Science.gov

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. PMID:26991482

  2. Aspergillus flavus Blast2GO gene ontology database: elevated growth temperature alters amino acid metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The availability of a representative gene ontology (GO) database is a prerequisite for a successful functional genomics study. Using online Blast2GO resources we constructed a GO database of Aspergillus flavus. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mea...

  3. MoS2-GO nanocomposites synthesized via a hydrothermal hydrogel method for solar light photocatalytic degradation of methylene blue

    NASA Astrophysics Data System (ADS)

    Ding, Yong; Zhou, Yifeng; Nie, Wangyan; Chen, Pengpeng

    2015-12-01

    In this work, molybdenum disulfide-graphene oxide (MoS2-GO) composite hydrogel was prepared via a one-step hydrothermal method. The morphology and structure of the as-prepared hydrogels with different proportions of MoS2 and GO were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, electrochemical impedance spectra and UV-vis absorption spectroscopy. The photocatalytic performance of MoS2-GO nanocomposites was studied toward the degradation of methylene blue (MB). Results showed that the MoS2-GO nanocomposites exhibited improved photocatalytic activities in the degradation of MB with a maximum degradation rate of 99% under solar lights irradiation within 60 min. The synthesized MoS2-GO composite hydrogel possesses great potential toward the development of newly synthesizable catalysts in the field of organic degradation in water.

  4. Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis.

    PubMed

    Aparicio, G; Götz, S; Conesa, A; Segrelles, D; Blanquer, I; García, J M; Hernandez, V; Robles, M; Talon, M

    2006-01-01

    The vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    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.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

  7. 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.

  8. 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.

  9. 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 that fit…

  10. 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.

  11. Magnetic solid-phase extraction of protein with deep eutectic solvent immobilized magnetic graphene oxide nanoparticles.

    PubMed

    Xu, Kaijia; Wang, Yuzhi; Ding, Xueqin; Huang, Yanhua; Li, Na; Wen, Qian

    2016-01-01

    As a new type of green solvent, four kinds of choline chloride (ChCl)-based deep eutectic solvents (DESs) have been synthesized, and then a core-shell structure magnetic graphene oxide (Fe3O4-NH2@GO) nanoparticles have been prepared and coated with the ChCl-based DESs. Magnetic solid-phase extraction (MSPE) based Fe3O4-NH2@GO@DES was studied for the first time for the extraction of proteins. The characteristic results of vibrating sample magnetometer (VSM), X-ray diffraction (XRD), Fourier transform infrared spectrometry (FT-IR), thermal gravimetric analysis (TGA) and field emission scanning electron microscopy (FESEM) indicated the successful preparation of Fe3O4-NH2@GO@DES. The concentrations of proteins in studies were determined by a UV-vis spectrophotometer. The advantages of Fe3O4-NH2@GO@DES in protein extraction were compared with Fe3O4-NH2@GO and Fe3O4-NH2, and Fe3O4-NH2@GO@ChCl-glycerol was selected as the suitable extraction solvent. The influence factors of the extraction process such as the pH value, the temperature, the extraction time, the concentration of protein and the amount of Fe3O4-NH2@GO@ChCl-glycerol were evaluated. Desorption experimental result showed 98.73% of BSA could be eluted from the solid extractant with 0.1 mol/L Na2HPO4 solution contained 1 mol/L NaCl. Besides, the conformation of BSA was not changed during the elution by the investigation of circular dichromism (CD) spectra. Furthermore, the analysis of real sample demonstrated that the prepared magnetic nanoparticles did have extraction ability on proteins in bovine whole blood.

  12. Fabrication of silica-decorated graphene oxide nanohybrids and the properties of composite epoxy coatings research

    NASA Astrophysics Data System (ADS)

    Ma, Yu; Di, Haihui; Yu, Zongxue; Liang, Ling; Lv, Liang; Pan, Yang; Zhang, Yangyong; Yin, Di

    2016-01-01

    With the purpose of preparing anticorrosive coatings, solvent-based epoxy resins often serve as raw material. Unfortunately, plentiful micro-pores are fabricated via solvent evaporation in the resin' curing process, which is an intrinsic shortcoming and it is thus necessary to obstacle their micro-pore for enhancing antiseptic property. To reduce the intrinsic defect and increase the corrosion resistance of coating, we synthesize a series of SiO2-GO hybrids through anchoring silica (SiO2) on graphene oxide (GO) sheets with the help of 3-aminopropyltriethoxysilane and 3-glycidoxypropyltrimethoxysilane, and disperse the hybrids into epoxy resin at a low weight fraction of 2%. Furthermore, we investigate the appropriate preparation proportion of SiO2-GO hybrids (namely: SiO2-GO (1:5)). The electrochemical impedance spectroscopy (EIS) test and coatings' morphology monitoring in corrosion process reveal that the anticorrosive performance of epoxy coatings is significantly enhanced by incorporation of SiO2-GO (1:5) hybrids to epoxy compared with neat epoxy and other nanofillers including SiO2 or GO at the same contents. The superiority of the SiO2-GO (1:5) hybrids is related to their excellent dispersion in resin and sheet-like structure.

  13. 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…

  14. Molecular imprinting method for fabricating novel glucose sensor: polyvinyl acetate electrode reinforced by MnO2/CuO loaded on graphene oxide nanoparticles.

    PubMed

    Farid, Mohammad Masoudi; Goudini, Leila; Piri, Farideh; Zamani, Abbasali; Saadati, Fariba

    2016-03-01

    An enzyme free glucose sensor was prepared by a molecular imprinting method (MIP). The procedure was developed by in situ preparation of a new polyvinyl acetate (PVA) electrode reinforced by MnO2/CuO loaded on graphene oxide (GO) nanoparticles (PVA/MnO2@GO/CuO). The nanocomposite was modified in the presence of glucose and then imprinted. A carbone paste method with voltammetry was used in the fabrication of the sensor from prepared MIP nanocomposite. PVA/MnO2@GO/CuO electrode was characterized by X-ray diffraction, FT-IR spectroscopy and scanning electron microscopy. Electrocatalytic activity of the electrode toward glucose oxidation was then investigated by cyclic voltammetry in alkaline medium. The results show that the response of PVA/MnO2@GO/CuO MIP is much higher than PVA/MnO2@GO/CuO non-imprinted electrode toward glucose oxidation. The detection limit was 53μM, and the sensor responses are linear for concentrations from 0.5 to 4.4mM. Relative standard deviations for intra- and inter-day determination were less than 6.0%. The relative recoveries for different samples were 96%.

  15. 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) "Look at Other…

  16. 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…

  17. 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 Issues in…

  18. 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…

  19. Write Grants, Get Money.

    ERIC Educational Resources Information Center

    Anderson, Cynthia

    This book provides information to help school librarians get grant money for their schools. Chapter 1, "Identify the Need and Make a Plan," discusses preparation, library technology, other needs, and objectives. Chapter 2, "Go Where the Grants Are," covers organizing the research, searching for funding sources, and types of grants. Chapter 3,…

  20. 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 missions); (4) "International…

  1. Transition to Old Age (Transition to Retirement).

    ERIC Educational Resources Information Center

    Bergman, Simon

    Several conceptualizations and definitions of retirement have been proposed. One of them--the three-stage transition process--can be illustrated from studies in Israel: (1) leaving the old role; (2) going through the act of formal separation; and (3) adjusting to the new situation and role. Today's higher rate of survival into later years means…

  2. Molecular imprinting method for fabricating novel glucose sensor: polyvinyl acetate electrode reinforced by MnO2/CuO loaded on graphene oxide nanoparticles.

    PubMed

    Farid, Mohammad Masoudi; Goudini, Leila; Piri, Farideh; Zamani, Abbasali; Saadati, Fariba

    2016-03-01

    An enzyme free glucose sensor was prepared by a molecular imprinting method (MIP). The procedure was developed by in situ preparation of a new polyvinyl acetate (PVA) electrode reinforced by MnO2/CuO loaded on graphene oxide (GO) nanoparticles (PVA/MnO2@GO/CuO). The nanocomposite was modified in the presence of glucose and then imprinted. A carbone paste method with voltammetry was used in the fabrication of the sensor from prepared MIP nanocomposite. PVA/MnO2@GO/CuO electrode was characterized by X-ray diffraction, FT-IR spectroscopy and scanning electron microscopy. Electrocatalytic activity of the electrode toward glucose oxidation was then investigated by cyclic voltammetry in alkaline medium. The results show that the response of PVA/MnO2@GO/CuO MIP is much higher than PVA/MnO2@GO/CuO non-imprinted electrode toward glucose oxidation. The detection limit was 53μM, and the sensor responses are linear for concentrations from 0.5 to 4.4mM. Relative standard deviations for intra- and inter-day determination were less than 6.0%. The relative recoveries for different samples were 96%. PMID:26471527

  3. 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 Teach Technology…

  4. Removal of Congo Red by magnetic mesoporous titanium dioxide-graphene oxide core-shell microspheres for water purification.

    PubMed

    Li, Leilei; Li, Xiangjun; Duan, Huimin; Wang, Xiaojiao; Luo, Chuannan

    2014-06-14

    Magnetic mesoporous titanium dioxide-graphene oxide (Fe3O4@mTiO2@GO) with a large surface area and a good magnetic responsiveness was synthesized by immobilizing a mesoporous titanium dioxide (mTiO2) shell on the surface of magnetic Fe3O4 nanoparticles prior to binding with graphene oxide (GO). It showed a tunable pore structure and surface properties, and was mechanically strong. The characteristic results of a Fourier transform infrared spectrometer (FTIR), a scanning electron microscope (SEM), a vibrating sample magnetometer (VSM) and X-ray diffraction (XRD) indicated that Fe3O4@mTiO2@GO has been prepared. Fe3O4@mTiO2@GO was used as an adsorbent for the removal of Congo Red (CR) from simulated wastewater with a fast solid-liquid separation in the presence of an external magnetic field. Batch adsorption experiments were performed to evaluate the adsorption conditions and reusability. The results showed that the maximum adsorption capacity was 89.95 mg g(-1), which is much higher than the previously reported values of other absorbent materials. Moreover, the Fe3O4@mTiO2@GO could be repeatedly used via simple treatment without any obvious structure and performance degradation. The adsorption kinetic data were best described by a pseudo-second-order model and the equilibrium adsorptions were well-described by the Freundlich isotherm model. The Fe3O4@mTiO2@GO may be suitable materials for use in CR pollution cleanup if synthesized on a large scale and at a low price in the near future. PMID:24741674

  5. Synthesis of double-clickable functionalised graphene oxide for biological applications.

    PubMed

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

    2015-10-18

    Azide- and alkyne-double functionalised graphene oxide (Click(2) 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 (MW = 3500), to the Click(2) GO. The final conjugate was characterised with ATR-FTIR and TGA. PMID:26295072

  6. 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

  7. Density functional theory study of interactions between glycine and TiO2/graphene nanocomposites

    NASA Astrophysics Data System (ADS)

    Wang, Meng-hao; Guo, Ya-nan; Wang, Qun; Zhang, Xia-shi-yao; Huang, Jing-jing; Lu, Xiong; Wang, Ke-feng; Zhang, Hong-ping; Leng, Yang

    2014-04-01

    The interactions of glycine (Gly) with TiO2, graphene (G), graphene oxide (GO), TiO2/G and TiO2/GO nanocomposites were investigated by density functional theory (DFT). The results indicate that the interactions between Gly and TiO2 in TiO2/G nanocomposites are stronger than that between Gly and bare TiO2 surfaces, which suggests G helps to strengthen the interaction of amino acids with TiO2 surfaces. In TiO2/GO nanocomposites, the interactions of Gly and TiO2 are slightly weaker than that between Gly and bare TiO2 surfaces, which reveals that GO is not conducive to the interaction of amino acids with TiO2 surfaces.

  8. Complete genome sequence of a giant Vibrio phage ValKK3 infecting Vibrio alginolyticus.

    PubMed

    Lal, Tamrin M; Sano, Motohiko; Hatai, Kishio; Ransangan, Julian

    2016-06-01

    This paper describes the complete sequence of a giant lytic marine myophage, Vibrio phage ValKK3 that is specific to Vibrio alginolyticus ATCC(®) 17749™. Vibrio phage ValKK3 was subjected to whole genome sequencing on MiSeq sequencing platform and annotated using Blast2Go. The complete sequence of ValKK3 genome was deposited in DBBJ/EMBL/GenBank under accession number KP671755. PMID:27114905

  9. 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.

  10. 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.

  11. Lipoxygenase-modified Ru-bpy/graphene oxide: Electrochemical biosensor for on-farm monitoring of non-esterified fatty acid.

    PubMed

    Veerapandian, Murugan; Hunter, Robert; Neethirajan, Suresh

    2016-04-15

    Elevated concentrations of non-esterified fatty acids (NEFA) in biological fluids are recognized as critical biomarkers for early diagnosis of dairy cow metabolic diseases. Herein, a cost-effective, electrochemically active, and bio-friendly sensor element based on ruthenium bipyridyl complex-modified graphene oxide nanosheets ([Ru(bpy)3](2+)-GO) is proposed as a biosensor platform for NEFA detection. Electrochemical analysis demonstrates that the [Ru(bpy)3](2+)-GO electrodes exhibit superior and durable redox properties compared to the pristine carbon and GO electrodes. Target specificity is accomplished through immobilization of the enzyme, lipoxygenase, which catalyzes the production of redox active species from NEFA. Lipoxygenases retain their catalytic ability upon immobilization and exhibit changes to amperometric signals upon interaction with various concentrations of standard NEFA and serum samples. Our study demonstrates that the [Ru(bpy)3](2+)-GO electrode has the potential to serve as a biosensor platform for developing a field deployable, rapid, and user-friendly detection tool for on-farm monitoring of dairy cow metabolic diseases.

  12. 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

  13. Comparison of electrorheological performance between urea-coated and graphene oxide-wrapped core-shell structured amorphous TiO2 nanoparticles

    NASA Astrophysics Data System (ADS)

    Dong, Xufeng; Huo, Shuang; Qi, Min

    2016-01-01

    Polar molecules and graphene oxide (GO) have been used as the shell materials to prepare core-shell structured particles with enhanced electrorheological (ER) properties. Nevertheless, few studies compared the ER performance and stability of the suspensions with the two kinds of shell. In this study, urea and GO are used as the shell materials to prepare TiO2/urea and TiO2/GO core-shell particles-based ER fluids, respectively. Particle characterization results indicate the two kinds of core-shell structured particles present little change in size, morphology and crystal structure compared with the bare amorphous TiO2. Some polar groups are distributed on the surface of the two kinds of core-shell structured particles, which is responsible for their improved ER performance with respect to the bare TiO2 particles. The TiO2/GO particles-based ER fluid presents higher yield stress, lower leakage current density, better sedimentation stability but lower ER efficiency than the TiO2/urea particles-based sample. The larger surface area, stronger connection with the bare TiO2 particles, and larger number of polar groups of the GO-coating is the possible reason for the different properties of TiO2/GO particles-based ER fluid compared with the TiO2/urea particles-based sample.

  14. Graphene oxide-immobilized NH₂-terminated silicon nanoparticles by cross-linked interactions for highly stable silicon negative electrodes.

    PubMed

    Sun, Cheng; Deng, Yuanfu; Wan, Lina; Qin, Xusong; Chen, Guohua

    2014-07-23

    There is a great interest in the utilization of silicon-based anodes for lithium-ion batteries. However, its poor cycling stability, which is caused by a dramatic volume change during lithium-ion intercalation, and intrinsic low electric conductivity hamper its industrial applications. A facile strategy is reported here to fabricate graphene oxide-immobilized NH2-terminated silicon nanoparticles (NPs) negative electrode (Si@NH2/GO) directed by hydrogen bonding and cross-linked interactions to enhance the capacity retention of the anode. The NH2-modified Si NPs first form strong hydrogen bonds and covalent bonds with GO. The Si@NH2/GO composite further forms hydrogen bonds and covalent bonds with sodium alginate, which acts as a binder, to yield a stable composite negative electrode. These two chemical cross-linked/hydrogen bonding interactions-one between NH2-modified Si NPs and GO, and another between the GO and sodium alginate-along with highly mechanically flexible graphene oxide, produced a robust network in the negative electrode system to stabilize the electrode during discharge and charge cycles. The as-prepared Si@NH2/GO electrode exhibits an outstanding capacity retention capability and good rate performance, delivering a reversible capacity of 1000 mAh g(-1) after 400 cycles at a current of 420 mA g(-1) with almost 100% capacity retention. The results indicated the importance of system-level strategy for fabricating stable electrodes with improved electrochemical performance.

  15. 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.

  16. Systematic analysis of palladium-graphene nanocomposites and their catalytic applications in Sonogashira reaction.

    PubMed

    Lee, Kyoung Hoon; Han, Sang-Wook; Kwon, Ki-Young; Park, Joon B

    2013-08-01

    Graphene has been modified with palladium nanoparticles (Pd NPs) to develop high performance catalysts for the Sonogashira cross coupling reaction. In this research, graphite oxide (GO) sheets exfoliated from graphite were impregnated with Pd(OAc)2 to prepare Pd(2+)/GO. Thermal treatments of the Pd(2+)/GO in H2 flow at 100°C produced Pd/graphene (Pd/G) nanocomposites. TEM images show that Pd NPs were distributed quite uniformly on the graphene sheet without obvious aggregation, and the mean size of Pd NPs was determined to be less than 2 nm in diameter. Morphological and chemical structures of the GO, Pd(2+)/GO, and Pd/G were investigated using FT-IR, XRD, XPS, and XAFS. The resulting Pd/G showed excellent catalytic efficiency in the Sonogashira reaction and offers significant advantages over inorganic supported catalysts such as simple recovery and recycling. Finally, deactivation process of the Pd/G in recycling was investigated. We believe that the remarkable reactivity of the Pd/G catalyst toward the Sonogashira reaction is attributed to the high degree of the Pd NP dispersion and thus the increased low coordination numbers of smaller Pd NPs. PMID:23673006

  17. 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.

  18. Functional prediction of hypothetical proteins in human adenoviruses.

    PubMed

    Dorden, Shane; Mahadevan, Padmanabhan

    2015-01-01

    Assigning functional information to hypothetical proteins in virus genomes is crucial for gaining insight into their proteomes. Human adenoviruses are medium sized viruses that cause a range of diseases. Their genomes possess proteins with uncharacterized function known as hypothetical proteins. Using a wide range of protein function prediction servers, functional information was obtained about these hypothetical proteins. A comparison of functional information obtained from these servers revealed that some of them produced functional information, while others provided little functional information about these human adenovirus hypothetical proteins. The PFP, ESG, PSIPRED, 3d2GO, and ProtFun servers produced the most functional information regarding these hypothetical proteins. PMID:26664031

  19. Semantic search among heterogeneous biological databases based on gene ontology.

    PubMed

    Cao, Shun-Liang; Qin, Lei; He, Wei-Zhong; Zhong, Yang; Zhu, Yang-Yong; Li, Yi-Xue

    2004-05-01

    Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

  20. 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

  1. 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.

  2. Ultrafine MnO2 nanoparticles decorated on graphene oxide as a highly efficient and recyclable catalyst for aerobic oxidation of benzyl alcohol.

    PubMed

    Hu, Zonggao; Zhao, Yafei; Liu, Jindun; Wang, Jingtao; Zhang, Bing; Xiang, Xu

    2016-12-01

    The highly active and selective aerobic oxidation of aromatic alcohols over earth-abundant, inexpensive and recyclable catalysts is highly desirable. We fabricated herein MnO2/graphene oxide (GO) composites by a facile in-situ growth approach at room temperature and used them in selective aerobic oxidation of benzyl alcohol to benzaldehyde. TEM, XRD, FTIR, XPS and N2 adsorption/desorption analysis were employed to systematically investigate the morphology, particle size, structure and surface properties of the catalysts. The 96.8% benzyl alcohol conversion and 100% benzaldehyde selectivity over the MnO2/GO (10/100) catalyst with well dispersive ultrafine MnO2 nanoparticles (ca. 3nm) can be obtained within 3h under 383K. Simultaneously, no appreciable loss of activity and selectivity occurred after recycling use up to six times. Due to their significant low cost, excellent catalytic performance, the MnO2/GO composites have huge application prospect in organic synthesis. PMID:27544446

  3. 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).

  4. 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.

  5. Electron Hopping Through Single-to-Few-Layer Graphene Oxide Films. Side-Selective Photocatalytic Deposition of Metal Nanoparticles.

    PubMed

    Lightcap, Ian V; Murphy, Sean; Schumer, Timothy; Kamat, Prashant V

    2012-06-01

    Single- to few-layer graphene oxide (GO) sheets have been successfully anchored onto TiO2 films using electrophoretic deposition. Upon UV illumination of TiO2-GO films, photogenerated electrons from TiO2 are captured by GO. These electrons are initially used in GO's reduction, while additional electron transfer results in storage across its sp(2) network. In the presence of silver ions, deposition of silver nanoparticles (NPs) is accomplished on the GO surface opposite the TiO2, thus confirming the ability of GO to transport electrons through its plane. Illumination-controlled reduction of silver ions allows for simple selection of particle size and loading, making these semiconductor-graphene-metal (SGM) films ideal for custom catalysis and sensor applications. Initial testing of SGM films as surface-enhanced resonance Raman (SERRS) sensors produced significant target molecule signal enhancements, enabling detection of nanomolar concentrations. PMID:26285621

  6. Origin of hole and electron traps in graphene oxide

    NASA Astrophysics Data System (ADS)

    Kotin, I. A.; Antonova, I. V.; Orlov, O. M.; Smagulova, S. A.

    2016-06-01

    Charge-carrier capture/emission processes proceeding with the participation of localized states in graphene oxide (GO) in test structures of Au/SiO2/GO/SiO2/Si were examined by charge deep-level transient spectroscopy (Q-DLTS). Two groups of traps capable of capturing both electrons and holes in GO were detected. The energy levels of these groups with reference to the electronic band structure of Si were found to be at EV + 0.75 eV (EC ‑ 0.37 eV) and EV + 0.55 eV (EC ‑ 0.55 eV). Such levels are proposed to be inherent to graphene islands in which charge carriers are emitted from energy levels in the vicinity of the Dirac point. Two groups of levels are suggested to be attributed to graphene islands, with and without p-doping with oxygen.

  7. Older women's experiences of living alone after heart surgery.

    PubMed

    Robinson, Anne White

    2002-08-01

    An increasing number of women who have coronary artery disease have undergone heart surgery and are living alone. This qualitative descriptive study identified four primary themes that constituted essential structures of the post-recovery experience for 12 older women living alone after coronary artery bypass surgery. Themes included (1) survival relief, experienced as awe and gratitude; (2) going on, described as an obligation; (3) living within a contracted world, structured by a sense of vulnerability; and (4) regained independence, characterized by affirmation of self-worth and personal freedom. Post-recovery meant restoring the identity the women had known before surgery together with actualizing the value of self-reliance. PMID:12173163

  8. Exosomes mediated pentose phosphate pathway in ovarian cancer metastasis: a proteomics analysis

    PubMed Central

    Yi, Huan; Zheng, Xiangqin; Song, Jianrong; Shen, Rongkai; Su, Yanzhao; Lin, Danmei

    2015-01-01

    Epithelial ovarian cancer is the most lethal gynecological malignancies for readily metastasis. Exosomes have played an influential role in carcinogenicity and cancer progression. Our aim is to discover exosome-related mechanisms in ovarian cancer progress and explore potential diagnostic biomarkers and therapeutic targets of ovarian cancer. We initially presented the proteomic profiles of exosomes derived from two late-stage ovarian cell lines, OVCA429 and HO8910PM. A total of 2940 exosomal proteins were recorded by MS. FunRich appropriately processed these exosomal proteins, manifesting some superiority in contrast to Blast2go. Moreover, we demonstrated the pentose phosphate pathway was a dominant mechanism in exosome mediated intracellular communication. Glucose-6-phosphate dehydrogenase, transketolase and transaldolase 1, three key enzymes regulated pentose phosphate pathway, were all marked in the same exosomal parts of proteins between two ovarian cell lines. Moreover, these key proteins might become diagnostic, prognostic biomarkers and therapeutic targets of ovarian cancer. PMID:26884841

  9. 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

  10. Amorphous carbon nanotube/MnO2/graphene oxide ternary composite electrodes for electrochemical capacitors.

    PubMed

    Im, Changbin; Yun, Young Soo; Kim, Bona; Park, Hyun Ho; Jin, Hyoung-Joon

    2013-03-01

    Ternary composites of amorphous carbon nanotube/MnO2/graphene oxide (a-CNT/MnO2/GO) were synthesized by a facile direct redox reaction between potassium permanganate and a-CNT, which was prepared by anodic aluminum oxide template method following co-filtration with GO. Needle-like, 100-nm-thick, MnO2 crystals were homogeneously coated on the a-CNT surface, which was then covered with GO. The electrochemical performance of the resulting MnO2-coated a-CNTs exhibited a specific capacitance of 473 F/g at a scan rate of 5 mV/s, and excellent charge/discharge stability after 500 cycles.

  11. 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. PMID:27130133

  12. 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

  13. 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.

  14. 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. PMID:23110046

  15. Two-step approach of fabrication of three-dimensional MnO2-graphene-carbon nanotube hybrid as a binder-free supercapacitor electrode

    NASA Astrophysics Data System (ADS)

    Xiong, Chuanyin; Li, Tiehu; Dang, Alei; Zhao, Tingkai; Li, Hao; Lv, Huiqin

    2016-02-01

    This paper describes the fabrication and characterization of a three-dimensional (3D) MnO2-graphene (GR)-CNT hybrid obtained by combining electrochemical deposition (ELD)-electrophoretic deposition (EPD) and chemical vapor deposition (CVD). Firstly, 3D MnO2-graphene oxide (GO) is fabricated via ELD-EPD. Secondly, the catalyst and xylene are mixed with solution of certain concentration. Thirdly, catalyst is loaded on the surface of MnO2-GO when the solution is sprayed into the furnace. Forth, MnO2-GO is restored to MnO2-GR at high temperature, meanwhile, MnO2-GR is served as a substrate to grow CNT, which is beneficial to provide high speed channel for carrier and obtain pseudocapacitance of MnO2. The as-prepared hybrid is characterized by scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray Diffraction (XRD) and Raman spectroscopy (Raman), and their supercapacitor properties are also investigated. The results show that a high specific capacitance of 330.75 F g-1 and high energy density of 36.68 Wh kg-1 while maintaining high power density of 8000 W kg-1 at a scan rate of 200 mV s-1. Furthermore, the hybrid displays a high specific capacitance of 187.53 F g-1 at ultrahigh scan rate of 400 mV s-1. These attractive results demonstrate that the hybrid is a promising electrode material for high performance supercapacitors.

  16. 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.

  17. Carbon dioxide within Venus and the earth

    NASA Technical Reports Server (NTRS)

    Ahrens, T. J.

    1981-01-01

    The maximum inventories of CO2 and H2O in the terrestrial and Venus mantles are calculated on the basis of shock wave data for magnesite and dunite to be approximately 1,000 times the observed atmospheric inventories. The CO2 fugacity determined for the buffered reaction MgCO3 plus SiO2 going to MgSiO3 plus CO2 yields values which increase from 0.0001 to 1.0 times the lithostatic pressure, going from 35 to 800 km depths in the earth. The major uncertainties in the fugacity calculations arise from lack of knowledge of effective activities. The calculated fugacity of CO2 and water brought to the surface from hypothetical mantle reservoirs on earth and Venus indicate that, in the case of the earth, the cool and dry atmosphere is strongly depleted in both CO2 and H2O compared to the low velocity zone. In contrast to the earth, on Venus, the 750 K surface temperature and 90 bar CO2 surface pressure are in equilibrium and probably in communication with an assumed upper mantle CO2 reservoir.

  18. 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

  19. 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

  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. PMID:26684618

  1. Contribution of Transcranial Direct Current Stimulation on Inhibitory Control to Assess the Neurobiological Aspects of Attention Deficit Hyperactivity Disorder: Randomized Controlled Trial

    PubMed Central

    Baptista, Abrahão Fontes; de Sena, Eduardo Pondé

    2015-01-01

    Background The applicability of transcranial direct current stimulation (tDCS) in individuals with attention deficit hyperactivity disorder (ADHD) has not yet been investigated. This low-cost, non-invasive, and safe technique optimized to modulate the inhibitory response might be a useful treatment option for those affected by this condition. Objective The aim of this single center, parallel, randomized, double-blinded, sham-controlled trial is to investigate the efficacy of transcranial direct current stimulation over the prefrontal cortex on the modulation of inhibitory control in adults with attention deficit hyperactivity disorder. Methods A total of 60 individuals will be divided into 2 groups by block randomization to receive active or sham stimulation. Anodal stimulation over the left dorsolateral prefrontal cortex will be applied at 1 mA during a single 20-minute session. Before and after interventions, subjects will perform 2 go/no go tasks and the brain electrical activity will be recorded by electroencephalogram (EEG) with 32 channels, according to the 10-20 international EEG system. Results The trial began in May 2013 and we are currently performing the statistical analysis for the secondary outcomes. Conclusions The findings from this study will provide preliminary results about the role of prefrontal cortex activation through tDCS on ADHD patients. Trial Registration Clinicaltrials.gov NCT01968512; http://clinicaltrials.gov/ct2/show/NCT01968512 (Archived by WebCite at www.webcitation.org/6YMSW2tkD). PMID:25986784

  2. Melatonin regulates proteomic changes during leaf senescence in Malus hupehensis.

    PubMed

    Wang, Ping; Sun, Xun; Xie, Yinpeng; Li, Mingjun; Chen, Wei; Zhang, Sheng; Liang, Dong; Ma, Fengwang

    2014-10-01

    Despite the relationship between melatonin and aging, the overall changes and regulation of proteome profiling by long-term melatonin exposure during leaf senescence is not well understood. In this study, leaf senescence in Malus hupehensis plants was delayed when exogenous melatonin was regularly applied to the roots for 2 months compared with natural leaf senescence. Proteins of samples 0 and 50 day for both treatments were extracted and labeled with TMT regents before being examined via NanoLC-MS/MS. The proteomics data showed that 622 and 309 proteins were altered by senescence and melatonin, respectively. Our GO analysis by Blast2GO revealed that most of the altered proteins that are involved in major metabolic processes exhibited hydrolase activity and were mainly located in the plastids. These proteins were classified into several senescence-related functional categories, including degradation of macromolecules, redox and stress responses, transport, photosynthesis, development, and other regulatory proteins. We found that melatonin treatment led to the downregulation of proteins that are normally upregulated during senescence. The melatonin-related delay in senescence might have occurred due to the altering of proteins involved in processes associated with senescence. And as well, there are many unknown regulatory proteins possibly being involved in the melatonin's function. This study is the first to demonstrate changes at the proteome level in response to exogenous melatonin in plants. Our findings provide a set of informative and fundamental data about the role of melatonin in apple leaf senescence.

  3. High-throughput sequencing of black pepper root transcriptome

    PubMed Central

    2012-01-01

    Background Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms. PMID:22984782

  4. 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.

  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. 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

  7. Generation and Analysis of Expressed Sequence Tags from Olea europaea L.

    PubMed Central

    Ozdemir Ozgenturk, Nehir; Oruç, Fatma; Sezerman, Ugur; Kuçukural, Alper; Vural Korkut, Senay; Toksoz, Feriha; Un, Cemal

    2010-01-01

    Olive (Olea europaea L.) is an important source of edible oil which was originated in Near-East region. In this study, two cDNA libraries were constructed from young olive leaves and immature olive fruits for generation of ESTs to discover the novel genes and search the function of unknown genes of olive. The randomly selected 3840 colonies were sequenced for EST collection from both libraries. Readable 2228 sequences for olive leaf and 1506 sequences for olive fruit were assembled into 205 and 69 contigs, respectively, whereas 2478 were singletons. Putative functions of all 2752 differentially expressed unique sequences were designated by gene homology based on BLAST and annotated using BLAST2GO. While 1339 ESTs show no homology to the database, 2024 ESTs have homology (under 80%) with hypothetical proteins, putative proteins, expressed proteins, and unknown proteins in NCBI-GenBank. 635 EST's unique genes sequence have been identified by over 80% homology to known function in other species which were not previously described in Olea family. Only 3.1% of total EST's was shown similarity with olive database existing in NCBI. This generated EST's data and consensus sequences were submitted to NCBI as valuable source for functional genome studies of olive. PMID:21197085

  8. Quantitative assessment of protein function prediction programs.

    PubMed

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-12-21

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate.

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

    PubMed

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

    2015-07-01

    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

  10. Gene expression analysis of volatile-rich male flowers of dioecious Pandanus fascicularis using expressed sequence tags.

    PubMed

    Vinod, M S; Sankararamasubramanian, H M; Priyanka, R; Ganesan, G; Parida, Ajay

    2010-07-15

    Pandanus fascicularis is dioecious with the female plant producing a non-scented fruit while the male produces a flower rich in volatiles. The essential oil extracted from the flowers is economically exploited as a natural flavouring agent as well as for its therapeutic properties. Molecular dissection of this distinct flower for identifying the genes responsible for its aroma by way of expressed sequence tags (ESTs) has not been initiated in spite of its economic viability. A male flower-specific cDNA library was constructed and 977 ESTs were generated. CAP3 analysis performed on the dataset revealed 83 contigs (549 ESTs) and 428 singlets, thereby yielding a total of 511 unigenes. Functional annotation using the BLAST2GO software resulted in 1952 Gene ontology (GO) functional classification terms for 621 sequences. Unknown proteins were further analysed with InterProScan to determine their functional motifs. RNA gel blot analysis of 26 functionally distinct transcripts potentially involved in flowering and volatile generation, using vegetative and reproductive tissues of both the sexes, revealed differential expression profiles. In addition to an overview of genes expressed, candidate genes with expression that are modulated predominantly in the male inflorescence were also identified. This is the first report on generation of ESTs to determine the subset of genes that can be used as potential candidates for future attempts aimed towards its genetic and genome analysis including metabolic engineering of floral volatiles in this economically important plant.

  11. 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.

  12. 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.

  13. 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

    2015-01-01

    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.

  14. The Transcriptome Sequence of Dientamoeba fragilis Offers New Biological Insights on its Metabolism, Kinome, Degradome and Potential Mechanisms of Pathogenicity.

    PubMed

    Barratt, Joel L N; Cao, Maisie; Stark, Damien J; Ellis, John T

    2015-09-01

    Dientamoeba fragilis is a human bowel parasite with a worldwide distribution. Dientamoeba was once described as a rare and harmless commensal though recent reports suggest it is common and potentially pathogenic. Molecular data on Dientamoeba is scarce which limits our understanding of this parasite. To address this, sequencing of the Dientamoeba transcriptome was performed. Messenger RNA was extracted from cultured Dientamoeba trophozoites originating from clinical stool specimens, and sequenced using Roche GS FLX and Illumina HiSeq technologies. In total 6,595 Dientamoeba transcripts were identified. These sequences were analysed using the BLAST2GO software suite and via BLAST comparisons to sequences available from TrichDB, GenBank, MEROPS and kinase.com. Several novel KEGG pathway maps were generated and gene ontology analysis was also performed. These results are thoroughly discussed guided by knowledge available for other related protozoa. Attention is paid to the novel biological insights afforded by this data including peptidases and kinases of Dientamoeba, as well as its metabolism, novel chemotherapeutics and possible mechanisms of pathogenicity. Currently, this work represents the largest contribution to our understanding of Dientamoeba molecular biology and also represents a major contribution to our understanding of the trichomonads generally, many of which are important pathogens of humans and animals.

  15. MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

    PubMed Central

    Huson, Daniel H.; Beier, Sina; Flade, Isabell; Ruscheweyh, Hans-Joachim; Tappu, Rewati

    2016-01-01

    There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce PMID:27327495

  16. 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 Central

    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. PMID:26684618

  17. MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

    PubMed

    Huson, Daniel H; Beier, Sina; Flade, Isabell; Górska, Anna; El-Hadidi, Mohamed; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Tappu, Rewati

    2016-06-01

    There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce. PMID:27327495

  18. Graphene oxide as a promising hole injection layer for MoS₂-based electronic devices.

    PubMed

    Musso, Tiziana; Kumar, Priyank V; Foster, Adam S; Grossman, Jeffrey C

    2014-11-25

    The excellent physical and semiconducting properties of transition metal dichalcogenide (TMDC) monolayers make them promising materials for many applications. The TMDC monolayer MoS2 has gained significant attention as a channel material for next-generation transistors. However, while n-type single-layer MoS2 devices can be made with relative ease, fabrication of p-type transistors remains a challenge as the Fermi-level of elemental metals used as contacts are pinned close to the conduction band leading to large p-type Schottky barrier heights (SBH). Here, we propose the utilization of graphene oxide (GO) as an efficient hole injection layer for single-layer MoS2-based electronic and optoelectronic devices. Using first-principles computations, we demonstrate that GO forms a p-type contact with monolayer MoS2, and that the p-type SBH can be made smaller by increasing the oxygen concentration and the fraction of epoxy functional groups in GO. Our analysis shows that this is possible due to the high work function of GO and the relatively weak Fermi-level pinning at the MoS2/GO interfaces compared to traditional MoS2/metal systems (common metals are Ag, Al, Au, Ir, Pd, Pt). The combination of easy-to-fabricate and inexpensive GO with MoS2 could be promising for the development of hybrid all-2D p-type electronic and optoelectronic devices on flexible substrates.

  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. Fabrication of Fe3O4@SiO2@TiO2 nanoparticles supported by graphene oxide sheets for the repeated adsorption and photocatalytic degradation of rhodamine B under UV irradiation.

    PubMed

    Chen, Fenghua; Yan, Fufeng; Chen, Qingtao; Wang, Yongwei; Han, Lifeng; Chen, Zhijun; Fang, Shaoming

    2014-09-28

    A quaternary nanocomposite Fe3O4@SiO2@TiO2/graphene oxide (GO) was for the first time successfully synthesized in this work for the repeated use in simultaneous adsorption and photocatalytic degradation of aromatically structured chemical pollutants. The resulting sample was characterized by TEM, XRD, FTIR, TG-DTG, XPS, PL, and VSM. Its photocatalytic activity was evaluated in the photocatalytic degradation of rhodamine B (RhB) under high-pressure mercury lamp irradiation. The results showed that about 63% of RhB was absorbed onto the prepared Fe3O4@SiO2@TiO2/GO nanocomposites by just 30 minute mixing, and after 120 min high-pressure mercury lamp irradiation, about 92.03% of RhB was converted. The photocatalytic degradation followed pseudo first-order reaction with an apparent rate constant of 0.0136 min(-1). Compared with the Fe3O4@SiO2@TiO2 nanoparticles, it exhibits an excellent ability to adsorb aromatic compounds via π-π stacking and a higher photocatalytic activity due to the presence of GO. In addition, the synthesized nanomaterial exhibited good magnetic response and the reusability study suggested that the prepared nanocomposites were stable enough and maintained high degradation rate and catalyst recovery even after five cycles, verifying their potential application in water purification.

  1. 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.

  2. 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

  3. 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

  4. Quantitative assessment of protein function prediction programs.

    PubMed

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-01-01

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate. PMID:26782400

  5. Effect of periodontal treatment on gingival overgrowth among cyclosporine A-treated renal transplant recipients.

    PubMed

    Pernu, H E; Pernu, L M; Knuuttila, M L

    1993-11-01

    No data exist on any association between combined cyclosporine A (Cy A) and dihydropyridine (DHP) medication and the effect of periodontal treatment on the occurrence of gingival overgrowth (GO) among renal transplant recipients. Clinical data on 27 renal transplant recipients treated with Cy A are presented here, including determinations of serum creatinine, whole blood Cy A concentration, existence of DHP treatment, and periodontal status. GO was classified into four categories according to the clinical changes: score 0 = no GO; score 1 = mild GO; score 2 = moderate GO; and score 3 = severe GO. All participants received hygiene phase periodontal treatment and gingivectomies were performed on 10 who originally had score 2 or 3 GO and pocketing. Fourteen (14) of the recipients had no overgrown gingiva or less than at the initial examination, and none of them had GO score 2 or 3 at the time of re-examination (group A). Thirteen (13) participants had more overgrown gingiva than initially or developed score 2 GO after gingivectomies (group B). Group B included significantly more DHP-medicated recipients than group A (6/13 and 1/14 respectively; P < 0.03). The concomitant administration of Cy A and DHP resulted in a significantly increased percentage of score 2 overgrown gingival units as compared with Cy A alone (P < 0.03). It is concluded that combined treatment with Cy A and DHP is a significant risk factor for progression or recurrence of GO after periodontal treatment among susceptible patients.

  6. Preparation of sulfonic-functionalized graphene oxide as ion-exchange material and its application into electrochemiluminescence analysis.

    PubMed

    Chen, Guifen; Zhai, Shengyong; Zhai, Yanling; Zhang, Ke; Yue, Qiaoli; Wang, Lei; Zhao, Jinsheng; Wang, Huaisheng; Liu, Jifeng; Jia, Jianbo

    2011-03-15

    Graphene oxide (GO) obtained from chemical oxidation of flake graphite was derivatized with sulfonic groups to form sulfonic-functionalized GO (GO-SO(3)(-)) through four sulfonation routes: through amide formation between the carboxylic group of GO and amine of sulfanilic acid (AA-GO-SO(3)(-)), aryl diazonium reaction of sulfanilic acid (AD-GO-SO(3)(-)), amide formation between the carboxylic group of GO and amine of cysteamine and oxidation by H(2)O(2) (CA-GO-SO(3)(-)), and alkyl diazonium reaction of cysteamine and oxidation by H(2)O(2) (CD-GO-SO(3)(-)). Results of Fourier transform infrared spectroscopy and X-ray photoelectrospectrocopy showed that -SO(3)(-) groups were attached onto GO. Thermo gravimetric analysis showed that derivatization with sulfonic groups improved thermo stability of GO. X-ray diffraction results indicated that GO-SO(3)(-) had more ordered π-π stacking structure than the original GO. GO-SO(3)(-) and cationic polyelectrote, poly (diallyldimethylammoniumchloride) (PDDA) were adsorbed at indium tin oxide (ITO) glass surface through layer-by-layer assembling to form (GO-SO(3)(-)/PDDA)(n)/ITO multilayers. After tris-(2,2'-bipyridyl) ruthenium (II) dichloride (Ru(bpy)(3)(2+)) was incorporated into the multilayers, the obtained Ru(bpy)(3)(2+)/(GO-SO(3)(-)/PDDA)(n)/ITO electrodes can be used as electrochemiluminescence sensors for detection of organic amine with high sensitivity (limit of detection of 1 nM) and stability.

  7. 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.

  8. 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. PMID:26971316

  9. 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. PMID:24055647

  10. 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.

  11. 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.

  12. Transit, Secondary Eclipse, and Phase Curve Modeling to Characterize Kepler Exoplanet Candidates

    NASA Astrophysics Data System (ADS)

    Tarnas, Jesse; Redfield, Seth

    2016-01-01

    The high sensitivity and continuous coverage of Kepler allows for analysis of optical phase curves, which provide detailed exoplanet characterization by fitting photometric features caused by thermal emission, reflected light, Doppler boosting, and ellipsoidal variations. Combined with transit and secondary eclipse analysis to reduce model degeneracy, phase curves can resolve atmospheric characteristics, dayside-nightside temperatures, and even mass using single-band photometry. We will present an integrated phase curve, transit, and secondary eclipse analysis of Kepler exoplanet candidates, building on the phase curve model constructed by Serindag & Redfield (2015). Phase curves can also be present in non-transiting systems. We will explore the feasibility of detecting and characterizing these non-transiting exoplanets. We will also investigate the possibility of analyzing exoplanet phase curves in K2 data. We gratefully acknowledge support through a grant (14-K2GO1_2-0071) associated with the K2 Guest Observer — Cycle 1 program of Research Opportunities in Space and Earth Sciences (ROSES-2014; NNH14ZDA001N).

  13. Spirit body healing--a hermeneutic, phenomenological study examining the lived experience of art and healing.

    PubMed

    Lane, Mary Rockwood

    2005-01-01

    Spirit-Body Healing was a hermeneutic, phenomenological research study that examined the lived experience of art and healing (using Max Van Manen's method of researching the lived experience) of 63 participants over a 4-year period. Data included taped interviews with artists and hospitalized cancer patients who could articulate their lived experience of art and healing, observations of artists at work, journal writings, and material from the Arts In Medicine program at Shands Hospital, University of Florida. The researcher interpreted data through Van Manen's method of writing as inquiry to elucidate the themes of the participants' experiences. The themes that emerged were (1) going into the darkness, (2) going elsewhere, (3) making art as a turning point, (4) slipping through the veil, (5) feeling the healing energy of love and compassion, (6) surrendering to the process, (7) knowing the truth, and (8) experiencing transcendence. Understanding the power of art to heal mind, body, and spirit has important implications for cancer nursing practice, and nurses can provide the leadership and commitment to integrate the arts into patient care.

  14. Center-of-Mass Reference Frame Technique applied to Conservation of Energy for Ideal Inelastic Collisions

    NASA Astrophysics Data System (ADS)

    Dowdye, Edward, Jr.

    2010-02-01

    Findings show that the law of conservation of kinetic energy directly applies to inelastic collisions as well as to elastic collisions. The kinetic energy transfer is consistent with the law of conservation of energy which states that energy can neither be created nor annihilated. In an ideal inelastic collision, two colliding masses, M1 and M2, will move jointly at their center-of-mass velocity, VCM=M1V1+M2V2 M1+M2. As a consequence, the equation 1 2M1V1^2+1 2M2V2^2-1 2M1( V1-VCM )^2-1 2M2( V2-VCM )^2=1 2( M1+M2 )VCM^2 applies to the ideal inelastic collision. The quantities 1 2M1V1^2 and 1 2M2V2^2 are the initial kinetic energies of the masses M1 and M2, respectively, that would be available in the rest frame if the two masses were to come to a complete stop, V1 = 0 and V2 = 0. The negative terms, -1 2M1( V1-VCM )^2 and -1 2M2( V2-VCM )^2, are the kinetic energies transferred into the center-of-mass frame as M1 and M2 go from velocities, V1 and V2 , respectively, to the velocity VCM. The kinetic equation leads directly to the valid conservation of momentum equation M1V1+M2V2=( M1+M2 )VCM , a mathematical proof that the kinetic energy is totally conserved for the ideal inelastic collision. For details: http://www.extinctionshift.com/SignificantFindingsInelastic.htm )

  15. De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.

    PubMed

    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

  16. Preparation and characterization of thin-film composite membrane with nanowire-modified support for forward osmosis process.

    PubMed

    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

  17. 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. PMID:25672325

  18. 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.

  19. Title and Abstract Screening and Evaluation in Systematic Reviews (TASER): a pilot randomised controlled trial of title and abstract screening by medical students

    PubMed Central

    2014-01-01

    Background The production of high quality systematic reviews requires rigorous methods that are time-consuming and resource intensive. Citation screening is a key step in the systematic review process. An opportunity to improve the efficiency of systematic review production involves the use of non-expert groups and new technologies for citation screening. We performed a pilot study of citation screening by medical students using four screening methods and compared students’ performance to experienced review authors. Methods The aims of this pilot randomised controlled trial were to provide preliminary data on the accuracy of title and abstract screening by medical students, and on the effect of screening modality on screening accuracy and efficiency. Medical students were randomly allocated to title and abstract screening using one of the four modalities and required to screen 650 citations from a single systematic review update. The four screening modalities were a reference management software program (EndNote), Paper, a web-based systematic review workflow platform (ReGroup) and a mobile screening application (Screen2Go). Screening sensitivity and specificity were analysed in a complete case analysis using a chi-squared test and Kruskal-Wallis rank sum test according to screening modality and compared to a final set of included citations selected by expert review authors. Results Sensitivity of medical students’ screening decisions ranged from 46.7% to 66.7%, with students using the web-based platform performing significantly better than the paper-based group. Specificity ranged from 93.2% to 97.4% with the lowest specificity seen with the web-based platform. There was no significant difference in performance between the other three modalities. Conclusions Medical students are a feasible population to engage in citation screening. Future studies should investigate the effect of incentive systems, training and support and analytical methods on screening

  20. Center-of-Mass Technique applied to the Ideal Inelastic Collisions Case

    NASA Astrophysics Data System (ADS)

    Dowdye, Edward, Jr.

    2009-10-01

    Findings show that the law of conservation of kinetic energy directly applies to inelastic collisions as well as to elastic collisions. The kinetic energy transfer is consistent with the law of conservation of energy which states that energy can neither be created nor annihilated. In an ideal inelastic collision, two colliding masses, M1 and M2, will move jointly at their center-of-mass velocity, VCM=M1V1+M2V2 M1+M2. As a consequence, the equation 1 2M1V1^2+1 2M2V2^2-1 2M1( V1-VCM )^2-1 2M2( V2-VCM )^2=1 2( M1+M2 )VCM^2 applies to the ideal inelastic collision. The quantities 1 2M1V1^2 and 1 2M2V2^2 are the initial kinetic energies of the masses M1 and M2, respectively, that would be available in the rest frame if the two masses were to come to a complete stop, V1 = 0 and V2 = 0. The negative terms, -1 2M1( V1-VCM )^2 and -1 2M2( V2-VCM )^2, are the kinetic energies transferred into the center-of-mass frame as M1 and M2 go from velocities, V1 and V2 , respectively, to the velocity VCM. The kinetic equation leads directly to the valid conservation of momentum equation M1V1+M2V2=( M1+M2 )VCM , a mathematical proof that the kinetic energy is totally conserved for the ideal inelastic collision. For details: http://www.extinctionshift.com/SignificantFindingsInelastic.htm

  1. 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. PMID:27442123

  2. 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. PMID:27111276

  3. A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population.

    PubMed

    Man, Wu; Zhang, Liyuan; Li, Xihua; Xie, Xiaobing; Pei, Wenfeng; Yu, Jiwen; Yu, Shuxun; Zhang, Jinfa

    2016-08-01

    Upland cotton (Gossypium hirsutum L.) is the most important fiber crop, and its lint-yield improvement is impeded due to its narrow genetic base and the lack of understanding of the genetic basis of yield. Backcross inbred lines (BILs) or near-isogenic lines (NILs) in the same genetic background differing in lint yield, developed through advanced backcrossing, provide an important genomic resource to study the molecular genetic basis of lint yield. In the present study, a high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense. Using a microarray-based comparative transcriptome analysis on developing fibers at 10 days post-anthesis (DPA) between the two groups, 1486 differentially expressed genes (DEGs) were identified. A total of 212 DEGs were further mapped in the regions of 24 yield QTL and 11 yield trait QTL hotspots as reported previously, and 81 DEGs mapped with the 7 lint-yield QTL identified in the BIL population from which the two sets of BILs were selected. Gene Ontology annotations and Blast-Mapping-Annotation-KEGG analysis via Blast2GO revealed that more DEGs were associated with catalytic activity and binding, followed by transporters, nucleic acid binding transcription factors, structural molecules and molecular transducer activities. Six DEGs were chosen for a quantitative RT-PCR assay, and the results were consistent with the microarray analysis. The development of DEGs-based markers revealed that 7 single strand conformation polymorphism-based single nucleotide polymorphic (SSCP-SNP) markers were associated with yield traits, and 3 markers with lint yield. In the present study, we identified a number of yield and yield component QTL-co-localizing DEGs and developed several DEG-based SSCP-SNP markers for the traits, thereby providing a set of candidate genes for molecular breeding and genetic manipulation of lint yield in cotton. PMID:27256327

  4. 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. PMID:27324587

  5. A transcriptome study on Macrobrachium rosenbergii hepatopancreas experimentally challenged with white spot syndrome virus (WSSV).

    PubMed

    Rao, Rama; Bhassu, Subha; Bing, Robin Zhu Ya; Alinejad, Tahereh; Hassan, Sharifah Syed; Wang, Jun

    2016-05-01

    The world production of shrimp such as the Malaysian giant freshwater prawn, Macrobrachium rosenbergii is seriously affected by the white spot syndrome virus (WSSV). There is an urgent need to understand the host pathogen interaction between M. rosenbergii and WSSV which will be able to provide a solution in controlling the spread of this infectious disease and lastly save the aquaculture industry. Now, using Next Generation Sequencing (NGS), we will be able to capture the response of the M. rosenbergii to the pathogen and have a better understanding of the host defence mechanism. Two cDNA libraries, one of WSSV-challenged M. rosenbergii and a normal control one, were sequenced using the Illumina HiSeq™ 2000 platform. After de novo assembly and clustering of the unigenes from both libraries, 63,584 standard unigenes were generated with a mean size of 698bp and an N50 of 1137bp. We successfully annotated 35.31% of all unigenes by using BLASTX program (E-value <10-5) against NCBI non-redundant (Nr), Swiss-Prot, Kyoto Encyclopedia of Genes and Genome pathway (KEGG) and Orthologous Groups of proteins (COG) databases. Gene Ontology (GO) assessment was conducted using BLAST2GO software. Differentially expressed genes (DEGs) by using the FPKM method showed 8443 host genes were significantly up-regulated whereas 5973 genes were significantly down-regulated. The differentially expressed immune related genes were grouped into 15 animal immune functions. The present study showed that WSSV infection has a significant impact on the transcriptome profile of M. rosenbergii's hepatopancreas, and further enhanced the knowledge of this host-virus interaction. Furthermore, the high number of transcripts generated in this study will provide a platform for future genomic research on freshwater prawns.

  6. 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.

  7. Analysis of Litopenaeus vannamei Transcriptome Using the Next-Generation DNA Sequencing Technique

    PubMed Central

    Li, Chaozheng; Weng, Shaoping; Chen, Yonggui; Yu, Xiaoqiang; Lü, Ling; Zhang, Haiqing; He, Jianguo; Xu, Xiaopeng

    2012-01-01

    Background Pacific white shrimp (Litopenaeus vannamei), the major species of farmed shrimps in the world, has been attracting extensive studies, which require more and more genome background knowledge. The now available transcriptome data of L. vannamei are insufficient for research requirements, and have not been adequately assembled and annotated. Methodology/Principal Findings This is the first study that used a next-generation high-throughput DNA sequencing technique, the Solexa/Illumina GA II method, to analyze the transcriptome from whole bodies of L. vannamei larvae. More than 2.4 Gb of raw data were generated, and 109,169 unigenes with a mean length of 396 bp were assembled using the SOAP denovo software. 73,505 unigenes (>200 bp) with good quality sequences were selected and subjected to annotation analysis, among which 37.80% can be matched in NCBI Nr database, 37.3% matched in Swissprot, and 44.1% matched in TrEMBL. Using BLAST and BLAST2Go softwares, 11,153 unigenes were classified into 25 Clusters of Orthologous Groups of proteins (COG) categories, 8171 unigenes were assigned into 51 Gene ontology (GO) functional groups, and 18,154 unigenes were divided into 220 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To primarily verify part of the results of assembly and annotations, 12 assembled unigenes that are homologous to many embryo development-related genes were chosen and subjected to RT-PCR for electrophoresis and Sanger sequencing analyses, and to real-time PCR for expression profile analyses during embryo development. Conclusions/Significance The L. vannamei transcriptome analyzed using the next-generation sequencing technique enriches the information of L. vannamei genes, which will facilitate our understanding of the genome background of crustaceans, and promote the studies on L. vannamei. PMID:23071809

  8. 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

  9. 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

  10. 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.

  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. 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.

  13. Enhanced photovoltaic performance of inverted hybrid bulk-heterojunction solar cells using TiO2/reduced graphene oxide films as electron transport layers

    NASA Astrophysics Data System (ADS)

    Morais, Andreia; Alves, João Paulo C.; Lima, Francisco Anderson S.; Lira-Cantu, Monica; Nogueira, Ana Flavia

    2015-01-01

    In this study, we investigated inverted hybrid bulk-heterojunction solar cells with the following configuration: fluorine-doped tin oxide (FTO) |TiO2/RGO|P3HT:PC61BM|V2O5 or PEDOT:PSS|Ag. The TiO2/GO dispersions were prepared by sol-gel method, employing titanium isopropoxide and graphene oxide (GO) as starting materials. The GO concentration was varied from 0.1 to 4.0 wt%. The corresponding dispersions were spin-coated onto FTO substrates and a thermal treatment was performed to remove organic materials and to reduce GO to reduced graphene oxide (RGO). The TiO2/RGO films were characterized by x-ray diffraction, Raman spectroscopy, and microscopy techniques. Atomic force microscopy (AFM) images showed that the addition of RGO significantly changes the morphology of the TiO2 films, with loss of uniformity and increase in surface roughness. Independent of the use of V2O5 or PEDOT: PSS films as the hole transport layer, the incorporation of 2.0 wt% of RGO into TiO2 films was the optimal concentration for the best organic photovoltaic performance. The solar cells based on TiO2/RGO (2.0 wt%) electrode exhibited a ˜22.3% and ˜28.9% short circuit current density (Jsc) and a power conversion efficiency enhancement, respectively, if compared with the devices based on pure TiO2 films. Kelvin probe force microscopy images suggest that the incorporation of RGO into TiO2 films can promote the appearance of regions with different charge dissipation capacities.

  14. ZERO EMISSION COAL POWER, A NEW CONCEPT

    SciTech Connect

    H. -J. ZIOCK; K. S. LACKNER; D. P. HARRISON

    2001-04-01

    The Zero Emission Coal Alliance (ZECA) is developing an integrated zero emission process that generates clean energy carriers (electricity or hydrogen) from coal. The process exothermically gasifies coal using hydrogen to produce a methane rich intermediate state. The methane is subsequently reformed using water and a CaO based sorbent. The sorbent supplies the energy needed to drive the reforming reaction and simultaneously removes the generated CO{sub 2} by producing CaCO{sub 3}. The resulting hydrogen product stream is split, approximately 1/2 going to gasify the next unit of coal, and the other half being the product. This product stream could then be split a second time, part being cleaned up with a high temperature hydrogen separation membrane to produce pure hydrogen, and the remainder used to generate electricity via a solid oxide fuel cell (SOFC). The inevitable high temperature waste heat produced by the SOFC would in turn be used to regenerate the CaO by calcining the CaCO{sub 3} product of the reforming stage thereby generating a pure stream of CO{sub 2}. The CO{sub 2} will be dealt with a mineral sequestration process discussed in other papers presented at this conference. The SOFC has the added advantage of doubling as an oxygen separation membrane, thereby keeping its exhaust stream, which is predominantly steam, free of any air. This exhaust stream is largely recycled back to the reforming stage to generate more hydrogen, with a slipstream being extracted and condensed. The slipstream carries with it the other initial contaminants present in the starting coal. Overall the process is effectively closed loop with zero gaseous emissions to the atmosphere. The process also achieves very high conversion efficiency from coal energy to electrical energy ({approximately} 70%) and naturally generates a pure stream of CO{sub 2} ready for disposal via the mineral sequestration process.

  15. 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

  16. 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

  17. 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.

  18. Gut response induced by weaning in piglet features marked changes in immune and inflammatory response.

    PubMed

    Bomba, Lorenzo; Minuti, Andrea; Moisá, Sonia J; Trevisi, Erminio; Eufemi, Elisa; Lizier, Michela; Chegdani, Fatima; Lucchini, Franco; Rzepus, Marcin; Prandini, Aldo; Rossi, Filippo; Mazza, Raffaele; Bertoni, Giuseppe; Loor, Juan J; Ajmone-Marsan, Paolo

    2014-12-01

    At weaning, piglets are exposed to many stressors, such as separation from the sow, mixing with other litters, end of lactational immunity, and a change in their environment and gut microbiota. The sudden change of feeding regime after weaning causes morphological and histological changes in the small intestine which are critical for the immature digestive system. Sixteen female piglets were studied to assess the effect of sorbic acid supplementation on the small intestine tissue transcriptome. At weaning day (T0, piglet age 28 days), four piglets were sacrificed and ileal tissue samples collected. The remaining 12 piglets were weighed and randomly assigned to different postweaning (T5, piglet age 33 days) diets. Diet A (n = 6) contained 5 g/kg of sorbic acid. In diet B (n = 6), the organic acids were replaced by barley flour. Total RNA was isolated and then hybridized to CombiMatrix CustomArray™ 90-K platform microarrays, screening about 30 K genes. Even though diet had no detectable effect on the transcriptome during the first 5 days after weaning, results highlighted some of the response mechanisms to the stress of weaning occurring in the piglet gut. A total of 205 differentially expressed genes were used for functional analysis using the bioinformatics tools BLAST2GO, Ingenuity Pathway Analysis 8.0, and Dynamic Impact Approach (DIA). Bioinformatic analysis revealed that apoptosis, RIG-I-like, and NOD-like receptor signaling were altered as a result of weaning. Interferons and caspases gene families were the most activated after weaning in response to piglets to multiple stressors. Results suggest that immune and inflammatory responses were activated and likely are a cause of small intestine atrophy as revealed by a decrease in villus height and villus/crypt ratio.

  19. 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

  20. 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.

  1. Retinoic acid-induced differentiation of human neuroblastoma SH-SY5Y cells is associated with changes in the abundance of G proteins.

    PubMed

    Ammer, H; Schulz, R

    1994-04-01

    Western blot analysis, using subtype-specific anti-G protein antibodies, revealed the presence of the following G protein subunits in human neuroblastoma SH-SY5Y cells: Gs alpha, Gi alpha 1, Gi alpha 2, Go alpha, Gz alpha, and G beta. Differentiation of the cells by all-trans-retinoic acid (RA) treatment (10 mumol/L; 6 days) caused substantial alterations in the abundance of distinct G protein subunits. Concomitant with an enhanced expression of mu-opioid binding sites, the levels of the inhibitory G proteins Gi alpha 1 and Gi alpha 2 were found to be significantly increased. This coordinate up-regulation is accompanied by functional changes in mu-opioid receptor-stimulated low-Km GTPase, mu-receptor-mediated adenylate cyclase inhibition, and receptor-independent guanosine 5'-(beta gamma-imido)triphosphate [Gpp(NH)p; 10 nmol/L]-mediated attenuation of adenylate cyclase activity. In contrast, increased levels of inhibitory G proteins had no effect on muscarinic cholinergic receptor-mediated adenylate cyclase inhibition. With respect to stimulatory receptor systems, a reciprocal regulation was observed for prostaglandin E1 (PGE1) receptors and Gs alpha, the G protein subunit activating adenylate cyclase. RA treatment of SH-SY5Y cells increases both the number of PGE1 binding sites and PGE1-stimulated adenylate cyclase activity, but significantly reduced amounts of Gs alpha were found. This down-regulation is paralleled by a decrease in the stimulatory activity of Gs alpha as assessed in S49 cyc- reconstitution assays.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8133263

  2. 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

  3. 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

  4. 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/.

  5. Analysis of expressed sequence tags from cDNA library of Fusarium culmorum infected barley (Hordeum vulgare L.) roots

    PubMed Central

    Tufan, Feyza; Uçarlı, Cüneyt; Gürel, Filiz

    2015-01-01

    Fusarium culmorum is one of the most common and globally important causal agent of root and crown rot diseases of cereals. These diseases cause grain yield loss and reduced grain quality in barley. In this study, we have analyzed an expressed sequence tag (EST) database derived from F. culmorum infected barley root tissues available at the National Center for Biotechnology Information (NCBI). The 2294 sequences were assembled into 1619 non-redundant sequences consisting of 359 contigs and 1260 singletons using the program CAP3. BLASTX analysis for these sequences was conducted in order to find similar sequences in all databases. Gene Ontology search, enzyme search, KEGG mapping and InterProScan search were done using Blast2GO 3.0.7 tool. By BLASTX analysis, 41.7%, 7.7%, 3.2% and 47.4% of ESTs were categorized as annotated, unannotated, not mapping and without blast hits, respectively. BLASTX analysis revealed that the majority of top hits were barley proteins (43.5%). Based on Gene Ontology classification, 38.3%, 31.3%, and 16% of ESTs were assigned to molecular function, biological process, and cellular component GO terms, respectively. Most abundant GO terms were as follows: 157 sequences were related to response to stress (biological process), 207 sequences were related to ion binding (molecular function), and 160 sequences were related to plastid (cellular component). Furthermore, based on KEGG mapping, 369 sequences could be assigned to 264 enzymes and 83 different KEGG pathways. According to Enzyme Commission (EC) distribution; 94 sequences were transferases (EC2) while 70 sequences were hydrolases (EC3). PMID:25780278

  6. Structure prediction and evolution of a halo-acid dehalogenase of Burkholderia mallei.

    PubMed

    Rai, Alok R; Singh, Raghvendra Pratap; Srivastava, Alok Kumar; Dubey, Ramesh Chandra

    2012-01-01

    Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. The structural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studies and are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capable of degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses the ability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows the cell to grow on MBA, a highly toxic and mutagenic environmental pollutant. For the structural and functional analysis, a 346 amino acid encoding protein sequence of haloacid dehalogenase is retrieve from NCBI data base. Primary and secondary structure analysis suggested that the high percentage of helices in the structure makes the protein more flexible for folding, which might increase protein interactions. The consensus protein sub-cellular localization predictions suggest that dehalogenase protein is a periplasmic protein 3D2GO server, suggesting that it is mainly employed in metabolic process followed by hydrolase activity and catalytic activity. The tertiary structure of protein was predicted by homology modeling. The result suggests that the protein is an unstable protein which is also an important characteristic of active enzyme enabling them to bind various cofactors and substrate for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and RMSD score. This predicted information will help in better understanding of mechanism underlying haloacid dehalogenase encoding protein and its evolutionary relationship.

  7. The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction

    PubMed Central

    2012-01-01

    Background Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry. Results We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371 bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638 bp and 354 bp, respectively. Functional annotation was performed using NCBI’s BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs. Conclusions We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other

  8. 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

  9. Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray

    PubMed Central

    2009-01-01

    Background It has recently been shown that the Trichoderma fungal species used for biocontrol of plant diseases are capable of interacting with plant roots directly, behaving as symbiotic microorganisms. With a view to providing further information at transcriptomic level about the early response of Trichoderma to a host plant, we developed a high-density oligonucleotide (HDO) microarray encompassing 14,081 Expressed Sequence Tag (EST)-based transcripts from eight Trichoderma spp. and 9,121 genome-derived transcripts of T. reesei, and we have used this microarray to examine the gene expression of T. harzianum either alone or in the presence of tomato plants, chitin, or glucose. Results Global microarray analysis revealed 1,617 probe sets showing differential expression in T. harzianum mycelia under at least one of the culture conditions tested as compared with one another. Hierarchical clustering and heat map representation showed that the expression patterns obtained in glucose medium clustered separately from the expression patterns observed in the presence of tomato plants and chitin. Annotations using the Blast2GO suite identified 85 of the 257 transcripts whose probe sets afforded up-regulated expression in response to tomato plants. Some of these transcripts were predicted to encode proteins related to Trichoderma-host (fungus or plant) associations, such as Sm1/Elp1 protein, proteases P6281 and PRA1, enchochitinase CHIT42, or QID74 protein, although previously uncharacterized genes were also identified, including those responsible for the possible biosynthesis of nitric oxide, xenobiotic detoxification, mycelium development, or those related to the formation of infection structures in plant tissues. Conclusion The effectiveness of the Trichoderma HDO microarray to detect different gene responses under different growth conditions in the fungus T. harzianum strongly indicates that this tool should be useful for further assays that include different stages of

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

    PubMed

    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 EA variables and

  11. 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.

  12. De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq

    PubMed Central

    2013-01-01

    Background Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism. Results In this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites. Conclusions Herein, we have described a

  13. 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

  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. 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

  16. Hydrological changes due to land-use change from Brazilian savanna to managed Eucalyptus

    NASA Astrophysics Data System (ADS)

    Siqueira, M. B.; Mota, F. C. M.

    2014-12-01

    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 from the Amazon tropical forest, in the north, to the edges of what used to be the Atlantic forest in the southeast. Today, somewhat 50% of this area has given place to agriculture, pasture and managed forests. 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 distinct seasons, a wet season (Nov-Mar) and dry season (May-Ago), with April and October being transitions between seasons. Typically, 75% of precipitation happens in the wet-season months and only 5% during dry-season. In this study, it is investigated the potential impacts of the substitution of Cerrado to the eco-hydrological characteristics of the region. The focus here is Eucalyptus plantation which have increased substantially in the last decade due to government incentives. Two eddy-covariance (EC) systems were installed, one in an undisturbed Cerrado Stricto area and other in a recently-established Eucalyptus plantation. The two areas are 1,400m apart and are subjected to the same meteorology and similar edaphic conditions. Besides instrumentation typical of EC towers, a soil-moisture profiling system were installed in each site. Data from the towers will be used to parameterized a Soil-Vegetation-Atmosphere (SVAT) model to simulate hydrological and atmospheric boundary layer (ABL) processes in order to understand how the two vegetation cover modulates the exchange of mass and energy between the biosphere and atmosphere. Simulations of 30-day dry down from saturation to complete water stress were performed and were analyzed on how ABL respond to soil moisture

  17. 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

  18. 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

  19. 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

  20. 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

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

    PubMed

    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 EA variables and

  2. 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

  3. 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

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

    PubMed

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

    2008-07-01

    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

  5. Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum

    PubMed Central

    2014-01-01

    Background The species of T. harzianum are well known for their biocontrol activity against plant pathogens. However, few studies have been conducted to further our understanding of its role as a biological control agent against S. sclerotiorum, a pathogen involved in several crop diseases around the world. In this study, we have used RNA-seq and quantitative real-time PCR (RT-qPCR) techniques in order to explore changes in T. harzianum gene expression during growth on cell wall of S. sclerotiorum (SSCW) or glucose. RT-qPCR was also used to examine genes potentially involved in biocontrol, during confrontation between T. harzianum and S. sclerotiorum. Results Data obtained from six RNA-seq libraries were aligned onto the T. harzianum CBS 226.95 reference genome and compared after annotation using the Blast2GO suite. A total of 297 differentially expressed genes were found in mycelia grown for 12, 24 and 36 h under the two different conditions: supplemented with glucose or SSCW. Functional annotation of these genes identified diverse biological processes and molecular functions required during T. harzianum growth on SSCW or glucose. We identified various genes of biotechnological value encoding proteins with functions such as transporters, hydrolytic activity, adherence, appressorium development and pathogenesis. To validate the expression profile, RT-qPCR was performed using 20 randomly chosen genes. RT-qPCR expression profiles were in complete agreement with the RNA-Seq data for 17 of the genes evaluated. The other three showed differences at one or two growth times. During the confrontation assay, some genes were up-regulated during and after contact, as shown in the presence of SSCW which is commonly used as a model to mimic this interaction. Conclusions The present study is the first initiative to use RNA-seq for identification of differentially expressed genes in T. harzianum strain TR274, in response to the phytopathogenic fungus S. sclerotiorum. It provides

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Superparamagnetic core-shells anchored onto graphene oxide grafted with phenylethyl amine as a nano-adsorbent for extraction and enrichment of organophosphorus pesticides from fruit, vegetable and water samples.

    PubMed

    Mahpishanian, Shokouh; Sereshti, Hassan; Baghdadi, Majid

    2015-08-01

    A novel adsorbent composed of silica coated magnetic microparticles (Fe3O4@SiO2) and graphene oxide (GO) functionalized with phenylethyl amine (PEA) was synthesized and characterized using Fourier transform-infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), vibrating sample magnetometry (VSM), and CHN elemental analysis techniques. The adsorbent (Fe3O4@SiO2@GO-PEA) was then used in a magnetic solid phase extraction (MSPE) of six organophosphorous pesticides (OPPs) including methyl parathion, fenitrothion, methidathion, ethion, methyl azinphos and coumaphos prior to gas chromatography-nitrogen phosphorus detection (GC-NPD). The fabricated adsorbent combines the advantages of superior adsorption capability of modified GO and magnetic separability of magnetite microparticles to provide high adsorption capacity, and easy isolation from sample solutions. The main experimental parameters affecting the extraction recovery of OPPs including extraction time, pH, adsorbent dosage, salt concentration, and desorption conditions were investigated and optimized. Under the optimal conditions, linear responses were obtained in the concentration range of 0.06-200μgL(-1) with the determination coefficients (R(2)) between 0.9945 and 0.9996. The limits of detection were from 0.02 to 0.1μgL(-1) and the intraday and inter-day relative standard deviations (RSDs) were less than 4.8 and 6.4%, respectively. The method was successfully applied for determination of the OPPs in apple, grape, pear, bell pepper, celery and water samples. The obtained recoveries were in the range of 90.4-108.0% (RSDs=1.9-6.6%, n=3) for fruits and vegetables, and 94.6-104.2% (RSDs=2.0-4.8%, n=3) for water samples. The excellent extraction performance of the adsorbent can be attributed to its structure characteristics where the phenyl rings of PEA grafted on the GO nanosheets are accessible to interact effectively with OPPs via delocalized π-electron system. PMID:26129984

  12. 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

  13. 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

  14. SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea

    PubMed Central

    2010-01-01

    Background Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L.) Walp). We aimed to use this method to enrich for genes expressed during drought stress in a drought tolerant cowpea line. However, current methods were inefficient in screening libraries and management of the sequence data, and thus there was a need to develop software tools to facilitate the process. Results Forward and reverse cDNA libraries enriched for cowpea drought response genes were screened on microarrays, and the R software package SSHscreen 2.0.1 was developed (i) to normalize the data effectively using spike-in control spot normalization, and (ii) to select clones for sequencing based on the calculation of enrichment ratios with associated statistics. Enrichment ratio 3 values for each clone showed that 62% of the forward library and 34% of the reverse library clones were significantly differentially expressed by drought stress (adjusted p value < 0.05). Enrichment ratio 2 calculations showed that > 88% of the clones in both libraries were derived from rare transcripts in the original tester samples, thus supporting the notion that suppression subtractive hybridization enriches for rare transcripts. A set of 118 clones were chosen for sequencing, and drought-induced cowpea genes were identified, the most interesting encoding a late embryogenesis abundant Lea5 protein, a glutathione S-transferase, a thaumatin, a universal stress protein, and a wound induced protein. A lipid transfer protein and several components of photosynthesis were down-regulated by the drought stress. Reverse transcriptase quantitative PCR confirmed the enrichment ratio values for the selected cowpea genes. SSHdb, a web-accessible database, was developed to manage the clone sequences and combine the SSHscreen data with sequence annotations derived from BLAST and Blast2GO. The self

  15. Detailed structure of the carbonated peridotite solidus ledge in the system CaO-MgO- Al2O3-SiO2-CO2

    NASA Astrophysics Data System (ADS)

    Ghosh, S.; Keshav, S.; Gudfinnsson, G.; Presnall, D.

    2008-12-01

    important implications, we are conducting high-pressure experiments to determine the melting relations at the solidus of CO2-bearing spinel-garnet peridotite in the system CMAS-CO2 at 2.1 to 3.0 GPa. We have found that the higher pressure invariant point, involving fo+opx+cpx+gt+CO2+dolomite+melt phase assemblage, occurs at 3 GPa/1225 C. The melt is calciocarbonatitic with roughly 40-42 wt.% CO2. Going along the solidus toward lower pressure, we have determined the following isobaric invariant points: 2.8 GPa/1275 C, 2.6 GPa/1375 C, 2.4 GPa/1400 C, 2.3 GPa/1425 C, and 2.1 GPa/1425 C. The first four points involve fo+opx+cpx+gt+CO2+melt, whereas the last one involves the fo+opx+cpx+sp+CO2+melt phase assemblage. Melt compositions at these isobaric invariant points resemble calciocarbonatites. These five points span a univariant curve in P-T space, lack crystalline carbonate, and hence define the famous carbonate ledge in the CMAS-CO2 system. Significantly, since two different isobaric invariant assemblages occur at 2.3 and 2.1 GPa, the lower pressure invariant point must occur at about 2.2 GPa/1425 C, consisting of fo+opx+cpx+sp+gt+CO2+melt. Experiments are currently under way to understand the melting relations where CO2 vapor coexists with the spinel lherzolite phase assemblage.

  16. Gravitational effects on weld pool shape and microstructural evolution during gas tungsten arc and laser beam welding on 304 stainless steel, nickel, and aluminum-4 wt.% copper alloy

    NASA Astrophysics Data System (ADS)

    Kang, Namhyun

    The objective of the present work was to investigate effects of gravitational (acceleration) level and orientation on Ni 200 alloy (99.5% Ni purity), 304 stainless steel, and Al-4 wt.% Cu alloy during gas tungsten arc welding (GTAW) and laser beam welding (LBW). Main characterization was focused on the weld pool shape, microstructure, and solute distribution as a function of gravitational level and orientation. The welds were divided into two classes, i.e., 'stable' and 'unstable' welds, in view of the variation of weld pool shape as a function of gravitational level and orientation. In general, higher arc current and translational GTAW produced more significant effects of gravitational orientation on the weld pool shape than the case of lower arc current and spot welding. Cross-sectional area (CSA) was a secondary factor in determining the stability of weld pool shape. For the 'stable' weld of 304 stainless steel GTAW, the II-U weld showed less convexity in the pool bottom and more depression of the free surface, therefore producing deeper penetration (10--20%) than the case of II-D weld. The II-D weld of 304 stainless steel showed 31% deeper penetration, 28% narrower width, and more hemispherical shape of the weld pool than the case of II-U weld. For GTAW on 304 stainless steel, gravitational level variation from low gravity (LG ≈ 1.2 go) to high gravity (HG ≈ 1.8 go) caused 10% increase in width and 10% decrease in depth while maintaining the overall weld pool volume. Furthermore, LBW on 304 stainless steels showed mostly constant shape of weld pool as a function of gravitational orientation. GTAW on Ni showed similar trends of weld pool shape compared with GTAW on 304 stainless steel, i.e., the weld pool became unstable by showing more penetration in the II-D weld for slower arc translational velocity (V a) and larger weld pool size. However, the Ni weld pool shape had greater stability of the weld pool shape with respect to the gravitational orientation