the reference when BLAST against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases available at NCBI. Numerous candidate genes associated with immune response, detoxification, apoptosis pathway were identified. Ten candidate genes related to immune responses and apoptosis were selected for validating the results of assembly and annotation by real-time quantitative PCR. Results revealed that the expressions of all these ten genes were up-regulated after nitrite exposure. Combining to our previous study, we speculate that all these selected genes may be involved in the response to nitrite stress. The study shows a systematic overview of the transcriptome analysis in L. vannamei, and provides valuable gene information for studying molecular mechanisms under nitrite exposure.

  11. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect L-Lysine Production in Corynebacterium glutamicum.

    PubMed

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-03-09

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in L-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport--NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885--were also expressed at significantly higher levels in the L-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, L-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production.

  12. [Characterization of hepatitis C virus structural proteins and HCV-like particles produced in recombinant baculovirus infected insect cells].

    PubMed

    Belzhelarskaia, S N; Koroleva, N N; Popenko, V V; Drutsa, V L; Orlova, O V; Rubtsov, P M; Kochetkov, S N

    2010-01-01

    Three proteins, namely: "core" protein C and glycoproteins E1 and E2, are main structural proteins forming a hepatitis C vius (HCV) virion. The virus structure and assembly, a role of the structural proteins in virion morphogenesis remain unknown because of the lack of an efficient culture system for HCV to be grown in vitro. Using recombinant baculoviruses expressing HCV structural protein genes in insect cells the specific structural proteins at the level of 25-35% relative to a common cell protein content, heterodimers of the glcoproteins, and HCV-like particles have been obtained. It has been demonstrated that recombinant proteins C, E1, and E2 go through the posttranslation modification, the glycoproteins form the non-covalent heterodimer, and HCV-like particles are located in endoplasmatic reticulum membrains of infected cells. An ability of the expressed proteins for forming E1E2 dimers and HCV-like particles was used for studying the role of E1 protein glcosylation upon expression and processing of the glycoproteins.

  13. iTRAQ-based profiling of grape berry exocarp proteins during ripening using a parallel mass spectrometric method.

    PubMed

    Martínez-Esteso, Maria José; Casado-Vela, Juan; Sellés-Marchart, Susana; Elortza, Felix; Pedreño, Maria Angeles; Bru-Martínez, Roque

    2011-03-01

    The 4-plex iTRAQ platform was utilized to analyze the protein profiles in four stages of grapevine berry skin ripening, from pre-veraison to fully ripening. Mass spectrometric data were acquired from three replicated analyses using a parallel acquisition method in an Orbitrap instrument by combining collision-induced dissociation (CID) and higher energy collision-induced dissociation (HCD) peptide ion fragmentations. As a result, the number of spectra suitable for peptide identification (either from CID or HCD) increased 5-fold in relation to those suitable for quantification (from HCD). Spectra were searched against an NCBInr protein database subset containing all the Vitis sequences, including those derived from whole genome sequencing. In general, 695 unique proteins were identified with more than one single peptide, and 513 of them were quantified. The sequence annotation and GO term enrichment analysis assisted by the automatic annotation tool Blast2GO permitted a pathway analysis which resulted in finding that biological processes and metabolic pathways de-regulated throughout ripening. A detailed analysis of the function-related proteins profiles helped discover a set of proteins of known Vitis gene origin as the potential candidates to play key roles in grapevine berry quality, growth regulation and disease resistance.

  14. Bubble formation in microgravity

    NASA Technical Reports Server (NTRS)

    Antar, Basil N.

    1996-01-01

    An extensive experimental program was initiated for the purpose of understanding the mechanisms leading to bubble generation during fluid handling procedures in a microgravity environment. Several key fluid handling procedures typical for PCG experiments were identified for analysis in that program. Experiments were designed to specifically understand how such procedures can lead to bubble formation. The experiments were then conducted aboard the NASA KC-135 aircraft which is capable of simulating a low gravity environment by executing a parabolic flight attitude. However, such a flight attitude can only provide a low gravity environment of approximately 10-2go for a maximum period of 30 seconds. Thus all of the tests conducted for these experiments were designed to last no longer than 20 seconds. Several experiments were designed to simulate some of the more relevant fluid handling procedures during protein crystal growth experiments. These include submerged liquid jet cavitation, filling of a cubical vessel, submerged surface scratch, attached drop growth, liquid jet impingement, and geysering experiments. To date, four separate KC-135 flight campaigns were undertaken specifically for performing these experiments. However, different experiments were performed on different flights.

  15. Controllable formation of graphene and graphene oxide sheets using photo-catalytic reduction and oxygen plasma treatment

    NASA Astrophysics Data System (ADS)

    Ostovari, Fatemeh; Abdi, Yaser; Ghasemi, Foad

    2012-12-01

    Au/SiO2/Si interdigital electrodes with thickness of 1 μm were created on silicon substrate. Graphene oxide (GO) sheets hanging from these electrodes were obtained by spin coating of chemically synthesized GO dispersed in water. We used UV-light-induced photo-catalytic activity of titanium oxide nanoparticles to reduce the GO layer. Effects of the photo-induced chemical reduction on the conductivity of the GO were investigated. Also, low power DC plasma was used for oxidation of the sheets. Oxygen bombardment leads to sheets with low electrical conductivity. Measurements show that graphene and GO sheets with the controlled electrical conductivity were obtained by these processes. Scanning electron and atomic force microscopy were used to study the morphology of the TiO2/GO and graphene structures. X-ray diffraction and Raman scattering analysis were used to verify the structural characteristics of the prepared sheets. Analysis showed a gradual increase in the number of C-O bonds on the surface of the graphene layer as a result of increasing the time of plasma bombardment. Based on the Raman spectroscopy, the photo-catalytic activity of TiO2 nanoparticles resulted in a decrease in the number of C-O bonds.

  16. Proteomic analysis of Toxocara canis excretory and secretory (TES) proteins.

    PubMed

    Sperotto, Rita Leal; Kremer, Frederico Schmitt; Aires Berne, Maria Elisabeth; Costa de Avila, Luciana F; da Silva Pinto, Luciano; Monteiro, Karina Mariante; Caumo, Karin Silva; Ferreira, Henrique Bunselmeyer; Berne, Natália; Borsuk, Sibele

    2017-01-01

    Toxocariasis is a neglected disease, and its main etiological agent is the nematode Toxocara canis. Serological diagnosis is performed by an enzyme-linked immunosorbent assay using T. canis excretory and secretory (TES) antigens produced by in vitro cultivation of larvae. Identification of TES proteins can be useful for the development of new diagnostic strategies since few TES components have been described so far. Herein, we report the results obtained by proteomic analysis of TES proteins using a liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach. TES fractions were separated by one-dimensional SDS-PAGE and analyzed by LC-MS/MS. The MS/MS spectra were compared with a database of protein sequences deduced from the genome sequence of T. canis, and a total of 19 proteins were identified. Classification according to the signal peptide prediction using the SignalP server showed that seven of the identified proteins were extracellular, 10 had cytoplasmic or nuclear localization, while the subcellular localization of two proteins was unknown. Analysis of molecular functions by BLAST2GO showed that the majority of the gene ontology (GO) terms associated with the proteins present in the TES sample were associated with binding functions, including but not limited to protein binding (GO:0005515), inorganic ion binding (GO:0043167), and organic cyclic compound binding (GO:0097159). This study provides additional information about the exoproteome of T. canis, which can lead to the development of new strategies for diagnostics or vaccination.

  17. Scalar current of created pairs by Schwinger mechanism in de Sitter spacetime

    NASA Astrophysics Data System (ADS)

    Bavarsad, Ehsan; Stahl, Clément; Xue, She-Sheng

    2016-11-01

    We consider a charged scalar field in a D -dimensional de Sitter spacetime and investigate pair creation by a Schwinger mechanism in a constant electric field background. Using a semiclassical approximation the current of the created pairs has been estimated. We find that the semiclassical current of the created pairs in the strong electric field limit responds as ED/2. Going further but restricting to D =3 dimensional de Sitter spacetime, the quantum expectation value of the spacelike component of the induced current has been computed in the in-vacuum state by applying an adiabatic subtraction scheme. We find that, in the strong electric field limit, the current responds as E3/2. In the weak electric field limit the current has a linear response in E and an inverse dependence on the mass of the scalar field. In the case of a massless scalar field, the current varies with E-1 which leads to a phenomenon of infrared hyperconductivity. A new relation between infrared hyperconductivity, tachyons, and conformality is discussed, and a scheme to avoid an infrared hyperconductivity regime is proposed. In D dimension, we eventually presented some first estimates of the backreaction of the Schwinger pairs to the gravitational field, and we find a decrease of the Hubble constant due to the pair creation.

  18. Date Fruits-Assisted Synthesis and Biocompatibility Assessment of Nickel Oxide Nanoparticles Anchored onto Graphene Sheets for Biomedical Applications.

    PubMed

    Alshatwi, Ali A; Athinarayanan, Jegan; Periasamy, Vaiyapuri Subbarayan; Alatiah, Khalid A

    2017-02-01

    Nanographene- and graphene-based nanohybrids have garnered attention in the biomedical community owing to their biocompatibility, excellent aqueous processability, ease of cellular uptake, facile surface functionalization, and thermal and electrical conductivities. NiO nanoparticle-graphene nanohybrid (G-NiO) was synthesized by first depositing Ni(OH)2 onto the surface of graphene oxide (GO) sheets. The Ni(OH)2-GO hybrids were then reduced to G-NiO using date palm syrup at 85 °C. The prepared G-NiO nanohybrids were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy, and energy-dispersive X-ray spectroscopy (EDX). The NiO nanoparticles, with a diameter of approximately 20-30 nm, were uniformly dispersed over the surface of the graphene sheets. The G-NiO hybrids exhibit biocompatibility in human mesenchymal stem cells (hMSCs) up to 100 μg/mL. The nanohybrids do not cause any significant changes in cellular and nuclear morphologies in hMSCs. The as-synthesized nanohybrids show excellent biocompatibility and could be a promising material for biomedical applications.

  19. Photocatalytic performance of titania nanospheres deposited on graphene in coumarin oxidation reaction

    NASA Astrophysics Data System (ADS)

    Wojtoniszak, M.; Zielinska, B.; Kalenczuk, R. J.; Mijowska, E.

    2012-03-01

    In this paper, we present a study on enhanced photocatalytic performance of TiO2 nanospheres deposited on graphene (n-TiO2-G) in a process of coumarin oxidation. The enhancement of the photoactivity has been observed in respect to commercial TiO2 P25. The presented material was prepared in two steps: (i) hydrolysis of titanium (IV) butoxide (TBT) in ethanol solution with simultaneous deposition on graphene oxide (GO) and (ii) calcination of TiO2-GO to form anatase-TiO2 and reduce GO to graphene. The nanomaterial was characterized by transmission electron microscopy (TEM), energy dispersive X-ray spectroscopy (EDX), thermogravimetric analysis (TGA), Fourier-Transformed Infrared spectroscopy and Raman spectroscopy. In the presented photocatalytic process the fluorescence was used to detect •OH formed on a photo-illuminated n-TiO2-G surface using coumarin which readily reacted with •OH to produce highly fluorescent 7-hydroxycoumarin.

  20. De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries).

    PubMed

    Yue, Y J; Liu, J B; Yang, M; Han, J L; Guo, T T; Guo, J; Feng, R L; Yang, B H

    2015-02-13

    Wool is produced via synthetic processes of wool follicles, which are embedded in the skin of sheep. The development of new-generation sequencing and RNA sequencing provides new approaches that may elucidate the molecular regulation mechanism of wool follicle development and facilitate enhanced selection for wool traits through gene-assisted selection or targeted gene manipulation. We performed de novo transcriptome sequencing of skin using the Illumina Hiseq 2000 sequencing system in sheep (Ovis aries). Transcriptome de novo assembly was carried out via short-read assembly programs, including SOAPdenovo and ESTScan. The protein function, clusters of orthologous group function, gene ontology function, metabolic pathway analysis, and protein coding region prediction of unigenes were annotated by BLASTx, BLAST2GO, and ESTScan. More than 26,266,670 clean reads were collected and assembled into 79,741 unigene sequences, with a final assembly length of 35,447,962 nucleotides. A total of 22,164 unigenes were annotated, accounting for 36.27% of the total number of unigenes, which were divided into 25 classes belonging to 218 signaling pathways. Among them, there were 17 signal paths related to hair follicle development. Based on mass sequencing data of sheepskin obtained by RNA-Seq, many unigenes were identified and annotated, which provides an excellent platform for future sheep genetic and functional genomic research. The data could be used for improving wool quality and as a model for human hair follicle development or disease prevention.

  1. Transcriptional profiling unravels potential metabolic activities of the olive leaf non-glandular trichome

    PubMed Central

    Koudounas, Konstantinos; Manioudaki, Maria E.; Kourti, Anna; Banilas, Georgios; Hatzopoulos, Polydefkis

    2015-01-01

    The olive leaf trichomes are multicellular peltate hairs densely distributed mainly at the lower leaf epidermis. Although, non-glandular, they have gained much attention since they significantly contribute to abiotic and biotic stress tolerance of olive leaves. The exact mechanisms by which olive trichomes achieve these goals are not fully understood. They could act as mechanical barrier but they also accumulate high amounts of flavonoids among other secondary metabolites. However, little is currently known about the exact compounds they produce and the respective metabolic pathways. Here we present the first EST analysis from olive leaf trichomes by using 454-pyrosequencing. A total of 5368 unigenes were identified out of 7258 high quality reads with an average length of 262 bp. Blast search revealed that 27.5% of them had high homologies to known proteins. By using Blast2GO, 1079 unigenes (20.1%) were assigned at least one Gene Ontology (GO) term. Most of the genes were involved in cellular and metabolic processes and in binding functions followed by catalytic activity. A total of 521 transcripts were mapped to 67 KEGG pathways. Olive trichomes represent a tissue of highly unique transcriptome as per the genes involved in developmental processes and the secondary metabolism. The results indicate that mature olive trichomes are trancriptionally active, mainly through the potential production of enzymes that contribute to phenolic compounds with important roles in biotic and abiotic stress responses. PMID:26322070

  2. Crumpling of graphene oxide through evaporative confinement in nanodroplets produced by electrohydrodynamic aerosolization

    NASA Astrophysics Data System (ADS)

    Kavadiya, Shalinee; Raliya, Ramesh; Schrock, Michael; Biswas, Pratim

    2017-02-01

    Restacking of graphene oxide (GO) nanosheets results in loss of surface area and creates limitations in its widespread use for applications. Previously, two-dimensional (2D) GO sheets have been crumpled into 3D structures to prevent restacking using different techniques. However, synthesis of nanometer size crumpled graphene particles and their direct deposition onto a substrate have not been demonstrated under room temperature condition so far. In this work, the evaporative crumpling of GO sheets into very small size (<100 nm) crumpled structures using an electrohydrodynamic atomization technique is described. Systematic study of the effect of different electrohydrodynamic atomization parameters, such as (1) substrate-to-needle distance, (2) GO concentration in the precursor solution, and (3) flow rate (droplet size) on the GO crumpling, is explored. Crumpled GO (CGO) particles are characterized online using a scanning mobility particle sizer (SMPS) and off-line using electron microscopy. The relation between the confinement force and the factors affecting the crumpled structure is established. Furthermore, to expand the application horizons of the structure, crumpled GO-TiO2 nanocomposites are synthesized. The method described here allows a simple and controlled production of graphene-based particles/composites with direct deposition onto any kind of substrate for a variety of applications.

  3. Real-time spectroscopic monitoring of photocatalytic activity promoted by graphene in a microfluidic reactor

    PubMed Central

    Li, Yifan; Lin, Beichen; Ge, Likai; Guo, Hongchen; Chen, Xinyi; Lu, Miao

    2016-01-01

    Photocatalytic microreactors have been utilized as rapid, versatile platforms for the characterization of photocatalysts. In this work, a photocatalytic microreactor integrated with absorption spectroscopy was proposed for the real-time monitoring of photocatalytic activity using different catalysts. The validity of this method was investigated by the rapid screening on the photocatalytic performance of a titanium oxide (TiO2)-decorated graphene oxide (GO) sheet for the degradation of methylene blue under monochromatic visible irradiation. The sampling interval time could be minimized to 10 s for achieving real-time detection. The best photocatalytic activity was observed for an optimized TiO2/GO weight mixing ratio of 7:11, with a reaction rate constant up to 0.067 min−1. The addition of GO into TiO2 enhances photocatalytic activity and adsorption of MB molecules. The synthetic reaction rate constant was up to approximately 0.11 min−1, which was also the highest among the catalysts. The microreactor exhibited good sensitivity and reproducibility without weakening the performance of the photocatalysts. Consequently, the photocatalytic microreactor is promising as a simple, portable, and rapid screening tool for new photocatalysts. PMID:27346555

  4. Investigation of high-rate lithium-thionyl chloride cells

    NASA Astrophysics Data System (ADS)

    Hayes, Catherine A.; Gust, Steven; Farrington, Michael D.; Lockwood, Judith A.; Donaldson, George J.

    Chemical analysis of a commercially produced high-rate D-size lithium-thionyl cell was carried out, as a function of rate of discharge (1 ohm and 5 ohms), depth of discharge, and temperature (25 C and -40 C), using specially developed methods for identifying suspected minor cell products or impurities which may effect cell performance. These methods include a product-retrieval system which involves solvent extraction to enhance the recovery of suspected semivolatile minor chemicals, and methods of quantitative GC analysis of volatile and semivolatile products. The nonvolatile products were analyzed by wet chemical methods. The results of the analyses indicate that the predominant discharge reaction in this cell is 4Li + 2SOCl2 going to 4LiCl + S + SO2, with SO2 formation decreasing towards the end of cell life (7 to 12 Ah). The rate of discharge had no effect on the product distribution. Upon discharge of the high-rate cell at -40 C, one cell exploded, and all others exhibited overheating and rapid internal pressure rise when allowed to warm up to room temperature.

  5. Graphite oxide incorporated crosslinked polyvinyl alcohol and sulfonated styrene nanocomposite membrane as separating barrier in single chambered microbial fuel cell

    NASA Astrophysics Data System (ADS)

    Rudra, Ruchira; Kumar, Vikash; Pramanik, Nilkamal; Kundu, Patit Paban

    2017-02-01

    Different membranes with varied molar concentrations of graphite oxide (GO), 'in situ' polymerized sulfonated polystyrene (SS) and glutaraldehyde (GA) cross linked polyvinyl alcohol (PVA), have been analyzed as an effective and low cost nanocomposite barrier in single chambered microbial fuel cells (MFCs). The synthesized composite membranes, namely GO0.2, GO0.4 and GO0.6 exhibited comparatively better results with reduced water uptake (WU) and swelling ratios (SR) over the native PVA. The variation in properties is illustrated with membrane analyses, where GO0.4 showed an increased proton conductivity (PC) and ion exchange capacity (IEC) of 0.128 S cm-1 and 0.33 meq g-1 amongst all of the used membranes. In comparison, reduced oxygen diffusivity with lower water uptake showed a two-fold decrease in GO0.4 over pure PVA membrane (∼2.09 × 10-4 cm s-1). A maximum power density of 193.6 mW m-2 (773.33 mW m-3) with a current density of 803.33 mA m-2 were observed with GO0.4 fitted MFC, where ∼81.89% of chemical oxygen demand (COD) was removed using mixed firmicutes, as biocatalyst, in 25 days operation. In effect, the efficacy of GO incorporated crosslinked PVA and SS nanocomposite membrane has been evaluated as a polymer electrolyte membrane for harnessing bio-energy from single chambered MFCs.

  6. Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq

    PubMed Central

    Tomalty, Katharine M. H.; Meek, Mariah H.; Stephens, Molly R.; Rincón, Gonzalo; Fangue, Nann A.; May, Bernie P.; Baerwald, Melinda R.

    2015-01-01

    Thermal exposure is a serious and growing challenge facing fish species worldwide. Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range are particularly likely to encounter warmer water due to a confluence of factors. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and pose a threat to dwindling salmon populations. To better understand how acute thermal exposure affects the biology of salmon, we performed a transcriptional analysis of gill tissue from Chinook salmon juveniles reared at 12° and exposed acutely to water temperatures ranging from ideal to potentially lethal (12° to 25°). Reverse-transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. In addition to a high degree of downregulation of a wide range of genes, we found upregulation of genes involved in protein folding/rescue, protein degradation, cell death, oxidative stress, metabolism, inflammation/immunity, transcription/translation, ion transport, cell cycle/growth, cell signaling, cellular trafficking, and structure/cytoskeleton. These results demonstrate the complex multi-modal cellular response to thermal stress in juvenile salmon. PMID:25911227

  7. The Comprehensive AOCMF Classification System: Midface Fractures - Level 3 Tutorial

    PubMed Central

    Cornelius, Carl-Peter; Audigé, Laurent; Kunz, Christoph; Buitrago-Téllez, Carlos H.; Rudderman, Randal; Prein, Joachim

    2014-01-01

    This tutorial outlines the details of the AOCMF image-based classification system for fractures of the midface at the precision level 3. The topography of the different midface regions (central midface—upper central midface, intermediate central midface, lower central midface—incorporating the naso-orbito-ethmoid region; lateral midface—zygoma and zygomatic arch, palate) is subdivided in much greater detail than in level 2 going beyond the Le Fort fracture types and its analogs. The level 3 midface classification system is presented along with guidelines to precisely delineate the fracture patterns in these specific subregions. It is easy to plot common fracture entities, such as nasal and naso-orbito-ethmoid, and their variants due to the refined structural layout of the subregions. As a key attribute, this focused approach permits to document the occurrence of fragmentation (i.e., single vs. multiple fracture lines), displacement, and bone loss. Moreover, the preinjury dental state and the degree of alveolar atrophy in edentulous maxillary regions can be recorded. On the basis of these individual features, tooth injuries, periodontal trauma, and fracture involvement of the alveolar process can be assessed. Coding rules are given to set up a distinctive formula for typical midface fractures and their combinations. The instructions and illustrations are elucidated by a series of radiographic imaging examples. A critical appraisal of the design of this level 3 midface classification is made. PMID:25489392

  8. Transcriptome analysis of sugar beet root maggot (Tetanops myopaeformis) genes modulated by the Beta vulgaris host.

    PubMed

    Li, Haiyan; Smigocki, Ann C

    2016-10-03

    Sugar beet root maggot (SBRM, Tetanops myopaeformis von Röder) is a major but poorly understood insect pest of sugar beet (Beta vulgaris L.). The molecular mechanisms underlying plant defense responses are well documented, however, little information is available about complementary mechanisms for insect adaptive responses to overcome host resistance. To date, no studies have been published on SBRM gene expression profiling. Suppressive subtractive hybridization (SSH) generated more than 300 SBRM ESTs differentially expressed in the interaction of the pest with a moderately resistant (F1016) and a susceptible (F1010) sugar beet line. Blast2GO v. 3.2 search indicated that over 40% of the differentially expressed genes had known functions, primarily driven by fruit fly D. melanogaster genes. Expression patterns of 18 selected EST clones were confirmed by RT-PCR analysis. Gene Ontology (GO) analysis predicted a dominance of metabolic and catalytic genes involved in the interaction of SBRM with its host. SBRM genes functioning during development, regulation, cellular process, signaling and under stress conditions were annotated. SBRM genes that were common or unique in response to resistant or susceptible interactions with the host were identified and their possible roles in insect responses to the host are discussed.

  9. Fear causes tears - Perineal injuries in home birth settings. A Swedish interview study

    PubMed Central

    2011-01-01

    Background Perineal injury is a serious complication of vaginal delivery that has a severe impact on the quality of life of healthy women. The prevalence of perineal injuries among women who give birth in hospital has increased over the last decade, while it is lower among women who give birth at home. The aim of this study was to describe the practice of midwives in home birth settings with the focus on the occurrence of perineal injuries. Methods Twenty midwives who had assisted home births for between one and 29 years were interviewed using an interview guide. The midwives also had experience of working in a hospital delivery ward. All the interviews were tape-recorded and transcribed. Content analysis was used. Results The overall theme was "No rushing and tearing about", describing the midwives' focus on the natural process taking its time. The subcategories 1) preparing for the birth; 2) going along with the physiological process; 3) creating a sense of security; 4) the critical moment and 5) midwifery skills illuminate the management of labor as experienced by the midwives when assisting births at home. Conclusions Midwives who assist women who give birth at home take many things into account in order to minimize the risk of complications during birth. Protection of the woman's perineum is an act of awareness that is not limited to the actual moment of the pushing phase but starts earlier, along with the communication between the midwife and the woman. PMID:21244665

  10. Multilevel resistive switching nonvolatile memory based on MoS2 nanosheet-embedded graphene oxide

    NASA Astrophysics Data System (ADS)

    Shin, Gwang Hyuk; Kim, Choong-Ki; Bang, Gyeong Sook; Kim, Jong Yun; Jang, Byung Chul; Koo, Beom Jun; Woo, Myung Hun; Choi, Yang-Kyu; Choi, Sung-Yool

    2016-09-01

    An increasing demand for nonvolatile memory has driven extensive research on resistive switching memory because it uses simple structures with high density, fast switching speed, and low power consumption. To improve the storage density, the application of multilevel cells is among the most promising solutions, including three-dimensional cross-point array architectures. Two-dimensional nanomaterials have several advantages as resistive switching media, including flexibility, low cost, and simple fabrication processes. However, few reports exist on multilevel nonvolatile memory and its switching mechanism. We herein present a multilevel resistive switching memory based on graphene oxide (GO) and MoS2 fabricated by a simple spin-coating process. Metallic 1T-MoS2 nanosheets, chemically exfoliated by Li intercalation, were successfully embedded between two GO layers as charge-trapping sites. The resulting stacks of GO/MoS2/GO exhibited excellent nonvolatile memory performance with at least four resistance states, >102 endurance cycles, and >104 s retention time. Furthermore, the charge transport mechanism was systematically investigated through the analysis of low-frequency 1/f noise in various resistance states, which could be modulated by the input voltage bias in the negative differential resistance region. Accordingly, we propose a strategy to achieve multilevel nonvolatile memory in which the stacked layers of two-dimensional nanosheets are utilized as resistive and charge-storage materials.

  11. DNA@Mn3(PO4)2 Nanoparticles Supported with Graphene Oxide as Photoelectrodes for Photoeletrocatalysis.

    PubMed

    Gao, Lixia; Xie, Jiale; Ma, Xiaoqing; Li, Man; Yu, Ling

    2017-12-01

    A novel deoxyribose nucleic acid (DNA)-based photoelectrode consisting of DNA@Mn3(PO4)2 nanoparticles on graphene oxide (GO) sheets was successfully fabricated for photoelectrocatalysis. DNA served as a soft template to guide the nucleation and growth of Mn3(PO4)2 nanoparticles in the synthesis of Mn3(PO4)2 nanoparticles. More importantly, the DNA also serves as semiconductor materials to adjust charge transport. Under UV light irradiation (180-420 nm, 15 mW/cm(2)), the photocurrent density of DNA@ Mn3(PO4)2/GO electrodes reached 9 μA/cm(2) at 0.7 V bias (vs. SCE). An applied bias photon-to-current efficiency (ABPE) of ~0.18% can be achieved, which was much higher than that of other control electrodes (<0.04%). In this DNA-based photoelectrode, well-matched energy levels can efficiently improve charge transfer and reduce the recombination of photogenerated electron-hole pairs.

  12. Comparative Genomics Analysis in Prunoideae to Identify Biologically Relevant Polymorphisms

    PubMed Central

    Koepke, Tyson; Schaeffer, Scott; Harper, Artemus; Dicenta, Federico; Edwards, Mark; Henry, Robert J.; Møller, Birger Lindberg; Meisel, Lee; Oraguzie, Nnadozie; Silva, Herman; Sánchez-Pérez, Raquel; Dhingra, Amit

    2013-01-01

    Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Nonsense mutations account for about 70,000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these nonsense SNPs revealed several interesting results. First, nonsense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison to peach, sweet cherry is found to have nonsense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the non-climacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of nonsense SNP abundance in a genus being linked to specific GO terms. PMID:23763653

  13. Spirit-body healing II: a nursing intervention model for spiritual/creative healing.

    PubMed

    Lane, Mary Rockwood

    2008-01-01

    This article describes an advanced intervention for spiritual healing that evolved from spirit-body healing, a hermeneutic phenomenological research study. The research study examined the lived experience of art and healing with cancer patients in the Arts in Medicine program at Shands Hospital, University of Florida. Max Van Manen's method of researching the lived experience was used in 63 patients over a 4-year period. Healing themes that emerged from the research were (1) go into darkness, (2) go elsewhere, (3) art becomes the turning point, (4) slip through the veil, (5) know the truth and trust the process, (6) embody your spirit, (7) feel the healing energy of love and compassion, and (8) experience transcendence. The intervention we offer allows nurses to apply creativity and guided imagery as advanced therapeutics and to continue to provide the leadership needed for integrating spiritual healing into patient care. It is one that personifies the nursing mission formalized by many hospitals: a commitment to treat the bodies, minds, and spirits of patients to the best of our ability as part of our routine care.

  14. Identification of differentially expressed genes in the oviduct of two rabbit lines divergently selected for uterine capacity using suppression subtractive hybridization.

    PubMed

    Ballester, M; Castelló, A; Peiró, R; Argente, M J; Santacreu, M A; Folch, J M

    2013-06-01

    Suppressive subtractive hybridization libraries from oviduct at 62 h post-mating of two lines of rabbits divergently selected for uterine capacity were generated to identify differentially expressed genes. A total of 438 singletons and 126 contigs were obtained by cluster assembly and sequence alignment of 704 expressed sequence tags (ESTs), of which 54% showed homology to known proteins of the non-redundant NCBI databases. Differential screening by dot blot validated 71 ESTs, of which 47 showed similarity to known genes. Transcripts of genes were functionally annotated in the molecular function and the biological process gene ontology categories using the BLAST2GO software and were assigned to reproductive developmental process, immune response, amino acid metabolism and degradation, response to stress and apoptosis terms. Finally, three interesting genes, PGR, HSD17B4 and ERO1L, were identified as overexpressed in the low line using RT-qPCR. Our study provides a list of candidate genes that can be useful to understanding the molecular mechanisms underlying the phenotypic differences observed in early embryo survival and development traits.

  15. Focused Rocket-Ejector RBCC Experiments

    NASA Technical Reports Server (NTRS)

    Santoro, Robert J.; Pal, Sibtosh

    2003-01-01

    This document reports the results of additional efforts for the Rocket Based Combined Cycle (RBCC) rocket-ejector mode research work carried out at the Perm State Propulsion Engineering Research Center in support of NASA s technology development efforts for enabling 3rd generation Reusable Launch Vehicles (RLV). The two tasks conducted under this program build on earlier NASA MSFC funded research program on rocket ejector investigations. The first task continued a systematic investigation of the improvements provided by a gaseous hydrogen (GHz)/oxygen (GO2) twin thruster RBCC rocket ejector system over a single rocket system. In a similar vein, the second task continued investigations into the performance of a hydrocarbon (liquid JP-7)/gaseous oxygen single thruster rocket-ejector system. To gain a systematic understanding of the rocket-ejector s internal fluid mechanic/combustion phenomena, experiments were conducted with both direct-connect and sea-level static diffusion and afterburning (DAB) configurations for a range of rocket operating conditions. For all experimental conditions, overall system performance was obtained through global measurements of wall static pressure profiles, heat flux profiles and engine thrust. For the GH2/GO2 propellant rocket ejector experiments, high frequency measurements of the pressure field within the system were also made to understand the unsteady behavior of the flowfield.

  16. Determining the Relative Criticality of Diverse Exploration Risks in NASA's Human Research Program

    NASA Technical Reports Server (NTRS)

    Kundrot, Craig E.; Edwards, J. Michelle; Anton, Wilma; Robotham, Kwesi

    2009-01-01

    The mission of NASA s Human Research Program (HRP) is to understand and reduce the risk to crew health and performance in exploration missions. The HRP addresses 27 specific risks, primarily in the context of Continuous Risk Management. Each risk is evaluated in terms of two missions (a six month stay on the Moon and a thirty month round trip to Mars) and three types of consequences (in-mission crew health, post-mission crew health, and in-mission performance). The lack of a common metric between the three consequence scales, such as financial costs or quality adjusted life years lost, makes it difficult to compare the relative criticality of the risks. We are, therefore, exploring the use of a ternary scale of criticality based on the common metric of influencing an operational decision. The three levels correspond to the level of concern the risk generates for a "go/no-go" decision to launch a mission: 1) no-go; 2) go with significant reservations; 3) go. The criticality of each of the 27 risks is scored for the three types of consequence in both types of mission. The scores are combined to produce an overall criticality rating for each risk. The overall criticality rating can then be used to guide the prioritization of resources to affect the greatest amount of risk reduction.

  17. Small rocket flowfield diagnostic chambers

    NASA Technical Reports Server (NTRS)

    Morren, Sybil; Reed, Brian

    1993-01-01

    Instrumented and optically-accessible rocket chambers are being developed to be used for diagnostics of small rocket (less than 440 N thrust level) flowfields. These chambers are being tested to gather local fluid dynamic and thermodynamic flowfield data over a range of test conditions. This flowfield database is being used to better understand mixing and heat transfer phenomena in small rockets, influence the numerical modeling of small rocket flowfields, and characterize small rocket components. The diagnostic chamber designs include: a chamber design for gathering wall temperature profiles to be used as boundary conditions in a finite element heat flux model; a chamber design for gathering inner wall temperature and static pressure profiles; and optically-accessible chamber designs, to be used with a suite of laser-based diagnostics for gathering local species concentration, temperature, density, and velocity profiles. These chambers were run with gaseous hydrogen/gaseous oxygen (GH2/GO2) propellants, while subsequent versions will be run on liquid oxygen/hydrocarbon (LOX/HC) propellants. The purpose, design, and initial test results of these small rocket flowfield diagnostic chambers are summarized.

  18. Deep, Staged Transcriptomic Resources for the Novel Coleopteran Models Atrachya menetriesi and Callosobruchus maculatus

    PubMed Central

    Conrads, Kai H.; Roth, Siegfried; Lynch, Jeremy A.

    2016-01-01

    Despite recent efforts to sample broadly across metazoan and insect diversity, current sequence resources in the Coleoptera do not adequately describe the diversity of the clade. Here we present deep, staged transcriptomic data for two coleopteran species, Atrachya menetriesi (Faldermann 1835) and Callosobruchus maculatus (Fabricius 1775). Our sampling covered key stages in ovary and early embryonic development in each species. We utilized this data to build combined assemblies for each species which were then analysed in detail. The combined A. menetriesi assembly consists of 228,096 contigs with an N50 of 1,598 bp, while the combined C. maculatus assembly consists of 128,837 contigs with an N50 of 2,263 bp. For these assemblies, 34.6% and 32.4% of contigs were identified using Blast2GO, and 97% and 98.3% of the BUSCO set of metazoan orthologs were present, respectively. We also carried out manual annotation of developmental signalling pathways and found that nearly all expected genes were present in each transcriptome. Our analyses show that both transcriptomes are of high quality. Lastly, we performed read mapping utilising our timed, stage specific RNA samples to identify differentially expressed contigs. The resources presented here will provide a firm basis for a variety of experimentation, both in developmental biology and in comparative genomic studies. PMID:27907180

  19. Differentially expressed genes and canonical pathway expression in human atherosclerotic plaques – Tampere Vascular Study

    PubMed Central

    Sulkava, Miska; Raitoharju, Emma; Levula, Mari; Seppälä, Ilkka; Lyytikäinen, Leo-Pekka; Mennander, Ari; Järvinen, Otso; Zeitlin, Rainer; Salenius, Juha-Pekka; Illig, Thomas; Klopp, Norman; Mononen, Nina; Laaksonen, Reijo; Kähönen, Mika; Oksala, Niku; Lehtimäki, Terho

    2017-01-01

    Cardiovascular diseases due to atherosclerosis are the leading cause of death globally. We aimed to investigate the potentially altered gene and pathway expression in advanced peripheral atherosclerotic plaques in comparison to healthy control arteries. Gene expression analysis was performed (Illumina HumanHT-12 version 3 Expression BeadChip) for 68 advanced atherosclerotic plaques (15 aortic, 29 carotid and 24 femoral plaques) and 28 controls (left internal thoracic artery (LITA)) from Tampere Vascular Study. Dysregulation of individual genes was compared to healthy controls and between plaques from different arterial beds and Ingenuity pathway analysis was conducted on genes with a fold change (FC) > ±1.5 and false discovery rate (FDR) < 0.05. 787 genes were significantly differentially expressed in atherosclerotic plaques. The most up-regulated genes were osteopontin and multiple MMPs, and the most down-regulated were cell death-inducing DFFA-like effector C and A (CIDEC, CIDEA) and apolipoprotein D (FC > 20). 156 pathways were differentially expressed in atherosclerotic plaques, mostly inflammation-related, especially related with leukocyte trafficking and signaling. In artery specific plaque analysis 50.4% of canonical pathways and 41.2% GO terms differentially expressed were in common for all three arterial beds. Our results confirm the inflammatory nature of advanced atherosclerosis and show novel pathway differences between different arterial beds. PMID:28128285

  20. De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms.

    PubMed

    He, Ziwen; Zhang, Zhang; Guo, Wuxia; Zhang, Ying; Zhou, Renchao; Shi, Suhua

    2015-01-01

    Nypa fruticans (Arecaceae) is the only monocot species of true mangroves. This species represents the earliest mangrove fossil recorded. How N. fruticans adapts to the harsh and unstable intertidal zone is an interesting question. However, the 60 gene segments deposited in NCBI are insufficient for solving this question. In this study, we sequenced, assembled and annotated the transcriptome of N. fruticans using next-generation sequencing technology. A total of 19,918,800 clean paired-end reads were de novo assembled into 45,368 unigenes with a N50 length of 1,096 bp. A total of 41.35% unigenes were functionally annotated using Blast2GO. Many genes annotated to "response to stress" and 15 putative positively selected genes were identified. Simple sequence repeats were identified and compared with other palms. The divergence time between N. fruticans and other palms was estimated at 75 million years ago using the genomic data, which is consistent with the fossil record. After calculating the synonymous substitution rate between paralogs, we found that two whole-genome duplication events were shared by N. fruticans and other palms. These duplication events provided a large amount of raw material for the more than 2,000 later speciation events in Arecaceae. This study provides a high quality resource for further functional and evolutionary studies of N. fruticans and palms in general.

  1. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.

    PubMed

    Sarah, Gautier; Homa, Felix; Pointet, Stéphanie; Contreras, Sandy; Sabot, François; Nabholz, Benoit; Santoni, Sylvain; Sauné, Laure; Ardisson, Morgane; Chantret, Nathalie; Sauvage, Christopher; Tregear, James; Jourda, Cyril; Pot, David; Vigouroux, Yves; Chair, Hana; Scarcelli, Nora; Billot, Claire; Yahiaoui, Nabila; Bacilieri, Roberto; Khadari, Bouchaib; Boccara, Michel; Barnaud, Adéline; Péros, Jean-Pierre; Labouisse, Jean-Pierre; Pham, Jean-Louis; David, Jacques; Glémin, Sylvain; Ruiz, Manuel

    2016-08-04

    We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.

  2. Deep, Staged Transcriptomic Resources for the Novel Coleopteran Models Atrachya menetriesi and Callosobruchus maculatus.

    PubMed

    Benton, Matthew A; Kenny, Nathan J; Conrads, Kai H; Roth, Siegfried; Lynch, Jeremy A

    2016-01-01

    Despite recent efforts to sample broadly across metazoan and insect diversity, current sequence resources in the Coleoptera do not adequately describe the diversity of the clade. Here we present deep, staged transcriptomic data for two coleopteran species, Atrachya menetriesi (Faldermann 1835) and Callosobruchus maculatus (Fabricius 1775). Our sampling covered key stages in ovary and early embryonic development in each species. We utilized this data to build combined assemblies for each species which were then analysed in detail. The combined A. menetriesi assembly consists of 228,096 contigs with an N50 of 1,598 bp, while the combined C. maculatus assembly consists of 128,837 contigs with an N50 of 2,263 bp. For these assemblies, 34.6% and 32.4% of contigs were identified using Blast2GO, and 97% and 98.3% of the BUSCO set of metazoan orthologs were present, respectively. We also carried out manual annotation of developmental signalling pathways and found that nearly all expected genes were present in each transcriptome. Our analyses show that both transcriptomes are of high quality. Lastly, we performed read mapping utilising our timed, stage specific RNA samples to identify differentially expressed contigs. The resources presented here will provide a firm basis for a variety of experimentation, both in developmental biology and in comparative genomic studies.

  3. Public Health Responses to a Dengue Outbreak in a Fragile State: A Case Study of Nepal

    PubMed Central

    Griffiths, Karolina; Banjara, Megha Raj; O'Dempsey, T.; Munslow, B.; Kroeger, Axel

    2013-01-01

    Objectives. The number of countries reporting dengue cases is increasing worldwide. Nepal saw its first dengue outbreak in 2010, with 96% of cases reported in three districts. There are numerous policy challenges to providing an effective public health response system in a fragile state. This paper evaluates the dengue case notification, surveillance, laboratory facilities, intersectoral collaboration, and how government and community services responded to the outbreak. Methods. Qualitative data were collected through 20 in-depth interviews, with key stakeholders, and two focus-group discussions, with seven participants. Results. Limitations of case recognition included weak diagnostic facilities and private hospitals not incorporated into the case reporting system. Research on vectors was weak, with no virological surveillance. Limitations of outbreak response included poor coordination and an inadequate budget. There was good community mobilization and emergency response but no routine vector control. Conclusions. A weak state has limited response capabilities. Disease surveillance and response plans need to be country-specific and consider state response capacity and the level of endemicity. Two feasible solutions for Nepal are (1) go upwards to regional collaboration for disease and vector surveillance, laboratory assistance, and staff training; (2) go downwards to expand upon community mobilisation, ensuring that vector control is anticipatory to outbreaks. PMID:23690789

  4. DArT Markers Effectively Target Gene Space in the Rye Genome

    PubMed Central

    Gawroński, Piotr; Pawełkowicz, Magdalena; Tofil, Katarzyna; Uszyński, Grzegorz; Sharifova, Saida; Ahluwalia, Shivaksh; Tyrka, Mirosław; Wędzony, Maria; Kilian, Andrzej; Bolibok-Brągoszewska, Hanna

    2016-01-01

    Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets. In total 515 DArT sequences could be incorporated into publicly available rye genome zippers providing a starting point for the integration of DArT- and transcript-based genomics resources in rye. Using Blast2Go pipeline we attributed putative gene functions to 1101 (29.4%) of the non-redundant DArT marker sequences, including 132 sequences with putative disease resistance-related functions, which were found to be preferentially located in the 4RL and 6RL chromosomes. Comparative analysis based on the DArT sequences revealed obvious inconsistencies between two recently published high density consensus maps of rye. Furthermore we demonstrated that DArT marker sequences can be a source of SSR polymorphisms. Obtained data demonstrate that DArT markers effectively target gene space in the large, complex, and repetitive rye genome. Through the annotation of putative gene functions and the alignment of DArT sequences relative to reference genomes we obtained information, that will complement the results of the studies, where DArT genotyping was deployed, by simplifying the gene ontology and microcolinearity based identification of candidate genes. PMID:27833625

  5. Nickel-iron battery system safety. Final report

    SciTech Connect

    Saltat, R.

    1984-06-01

    Eagle-Picher Industries conducted a literature search and experimental tests to characterize the generated flow rates of gaseous hydrogen (GH/sub 2/) and gaseous oxygen (GO/sub 2/) from an electrical vehicle (EV) nickel-iron battery system. The resulting gassing rates were used to experimentally evaluate the flame quenching capabilities of several candidate devices to prevent the propagation of flame within batteries having central watering/venting systems. The battery generated hydrogen (GH/sub 2/) and oxygen (GO/sub 2/) gasses were measured for a complete charge and discharge cycle. The data correlates well with accepted theory during strong overcharge conditions indicating that the measurements are valid for other portions of the cycle. Tests have confirmed that the gas mixture in the cells is always flammable regardless of the battery status. Research of flame arrestor literature yielded little information regarding their operation with hydrogen-oxygen mixtures. It was indicated that a conventional flame arrestor would not be effective over the broad spectrum of gassing conditions presented by a nickel-iron battery. Four different types of protective devices were evaluated. A foam-metal arrestor design was successful in quenching GH/sub 2/-GO/sub 2/ flames, however; the application of this flame arrestor to individual cell or module protection in a battery is problematic. A possible rearrangement of the watering/venting system to accept the partial protection of simple one-way valves is presented. This in combination with the successful foam-metal arrestor as main vent protection, could result in a significant improvement in battery protection. This concept was not tested.

  6. Results of Experimental Investigations to Determine External Tank Protuberance Loads Using a 0.03-Scale Model of the Space Shuttle Launch Configuration (Model 47-OTS) in the NASA/ARC Unitary Plan Wind Tunnel, Volume 2

    NASA Technical Reports Server (NTRS)

    Houlihan, S. R.

    1992-01-01

    Data were obtained on a 3-percent model of the Space Shuttle launch vehicle in the NASA/Ames Research Center 11x11-foot and 9x7-foot Unitary Plan Wind Tunnels. This test series has been identified as IA19OA/B and was conducted from 7 Feb. 1980 to 19 Feb. 1980 (IA19OA) and from 17 March 1980 to 19 March 1980 and from 8 May 1980 to 30 May 1980 (IA19OB). The primary test objective was to obtain structural loads on the following external tank protuberances: (1) LO2 feedline; (2) GO2 pressure line; (3) LO2 antigeyser line; (4) GH2 pressure line; (5) LH2 tank cable tray; (6) LO2 tank cable tray; (7) Bipod; (8) ET/SRB cable tray; and (9) Crossbeam/Orbiter cable tray. To fulfill these objectives the following steps were taken: Eight 3-component balances were used to measure forces on various sections of 1 thru 6 above; 315 pressure orifices were distributed over all 9 above items. The LO2 feedline was instrumented with 96 pressure taps and was rotated to four positions to yield 384 pressure measurements. The LO2 antigeyser line was instrumented with 64 pressure taps and was rotated to two positions to yield 128 pressure measurements; Three Chrysler miniature flow direction probes were mounted on a traversing mechanism on the tank upper surface centerline to obtain flow field data between the forward and aft attach structures; and Schlieren photographs and ultraviolet flow photographs were taken at all test conditions. Data from each of the four test phases are presented.

  7. Results of experimental investigations to determine external tank protuberance loads using a 0.03-scale model of the Space Shuttle launch configuration (model 47-OTS) in the NASA/ARC unitary plan wind tunnel, volume 1

    NASA Technical Reports Server (NTRS)

    Houlihan, S. R.

    1992-01-01

    Data were obtained on a 3-percent model of the Space Shuttle launch vehicle in the NASA/Ames Research Center 11x11-foot and 9x7-foot Unitary Plan Wind Tunnels. This test series has been identified as IA190A/B and was conducted from 7 Feb. 1980 to 19 Feb. 1980 (IA190A) and from 17 March 1980 to 19 March 1980 and from 8 May 1980 to 30 May 1980 (IA190B). The primary test objective was to obtain structural loads on the following external tank protuberances: (1) LO2 feedline, (2) GO2 pressure line, (3) LO2 antigeyser line, (4) GH2 pressure line, (5) LH2 tank cable tray, (6) LO2 tank cable tray, (7) Bipod, (8) ET/SRB cable tray, and (9) Crossbeam/Orbiter cable tray. To fulfill these objectives the following steps were taken: (1) Eight 3-component balances were used to measure forces on various sections of 1 thru 6 above. (2) 315 pressure orifices were distributed over all 9 above items. The LO2 feedline was instrumented with 96 pressure taps and was rotated to four positions to yield 384 pressure measurements. The LO2 antigeyser line was instrumented with 64 pressure taps and was rotated to two positions to yield 128 pressure measurements. (3) Three Chrysler miniature flow direction probes were mounted on a traversing mechanism on the tank upper surface centerline to obtain flow field data between the forward and aft attach structures. (4) Schlieren photographs and ultraviolet flow photographs were taken at all test conditions. Data from each of the four test phases are presented.

  8. Transcriptome analysis of integument differentially expressed genes in the pigment mutant (quail) during molting of silkworm, Bombyx mori.

    PubMed

    Nie, Hongyi; Liu, Chun; Cheng, Tingcai; Li, Qiongyan; Wu, Yuqian; Zhou, Mengting; Zhang, Yinxia; Xia, Qingyou

    2014-01-01

    In the silkworm Bombyx mori, pigment mutants with diverse body colors have been maintained throughout domestication for about 5000 years. The silkworm larval body color is formed through the mutual interaction of melanin, ommochromes, pteridines and uric acid. These pigments/compounds are synthesized by the cooperative action of various genes and enzymes. Previous reports showed that melanin, ommochrome and pteridine are increased in silkworm quail (q) mutants. To understand the pigment increase and alterations in pigment synthesis in q mutant, transcriptome profiles of the silkworm integument were investigated at 16 h after head capsule slippage in the fourth molt in q mutants and wild-type (Dazao). Compared to the wild-type, 1161 genes were differentially expressed in the q mutant. Of these modulated genes, 62.4% (725 genes) were upregulated and 37.6% (436 genes) were downregulated in the q mutant. The molecular function of differently expressed genes was analyzed by Blast2GO. The results showed that upregulated genes were mainly involved in protein binding, small molecule binding, transferase activity, nucleic acid binding, specific DNA-binding transcription factor activity and chromatin binding, while exclusively down-expressed genes functioned in oxidoreductase activity, cofactor binding, tetrapyrrole binding, peroxidase activity and pigment binding. We focused on genes related to melanin, pteridine and ommochrome biosynthesis; transport of uric acid; and juvenile hormone metabolism because of their importance in integument coloration during molting. This study identified differently expressed genes implicated in silkworm integument formation and pigmentation using silkworm q mutant. The results estimated the number and types of genes that drive new integument formation.

  9. Transcriptome Analysis of Integument Differentially Expressed Genes in the Pigment Mutant (quail) during Molting of Silkworm, Bombyx mori

    PubMed Central

    Cheng, Tingcai; Li, Qiongyan; Wu, Yuqian; Zhou, Mengting; Zhang, Yinxia; Xia, Qingyou

    2014-01-01

    In the silkworm Bombyx mori, pigment mutants with diverse body colors have been maintained throughout domestication for about 5000 years. The silkworm larval body color is formed through the mutual interaction of melanin, ommochromes, pteridines and uric acid. These pigments/compounds are synthesized by the cooperative action of various genes and enzymes. Previous reports showed that melanin, ommochrome and pteridine are increased in silkworm quail (q) mutants. To understand the pigment increase and alterations in pigment synthesis in q mutant, transcriptome profiles of the silkworm integument were investigated at 16 h after head capsule slippage in the fourth molt in q mutants and wild-type (Dazao). Compared to the wild-type, 1161 genes were differentially expressed in the q mutant. Of these modulated genes, 62.4% (725 genes) were upregulated and 37.6% (436 genes) were downregulated in the q mutant. The molecular function of differently expressed genes was analyzed by Blast2GO. The results showed that upregulated genes were mainly involved in protein binding, small molecule binding, transferase activity, nucleic acid binding, specific DNA-binding transcription factor activity and chromatin binding, while exclusively down-expressed genes functioned in oxidoreductase activity, cofactor binding, tetrapyrrole binding, peroxidase activity and pigment binding. We focused on genes related to melanin, pteridine and ommochrome biosynthesis; transport of uric acid; and juvenile hormone metabolism because of their importance in integument coloration during molting. This study identified differently expressed genes implicated in silkworm integument formation and pigmentation using silkworm q mutant. The results estimated the number and types of genes that drive new integument formation. PMID:24718369

  10. Preparation and Characterization of Thin-Film Composite Membrane with Nanowire-Modified Support for Forward Osmosis Process

    PubMed Central

    Low, Ze-Xian; Liu, Qi; Shamsaei, Ezzatollah; Zhang, Xiwang; Wang, Huanting

    2015-01-01

    Internal concentration polarization (ICP) in forward osmosis (FO) process is a characteristic problem for asymmetric thin-film composite (TFC) FO membrane which leads to lower water flux. To mitigate the ICP effect, modification of the substrates’ properties has been one of the most effective methods. A new polyethersulfone-based ultrafiltration membrane with increased surface porosity and high water flux was recently produced by incorporating Zn2GeO4 nanowires. The composite membrane was used as a substrate for the fabrication of TFC FO membrane, by coating a thin layer of polyamide on top of the substrate. The substrate and the nanowires were characterized by a range of techniques such as SEM, XRD, and contact angle goniometry. The water permeability and molecular weight cut-offs (MWCO) of the substrate; and the FO performance of the TFC membrane were also determined. The Zn2GeO4-modified membrane showed ~45% increase in water permeability and NaCl salt rejection of 80% under RO mode. In FO mode, the ratio of water flux to reverse solute flux was also improved. However, lower FO flux was obtained which could be due to ICP. The result shows that Zn2GO4 nanowire may be used as a modifier to the substrate to improve the quality of the polyamide layer on the substrate to improve the flux and selectivity, but not as effective in reducing ICP. This work demonstrates that the incorporation of nanomaterials to the membrane substrate may be an alternative approach to improve the formation of polyamide skin layer to achieve better FO performance. PMID:25803239

  11. Transcriptomic Analysis of Endangered Chinese Salamander: Identification of Immune, Sex and Reproduction-Related Genes and Genetic Markers

    PubMed Central

    Che, Rongbo; Sun, Yuena; Wang, Rixin; Xu, Tianjun

    2014-01-01

    Background The Chinese salamander (Hynobius chinensis), an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it. Principal Findings We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66%) unigenes showed homologous matches in at least one database and 33,537 (22.58%) unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs) and 460,923 putative single nucleotide polymorphisms (SNPs). Conclusion This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis), an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species. PMID:24498226

  12. Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing

    PubMed Central

    Patnaik, Bharat Bhusan; Hwang, Hee-Ju; Kang, Se Won; Park, So Young; Wang, Tae Hun; Park, Eun Bi; Chung, Jong Min; Song, Dae Kwon; Kim, Changmu; Kim, Soonok; Lee, Jae Bong; Jeong, Heon Cheon; Park, Hong Seog; Han, Yeon Soo; Lee, Yong Seok

    2015-01-01

    The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10−5) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species. PMID:26694362

  13. Identification of differentially expressed genes from Trichoderma harzianum during growth on cell wall of Fusarium solani as a tool for biotechnological application

    PubMed Central

    2013-01-01

    Background The species of T. harzianum are well known for their biocontrol activity against many plant pathogens. However, there is a lack of studies concerning its use as a biological control agent against F. solani, a pathogen involved in several crop diseases. In this study, we have used subtractive library hybridization (SSH) and quantitative real-time PCR (RT-qPCR) techniques in order to explore changes in T. harzianum genes expression during growth on cell wall of F. solani (FSCW) or glucose. RT-qPCR was also used to examine the regulation of 18 genes, potentially involved in biocontrol, during confrontation between T. harzianum and F. solani. Results Data obtained from two subtractive libraries were compared after annotation using the Blast2GO suite. A total of 417 and 78 readable EST sequence were annotated in the FSCW and glucose libraries, respectively. Functional annotation of these genes identified diverse biological processes and molecular functions required during T. harzianum growth on FSCW or glucose. We identified various genes of biotechnological value encoding to proteins which function such as transporters, hydrolytic activity, adherence, appressorium development and pathogenesis. Fifteen genes were up-regulated and sixteen were down-regulated at least at one-time point during growth of T. harzianum in FSCW. During the confrontation assay most of the genes were up-regulated, mainly after contact, when the interaction has been established. Conclusions This study demonstrates that T. harzianum expressed different genes when grown on FSCW compared to glucose. It provides insights into the mechanisms of gene expression involved in mycoparasitism of T. harzianum against F. solani. The identification and evaluation of these genes may contribute to the development of an efficient biological control agent. PMID:23497274

  14. Transposon variation by order during allopolyploidisation between Brassica oleracea and Brassica rapa.

    PubMed

    An, Z; Tang, Z; Ma, B; Mason, A S; Guo, Y; Yin, J; Gao, C; Wei, L; Li, J; Fu, D

    2014-07-01

    Although many studies have shown that transposable element (TE) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE-associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE, and determined the impact of TE-associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the Inter-Retrotransposon Amplified Polymorphism (IRAP) method to detect variation in TE-associated sequences during the process of allopolyploidisation between Brassica rapa (AA) and Brassica oleracea (CC), and in successive generations of self-pollinated progeny. In addition, fragments with TE insertions were used to perform Blast2GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety-two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TEs could be classed in ascending frequency into LTR-REs, TIRs, LINEs, SINEs and unknown TEs. The frequency of novel variation (putative activation) detected for the four orders of TEs was highest from the F1 to F2 generations, and lowest from the F2 to F3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation.

  15. Major putative pesticide receptors, detoxification enzymes, and transcriptional profile of the midgut of the tobacco budworm, Heliothis virescens (Lepidoptera: Noctuidae).

    PubMed

    Zhu, Yu Cheng; Guo, Zibiao; Chen, Ming-Shun; Zhu, Kun Yan; Liu, Xiaofen F; Scheffler, Brian

    2011-02-01

    Insecticide resistance mechanisms, including those for Cry proteins (Bt), in Heliothis virescens are not well understood. Sequencing of midgut transcriptomes may facilitate the discovery of the genes responsible for resistance development. In this study, a total of 5856 Sanger sequences were obtained and assembled to 1687 contigs (464) and singletons (1233) with average length of 507 bp. Blast similarity search showed that 1372 cDNAs from this study matched different genes or cDNAs in the GenBank and other sequence databases. Blast2go annotation identified 611 highly similar proteins with metabolic and cellular processes as major biological functions and catalytic activity and binding as major molecular functions. At least 143 contigs and singletons were associated with pesticide activation, detoxification, and resistance development. These cDNAs, with average length of 601 bp, matched nine groups of pesticide resistance related genes. At least 80 cDNAs coded for Bt resistance related enzymes and potential receptors, including 58 proteinases, 4 cadherins, 13 aminopeptidase, and 5 alkaline phosphatases. Other putative detoxification enzymes included 20 cytochrome P450 oxidases, 11 glutathione S-transferases, 9 esterases, 8 sodium channels, and 15 cytochrome oxidases. Of the 143 contigs and singletons, 111 cDNA sequences seemed to be new resistance candidate gene transcripts in GenBank because they either priorly matched resistance candidate cDNAs of other species, or had low sequence identity with those previously sequenced from H. virescens. This study provides a foundation for future research to develop a gut-specific DNA microarray for analysis of the global changes of gene expression in response to biological and chemical pesticides. Future development resistance management strategies could benefit from this study and help continue research to identify key genes targetable by classic and novel approaches.

  16. De novo Assembly of the Indo-Pacific Humpback Dolphin Leucocyte Transcriptome to Identify Putative Genes Involved in the Aquatic Adaptation and Immune Response

    PubMed Central

    Xia, Jia; Yang, Lili; Chen, Jialin; Wu, Yuping; Yi, Meisheng

    2013-01-01

    Background The Indo-Pacific humpback dolphin (Sousa chinensis), a marine mammal species inhabited in the waters of Southeast Asia, South Africa and Australia, has attracted much attention because of the dramatic decline in population size in the past decades, which raises the concern of extinction. So far, this species is poorly characterized at molecular level due to little sequence information available in public databases. Recent advances in large-scale RNA sequencing provide an efficient approach to generate abundant sequences for functional genomic analyses in the species with un-sequenced genomes. Principal Findings We performed a de novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome by Illumina sequencing. 108,751 high quality sequences from 47,840,388 paired-end reads were generated, and 48,868 and 46,587 unigenes were functionally annotated by BLAST search against the NCBI non-redundant and Swiss-Prot protein databases (E-value<10−5), respectively. In total, 16,467 unigenes were clustered into 25 functional categories by searching against the COG database, and BLAST2GO search assigned 37,976 unigenes to 61 GO terms. In addition, 36,345 unigenes were grouped into 258 KEGG pathways. We also identified 9,906 simple sequence repeats and 3,681 putative single nucleotide polymorphisms as potential molecular markers in our assembled sequences. A large number of unigenes were predicted to be involved in immune response, and many genes were predicted to be relevant to adaptive evolution and cetacean-specific traits. Conclusion This study represented the first transcriptome analysis of the Indo-Pacific humpback dolphin, an endangered species. The de novo transcriptome analysis of the unique transcripts will provide valuable sequence information for discovery of new genes, characterization of gene expression, investigation of various pathways and adaptive evolution, as well as identification of genetic markers. PMID:24015242

  17. Identification of Genes Potentially Responsible for extra-Oral Digestion and Overcoming Plant Defense from Salivary Glands of the Tarnished Plant Bug (Hemiptera: Miridae) Using cDNA Sequencing

    PubMed Central

    Zhu, Yu-Cheng; Yao, Jianxiu; Luttrell, Randall

    2016-01-01

    Saliva is known to play a crucial role in tarnished plant bug (TPB, Lygus lineolaris [Palisot de Beauvois]) feeding. By facilitating the piercing, the enzyme-rich saliva may be used for extra-oral digestion and for overcoming plant defense before the plant fluids are ingested by TPBs. To identify salivary gland genes, mRNA was extracted from salivary glands and cDNA library clones were sequenced. A de novo-assembling of 7,000 Sanger sequences revealed 666 high-quality unique cDNAs with an average size of 624 bp, in which the identities of 347 cDNAs were determined using Blast2GO. Kyoto Encyclopedia of Genes and Genomes analysis indicated that these genes participate in eighteen metabolic pathways. Identifications of large number of enzyme genes in TPB salivary glands evidenced functions for extra-oral digestion and feeding damage mechanism, including 45 polygalacturonase, two α- amylase, one glucosidase, one glycan enzyme, one aminopeptidase, four lipase, and many serine protease cDNAs. The presence of multiple transcripts, multigene members, and high abundance of cell wall degradation enzymes (polygalacturonases) indicated that the enzyme-rich saliva may cause damage to plants by breaking down plant cell walls to make nutrients available for feeding. We also identified genes potentially involved in insect adaptation and detoxifying xenobiotics that may allow insects to overcome plant defense responses, including four glutathione S-transferases, three esterases, one cytochrome P450, and several serine proteases. The gene profiles of TPB salivary glands revealed in this study provides a foundation for further understanding and potential development of novel enzymatic inhibitors, or other RNAi approaches that may interrupt or minimize TPB feeding damage. PMID:27324587

  18. Chronic fluoxetine treatment directs energy metabolism towards the citric acid cycle and oxidative phosphorylation in rat hippocampal nonsynaptic mitochondria.

    PubMed

    Filipović, Dragana; Costina, Victor; Perić, Ivana; Stanisavljević, Andrijana; Findeisen, Peter

    2017-03-15

    Fluoxetine (Flx) is the principal treatment for depression; however, the precise mechanisms of its actions remain elusive. Our aim was to identify protein expression changes within rat hippocampus regulated by chronic Flx treatment versus vehicle-controls using proteomics. Fluoxetine-hydrohloride (15mg/kg) was administered daily to adult male Wistar rats for 3weeks, and cytosolic and nonsynaptic mitochondrial hippocampal proteomes were analyzed. All differentially expressed proteins were functionally annotated according to biological process and molecular function using Uniprot and Blast2GO. Our comparative study revealed that in cytosolic and nonsynaptic mitochondrial fractions, 60 and 3 proteins respectively, were down-regulated, and 23 and 60 proteins, respectively, were up-regulated. Proteins differentially regulated in cytosolic and nonsynaptic mitochondrial fractions were primarily related to cellular and metabolic processes. Of the identified proteins, the expressions of calretinin and parvalbumine were confirmed. The predominant molecular functions of differentially expressed proteins in both cell hippocampal fractions were binding and catalytic activity. Most differentially expressed proteins in nonsynaptic mitochondria were catalytic enzymes involved in the pyruvate metabolism, citric acid cycle, oxidative phosphorylation, ATP synthesis, ATP transduction and glutamate metabolism. Results indicate that chronic Flx treatment may influence proteins involved in calcium signaling, cytoskeletal structure, chaperone system and stimulates energy metabolism via the upregulation of GAPDH expression in cytoplasm, as well as directing energy metabolism toward the citric acid cycle and oxidative phosphorylation in nonsynaptic mitochondria. This approach provides new insight into the chronic effects of Flx treatment on protein expression in a key brain region associated with stress response and memory.

  19. Conductive reduced graphene oxide/MnO2 carbonized cotton fabrics with enhanced electro -chemical, -heating, and -mechanical properties

    NASA Astrophysics Data System (ADS)

    Tian, Mingwei; Du, Minzhi; Qu, Lijun; Zhang, Kun; Li, Hongliang; Zhu, Shifeng; Liu, Dongdong

    2016-09-01

    Versatile and ductile conductive carbonized cotton fabrics decorated with reduced graphene oxide (rGO)/manganese dioxide (MnO2) are prepared in this paper. In order to endow multifunction to cotton fabric, graphene oxide (GO) is deposited on cotton fibers by simple dip-coating route. MnO2 nanoparticles are assembled on the surface of cotton fabric through in-situ chemical solution deposition. MnO2/GO@cotton fabrics are carbonized to achieve conductive fabric (MnO2/rGO@C). The morphologies and structures of obtained fabrics are characterized by SEM, XRD, ICP and element analysis, and their electro-properties including electro-chemical, electro-heating and electro-mechanical properties are evaluated. The MnO2/rGO@C yields remarkable specific capacitance of 329.4 mA h/g at the current density of 100 mA/g, which is more than 40% higher than that of the control carbonized cotton fabric (231 mA h/g). Regarding electro-heating properties, the temperature of MnO2/rGO@C fabric could be monotonically increased to the steady-state maximum temperatures (ΔTmax) of 36 °C within 5 min under the applied voltage 15 V while the ΔTmax = 17 °C of the control case. In addition, MnO2/rGO@C exhibits repeatable electro-mechanical properties and its normalized resistance (R-R0)/R0 could reach 0.78 at a constant strain (curvature = 0.6 cm-1). The MnO2/rGO@C fabric is versatile, scalable, and adaptable to a wide variety of smart textiles applications.

  20. Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions

    PubMed Central

    Yadav, Inderjit S.; Sharma, Amandeep; Kaur, Satinder; Nahar, Natasha; Bhardwaj, Subhash C.; Sharma, Tilak R.; Chhuneja, Parveen

    2016-01-01

    Leaf rust caused by Puccinia triticina (Pt) is one of the most important diseases of bread wheat globally. Recent advances in sequencing technologies have provided opportunities to analyse the complete transcriptomes of the host as well as pathogen for studying differential gene expression during infection. Pathogen induced differential gene expression was characterized in a near isogenic line carrying leaf rust resistance gene Lr57 and susceptible recipient genotype WL711. RNA samples were collected at five different time points 0, 12, 24, 48, and 72 h post inoculation (HPI) with Pt 77-5. A total of 3020 transcripts were differentially expressed with 1458 and 2692 transcripts in WL711 and WL711+Lr57, respectively. The highest number of differentially expressed transcripts was detected at 12 HPI. Functional categorization using Blast2GO classified the genes into biological processes, molecular function and cellular components. WL711+Lr57 showed much higher number of differentially expressed nucleotide binding and leucine rich repeat genes and expressed more protein kinases and pathogenesis related proteins such as chitinases, glucanases and other PR proteins as compared to susceptible genotype. Pathway annotation with KEGG categorized genes into 13 major classes with carbohydrate metabolism being the most prominent followed by amino acid, secondary metabolites, and nucleotide metabolism. Gene co-expression network analysis identified four and eight clusters of highly correlated genes in WL711 and WL711+Lr57, respectively. Comparative analysis of the differentially expressed transcripts led to the identification of some transcripts which were specifically expressed only in WL711+Lr57. It was apparent from the whole transcriptome sequencing that the resistance gene Lr57 directed the expression of different genes involved in building the resistance response in the host to combat invading pathogen. The RNAseq data and differentially expressed transcripts identified in

  1. Self-assembly of photo-reduced graphene-titania films.

    SciTech Connect

    Lambert, Timothy N.; Chavez, Carlos A.; Bell, Nelson Simmons; Washburn, Cody M.; Brumbach, Michael Todd; Wheeler, David Roger; McKenzie, Bonnie Beth

    2010-07-01

    In an aim to develop photo-responsive composites, the UV photo-reduction of aqueous titanium oxide nanoparticle-graphene oxide (TiO{sub 2}-GO) dispersions (Lambert et al. J Phys. Chem. 2010 113 (46), 19812-19823) was undertaken. Photo-reduction led to the formation of a black precipitate as well as a soluble portion, comprised of titanium oxide nanoparticle-reduced graphene oxide (TiO{sub 2}-RGO). When allowed to slowly evaporate, self assembled titanium oxide nanoparticle-graphene oxide (SA-TiO{sub 2}-RGO) films formed at the air-liquid interface of the solution. The thickness of SARGO-TiO{sub 2} films range from {approx}30-100 nm when deposited on substrates, and appear to be comprised of a mosaic assembly of graphene nanosheets and TiO{sub 2}, as observed by scanning electron microscopy. Raman spectroscopy and X-ray photoelectron spectroscopy indicate that the graphene oxide is only partially reduced in the SA-TiO{sub 2}-RGO material. These films were also deposited onto inter-digitated electrodes and their photo-responsive behavior was examined. UV-exposure lead to a {approx} 200 kOhm decrease in resistance across the device, resulting in a cathodically biased film. The cathodic bias of the films was utilized for the subsequent reduction of Ag(NO{sub 3}) into silver (Ag) nanoparticles, forming a ternary Ag-(SA-RGO-TiO{sub 2}) composite. Various aspects of the self assembled films, their photoconductive properties as well as potential applications will be presented.

  2. SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions.

    PubMed

    Bhattacharya, Anindya; Cui, Yan

    2016-01-04

    SomamiR 2.0 (http://compbio.uthsc.edu/SomamiR) is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). Here, we describe the recent major updates to the SomamiR database. We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. Recently, a large number of miRNA target sites have been discovered by newly emerged high-throughput technologies for mapping the miRNA interactome. We have mapped 388 247 somatic mutations to the experimentally identified miRNA target sites. The updated database also includes a list of somatic mutations in the miRNA seed regions, which contain the most important guiding information for miRNA target recognition. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA-ceRNA interactions.

  3. Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC.

    PubMed

    Chen, Yuehong; Cao, Qinghua; Tao, Xiang; Shao, Huanhuan; Zhang, Kun; Zhang, Yizheng; Tan, Xuemei

    2017-03-01

    White-rot basidiomycete Coriolopsis gallica HTC is one of the main biodegraders of poplar. In our previous study, we have shown the strong capacity of C. gallica HTC to degrade lignocellulose. In this study, equal amounts of total RNA fromC. Gallica HTC cultures grown in different conditions were pooled together. Illumina paired-end RNA sequencing was performed, and 13.2 million 90-bp paired-end reads were generated. We chose the Merged Assembly of Oases data-set for the following blast searches and gene ontology analyses. The reads were assembled de novo into 28,034 transcripts (≥ 100 bp) using combined assembly strategy MAO. The transcripts were annotated using Blast2GO. In all, 18,810 transcripts (≥100 bp) achieved BLASTX hits, of which, 7048 transcripts had GO term and 2074 had ECs. The expression level of 11 lignocellulolytic enzyme genes from the assembled C. gallica HTC transcriptome were detected by real-time quantitative polymerase chain reaction. The results showed that expression levels of these genes were affected by carbon source and nitrogen source at the level of transcription. The current abundant transcriptome data allowed the identification of many new transcripts in C. gallica HTC. Data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest from C. gallica HTC. Characterization of C. gallica HTC transcriptome provides an effective tool to understand mechanisms underlying cellular and molecular functions of C. gallica HTC.

  4. Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns

    PubMed Central

    Morales, Andrea; Zurita-Silva, Andres; Maldonado, Jonathan; Silva, Herman

    2017-01-01

    HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. Chenopodium quinoa (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (Fv/Fm) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses. PMID:28337209

  5. Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns.

    PubMed

    Morales, Andrea; Zurita-Silva, Andres; Maldonado, Jonathan; Silva, Herman

    2017-01-01

    HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. Chenopodium quinoa (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (Fv/Fm) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses.

  6. Transcriptome analysis of the copepod Eurytemora affinis upon exposure to endocrine disruptor pesticides: Focus on reproduction and development.

    PubMed

    Legrand, Eléna; Forget-Leray, Joëlle; Duflot, Aurélie; Olivier, Stéphanie; Thomé, Jean-Pierre; Danger, Jean-Michel; Boulangé-Lecomte, Céline

    2016-07-01

    Copepods-which include freshwater and marine species-represent the most abundant group of aquatic invertebrates. Among them, the calanoid copepod Eurytemora affinis is widely represented in the northern hemisphere estuaries and has become a species of interest in ecotoxicology. Like other non-target organisms, E. affinis may be exposed to a wide range of chemicals such as endocrine disruptors (EDs). This study investigated the gene expression variation in E. affinis after exposure to ED pesticides-chosen as model EDs-in order to (i) improve the knowledge on their effects in crustaceans, and (ii) highlight relevant transcripts for further development of potential biomarkers of ED exposure/effect. The study focused on the reproduction function in response to ED. Copepods were exposed to sublethal concentrations of pyriproxyfen (PXF) and chlordecone (CLD) separately. After 48h, males and females (400 individuals each) were sorted for RNA extraction. Their transcriptome was pyrosequenced using the Illumina(®) technology. Contigs were blasted and functionally annotated using Blast2GO(®). The differential expression analysis between ED- and acetone-exposed organisms was performed according to sexes and contaminants. Half of the 19,721 contigs provided by pyrosequencing were annotated, mostly (80%) from arthropod sequences. Overall, 2,566 different genes were differentially expressed after ED exposures in comparison with controls. As many genes were differentially expressed after PXF exposure as after CLD exposure. In contrast, more genes were differentially expressed in males than in females after both exposures. Ninety-seven genes overlapped in all conditions. Finally, 31 transcripts involved in reproduction, growth and development, and changed in both chemical exposures were selected as potential candidates for future development of biomarkers.

  7. Genome sequence and comparative analysis of Avibacterium paragallinarum

    PubMed Central

    Requena, David; Chumbe, Ana; Torres, Michael; Alzamora, Ofelia; Ramirez, Manuel; Valdivia-Olarte, Hugo; Gutierrez, Andres Hazaet; Izquierdo-Lara, Ray; Saravia, Luis Enrique; Zavaleta, Milagros; Tataje-Lavanda, Luis; Best, Ivan; Fernández-Sánchez, Manolo; Icochea, Eliana; Zimic, Mirko; Fernández-Díaz, Manolo

    2013-01-01

    Background: Avibacterium paragallinarum, the causative agent of infectious coryza, is a highly contagious respiratory acute disease of poultry, which affects commercial chickens, laying hens and broilers worldwide. Methodology: In this study, we performed the whole genome sequencing, assembly and annotation of a Peruvian isolate of A. paragallinarum. Genome was sequenced in a 454 GS FLX Titanium system. De novo assembly was performed and annotation was completed with GS De Novo Assembler 2.6 using the H. influenzae str. F3031 gene model. Manual curation of the genome was performed with Artemis. Putative function of genes was predicted with Blast2GO. Virulence factors were identified by comparison with the Virulence Factor Database. Results: The genome obtained has a length of 2.47 Mb with 40.66% of GC content. Seventy five large contigs (>500 nt) were obtained, which comprised 1,204 predicted genes. All the contigs are available in Genbank [GenBank: PRJNA64665]. A total of 103 virulence factors, reported in the Virulence Factor Database, were found in A. paragallinarum. Forty four of them are present in 7 species of Haemophilus, which are related with pathogenesis, virulence and host immune system evasion. A tetracycline-resistance associated transposon (Tn10), was found in A. paragallinarum, possibly acting as a defense mechanism. Discussion and conclusion: The availability of A. paragallinarum genome represents an important source of information for the development of diagnostic tests, genotyping, and novel antigens for potential vaccines against infectious coryza. Identification of virulence factors contributes to better understanding the pathogenesis, and planning efforts for prevention and control of the disease. PMID:23861570

  8. Identification and characterization of low temperature stress responsive genes in Poncirus trifoliata by suppression subtractive hybridization.

    PubMed

    Peng, T; Zhu, X F; Fan, Q J; Sun, P P; Liu, J H

    2012-01-15

    Trifoliate orange (Poncirus trifoliata (L.) Raf.) is extremely cold hardy when fully acclimated, but knowledge relevant to the molecular events underlying the acclimation is still limited so far. In this study, forward (4 °C over 25 °C) and reverse (25 °C over 4 °C) suppression subtractive hybridization (SSH) libraries were constructed in order to identify the genes involved in cold acclimation in trifoliate orange. After reverse northern blotting analysis and sequencing, a total of 105 and 117 non-redundant differentially expressed sequence tags (ESTs) were obtained from the forward and reverse libraries, respectively. Blast2go analysis revealed that 91 ESTs, 31 from the forward library and 60 from the reverse library, displayed significant sequence homology to the genes with known or putative functions. They were categorized into various functional groups, including catalytic activity, binding protein, structural molecule, enzyme regulator, molecular transducer, electron carrier, and transport activity/transcription regulation. Expression analysis of the selected ESTs by reverse transcriptase polymerase chain reaction was consistent with the results of differential screening. In addition, time-course expression patterns of the genes further confirmed that they were responsive to low temperature treatment. Among the genes of known functions, many are related to maintenance of cell wall integrity, adjustment of osmotic potential and maintenance of reactive oxygen species homeostasis, implying that these physiological processes might be of paramount significance in rendering protective mechanisms against the low temperature stress. The data presented here gain an insight into the molecular changes underlying the cold acclimation of trifoliate orange, and the results can be of reference for unraveling candidate genes that hold great potential for genetic engineering in an effort to create novel germplasms with enhanced cold stress tolerance.

  9. The core stimulon of Corynebacterium pseudotuberculosis strain 1002 identified using ab initio methodologies.

    PubMed

    Pinto, Anne Cybelle; Ramos, Rommel T J; Silva, Wanderson Marques; Rocha, Flávia Souza; Barbosa, Silvanira; Miyoshi, Anderson; Schneider, Maria P C; Silva, Artur; Azevedo, Vasco

    2012-07-01

    Corynebacterium pseudotuberculosis is a bacterium which causes diseases such as caseous lymphadenitis in small ruminants, resulting in large-scale economic losses for agribusiness worldwide. Consequently, this bacterium including its transcriptional profile analysis has been the focus of various studies. Identification of the transcripts that appear under conditions that simulate the environment encountered by this bacterial species in the host is of great importance in discovering new targets for the production of more efficient vaccines. We sequenced the cDNA of Corynebacterium pseudotuberculosis strain 1002, using the SOLiD V3 system, under the following conditions: osmotic stress (2 M), acidity (pH), heat shock (50 °C) and control condition (N). To identify the transcripts shared among the stimulons and integrate this information with the results from BLAST and BLAST2GO, we developed the software CoreStImulon (CSI) which allows the user to individually distinguish the genes in terms of their participation in biological processes, their function and cellular location. In the biosynthetic processes, eleven genes represented in the core stimulon and twenty genes in the control were observed. This validates the hypothesis that the organisms strategy for surviving in a hostile environment is through growth reduction. The oxidation reduction process, response to stress process, and cell adhesion are controlled by genes that contribute to bacterial cell maintenance under stress conditions; these could be involved in their pathogenicity. The methodology for identification of transcripts obtained by ab initio assembly and shared among the stimulons permitted candidates selection for vaccine studies. CSI is available at https://sourceforge.net/projects/corestimulon/.

  10. CircRNA expression pattern and circRNA-miRNA-mRNA network in the pathogenesis of nonalcoholic steatohepatitis

    PubMed Central

    Jin, Xi; Feng, Chun-yan; Xiang, Zun; Chen, Yi-peng; Li, You-ming

    2016-01-01

    The pathogenesis of nonalcoholic steatohepatitis (NASH) is still unclear, where involvement of circRNA is considered for its active role as “miRNA sponge”. Therefore, we aimed to investigate the circRNA expression pattern in NASH and further construct the circRNA-miRNA-mRNA network for in-depth mechanism exploration. Briefly, NASH mice model was established by Methionine and choline deficiency (MCD) diet feeding. Liver circRNA and mRNA profile was initially screened by microarray and ensuing qRT-PCR verification was carried out. The overlapped predicted miRNAs as downstream targets of circRNAs and upstream regulators of mRNAs were verified by qRT-PCR and final circRNA-miRNA-mRNA network was constructed. Gene Ontology (GO) and KEGG pathway analysis were further applied to enrich the huge mRNA microarray data. To sum up, there were 69 up and 63 down regulated circRNAs as well as 2760 up and 2465 down regulated mRNAs in NASH group, comparing with control group. Randomly selected 13 of 14 mRNAs and 2 of 8 circRNAs were successfully verified by qRT-PCR. Through predicted overlapped miRNA verification, four circRNA-miRNA-mRNA pathways were constructed, including circRNA_002581-miR-122-Slc1a5, circRNA_002581- miR-122-Plp2, circRNA_002581-miR-122-Cpeb1 and circRNA_007585-miR-326- UCP2. GO and KEGG pathway analysis also enriched specific mRNAs. Therefore, circRNA profile may serve as candidate for NASH diagnosis and circRNA-miRNA -mRNA pathway may provide novel mechanism for NASH. PMID:27677588

  11. Identification of Genes Potentially Responsible for extra-Oral Digestion and Overcoming Plant Defense from Salivary Glands of the Tarnished Plant Bug (Hemiptera: Miridae) Using cDNA Sequencing.

    PubMed

    Zhu, Yu-Cheng; Yao, Jianxiu; Luttrell, Randall

    2016-01-01

    Saliva is known to play a crucial role in tarnished plant bug (TPB, Lygus lineolaris [Palisot de Beauvois]) feeding. By facilitating the piercing, the enzyme-rich saliva may be used for extra-oral digestion and for overcoming plant defense before the plant fluids are ingested by TPBs. To identify salivary gland genes, mRNA was extracted from salivary glands and cDNA library clones were sequenced. A de novo-assembling of 7,000 Sanger sequences revealed 666 high-quality unique cDNAs with an average size of 624 bp, in which the identities of 347 cDNAs were determined using Blast2GO. Kyoto Encyclopedia of Genes and Genomes analysis indicated that these genes participate in eighteen metabolic pathways. Identifications of large number of enzyme genes in TPB salivary glands evidenced functions for extra-oral digestion and feeding damage mechanism, including 45 polygalacturonase, two α- amylase, one glucosidase, one glycan enzyme, one aminopeptidase, four lipase, and many serine protease cDNAs. The presence of multiple transcripts, multigene members, and high abundance of cell wall degradation enzymes (polygalacturonases) indicated that the enzyme-rich saliva may cause damage to plants by breaking down plant cell walls to make nutrients available for feeding. We also identified genes potentially involved in insect adaptation and detoxifying xenobiotics that may allow insects to overcome plant defense responses, including four glutathione S-transferases, three esterases, one cytochrome P450, and several serine proteases. The gene profiles of TPB salivary glands revealed in this study provides a foundation for further understanding and potential development of novel enzymatic inhibitors, or other RNAi approaches that may interrupt or minimize TPB feeding damage.

  12. De Novo Transcriptome Analysis Provides Insights into Immune Related Genes and the RIG-I-Like Receptor Signaling Pathway in the Freshwater Planarian (Dugesia japonica)

    PubMed Central

    Deng, Hongkuan; Zhang, Yichao; Sun, Xiaowen; Zhu, Guangzhong; Liu, Baohua; Zhao, Bosheng

    2016-01-01

    Background The freshwater planarian Dugesia japonica (D. japonica) possesses extraordinary ability to regenerate lost organs or body parts. Interestingly, in the process of regeneration, there is little wound infection, suggesting that D. japonica has a formidable innate immune system. The importance of immune system prompted us to search for immune-related genes and RIG-I-like receptor signaling pathways. Results Transcriptome sequencing of D. japonica was performed on an IlluminaHiSeq2000 platform. A total of 27,180 transcripts were obtained by Trinity assembler. CEGMA analysis and mapping of all trimmed reads back to the assembly result showed that our transcriptome assembly covered most of the whole transcriptome. 23,888 out of 27,180 transcripts contained ORF (open reading fragment), and were highly similar to those in Schistosoma mansoni using BLASTX analysis. 8,079 transcripts (29.7%) and 8,668 (31.9%) were annotated by Blast2GO and KEGG respectively. A DYNLRB-like gene was cloned to verify its roles in the immune response. Finally, the expression patterns of 4 genes (RIG-I, TRAF3, TRAF6, P38) in the RIG-I-like receptor signaling pathway were detected, and the results showed they are very likely to be involved in planarian immune response. Conclusion RNA-Seq analysis based on the next-generation sequencing technology was an efficient approach to discover critical genes and to understand their corresponding biological functions. Through GO and KEGG analysis, several critical and conserved signaling pathways and genes related to RIG-I-like receptor signaling pathway were identified. Four candidate genes were selected to identify their expression dynamics in the process of pathogen stimulation. These annotated transcripts of D. japonica provide a useful resource for subsequent investigation of other important pathways. PMID:26986572

  13. Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing.

    PubMed

    Patnaik, Bharat Bhusan; Hwang, Hee-Ju; Kang, Se Won; Park, So Young; Wang, Tae Hun; Park, Eun Bi; Chung, Jong Min; Song, Dae Kwon; Kim, Changmu; Kim, Soonok; Lee, Jae Bong; Jeong, Heon Cheon; Park, Hong Seog; Han, Yeon Soo; Lee, Yong Seok

    2015-12-16

    The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10(-5)) against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB). BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO) terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs) were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species.

  14. Transcriptome and Gene Ontology (GO) Enrichment Analysis Reveals Genes Involved in Biotin Metabolism That Affect l-Lysine Production in Corynebacterium glutamicum

    PubMed Central

    Kim, Hong-Il; Kim, Jong-Hyeon; Park, Young-Jin

    2016-01-01

    Corynebacterium glutamicum is widely used for amino acid production. In the present study, 543 genes showed a significant change in their mRNA expression levels in l-lysine-producing C. glutamicum ATCC21300 than that in the wild-type C. glutamicum ATCC13032. Among these 543 differentially expressed genes (DEGs), 28 genes were up- or downregulated. In addition, 454 DEGs were functionally enriched and categorized based on BLAST sequence homologies and gene ontology (GO) annotations using the Blast2GO software. Interestingly, NCgl0071 (bioB, encoding biotin synthase) was expressed at levels ~20-fold higher in the l-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain. Five other genes involved in biotin metabolism or transport—NCgl2515 (bioA, encoding adenosylmethionine-8-amino-7-oxononanoate aminotransferase), NCgl2516 (bioD, encoding dithiobiotin synthetase), NCgl1883, NCgl1884, and NCgl1885—were also expressed at significantly higher levels in the l-lysine-producing ATCC21300 strain than that in the wild-type ATCC13032 strain, which we determined using both next-generation RNA sequencing and quantitative real-time PCR analysis. When we disrupted the bioB gene in C. glutamicum ATCC21300, l-lysine production decreased by approximately 76%, and the three genes involved in biotin transport (NCgl1883, NCgl1884, and NCgl1885) were significantly downregulated. These results will be helpful to improve our understanding of C. glutamicum for industrial amino acid production. PMID:27005618

  15. Draft Genome of Toxocara canis, a Pathogen Responsible for Visceral Larva Migrans

    PubMed Central

    Kong, Jinhwa; Won, Jungim; Yoon, Jeehee; Lee, UnJoo; Kim, Jong-Il; Huh, Sun

    2016-01-01

    This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out. Besides them, recently developed tools such as MAKER, PASA, Evidence Modeler, and Blast2GO were used. The scaffold DNA was obtained, the N50 was 108,950 bp, and the overall length was 341,776,187 bp. The N50 of the transcriptome was 940 bp, and its length was 53,046,952 bp. The GC content of the entire genome was 39.3%. The total number of genes was 20,178, and the total number of protein sequences was 22,358. Of the 22,358 protein sequences, 4,992 were newly observed in T. canis. Following proteins previously unknown were found: E3 ubiquitin-protein ligase cbl-b and antigen T-cell receptor, zeta chain for T-cell and B-cell regulation; endoprotease bli-4 for cuticle metabolism; mucin 12Ea and polymorphic mucin variant C6/1/40r2.1 for mucin production; tropomodulin-family protein and ryanodine receptor calcium release channels for muscle movement. We were able to find new hypothetical polypeptides sequences unique to T. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding of T. canis. PMID:28095660

  16. Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

    PubMed Central

    2012-01-01

    Background Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioinformatics tools, easy to use and able to provide automatic and reliable annotations at a genomic scale, are necessary and urgent. In this scenario, the Gene Ontology has provided the means to standardize the annotation classification with a structured vocabulary which can be easily exploited by computational methods. Results Argot2 is a web-based function prediction tool able to annotate nucleic or protein sequences from small datasets up to entire genomes. It accepts as input a list of sequences in FASTA format, which are processed using BLAST and HMMER searches vs UniProKB and Pfam databases respectively; these sequences are then annotated with GO terms retrieved from the UniProtKB-GOA database and the terms are weighted using the e-values from BLAST and HMMER. The weighted GO terms are processed according to both their semantic similarity relations described by the Gene Ontology and their associated score. The algorithm is based on the original idea developed in a previous tool called Argot. The entire engine has been completely rewritten to improve both accuracy and computational efficiency, thus allowing for the annotation of complete genomes. Conclusions The revised algorithm has been already employed and successfully tested during in-house genome projects of grape and apple, and has proven to have a high precision and recall in all our benchmark conditions. It has also been successfully compared with Blast2GO, one of the methods most commonly employed for sequence annotation. The server is freely accessible at http://www.medcomp.medicina.unipd.it/Argot2. PMID:22536960

  17. The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus

    PubMed Central

    Sayadi, Ahmed; Immonen, Elina; Bayram, Helen

    2016-01-01

    Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally. PMID:27442123

  18. The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

    PubMed

    Sayadi, Ahmed; Immonen, Elina; Bayram, Helen; Arnqvist, Göran

    2016-01-01

    Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.

  19. De Novo Assembly of a Transcriptome for Calanus finmarchicus (Crustacea, Copepoda) – The Dominant Zooplankter of the North Atlantic Ocean

    PubMed Central

    Lenz, Petra H.; Roncalli, Vittoria; Hassett, R. Patrick; Wu, Le-Shin; Cieslak, Matthew C.; Hartline, Daniel K.; Christie, Andrew E.

    2014-01-01

    Assessing the impact of global warming on the food web of the North Atlantic will require difficult-to-obtain physiological data on a key copepod crustacean, Calanus finmarchicus. The de novo transcriptome presented here represents a new resource for acquiring such data. It was produced from multiplexed gene libraries using RNA collected from six developmental stages: embryo, early nauplius (NI-II), late nauplius (NV-VI), early copepodite (CI-II), late copepodite (CV) and adult (CVI) female. Over 400,000,000 paired-end reads (100 base-pairs long) were sequenced on an Illumina instrument, and assembled into 206,041 contigs using Trinity software. Coverage was estimated to be at least 65%. A reference transcriptome comprising 96,090 unique components (“comps”) was annotated using Blast2GO. 40% of the comps had significant blast hits. 11% of the comps were successfully annotated with gene ontology (GO) terms. Expression of many comps was found to be near zero in one or more developmental stages suggesting that 35 to 48% of the transcriptome is “silent” at any given life stage. Transcripts involved in lipid biosynthesis pathways, critical for the C. finmarchicus life cycle, were identified and their expression pattern during development was examined. Relative expression of three transcripts suggests wax ester biosynthesis in late copepodites, but triacylglyceride biosynthesis in adult females. Two of these transcripts may be involved in the preparatory phase of diapause. A key environmental challenge for C. finmarchicus is the seasonal exposure to the dinoflagellate Alexandrium fundyense with high concentrations of saxitoxins, neurotoxins that block voltage-gated sodium channels. Multiple contigs encoding putative voltage-gated sodium channels were identified. They appeared to be the result of both alternate splicing and gene duplication. This is the first report of multiple NaV1 genes in a protostome. These data provide new insights into the transcriptome and

  20. Coincident frequencies and relative phases among brain activity and hormonal signals

    PubMed Central

    Solís-Ortíz, Silvia; Campos, Rafael G; Félix, Julián; Obregón, Octavio

    2009-01-01

    Background Fourier transform is a basic tool for analyzing biological signals and is computed for a finite sequence of data sample. The electroencephalographic (EEG) signals analyzed with this method provide only information based on the frequency range, for short periods. In some cases, for long periods it can be useful to know whether EEG signals coincide or have a relative phase between them or with other biological signals. Some studies have evidenced that sex hormones and EEG signals show oscillations in their frequencies across a period of 28 days; so it seems of relevance to seek after possible patterns relating EEG signals and endogenous sex hormones, assumed as long time-periodic functions to determine their typical periods, frequencies and relative phases. Methods In this work we propose a method that can be used to analyze brain signals and hormonal levels and obtain frequencies and relative phases among them. This method involves the application of a discrete Fourier Transform on previously reported datasets of absolute power of brain signals delta, theta, alpha1, alpha2, beta1 and beta2 and the endogenous estrogen and progesterone levels along 28 days. Results Applying the proposed method to exemplary datasets and comparing each brain signal with both sex hormones signals, we found a characteristic profile of coincident periods and typical relative phases. For the corresponding coincident periods the progesterone seems to be essentially in phase with theta, alpha1, alpha2 and beta1, while delta and beta2 go oppositely. For the relevant coincident periods, the estrogen goes in phase with delta and theta and goes oppositely with alpha2. Conclusion Findings suggest that the procedure applied here provides a method to analyze typical frequencies, or periods and phases between signals with the same period. It generates specific patterns for brain signals and hormones and relations among them. PMID:19284671

  1. Proteomic analysis of mature Lagenaria siceraria seed.

    PubMed

    Kumari, Neha; Tajmul, Md; Yadav, Savita

    2015-04-01

    Lagenaria siceraria (bottle gourd) class belongs to Magnoliopsida family curcurbitaceae that is a traditionally used medicinal plant. Fruit of this plant are widely used as a therapeutic vegetable in various diseases, all over the Asia and Africa. Various parts of this plant like fruit, seed, leaf and root are used as alternative medicine. In the present study, primarily, we have focused on proteomic analysis of L. siceraria seed using phenol extraction method for protein isolation. Twenty-four colloidal coomassie blue stained protein spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) after resolving on two-dimensional gel electrophoresis. Out of 24 identified protein spots, four were grouped as unidentified proteins which clearly suggest that less work has been done in the direction of plant seed proteomics. These proteins have been found to implicate in various functions such as biosynthesis of plant cell wall polysaccharides and glycoproteins, serine/threonine kinase activity, plant disease resistance and transferase activity against insects by means of insecticidal and larval growth inhibitory, anti-HIV, antihelmintic and antimicrobial properties. By Blast2GO annotation analysis, amongst the identified proteins of L. siceraria, molecular function for majority of proteins has indispensable role in catalytic activity, few in binding activity and antioxidant activity; it is mostly distributed in cell, organelle, membrane and macromolecular complex. Most of them involved in biological process such as metabolic process, cellular process, response to stimulus, single organism process, signalling, biological recognition, cellular component organization or biogenesis and localization.

  2. The First Illumina-Based De Novo Transcriptome Sequencing and Analysis of Safflower Flowers

    PubMed Central

    Lulin, Huang; Xiao, Yang; Pei, Sun; Wen, Tong; Shangqin, Hu

    2012-01-01

    Background The safflower, Carthamus tinctorius L., is a worldwide oil crop, and its flowers, which have a high flavonoid content, are an important medicinal resource against cardiovascular disease in traditional medicine. Because the safflower has a large and complex genome, the development of its genomic resources has been delayed. Second-generation Illumina sequencing is now an efficient route for generating an enormous volume of sequences that can represent a large number of genes and their expression levels. Methodology/Principal Findings To investigate the genes and pathways that might control flavonoids and other secondary metabolites in the safflower, we used Illumina sequencing to perform a de novo assembly of the safflower tubular flower tissue transcriptome. We obtained a total of 4.69 Gb in clean nucleotides comprising 52,119,104 clean sequencing reads, 195,320 contigs, and 120,778 unigenes. Based on similarity searches with known proteins, we annotated 70,342 of the unigenes (about 58% of the identified unigenes) with cut-off E-values of 10−5. In total, 21,943 of the safflower unigenes were found to have COG classifications, and BLAST2GO assigned 26,332 of the unigenes to 1,754 GO term annotations. In addition, we assigned 30,203 of the unigenes to 121 KEGG pathways. When we focused on genes identified as contributing to flavonoid biosynthesis and the biosynthesis of unsaturated fatty acids, which are important pathways that control flower and seed quality, respectively, we found that these genes were fairly well conserved in the safflower genome compared to those of other plants. Conclusions/Significance Our study provides abundant genomic data for Carthamus tinctorius L. and offers comprehensive sequence resources for studying the safflower. We believe that these transcriptome datasets will serve as an important public information platform to accelerate studies of the safflower genome, and may help us define the mechanisms of flower tissue

  3. Cold Responsive Gene Expression Profiling of Sugarcane and Saccharum spontaneum with Functional Analysis of a Cold Inducible Saccharum Homolog of NOD26-Like Intrinsic Protein to Salt and Water Stress.

    PubMed

    Park, Jong-Won; Benatti, Thiago R; Marconi, Thiago; Yu, Qingyi; Solis-Gracia, Nora; Mora, Victoria; da Silva, Jorge A

    2015-01-01

    Transcriptome analysis of sugarcane hybrid CP72-1210 (cold susceptible) and Saccharum spontaneum TUS05-05 (cold tolerant) using Sugarcane Assembled Sequences (SAS) from SUCEST-FUN Database showed that a total of 35,340 and 34,698 SAS genes, respectively, were expressed before and after chilling stress. The analysis revealed that more than 600 genes are differentially expressed in each genotype after chilling stress. Blast2Go annotation revealed that the major difference in gene expression profiles between CP72-1210 and TUS05-05 after chilling stress are present in the genes related to the transmembrane transporter activity. To further investigate the relevance of transmembrane transporter activity against abiotic stress tolerance, a S. spontaneum homolog of a NOD26-like major intrinsic protein gene (SspNIP2) was selected for functional analysis, of which expression was induced after chilling stress in the cold tolerant TUS05-05. Quantitative real-time PCR showed that SspNIP2 expression was increased ~2.5 fold at 30 minutes after cold treatment and stayed induced throughout the 24 hours of cold treatment. The amino acid sequence analysis of the cloned SspNIP2 confirmed the presence of six transmembrane domains and two NPA (Asn-Pro-Ala) motifs, signature features of major intrinsic protein families. Amino acid analysis confirmed that four amino acids, comprising the ar/R (aromatic residue/arginine) region responsible for the substrate specificity among MIPs, are conserved among monocot silicon transporters and SspNIP2. Salinity stress test on SspNIP2 transgenic tobacco plants resulted in more vigorous transgenic lines than the non-transgenic tobacco plants, suggesting some degree of tolerance to salt stress conferred by SspNIP2. SspNIP2-transgenic plants, exposed to 2 weeks of water stress without irrigation, developed various degrees of water stress symptom. The water stress test confirmed that the SspNIP2 transgenic lines had lower evapotranspiration rates than non

  4. CycADS: an annotation database system to ease the development and update of BioCyc databases

    PubMed Central

    Vellozo, Augusto F.; Véron, Amélie S.; Baa-Puyoulet, Patrice; Huerta-Cepas, Jaime; Cottret, Ludovic; Febvay, Gérard; Calevro, Federica; Rahbé, Yvan; Douglas, Angela E.; Gabaldón, Toni; Sagot, Marie-France; Charles, Hubert; Colella, Stefano

    2011-01-01

    In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL: http

  5. CycADS: an annotation database system to ease the development and update of BioCyc databases.

    PubMed

    Vellozo, Augusto F; Véron, Amélie S; Baa-Puyoulet, Patrice; Huerta-Cepas, Jaime; Cottret, Ludovic; Febvay, Gérard; Calevro, Federica; Rahbé, Yvan; Douglas, Angela E; Gabaldón, Toni; Sagot, Marie-France; Charles, Hubert; Colella, Stefano

    2011-01-01

    In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL: http://www.cycadsys.org.

  6. Cold Responsive Gene Expression Profiling of Sugarcane and Saccharum spontaneum with Functional Analysis of a Cold Inducible Saccharum Homolog of NOD26-Like Intrinsic Protein to Salt and Water Stress

    PubMed Central

    Park, Jong-Won; Benatti, Thiago R.; Marconi, Thiago; Yu, Qingyi; Solis-Gracia, Nora; Mora, Victoria; da Silva, Jorge A.

    2015-01-01

    Transcriptome analysis of sugarcane hybrid CP72-1210 (cold susceptible) and Saccharum spontaneum TUS05-05 (cold tolerant) using Sugarcane Assembled Sequences (SAS) from SUCEST-FUN Database showed that a total of 35,340 and 34,698 SAS genes, respectively, were expressed before and after chilling stress. The analysis revealed that more than 600 genes are differentially expressed in each genotype after chilling stress. Blast2Go annotation revealed that the major difference in gene expression profiles between CP72-1210 and TUS05-05 after chilling stress are present in the genes related to the transmembrane transporter activity. To further investigate the relevance of transmembrane transporter activity against abiotic stress tolerance, a S. spontaneum homolog of a NOD26-like major intrinsic protein gene (SspNIP2) was selected for functional analysis, of which expression was induced after chilling stress in the cold tolerant TUS05-05. Quantitative real-time PCR showed that SspNIP2 expression was increased ~2.5 fold at 30 minutes after cold treatment and stayed induced throughout the 24 hours of cold treatment. The amino acid sequence analysis of the cloned SspNIP2 confirmed the presence of six transmembrane domains and two NPA (Asn-Pro-Ala) motifs, signature features of major intrinsic protein families. Amino acid analysis confirmed that four amino acids, comprising the ar/R (aromatic residue/arginine) region responsible for the substrate specificity among MIPs, are conserved among monocot silicon transporters and SspNIP2. Salinity stress test on SspNIP2 transgenic tobacco plants resulted in more vigorous transgenic lines than the non-transgenic tobacco plants, suggesting some degree of tolerance to salt stress conferred by SspNIP2. SspNIP2-transgenic plants, exposed to 2 weeks of water stress without irrigation, developed various degrees of water stress symptom. The water stress test confirmed that the SspNIP2 transgenic lines had lower evapotranspiration rates than non

  7. High Through-Put Sequencing of the Parhyale hawaiensis mRNAs and microRNAs to Aid Comparative Developmental Studies

    PubMed Central

    Everall, Richard; Shih, Yu-huan; Lemay, Virginie; Moreton, Joanna; Wilson, Raymond; Aboobaker, A. Aziz

    2012-01-01

    Understanding the genetic and evolutionary basis of animal morphological diversity will require comparative developmental studies that use new model organisms. This necessitates development of tools for the study of genetics and also the generation of sequence information of the organism to be studied. The development of next generation sequencing technology has enabled quick and cost effective generation of sequence information. Parhyale hawaiensis has emerged as a model organism of choice due to the development of advanced molecular tools, thus P. hawaiensis genetic information will help drive functional studies in this organism. Here we present a transcriptome and miRNA collection generated using next generation sequencing platforms. We generated approximately 1.7 million reads from a P. hawaiensis cDNA library constructed from embryos up to the germ band stage. These reads were assembled into a dataset comprising 163,501 transcripts. Using the combined annotation of Annot8r and pfam2go, Gene Ontology classifications was assigned to 20,597 transcripts. Annot8r was used to provide KEGG orthology to our transcript dataset. A total of 25,292 KEGG pathway assignments were defined and further confirmed with reciprocal blast against the NCBI nr protein database. This has identified many P. hawaiensis gene orthologs of key conserved signalling pathways involved in development. We also generated small RNA sequences from P. hawaiensis, identifying 55 conserved miRNAs. Sequenced small RNAs that were not annotated by stringent comparison to mirBase were used to search the Daphnia pulex for possible novel miRNAs. Using a conservative approach, we have identified 51 possible miRNA candidates conserved in the Daphnia pulex genome, which could be potential crustacean/arthropod specific miRNAs. Our study presents gene and miRNA discovery in a new model organism that does not have a sequenced genome. The data provided by our work will be valuable for the P. hawaiensis community

  8. Emotional Availability Modulates Electrophysiological Correlates of Executive Functions in Preschool Children

    PubMed Central

    Schneider-Hassloff, Henriette; Zwönitzer, Annabel; Künster, Anne K.; Mayer, Carmen; Ziegenhain, Ute; Kiefer, Markus

    2016-01-01

    Executive functions (EFs) – a set of cognitive control abilities – mediate resilience to stress and are associated with academic achievement and health throughout life. They are crucially linked to prefrontal cortex function as well as to other cortical and subcortical brain functions, which are maturing throughout childhood at different rates. Recent behavioral research suggested that children’s EFs were related to parenting quality and child attachment security, but the neural correlates of these associations are unknown. With this study we tested in 4- to 6-year-old healthy children (N = 27) how emotional availability (EA) of the mother-child-interaction was associated with behavioral and electrophysiological correlates of response inhibition (a core EF) in a Go/Nogo task, using event-related potential recordings (ERPs), and with behavioral performance in a Delay of Gratification (DoG) and a Head-Toes-Knees-Shoulders task (HTKS). Our data showed that the Go/Nogo task modulated children’s ERP components resembling adult electrophysiological indices of response inhibition - the N2 and P3/LPC ERPs-, but the children’s N2 and P3/LPC ERPs showed longer latencies. Higher maternal autonomy-fostering behavior and greater child responsiveness were significantly associated with smaller children’s N2 Go/Nogo effects at fronto-central and parietal sites and with greater Go/Nogo effects in the N2 time window at occipital sites, over and above children’s age and intelligence. Additionally, greater maternal sensitivity and a higher dyadic EA quality of the mother-child-interaction went along with greater occipital Go/Nogo effects in the N2 time window, but this effect clearly diminished when we controlled for children’s age and intelligence. Higher maternal autonomy-support was also positively associated with better HTKS performance, and higher dyadic EA quality went along with higher HTKS and DoG scores. However, no significant associations were found between

  9. Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem.

    PubMed

    Mahadevan, Chidambareswaren; Krishnan, Anu; Saraswathy, Gayathri G; Surendran, Arun; Jaleel, Abdul; Sakuntala, Manjula

    2016-01-01

    Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset

  10. Interactions between soil moisture and Atmospheric Boundary Layer at the Brazilian savana-type vegetation Cerrado

    NASA Astrophysics Data System (ADS)

    Pinheiro, L. R.; Siqueira, M. B.

    2013-05-01

    Before the large people influx and development of the central part of Brazil in the sixties, due to new capital Brasília, Cerrado, a typical Brazilian savanna-type vegetation, used to occupy about 2 million km2, going all the way from the Amazon tropical forest, in the north of the country, to the edges of what used to be of the Atlantic forest in the southeast. Today, somewhat 50% of this area has given place to agriculture, pasture and managed forests. It is forecasted that, at the current rate of this vegetation displacement, Cerrado will be gone by 2030. Understanding how Cerrado interacts with the atmosphere and how this interaction will be modified with this land-use change is a crucial step towards improving predictions of future climate-change scenarios. Cerrado is a vegetation adapted to a climate characterized by two very distinct seasons, a wet season (Nov-Mar) and dry season (May-Ago), with April and October being transitions between seasons. Typically, based on measurements in a weather station located in Brasilia, 75% of precipitation happens in the wet-season months and only 5% during dry-season. Under these circumstances, it is clear that the vegetation will have to cope with long periods of water stress. In this work we studied using numerical simulations, the interactions between soil-moisture, responsible for the water stress, with the Atmospheric Boundary Layer (ABL). The numerical model comprises of a Soil-Vegetation-Atmosphere model where the biophysical processes are represented with a big-leaf approach. Soil water is estimated with a simple logistic model and with water-stress effects on stomatal conductance are parameterized from local measurements of simultaneous latent-heat fluxes and soil moisture. ABL evolution is calculate with a slab model that considers independently surface and entrainment fluxes of sensible- and latent- heat. Temperature tropospheric lapse-rate is taken from soundings at local airport. Simulations of 30-day dry

  11. A "tropical" Early Eocene marine environment on the Antarctic margin: TEX86 results from IODP expedition 318

    NASA Astrophysics Data System (ADS)

    Bendle, J. A.; Bijl, P.; Toney, J. L.; Pross, J.; Contreras, L.; Schouten, S.; Roehl, U.; Tauxe, L.; Huber, M.; Brinkhuis, H.; Scientific Team of IODP Drilling Leg 318

    2011-12-01

    temperatures are substantially higher than can be simulated by most models without assuming exceptionally high pCO2 levels. Recent model runs of the Eocene climate using the Community Climate System Model version 3 forced by 4480ppm pCO2 go someway to resolving this mismatch, with summer month temperatures on the Wilkes margin of 25 - 27°C. However, even the 4480ppm runs do not agree with the mean annual TEX86-H estimates of 27 - 33°C (Av. 32°C).

  12. Identification of Differentially-Expressed Genes in Response to Mycosphaerella fijiensis in the Resistant Musa Accession ‘Calcutta-4’ Using Suppression Subtractive Hybridization

    PubMed Central

    Pacheco Coello, Ricardo; Chávez Navarrete, Tatiana; Navarrete Villegas, Oscar; Santos Ordóñez, Efrén

    2016-01-01

    Bananas and plantains are considered an important crop around the world. Banana production is affected by several constraints, of which Black Sigatoka Disease, caused by the fungus Mycosphaerella fijiensis, is considered one of the most important diseases in banana plantations. The banana accession ‘Calcutta-4’ has a natural resistance to Black Sigatoka; however, the fruit is not valuable for commercialization. Gene identification and expression studies in ‘Calcutta-4’ might reveal possible gene candidates for resistant to the disease and elucidate mechanisms for resistance. A subtracted cDNA library was generated from leaves after 6, 9 and 12 days inoculated with M. fijiensis conidia on greenhouse banana plants of the accession ‘Calcutta-4’. Bioinformatic analysis revealed 99 good quality sequences. Blast2go analysis revealed that 31% of the sequences could not be categorized and, according to the Biological Process Category, 32 and 28 ESTs are related to general metabolic and cellular processes, respectively; while 10 ESTs response to stimulus. Seven sequences were redundant and one was similar to genes that may be involved in pathogen resistance including the putative disease resistance protein RGA1. Genes encoding zinc finger domains were identified and may play an important role in pathogen resistance by inducing the expression of downstream genes. Expression analysis of four selected genes was performed using RT-qPCR during the early stage of the disease development at 6, 9, 12 and 15 days post inoculation showing a peak of up regulation at 9 or 12 days post inoculation. Three of the four genes showed an up-regulation of expression in ‘Calcutta-4’ when compared to ‘Williams’ after inoculation with M. fijiensis, suggesting a fine regulation of specific gene candidates that may lead to a resistance response. The genes identified in early responses in a plant-pathogen interaction may be relevant for the resistance response of ‘Calcutta-4

  13. 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes.

    PubMed

    Hook, Sharon E; Twine, Natalie A; Simpson, Stuart L; Spadaro, David A; Moncuquet, Philippe; Wilkins, Marc R

    2014-08-01

    Next generation sequencing using Roche's 454 pyrosequencing platform can be used to generate genomic information for non-model organisms, although there are bioinformatic challenges associated with these studies. These challenges are compounded by a lack of a standardized protocol to either assemble data or to evaluate the quality of a de novo transcriptome. This study presents an assembly of the control and toxicant responsive transcriptome of Melita plumulosa, an Australian amphipod commonly used in ecotoxicological studies. RNA was harvested from control amphipods, juvenile amphipods, and from amphipods exposed to either metal or diesel contaminated sediments. This RNA was used as the basis for a 454 based transcriptome sequencing effort. Sequencing generated 1.3 million reads from control, juvenile, metal-exposed and diesel-exposed amphipods. Different read filtering and assembly protocols were evaluated to generate an assembly that (i) had an optimal number of contigs; (ii) had long contigs; (iii) contained a suitable representation of conserved genes; and (iv) had long ortholog alignment lengths relative to the length of each contig. A final assembly, generated using fixed-length trimming based on the sequence quality scores, followed by assembly using the MIRA algorithm, produced the best results. The 26,625 contigs generated via this approach were annotated using Blast2GO, and the differential expression between treatments and control was determined by mapping with BWA followed by DESeq. Although the mapping generated low coverage, many differentially expressed contigs, including some with known developmental or toxicological function, were identified. This study demonstrated that 454 pyrosequencing is an effective means of generating reference transcriptome information for organisms, such as the amphipod M. plumulosa, that have no genomic information available in databases or in closely related sequenced species. It also demonstrated how optimization of

  14. Development of Molten-Salt Heat Transfer Fluid Technology for Parabolic Trough Solar Power Plants - Public Final Technical Report

    SciTech Connect

    Grogan, Dylan C. P.

    2013-08-15

    /kWhe , which achieved the Phase 2 Go/No Go target of less than 0.12¢/kWhe. Abengoa Solar has high confidence that the primary risk areas have been addressed in the project and a commercial plant utilizing molten salt is economically and technically feasible. The strong results from the Phase 1 and 2 research, testing, and analyses, summarized in this report, led Abengoa Solar to recommend that the project proceed to Phase 3. However, a commercially viable collector interconnection was not fully validated by the end of Phase 2, combined with the uncertainty in the federal budget, forced the DOE and Abengoa Solar to close the project. Thus the resources required to construct and operate a molten salt pilot plant will be solely supplied by Abengoa Solar.

  15. Gene Classification and Mining of Molecular Markers Useful in Red Clover (Trifolium pratense) Breeding

    PubMed Central

    Ištvánek, Jan; Dluhošová, Jana; Dluhoš, Petr; Pátková, Lenka; Nedělník, Jan; Řepková, Jana

    2017-01-01

    Red clover (Trifolium pratense) is an important forage plant worldwide. This study was directed to broadening current knowledge of red clover's coding regions and enhancing its utilization in practice by specific reanalysis of previously published assembly. A total of 42,996 genes were characterized using Illumina paired-end sequencing after manual revision of Blast2GO annotation. Genes were classified into metabolic and biosynthetic pathways in response to biological processes, with 7,517 genes being assigned to specific pathways. Moreover, 17,727 enzymatic nodes in all pathways were described. We identified 6,749 potential microsatellite loci in red clover coding sequences, and we characterized 4,005 potential simple sequence repeat (SSR) markers as generating polymerase chain reaction products preferentially within 100–350 bp. Marker density of 1 SSR marker per 12.39 kbp was achieved. Aligning reads against predicted coding sequences resulted in the identification of 343,027 single nucleotide polymorphism (SNP) markers, providing marker density of one SNP marker per 144.6 bp. Altogether, 95 SSRs in coding sequences were analyzed for 50 red clover varieties and a collection of 22 highly polymorphic SSRs with pooled polymorphism information content >0.9 was generated, thus obtaining primer pairs for application to diversity studies in T. pratense. A set of 8,623 genome-wide distributed SNPs was developed and used for polymorphism evaluation in individual plants. The polymorphic information content ranged from 0 to 0.375. Temperature switch PCR was successfully used in single-marker SNP genotyping for targeted coding sequences and for heterozygosity or homozygosity confirmation in validated five loci. Predicted large sets of SSRs and SNPs throughout the genome are key to rapidly implementing genome-based breeding approaches, for identifying genes underlying key traits, and for genome-wide association studies. Detailed knowledge of genetic relationships among

  16. Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum—Phytophthora capsici Phytopathosystem

    PubMed Central

    Mahadevan, Chidambareswaren; Krishnan, Anu; Saraswathy, Gayathri G.; Surendran, Arun; Jaleel, Abdul; Sakuntala, Manjula

    2016-01-01

    Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset

  17. iTRAQ-based protein profiling provides insights into the central metabolism changes driving grape berry development and ripening

    PubMed Central

    2013-01-01

    Background Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components such as sugars, acids, flavors, anthocyanins, tannins, etc., accumulate in the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance in our understanding of berry development and ripening processes. Results We report the developmental analysis of Vitis vinifera cv. Muscat Hamburg berries at the protein level from fruit set to full ripening. An iTRAQ-based bottom-up proteomic approach followed by tandem mass spectrometry led to the identification and quantitation of 411 and 630 proteins in the green and ripening phases, respectively. Two key points in development relating to changes in protein level were detected: end of the first growth period (7 mm-to-15 mm) and onset of ripening (15 mm-to-V100, V100-to-110). A functional analysis was performed using the Blast2GO software based on the enrichment of GO terms during berry growth. Conclusions The study of the proteome contributes to decipher the biological processes and metabolic pathways involved in the development and quality traits of fruit and its derived products. These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry. In addition, some key steps in carbohydrate and malate metabolism have been identified in this study, i.e., PFP-PFK or SuSy-INV switches among others, which may influence the final sugar and acid balance in ripe fruit. In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development. These results open up

  18. Identification of Differentially-Expressed Genes in Response to Mycosphaerella fijiensis in the Resistant Musa Accession 'Calcutta-4' Using Suppression Subtractive Hybridization.

    PubMed

    Sánchez Timm, Eduardo; Hidalgo Pardo, Lisette; Pacheco Coello, Ricardo; Chávez Navarrete, Tatiana; Navarrete Villegas, Oscar; Santos Ordóñez, Efrén

    2016-01-01

    Bananas and plantains are considered an important crop around the world. Banana production is affected by several constraints, of which Black Sigatoka Disease, caused by the fungus Mycosphaerella fijiensis, is considered one of the most important diseases in banana plantations. The banana accession 'Calcutta-4' has a natural resistance to Black Sigatoka; however, the fruit is not valuable for commercialization. Gene identification and expression studies in 'Calcutta-4' might reveal possible gene candidates for resistant to the disease and elucidate mechanisms for resistance. A subtracted cDNA library was generated from leaves after 6, 9 and 12 days inoculated with M. fijiensis conidia on greenhouse banana plants of the accession 'Calcutta-4'. Bioinformatic analysis revealed 99 good quality sequences. Blast2go analysis revealed that 31% of the sequences could not be categorized and, according to the Biological Process Category, 32 and 28 ESTs are related to general metabolic and cellular processes, respectively; while 10 ESTs response to stimulus. Seven sequences were redundant and one was similar to genes that may be involved in pathogen resistance including the putative disease resistance protein RGA1. Genes encoding zinc finger domains were identified and may play an important role in pathogen resistance by inducing the expression of downstream genes. Expression analysis of four selected genes was performed using RT-qPCR during the early stage of the disease development at 6, 9, 12 and 15 days post inoculation showing a peak of up regulation at 9 or 12 days post inoculation. Three of the four genes showed an up-regulation of expression in 'Calcutta-4' when compared to 'Williams' after inoculation with M. fijiensis, suggesting a fine regulation of specific gene candidates that may lead to a resistance response. The genes identified in early responses in a plant-pathogen interaction may be relevant for the resistance response of 'Calcutta-4' to Black Sigatoka

  19. Fritz London

    NASA Astrophysics Data System (ADS)

    Gavroglu, Kostas

    2005-11-01

    Preface; Acknowledgements; Part I. From Philosophy to Physics: The years that left nothing unaffected; 1. The appeal of ideas; 2. Goëthe as a scientist; 3. How absolute is our knowledge?; 4. How do we come to know things?; 5. London's teachers in philosophy; 6. Husserl's teachings; 7. Expectations of things to come; 8. The thesis in philosophy; 9. Tolman's principle of similitude; 10. The necessary clarifications; 11. Work on quantum theory; 12. Transformation theory; 13. Unsuccessful attempts at unification; Part II. The Years in Berlin and the Beginnings of Quantum Chemistry: The mysterious bond; 14. London in Zürich; 15. Binding forces; 16. The Pauli principle; 17. Reactions to the Heitler-London paper; 18. Polyelectronic molecules and the application of group theory to problems of chemical valence; 19. Chemists as physicists?; 20. London's first contacts in Berlin; 21. Marriage; 22. Job offers; 23. Intermolecular forces; 24. The book which could not be written; 25. Leningrad and Rome; 26. Difficulties with group theory; 27. Linus Pauling's resonance structures; 28. Robert Mulliken's molecular orbitals; Part III. Oxford and Superconductivity: The rise of the Nazis; 29. Going to Oxford; 30. Lindemann, Simon and Heinz London; 31. Electricity in the very cold; 32. The end of old certainties; 33. The thermodynamic treatment; 34. The theory of Fritz and Heinz London; 35. Initial reactions by von Laue; 36. The discussion at the Royal Society; 37. Termination of the ICI fellowship; Part IV. Paris and Superfluidity: The Front Populaire; 38. The article in Nature 1937 and 'Nouvelle Conception'; 39. Laue again; 40. The structure of solid helium; 41. The peculiar properties of helium; 42. Bose-Einstein condensation; 43. The note in Nature; 44. The two-fluid model; 45. The trip to Jerusalem; 46. Leaving again; 47. The observer in quantum mechanics; Part V. United States and the Typing up of Loose Ends: Duke University, North Carolina; 48. The Soviet Union, Kapitza and

  20. Development of expressed sequence tag and expressed sequence tag–simple sequence repeat marker resources for Musa acuminata

    PubMed Central

    Passos, Marco A. N.; de Oliveira Cruz, Viviane; Emediato, Flavia L.; de Camargo Teixeira, Cristiane; Souza, Manoel T.; Matsumoto, Takashi; Rennó Azevedo, Vânia C.; Ferreira, Claudia F.; Amorim, Edson P.; de Alencar Figueiredo, Lucio Flavio; Martins, Natalia F.; de Jesus Barbosa Cavalcante, Maria; Baurens, Franc-Christophe; da Silva, Orzenil Bonfim; Pappas, Georgios J.; Pignolet, Luc; Abadie, Catherine; Ciampi, Ana Y.; Piffanelli, Pietro; Miller, Robert N. G.

    2012-01-01

    Background and aims Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana–Mycosphaerella fijiensis (Mf) interactions. Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of banana. Microsatellite markers were developed as a resource for crop improvement. Methodology cDNA libraries were constructed from in vitro-infected leaves from BLSD-resistant M. acuminata ssp. burmaniccoides Calcutta 4 (MAC4) and susceptible M. acuminata cv. Cavendish Grande Naine (MACV). Clones were 5′-end Sanger sequenced, ESTs assembled with TGICL and unigenes annotated using BLAST, Blast2GO and InterProScan. Mreps was used to screen for simple sequence repeats (SSRs), with markers evaluated for polymorphism using 20 diploid (AA) M. acuminata accessions contrasting in resistance to Mycosphaerella leaf spot diseases. Principal results A total of 9333 high-quality ESTs were obtained for MAC4 and 3964 for MACV, which assembled into 3995 unigenes. Of these, 2592 displayed homology to genes encoding proteins with known or putative function, and 266 to genes encoding proteins with unknown function. Gene ontology (GO) classification identified 543 GO terms, 2300 unigenes were assigned to EuKaryotic orthologous group categories and 312 mapped to Kyoto Encyclopedia of Genes and Genomes pathways. A total of 624 SSR loci were identified, with trinucleotide repeat motifs the most abundant in MAC4 (54.1 %) and MACV (57.6 %). Polymorphism across M. acuminata accessions was observed with 75 markers. Alleles per polymorphic locus ranged from 2 to 8, totalling 289. The polymorphism information content ranged from 0.08 to 0.81. Conclusions This EST collection offers a resource for studying functional genes, including

  1. Onto-CC: a web server for identifying Gene Ontology conceptual clusters

    PubMed Central

    Romero-Zaliz, R.; del Val, C.; Cobb, J. P.; Zwir, I.

    2008-01-01

    gene expression profiles resulting from the host response to injuries in the inflammatory problem. Onto-CC provides two versions: Ready2GO, a precalculated EMO-CC for several genomes and an Advanced Onto-CC for custom annotation files (http://gps-tools2.wustl.edu/onto-cc/index.html). PMID:18544607

  2. Identification and computational annotation of genes differentially expressed in pulp development of Cocos nucifera L. by suppression subtractive hybridization

    PubMed Central

    2014-01-01

    Background Coconut (Cocos nucifera L.) is one of the world’s most versatile, economically important tropical crops. Little is known about the physiological and molecular basis of coconut pulp (endosperm) development and only a few coconut genes and gene product sequences are available in public databases. This study identified genes that were differentially expressed during development of coconut pulp and functionally annotated these identified genes using bioinformatics analysis. Results Pulp from three different coconut developmental stages was collected. Four suppression subtractive hybridization (SSH) libraries were constructed (forward and reverse libraries A and B between stages 1 and 2, and C and D between stages 2 and 3), and identified sequences were computationally annotated using Blast2GO software. A total of 1272 clones were obtained for analysis from four SSH libraries with 63% showing similarity to known proteins. Pairwise comparing of stage-specific gene ontology ids from libraries B-D, A-C, B-C and A-D showed that 32 genes were continuously upregulated and seven downregulated; 28 were transiently upregulated and 23 downregulated. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that 1-acyl-sn-glycerol-3-phosphate acyltransferase (LPAAT), phospholipase D, acetyl-CoA carboxylase carboxyltransferase beta subunit, 3-hydroxyisobutyryl-CoA hydrolase-like and pyruvate dehydrogenase E1 β subunit were associated with fatty acid biosynthesis or metabolism. Triose phosphate isomerase, cellulose synthase and glucan 1,3-β-glucosidase were related to carbohydrate metabolism, and phosphoenolpyruvate carboxylase was related to both fatty acid and carbohydrate metabolism. Of 737 unigenes, 103 encoded enzymes were involved in fatty acid and carbohydrate biosynthesis and metabolism, and a number of transcription factors and other interesting genes with stage-specific expression were confirmed by real-time PCR, with validation of the SSH results as

  3. News and Announcements

    NASA Astrophysics Data System (ADS)

    1999-07-01

    New Source of Information from Advertisers The Journal has a new feature effective with the June 1999 issue. If you would like additional information about our advertisers or their products, the quickest and easiest way to get it is via JCE Online: go to http://jchemed.chem.wisc.edu click on Ad Index This will take you to the list of advertisers, each conveniently linked to their home page. When you do contact our advertisers, be sure to tell them that you saw their ad in the Journal of Chemical Education. This is important to them, and to us. JCE Software Receives Award The Journal recently received notice that JCE Software portion of JCE Online has been selected as a Links2Go Key Resource for the topic of chemistry software. According to Links2Go (www.links2go.com), JCE Software's home page is one of the top fifty most accessed online resources in the area of chemistry software (currently ranked 45). Thanks to all of you who have visited JCE Online and the JCE Software area to make this possible. If you haven't visited the site yet, you can go there directly (http://jchemed.chem.wisc.edu/JCESoft/index.html ) as well as via our JCE Online home page. You will be greeted with a short video of nitrogen triiodide exploding and be able to get a wealth of information about our latest releases, software, CD-ROMs/Video, student resources, materials for authors and software developers. You can see color graphics from our CD-ROMs, video, and software,... Actually, if you are familiar with our Catalog, this is much better. 1999 Welch Chemistry Prize Richard N. Zare, the Marguerite Blake Wilbur Professor of Natural Science at Stanford University, has been named the 1999 recipient of the Welch Award in Chemistry for his lifetime achievements in physical and analytical chemistry. Zare's interests focus on the development and application of lasers and other novel instruments to explore chemical frontiers, ranging from molecules to chemical processes, from the inside of cells to

  4. Experimental and modeling analyses for interactions between graphene oxide and quartz sand.

    PubMed

    Kang, Jin-Kyu; Park, Jeong-Ann; Yi, In-Geol; Kim, Song-Bae

    2017-03-21

    The aim of this study was to quantify the interactions between graphene oxide (GO) and quartz sand by conducting experimental and modeling analyses. The results show that both GO and quartz sand were negatively charged in the presence of 0-50 mM NaCl and 5 mM CaCl2 (GO = -43.10 to -17.60 mV, quartz sand = -40.97 to -8.44 mV). In the Derjaguin-Landau-Verwey-Overbeek (DLVO) energy profiles, the adhesion of GO to quartz sand becomes more favorable with increasing NaCl concentration from 0 to 10 mM because the interaction energy profile was compressed and the primary maximum energy barrier was lowered. At 50 mM NaCl and 5 mM CaCl2, the primary maximum energy barrier even disappeared, resulting in highly favorable conditions for GO retention to quartz sand. In the Maxwell model analysis, the probability of GO adhesion to quartz sand (αm) increased from 2.46 × 10(-4) to 9.98 × 10(-1) at ionic strengths of 0-10 mM NaCl. In the column experiments (column length = 10 cm, inner diameter = 2.5 cm, flow rate = 0.5 mL min(-1)), the mass removal (Mr) of GO in quartz sand increased from 5.4% to 97.8% as the NaCl concentration was increased from 0 to 50 mM, indicating that the mobility of GO was high in low ionic strength solutions and decreased with increasing ionic strength. The Mr value of GO at 5 mM CaCl2 was 100%, demonstrating that Ca(2+) had a much stronger effect than Na(+) on the mobility of GO. In addition, the mobility of GO was lower than that of chloride (Mr = 1.4%) but far higher than that of multi-walled carbon nanotubes (Mr = 87.0%) in deionized water. In aluminum oxide-coated sand, the Mr value of GO was 98.1% at 0 mM NaCl, revealing that the mobility of GO was reduced in the presence of metal oxides. The transport model analysis indicates that the value of the dimensionless attachment rate coefficient (Da) increased from 0.11 to 4.47 as the NaCl concentration was increased from 0 to 50 mM. In the colloid filtration model analysis, the

  5. A new approach to UNESCO-IOC Post-Tsunami Field Surveys

    NASA Astrophysics Data System (ADS)

    Kong, L. S.; Steffen, J.; Dominey-Howes, D.; Biukoto, L.; Titimaea, A.; Thaman, R.; Vaa, R.

    2009-12-01

    -sensitive and appropriate way and, (b) outputs achieved were relevant to both GoS and ITST scientists; (2) was interdisciplinary and multisectoral to capture a thorough understanding; and (3) used a ‘coupled human-environment systems framework’ to examine vulnerability and resilience before, during and after the tsunami. ITST succeeded because of (1) the scientists’ strong desire to share their knowledge; (2) GoS’s belief that science will improve disaster risk reduction practices; (3) immediate engagement of UN and regional organizations to provide an umbrella framework for working together; (4) local support to provide the ITST’s command center and; (5) dedicated Science Coordinators to manage the scientific planning, logistics, information sharing, and Report preparation. In 2010, UNESCO/IOC will revise its Post-Tsunami Field Survey Guide to document ITST-Samoa best practices and so provide guidance for future International Tsunami Survey Teams.

  6. Initiation of plate tectonics from post-magma ocean thermo-chemical convection

    NASA Astrophysics Data System (ADS)

    Foley, B. J.; Bercovici, D. A.

    2013-12-01

    We investigate the initiation of plate tectonics on Earth from scaling laws for plate tectonic style convection with grain-damage, and from numerical models of mantle convection immediately after magma ocean solidification. Using scaling laws for convection with grain-damage we constrain the likelihood of plate tectonics on the early Earth. Both mantle temperature and surface temperature play key roles in how plate speed and heat flow scale, and thus whether plate tectonics would be likely on the early Earth. Specifically either high mantle temperatures or high surface temperatures decrease plate speed because grain-growth (or healing) increases in lithospheric shear zones, causing viscosity to go up in these regions. When applied to the early Earth, we find that while higher mantle temperatures decrease plate speed, it is not enough to shut off plate tectonics; plate speed only decreases by a factor of 2 going from the present day to Hadean mantle temperatures. Surface temperature has a bigger influence as it more directly controls the temperature in lithospheric shear zones; at a Venusian surface temperature plate tectonics can be effectively shut off. Earth's surface temperature in the Hadean is unknown, however, given that Hadean zircons show evidence for liquid water, the surface temperature was lower than that of present day Venus. Even under hot greenhouse conditions plate speeds on the order of 1 cm/yr could exist in the Hadean. Therefore early Earth conditions were favorable for plate tectonics, even with a higher surface temperature, although Hadean plate tectonics would be sluggish (slower plate speed and thicker lithosphere) compared to the present day. We perform numerical convection experiments to constrain the timescales over which plate tectonics would initiate in the early Earth, starting from post-magma ocean conditions. Rapid solidification of the magma ocean leaves behind a solid mantle with a temperature profile following the solidus. There is