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Sample records for 2-go kontura vvehr-1000

  1. Genes2GO: A web application for querying gene sets for specific GO terms.

    PubMed

    Chawla, Konika; Kuiper, Martin

    2016-01-01

    Gene ontology annotations have become an essential resource for biological interpretations of experimental findings. The process of gathering basic annotation information in tables that link gene sets with specific gene ontology terms can be cumbersome, in particular if it requires above average computer skills or bioinformatics expertise. We have therefore developed Genes2GO, an intuitive R-based web application. Genes2GO uses the biomaRt package of Bioconductor in order to retrieve custom sets of gene ontology annotations for any list of genes from organisms covered by the Ensembl database. Genes2GO produces a binary matrix file, indicating for each gene the presence or absence of specific annotations for a gene. It should be noted that other GO tools do not offer this user-friendly access to annotations. Genes2GO is freely available and listed under http://www.semantic-systems-biology.org/tools/externaltools/.

  2. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.

    PubMed

    Conesa, Ana; Götz, Stefan; García-Gómez, Juan Miguel; Terol, Javier; Talón, Manuel; Robles, Montserrat

    2005-09-15

    We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Blast2GO is freely available via Java Web Start at http://www.blast2go.de. http://www.blast2go.de -> Evaluation.

  3. 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.

  4. Blast2GO: A comprehensive suite for functional analysis in plant genomics.

    PubMed

    Conesa, Ana; Götz, Stefan

    2008-01-01

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

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

    PubMed Central

    Conesa, Ana; Götz, Stefan

    2008-01-01

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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed

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

    2008-06-01

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

  9. 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.

  10. MnO2-GO double-shelled sulfur (S@MnO2@GO) as a cathode for Li-S batteries with improved rate capability and cyclic performance

    NASA Astrophysics Data System (ADS)

    Huang, Xingkang; Shi, Keying; Yang, Joseph; Mao, George; Chen, Junhong

    2017-07-01

    Sulfur cathodes have attracted much attention recently because of their high energy density and power density. However, sulfur possesses very poor electrical conductivity, and lithium polysulfides, resulting from the lithiation of sulfur, are prone to dissolving into electrolytes, which leads to the loss of active materials and poor cyclic performance of the sulfur cathodes. Here we report an MnO2-graphene oxide (GO) double-shelled sulfur (S@MnO2@GO) with improved rate capability and cyclic performance, in which we propose a new reaction using sulfur-reducing KMnO4 to produce MnO2 that covers the surface of the excess sulfur in situ. The resulting MnO2 with honeycomb-like morphology provides excellent voids for storing polysulfides. The outermost GO was assembled to block the open pores of MnO2, thereby minimizing the opportunity for polysulfides to leach into the electrolytes. The GO significantly improved the electrical conductivity of the sulfur cathode, and the S@MnO2@GO exhibited excellent rate capability and long cycle life.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

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

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

    PubMed

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

    2017-05-05

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

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

    PubMed

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

    2016-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  16. A novel fabrication of a high performance SiO(2)-graphene oxide (GO) nanohybrids: Characterization of thermal properties of epoxy nanocomposites filled with SiO(2)-GO nanohybrids.

    PubMed

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

    2017-05-01

    In this study it has been aimed to enhance the thermal resistance of epoxy coating through incorporation of SiO2-GO nanohybrids. SiO2-GO nanohybrids were synthesized through one-step sol-gel route using a mixture of Tetraethylorthosilane (TEOS) and 3-Aminopropyl triethoxysilane (APTES) silanes. The SiO2-GO nanohybrids were prepared at various hydrolysis times of 24, 48 and 72h. Then 0.2wt.% of GO and SiO2-GO nanohybrids were separately incorporated into the epoxy coating. Results revealed that amino functionalized SiO2 nanoparticles with particle size around 20-30nm successfully synthesized on the basal plane of GO. Results showed significant improvement of dispersion and interfacial interactions between nanohybrids and epoxy composite arising from covalent bonding between the SiO2-GO and the epoxy matrix. It was found that the thermal resistance of SiO2-GO nanohybrids and SiO2-GO/Epoxy nanocomposite was noticeably higher than GO and epoxy matrix, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data.

    PubMed

    Ahadi, Alireza; Sablok, Gaurav; Hutvagner, Gyorgy

    2017-04-07

    MicroRNAs (miRNAs) are ∼19-22 nucleotides (nt) long regulatory RNAs that regulate gene expression by recognizing and binding to complementary sequences on mRNAs. The key step in revealing the function of a miRNA, is the identification of miRNA target genes. Recent biochemical advances including PAR-CLIP and HITS-CLIP allow for improved miRNA target predictions and are widely used to validate miRNA targets. Here, we present miRTar2GO, which is a model, trained on the common rules of miRNA-target interactions, Argonaute (Ago) CLIP-Seq data and experimentally validated miRNA target interactions. miRTar2GO is designed to predict miRNA target sites using more relaxed miRNA-target binding characteristics. More importantly, miRTar2GO allows for the prediction of cell-type specific miRNA targets. We have evaluated miRTar2GO against other widely used miRNA target prediction algorithms and demonstrated that miRTar2GO produced significantly higher F1 and G scores. Target predictions, binding specifications, results of the pathway analysis and gene ontology enrichment of miRNA targets are freely available at http://www.mirtar2go.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Design and methods for a community-based intervention to reduce sugar-sweetened beverage consumption among youth: H2GO! study.

    PubMed

    Wang, Monica L; Lemon, Stephenie C; Clausen, Kristian; Whyte, Julie; Rosal, Milagros C

    2016-11-09

    Reducing sugar-sweetened beverage (SSB) intake is an important dietary target among underserved children at high risk for obesity and associated morbidities. Community-based approaches to reduce SSB intake are needed. The use of narrative-based approaches (presenting messages within the context of a story) can facilitate connection with target health messages and empower children as behavior change agents within their families. The H2GO! program is a community-based behavioral intervention that integrates narrative-based strategies to reduce SSB consumption and promote water intake among school-age youth and parents. Guided by the Social Cognitive Theory and the Social Ecological Model, the H2GO! intervention consists of 6 weekly sessions that target beverage knowledge, attitudes, and behaviors through youth-produced messages and narratives to reduce SSB intake and encourage water intake and parent-child activities. To reach underserved youth and families, we identified Boys & Girls Clubs (B&GC) (youth-based community centers that serve an ethnically diverse and predominantly low socioeconomic status population) as a community partner and study setting. Participants (children ages 9-12 years and their parents) will be recruited from B&GC sites in Massachusetts, USA. Intervention efficacy will be assessed through a site-randomized trial (N = 2 youth-based community sites, pair-matched for size and racial/ethnic composition) with 54 parent-child pairs (N = 108) enrolled per site (N = 216 total). The comparison site will carry on with usual practice. Child and parental SSB and water consumption (primary outcomes) and parent and child beverage knowledge and attitudes (secondary outcomes) will be measured via self-report surveys. Additional outcomes include children's anthropometric data, additional dietary behaviors, and physical activity. Measures will be collected at baseline, 2 and 6 months follow-up. With an estimated 20 % dropout rate, the study will

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  20. Evaluation of Healthy2Go: A country store transformation project to improve the food environment and consumer choices in Appalachian Kentucky.

    PubMed

    Rushakoff, Joshua A; Zoughbie, Daniel E; Bui, Nancy; DeVito, Katerina; Makarechi, Leila; Kubo, Hitomi

    2017-09-01

    Rates of obesity and type 2 diabetes in Kentucky's Cumberland Valley region are among the highest in the United States and limited access to healthy food contributes to these epidemics. The aim of Healthy2Go (H2G), a country store transformation project launched by Spread the Health Appalachia (STHA), was to improve awareness and availability of healthy options in small, rural stores. Ten country stores participated in H2G and received training and technical assistance to increase availability and awareness of healthy foods. Stores made inventory changes; installed point-of-purchase educational and in-store marketing materials directing shoppers to healthier options; provided nutrition education such as healthy recipes; and altered the display and location of healthy items. To measure changes within stores and the potential impact on resident eating and purchasing habits, STHA used four instruments: a modified version of the Nutrition Environs Measures Survey - Corner Stores at baseline and follow-up, a bimonthly store inventory assessment, a final store owner survey, and a Community Nutrition Survey at baseline (n = 287) and follow-up (n = 281). The stores in the H2G program (n = 10) had a 40% increase in stocking fresh produce, a 20% increase in produce variety, and trends towards increasing healthy inventory. During the same period, surveyed residents reported a statistically significant increase in the frequency of healthy food consumption. Small store transformation programs can improve availability of and access to healthy food in rural settings and influence local purchasing patterns.

  1. 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.

  2. Investigation of GH2-GO2 combustion

    NASA Technical Reports Server (NTRS)

    Calhoon, D. F.

    1972-01-01

    Data from prototype GO2-GH2 injection elements were obtained and analyzed. The bulk of the testing was conducted with nonreacting propellants, N2 to simulate the O2 and H2. A limited number of tests were conducted in combusting environment, with the purpose of this testing being to evaluate the effects of combustion on cold flow mixture ratio and mass profiles. The cold flow testing was completed in 223 tests. Analytical model correlations of these data are under way. The hot flow testing was completed in 36 tests. These data have been reduced and are documented in the report.

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

    NASA Astrophysics Data System (ADS)

    Skarmoutsos, Ioannis; Mossa, Stefano; Samios, Jannis

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Hagley, Edward Walter

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

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

    PubMed

    Fekete, Ágnes A; Giromini, Carlotta; Chatzidiakou, Yianna; Givens, D Ian; Lovegrove, Julie A

    2016-12-01

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

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

    PubMed Central

    Givens, D Ian

    2016-01-01

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

  7. 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…

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

    PubMed

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

    2016-12-15

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

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

    PubMed Central

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

    2017-01-01

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

  11. 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.

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

    PubMed

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

    2017-01-01

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

  13. Preparation and characterization of amine functionalized graphene oxide with water soluble quantum dots for sensing material

    NASA Astrophysics Data System (ADS)

    Zaid, Mohd Hazani Mat; Abdullah, Jaafar

    2017-09-01

    Nanocomposite material has been prepared comprises of amine functionalized graphene oxide (NH2-GO) incorporation with water solube CdS Quantum dots nanoparticle to form a new composite material (NH2-GO/QDs). This composite mixture shows highly homogenous without precipitation and have been characterize by using Raman, Fourier transform infrared spectroscopy (FTIR) and the scan electron microscopy (SEM-EDX). Kinetic investigation based on DNA hybridization by cyclic voltammetry shows modified electrode able to achieve high hybridization rate can be used as electrochemical biosensor platform.

  14. 26 CFR 1.197-0 - Table of contents.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... other intangibles. (a) Overview. (1) In general. (2) Section 167(f) property. (3) Amounts otherwise deductible. (b) Section 197 intangibles; in general. (1) Goodwill. (2) Going concern value. (3) Workforce in place. (4) Information base. (5) Know-how, etc. (6) Customer-based intangibles. (7) Supplier-based...

  15. 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…

  16. Titanium nanoparticles (TiO2)/graphene oxide nanosheets (GO): an electrochemical sensing platform for the sensitive and simultaneous determination of benzocaine in the presence of antipyrine.

    PubMed

    Mohamed, Mona A; Atty, Shimaa A; Merey, Hanan A; Fattah, Taghreed A; Foster, Christopher W; Banks, Craig E

    2017-10-07

    An effective electrochemical sensing platform for the simultaneous determination of benzocaine (BEN) and antipyrine (ANT) based upon titanium dioxide nanoparticle (TiO2)/graphene oxide nanosheet (GO) bulk modified carbon paste electrodes (TiO2-GO/CPE) is reported. The TiO2-GO/CPE electrochemical sensing platform is found to exhibit linear ranges from 1.0 × 10(-6) to 1.0 × 10(-4) M and 1.2 × 10(-8) to 8.0 × 10(-5) M for BEN and ANT, respectively. The TiO2-GO/CPE sensor is explored towards the analysis of BEN and ANT in oral fluid (saliva) and pharmaceutical products. The synergy between the graphene oxide nanosheets and titanium dioxide nanoparticles results in a dramatic enhancement in the sensitivity of the sensor through a combination of increased surface area and improved electron transfer kinetics compared to other electrode alternatives. The fabricated TiO2-GO/CPE exhibits high sensitivity and good stability towards the sensing of BEN and ANT and has the potential to be utilised as a clinical assay and QA in pharmaceutical products.

  17. Digital Geogames to Foster Local Biodiversity

    ERIC Educational Resources Information Center

    Schaal, Sonja; Schaal, Steffen; Lude, Armin

    2015-01-01

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

  18. 26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... due to the name or reputation of a trade or business or any other factor. (2) Going concern value. Section 197 intangibles include going concern value. Going concern value is the additional value that... exception applies: (1) Goodwill. Section 197 intangibles include goodwill. Goodwill is the value of a...

  19. 26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... due to the name or reputation of a trade or business or any other factor. (2) Going concern value. Section 197 intangibles include going concern value. Going concern value is the additional value that... exception applies: (1) Goodwill. Section 197 intangibles include goodwill. Goodwill is the value of a...

  20. 26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... due to the name or reputation of a trade or business or any other factor. (2) Going concern value. Section 197 intangibles include going concern value. Going concern value is the additional value that... exception applies: (1) Goodwill. Section 197 intangibles include goodwill. Goodwill is the value of a...

  1. 26 CFR 1.197-2 - Amortization of goodwill and certain other intangibles.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... due to the name or reputation of a trade or business or any other factor. (2) Going concern value. Section 197 intangibles include going concern value. Going concern value is the additional value that... exception applies: (1) Goodwill. Section 197 intangibles include goodwill. Goodwill is the value of a...

  2. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  4. Digital Geogames to Foster Local Biodiversity

    ERIC Educational Resources Information Center

    Schaal, Sonja; Schaal, Steffen; Lude, Armin

    2015-01-01

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

  5. 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,…

  6. Preparation and tribological properties of MoS2/graphene oxide composites

    NASA Astrophysics Data System (ADS)

    Song, Haojie; Wang, Biao; Zhou, Qiang; Xiao, Jiaxuan; Jia, Xiaohua

    2017-10-01

    A hydrothermal route is developed for the synthesis of MoS2/graphene oxide (GO) composites based on the hydrothermal reduction of Na2MoO4 and GO sheets with L-cysteine. The MoS2/GO composites in improving friction and wear of the sunshine oil on sliding steel surfaces under low or high applied load were demonstrated. In tests with sliding steel surfaces, the sunshine oil that contains small amounts of MoS2/GO composites exhibited the lowest specific friction coefficient and wear rate under all of the sliding conditions. Scanning electron microscopy and energy dispersive spectrometer performed to analyze the wear scar surfaces after friction confirmed that the outstanding lubrication performance of MoS2/GO composites could be attributed to their good dispersion stability and extremely thin laminated structure, which allow the MoS2/GO composites to easily enter the contact area, thereby preventing the rough surfaces from coming into direct contact.

  7. 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…

  8. 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…

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. SQUID (Superconducting Quantum Interference Device) Arrays for Simultaneous Magnetic Measurements: Calibration and Source Localization Performance.

    DTIC Science & Technology

    1988-02-29

    P. Com Ribeiro, was supported by the Guggenheim Foundation and is with the Departamento de Fisica , Pontificia Universidade Catolica do Rio de Janeiro...field at the center of the coil is Bc = F2 go Nc Ic/wSc (2) where Nc is the number of turns and Ic is the current in the coil. It is conceptually

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

    ERIC Educational Resources Information Center

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

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

  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)…

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

    PubMed

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

    2016-10-12

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

  17. 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

  18. 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.

  19. Effectiveness and Cost of Alcohol Rehabilitation in the United States Air Force.

    DTIC Science & Technology

    1981-12-01

    the influence of alcohol . . .. 1 2 32/ R. Vitamin deficiencies or anemia ........ .l..1 2 33/ S. Trouble focusing eyes when not under the influence of...when not under the influence of alcohol .......... ... 1 2 i, T. Vitamin deficiencies or anemia ............. ... 1 2 U. Trouble focusing eyes when not...IN THE ALCOHOL TREATIEINT CENTER PROGRAII(S) HARIFUL IN ANY WAY? (Circle one) Yes ............... nswer No ..... ............ 2 GO to Tuestion *0 I A

  20. A Computational Procedure for the Protection of Industrial Power Systems.

    DTIC Science & Technology

    1981-11-01

    the longest programs in the series . The program asks for the zero-sequence impedance for all loads in the system and the mutual-coupling impedances. If...IF(NN2.EQ.NN) GO TO 74 IF(NNI.EQ.0)GO TO 86 GO TO 85 70 FCUR( NIIf ,1,2)-((EFALT(IBJI,1,2)-EFALT(IBJJ,1,2))/ 1(ZN2) )+FCUR(NN, 1,2) GO TO 85 74 FCUR(NN

  1. 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.

  2. 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.

  3. MoS2-nanosheet/graphene-oxide composite hole injection layer in organic light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Park, Minjoon; Nguyen, Thang Phan; Choi, Kyoung Soon; Park, Jongee; Ozturk, Abdullah; Kim, Soo Young

    2017-07-01

    In this work, composite layers comprising two-dimensional MoS2 and graphene oxide (GO) were employed as hole injection layers (HILs) in organic light-emitting diodes (OLEDs). MoS2 was fabricated by the butyllithium (BuLi) intercalation method, while GO was synthesized by a modified Hummers method. The X-ray diffraction patterns showed that the intensity of the MoS2 (002) peak at 14.15° decreased with increase in GO content; the GO (001) peak was observed at 10.07°. In the C 1s synchrotron radiation photoemission spectra, the contributions of the C-O, C=O, and O-C=O components increased with increase in GO content. These results indicated that GO was well mixed with MoS2. The lateral size of MoS2 spanned from a few hundreds of nanometers to 1 μm, while the size of GO was between 400 nm and a few micrometers. Thus, the coverage of the MoS2-GO composite on the ITO surface improved as the GO content increased, owing to the large particle size of GO. Notably, GO with large size could fully cover the indium tin oxide film surface, thus, lowering the roughness. The highest maximum power efficiency (PEmax) was exhibited by the OLED with MoS2-GO 6:4 composite HIL, indicating that similar contents of MoS2 and GO in MoS2-GO composites provide the best results. The OLED with GO HIL showed very high PEmax (4.94 lm W-1) because of very high surface coverage and high work function of GO. These results indicate that the MoS2-GO composites can be used to fabricate HILs in OLEDs.[Figure not available: see fulltext.

  4. Application of Computational and Visualization Methods to Groundwater Modeling

    DTIC Science & Technology

    1994-09-01

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

  5. Preparation of RHA-silica/graphene oxide nanocomposite for removal of nickel ions from water

    NASA Astrophysics Data System (ADS)

    Tien, Tran Thi Thuy; Tu, Tran Hoang; Thao, Huynh Nguyen Phuong; Hieu, Nguyen Huu

    2017-09-01

    In this study, silica was synthesized from rice husk ash (RHA-SiO2) by precipitation method. Graphene oxide (GO) was prepared by modified Hummers method. RHA-SiO2/GO nanocomposite was fabricated by in-situ one-step method using 3-Aminopropyltriethoxysilane (APS) as a coupling agent. The nanocomposite was characterized by using X-ray Fluorescence, X-ray diffraction, transmission electron microscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, and Brunauer-Emmett-Teller (BET) specific surface area. The adsorption of RHA-SiO2/GO for Ni2+ ions from water was investigated and compared with the precursors. Ultraviolet-visible (UV-Vis) spectroscopy was used to quantify the amount of the initial and the residual Ni2+ concentration. The maximum adsorption capacity of the nanocomposite for Ni2+ calculated from Langmuir isotherm model, which was 256.4 mg/g. In addition, the adsorption data were well-fitted to the pseudo-second-order kinetic equation. Accordingly, this study demonstrated that RHA-SiO2/GO could be used as a highly efficient adsorbent for removal Ni2+ ions from aqueous solution.

  6. 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

  7. A novel magnetic β-cyclodextrin modified graphene oxide adsorbent with high recognition capability for 5 plant growth regulators.

    PubMed

    Chen, Jiu-Yan; Cao, Shu-Rui; Xi, Cun-Xian; Chen, Yu; Li, Xian-Liang; Zhang, Lei; Wang, Guo-Min; Chen, Ya-Ling; Chen, Zhi-Qiong

    2018-01-15

    β-Cyclodextrin (β-CD) modified magnetic graphene oxide material (Fe3O4@SiO2/GO/β-CD), a novel magnetic sorbent for enrichment and purification of plant growth regulators (PGRs) in vegetables prior to gas chromatograph mass spectrometer (GC-MS) detection, was successfully fabricated. The novel magnetic sorbent geometrically fitted to selectively recognize and enrich PGR analytes especially containing aromatic structure. The selectivity experiment demonstrated the higher selectivity of Fe3O4@SiO2/GO/β-CD toward 5 PGR compounds than that of Fe3O4@SiO2/GO. Several parameters affecting extraction efficiency including the volume of extraction solvent, amount of adsorbent, extraction time, type and the volume of desorption solvent were optimized. Under the optimized condition, good linear relationships were obtained in the range of 1-100μg/kg with determination coefficients (R(2)) from 0.9983 to 0.9996. The limits of detection (LODs) of 5 PGRs were from 0.04 to 0.28μg/kg. The proposed method had good potential for the analysis of trace level of 5 PGRs in real vegetable samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. pH-Controlled drug delivery with hybrid aerogel of chitosan, carboxymethyl cellulose and graphene oxide as the carrier.

    PubMed

    Wang, Ren; Shou, Dan; Lv, Ouyang; Kong, Yong; Deng, Linhong; Shen, Jian

    2017-10-01

    Hybrid aerogels of chitosan (CS), carboxymethyl cellulose (CMC) and graphene oxide (GO) are successfully prepared by using calcium ion (Ca(2+)) as the crosslinker. The resultant hybrid aerogels, CS/CMC/Ca(2+)/GO, are characterized by field emission scanning electron microscopy (FESEM) and Fourier transform infrared (FT-IR) spectroscopy. Due to the pH sensitivity of CS and CMC, pH-controlled drug delivery with CS/CMC/Ca(2+)/GO as the carrier is investigated using 5-fluorouracil (5-FU), an effective chemotherapeutic agent in the treatment of cancers, as the model drug. Finally, Higuchi model and Korsmeyer-Peppas model are used to study the release kinetics, and it reveals that the release of 5-FU from the hybrid aerogels is controlled by Fickian diffusion. Collectively, the findings demonstrate the CS/CMC/Ca(2+)/GO would be a potential material for the construction of pH-controlled drug delivery platform. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2009-01-01

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

  10. 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.

  11. Water and Carbon as Creators of Imbalances in Nature

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  12. 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.

  13. The Military Procurement System--Can It Be Improved?

    DTIC Science & Technology

    1983-05-03

    CLASSOICATION OF ?ŘIS PACE e(1b D. O r ________________ REPRT REPORT DOCUMENTATION PAGE NO . 310U COUPLZIUU V~m NUMBER 2. GO T ACCESION NO .RECIPIENT’S CATALOG...PA&E was heavily in the financial area as it should be. In this capacity they could offer up alternatives to the Secretary of Defense based on what...responsible, coordinated position with the financial people in OSD. As it is now, the financial aspects are only given a cursory glance during the program

  14. Statistics on Aircraft Gas Turbine Engine Rotor Failures That Occurred in U.S. Commercial Aviation during 1985

    DTIC Science & Technology

    1989-07-01

    Report No. 2. Go vrmen.t Accesion No. 3 . Recipient’ 0 Ca.talog No.- DOT/FAA/CT-89-7 4. Title end Subticly 5. Repert nOAte July 1989 STATISTICS ON...R4eport an- Period Covered 12. Sponsoring Agency Name and Address Department of Transportation F nlRp rFederal Aviation Administration FnlRpr...CONCLUSIONS 3 APPENDIX A - Data of Engine Rotor Failures in U.S. Commercial Aviation for 1985 LIST OF ILLUSTRATIONS Figure Page 1 Incidence of Engine Rotor

  15. Notes on Clinical Simulations for the Problem Oriented Medical Curriculum at Sheppard Air Force Base

    DTIC Science & Technology

    1976-06-01

    No edema. Pulses full (0) B -9 Genital and rectal exam B -9 Genitalia normal. No hernias . Hard stool in rectum, but no masses. (0) B -10 Lymph node exam B ...testing without contributing to test score (e.g., problem II, section B -i, 2, 3, 4, 6). Such options should either be chosen as standard practice in...patient’s medical A-2 Go to Section B record (-2) A-3 Exaqpine the patient A-3 Go to Section F (-4) A-4 Order diagnostic studies A-4 Go to Section E

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

    PubMed

    González, Francisco Javier; Vizcaíno, Juan Antonio

    2011-01-01

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

  17. Animal Preparations to Assess Neurophysiological Effects of Bio-Dynamic Environments.

    DTIC Science & Technology

    1980-07-17

    lateral hypothalmic lesions in the cat: parallels with development. J . Comp. Physiol. Psychol. (1980) in press. Whittington, D ., Pettijohn, D . and Hein...Biological Sciences Division of the Office of Naval Research ......... , D T C ,5I 90 /( l0 ELECTE , / fl~~l4-8’-C-O𔄃/.l.J" ’ SEp , 2 goSP2980D dAlan...Department of Psychology Cambridge, Massachusetts 02139 J A. Hein GENERAL INTRODUCTION eridical perception of the visual world and motor performance

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

    DTIC Science & Technology

    1984-05-25

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

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

    PubMed

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

    2016-12-01

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

  20. Far UV Observations of Interstellar Shocks

    NASA Technical Reports Server (NTRS)

    Raymond, John C.

    1998-01-01

    This grant covered analysis of Hopkins Ultraviolet Telescope data from the Astro-2 mission. The proposed research was aimed primarily at SNR shock waves, but the ASTRO-2 GO program was intended to make the GOs part of the instrument teams. The grant therefore covered extensive travel to Marshall Space Flight Center for mission simulations and the mission itself. In keeping with the unique nature of the ASTRO-2 GO program, I participated actively in the instrument team's investigations of HH objects and cataclysmic variables. Over the course of the Astro-2 mission, we obtained good observations of the supernova remnants SN1006 (1 position), Vela (3 positions), the Cygnus Loop (7 positions) and 0519-69 in the LMC (1 position) as part of this GI program, along with Puppis A (1 position), Vela (1 position), the Cygnus Loop (7 positions) and the Schweizer- Middleditch star (HUT PI program on SNRS). We also observed the Herbig-Haro object HH2 and about a dozen cataclysmic variables, including magnetic systems and dwarf novae. This GI grant covered modest travel for data analysis. We anticipate submitting papers on the non-radiative shock in northern Cygnus Loop, on the LMC Balmer-dominated remnant LMC 0519-69, on the radiative shocks in the Eastern Cygnus Loop (the XA region), and on the cataclysmic variable YZ Cnc over the course of the coming year. We have obtained extensive supporting data from ground-based telescopes for the Cygnus Loop spectra.

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

    PubMed

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

    2012-08-01

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

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

    PubMed

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

    2017-03-01

    In this research, a modified Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) method based on graphene oxide@SiO2(SiO2@GO) nanocomposite as adsorbent of dispersive solid-phase extraction (dSPE) combined with high performance liquid chromatography (HPLC) for the analysis of four plant hormones in different plants was established. The as-prepared SiO2@GO was characterized by scanning electron microscopy, transmission electron microscopy and infrared spectroscopy. The experimental conditions for dSPE, including the ratio of material to liquid, pH of sample, adsorption and desorption time, desorption temperature as well as desorption solution, were investigated. The detection limits for the analysis of indole-3-acetic acid, indole-3-butyric acid, 1-naphthylacetic acid and abscisic acid were achieved below 0.05μgmL(-1). The established method was applied to the analysis of the plant hormones in fruits, vegetables and other food samples. The obtained results indicated that the method was sensitive, accurate, convenient and quick, which provided an alternative analytical approach for plant hormones in complex matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. 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

  4. 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.

  5. Photocatalytic synthesis of TiO(2) and reduced graphene oxide nanocomposite for lithium ion battery.

    PubMed

    Qiu, Jingxia; Zhang, Peng; Ling, Min; Li, Sheng; Liu, Porun; Zhao, Huijun; Zhang, Shanqing

    2012-07-25

    In this work, we synthesized graphene oxide (GO) using the improved Hummers' oxidation method. TiO2 nanoparticles can be anchored on the GO sheets via the abundant oxygen-containing functional groups such as epoxy, hydroxyl, carbonyl, and carboxyl groups on the GO sheets. Using the TiO2 photocatalyst, the GO was photocatalytically reduced under UV illumination, leading to the production of TiO2-reduced graphene oxide (TiO2-RGO) nanocomposite. The as-prepared TiO2, TiO2-GO, and TiO2-RGO nanocomposite were used to fabricate lithium ion batteries (LIBs) as the active anode materials and their corresponding lithium ion insertion/extraction performance was evaluated. The resultant LIBs of the TiO2-RGO nanocomposite possesses more stable cyclic performance, larger reversible capacity, and better rate capability, compared with that of the pure TiO2 and TiO2-GO samples. The electrochemical and materials characterization suggest that the graphene network provides efficient pathways for electron transfer, and the TiO2 nanoparticles prevent the restacking of the graphene nanosheets, resulting in the improvement in both electric conductivity and specific capacity, respectively. This work suggests that the TiO2 based photocatalytic method could be a simple, low-cost, and efficient approach for large-scale production of anode materials for lithium ion batteries.

  6. 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).

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

    DTIC Science & Technology

    1987-12-01

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

  8. A User’s Manual for the DTNSRDC Momentum Integral Boundary-Layer Code for Ship Hulls.

    DTIC Science & Technology

    1980-12-01

    ISTI.IST2,KP1,KP2,TOL,BL) 370 CALL CONTRA(K,N,TOL 380 IF(K.LE.2) GO TO 5 390 CALL POLY(1,IST1,N,KP1) 400 5 CALL OUTPUT(I,IST1,N,KP1,BL) 410 IF(IST1-K...VE(25) 3800 INT=0 3810 DO 12 1-=I., ,KE 3820 IS=11FS(I) .3830 GO TO (12,13,13,28,28,4 ),IS 380 28 INI=INT+2 3850 (3O TO 12 3860 13 lNf=INI+l 381-1...I1,<Pl-) i60 1 - CONTINUE 31-0 URITEU(i,414) 380 WRITE(9,415) 390 WRITE(9.416) 400 WRITE(?.41.7) 410 WRITE(9.418) � iE,’Ab’,412) NINPI 430 GOTO

  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. A Computer System for Generating Single and Double Sampling Plans for Attributes Data.

    DTIC Science & Technology

    1984-08-01

    THE DIFFRENT INSPECIION LEVELS. 0149 C THE USER IS ASKED IF SCHEME EVALUATION IS 0150 C DESIRED IF SO THEN SUBROUTINE OC IS INVOKED. 0151 C 0152 C...0008 C 0009 REAL*8 AG(20,20),BG(20,20) 0010 DIMENSION N(30).PR(30),V(100,50),P(30),TPA(30,4),ASN(30,4) 0011 DIMENSION AOG(30,4),ATI(30,4...NN(4),TM(20,20),ZP(20,20) 0012 DIMENSION ASNC(30),AOQC(30).ATIC(30),AFI(30),PA(30) 0013 INTEGER A(50),R(50),HI,AA(2o4),RR(2,4) 0014 IF(J. EQ. 2) GO

  11. TSARINA: User’s Guide to a Computer Model for Damage Assessment of Complex Airbase Targets.

    DTIC Science & Technology

    1980-07-01

    Y(1I)CT*(XT-X(1)))) GO TO 30 2024 . IF (YT .GT. (Y(2)- T*(IT-X(2)))) GO TO 3? 2025. IF (YT .LT.(Y(4) CT*(XT-X(4)))) GO TO 3C 2026. IF (IT .LT. (Y(1...13*LU + 1 2119. LU = LU + 1 2120. DO 00 J = 1,40 2121o I = 41-J 2122. DO 10 N = 1,129 2123. 10 ICOL(N) = IBK 2124 . ICOL(l) = IE 2125. ICOL(LEN...JUI.OPE.ORL( 2024 )AGE1I14)PATS(4014), 2738. 1 AKRO(126,14).THAP(26,4) .IATERL(26,𔃾).E0LA10.14),SIOCKS(1000.3). 2739. 1 REjUIV(4O0) 27140. COMMON /SIATS / STAY

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

    SciTech Connect

    Marsillac, Sylvain

    2015-11-30

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  14. Combined effects of graphene oxide and Cd on the photosynthetic capacity and survival of Microcystis aeruginosa.

    PubMed

    Tang, Yulin; Tian, Jinglin; Li, Shuyan; Xue, Chonghua; Xue, Zhehua; Yin, Daqiang; Yu, Shuili

    2015-11-01

    In this work, the combined effects of graphene oxide (GO) and Cd(2+) solution on Microcystis aeruginosa were investigated. Chlorophyll fluorescence parameters were measured by a pulse-amplitude modulated fluorometer. GO at low concentrations exhibited no significant toxicity. The presence of GO at low concentrations significantly enhanced Cd(2+) toxicity as the 96 h half maximal effective concentration of the Cd(2+) reduced from 0.51 ± 0.01 to 0.474 ± 0.01 mg/L. However, concentrations of GO above 5mg/L did not significantly increase the toxicity of the Cd(2+)/GO system. Observations through scanning and transmission electron microscopy revealed that GO, with Cd(2+), easily attached to and entered into the algae. Reactive oxygen species and malondialdehyde were measured to explain the toxicity mechanism. The photosynthetic parameters were useful in measuring the combined toxicity of the nanoparticles and heavy metals. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. 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

    2012-06-07

    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.

  16. Anticipation in manual tracking with multiple delays.

    PubMed

    Stepp, Nigel; Turvey, Michael T

    2017-05-01

    Two experiments are reported showing that behavior exhibited in manual tracking is consistent with behavior predicted by a dynamical systems phenomenon known as anticipating synchronization (Voss, 2000). They extend a prior investigation of the effect of delay on anticipatory manual tracking (Stepp, 2009) by also manipulating coupling strength. The coupling scheme in Experiment 1 and that in Experiment 2 go beyond the single delayed feedback coupling used in previous research and articulations of anticipating synchronization. These advanced coupling arrangements are addressed using an extended formulation which allows for multiple feedback delays, a continuous range of delay, or even coupling to real future values. The latter case is specifically investigated in Experiment 2, which utilizes a navigation task that provides a natural way to speak about coupling to future values. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  17. 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.

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

    PubMed

    Peng, Jian; Weng, Jian

    2017-03-15

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

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

    PubMed

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  1. 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

  2. B2G-FAR, a species-centered GO annotation repository.

    PubMed

    Götz, Stefan; Arnold, Roland; Sebastián-León, Patricia; Martín-Rodríguez, Samuel; Tischler, Patrick; Jehl, Marc-André; Dopazo, Joaquín; Rattei, Thomas; Conesa, Ana

    2011-04-01

    Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data. The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips. B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms. The annotation resource is available at http://www.b2gfar.org.

  3. 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.

  4. B2G-FAR, a species-centered GO annotation repository

    PubMed Central

    Götz, Stefan; Arnold, Roland; Sebastián-León, Patricia; Martín-Rodríguez, Samuel; Tischler, Patrick; Jehl, Marc-André; Dopazo, Joaquín; Rattei, Thomas; Conesa, Ana

    2011-01-01

    Motivation: Functional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data. Results: The Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips. Conclusions: B2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms. Availability: The annotation resource is available at http://www.b2gfar.org. Contact: aconesa@cipf.es; sgoetz@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21335611

  5. De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

    PubMed Central

    2012-01-01

    Background Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Results Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80–120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were

  6. De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.

    PubMed

    Ashrafi, Hamid; Hill, Theresa; Stoffel, Kevin; Kozik, Alexander; Yao, Jiqiang; Chin-Wo, Sebastian Reyes; Van Deynze, Allen

    2012-10-30

    Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80-120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  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. 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.

  13. A comprehensive analysis of the Manduca sexta immunotranscriptome

    PubMed Central

    Gunaratna, Ramesh T.; Jiang, Haobo

    2012-01-01

    As a biochemical model, Manduca sexta has substantially contributed to our knowledge on insect innate immunity. The RNA-Seq approach was implemented in three studies to examine tissue immunotranscriptomes of this species. With the latest and largest focusing on highly regulated process- and tissue-specific genes, we further analyzed the same set of data using BLAST2GO to explore functional aspects of the larval fat body (F) and hemocyte (H) transcriptomes with (I) or without (C) immune challenge. Using immunity-related sequences from other insects, we found 383 homologous contigs and compared them with those discovered based on relative abundance changes. The major overlap of the two lists validated our previous research designed for gene discovery and transcript profiling in organisms lacking sequenced genomes. By concatenating the contigs, we established a repertoire of 232 immunity-related genes encoding proteins for pathogen recognition (16%), signal transduction (53%), microbe killing (13%), and others (18%). We examined their transcript levels along with attribute classifications and detected prominent differences in nine of the thirty level 2 gene ontology (GO) categories. The increase in extracellular proteins (155%) was consistent with the highly induced synthesis of defense molecules (e.g., antimicrobial peptides) in fat body after the immune challenge. We identified most members of the putative Toll, IMD, MAPK-JNK-p38, and JAK-STAT pathways and small changes in their mRNA levels. Together, these findings set the stage for on-going analysis of the M. sexta immunogenome. PMID:23178408

  14. 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

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

    PubMed Central

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

    2017-01-01

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

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  18. Removal of sulfamethoxazole and ciprofloxacin from aqueous solutions by graphene oxide.

    PubMed

    Chen, Hao; Gao, Bin; Li, Hui

    2015-01-23

    As a promising nanomaterial, graphene-oxide (GO) has shown great sorption potential for environmental contaminants. This study evaluated the ability and mechanism of GO to remove sulfamethoxazole (SMX) and ciprofloxacin (CIP) from aqueous solution. Experimental and modeling results showed that GO effectively sorbed both CIP and SMX with maximum sorption capacity of 379 and 240 mg g(-1), respectively. The sorption of CIP was mainly controlled by the electrostatic attractions; while SMX sorption was mainly though π-π EDA attraction on the basal planes of the GO. Solution pH showed strong effect on the sorption ability of GO to the two antibiotics: at pH of 2, GO sorption ability decreased for both CIP and SMX; at pH of 9, GO completely lost SMX sorption ability but still showed strong sorption to CIP. Both NaCl and CaCl2 decreased CIP sorption onto GO and CaCl2 showed high efficiency even at low ionic strength. The effect of NaCl and CaCl2 on SMX sorption was weaker, but higher ionic strength also reduced the sorption of SMX onto GO. At solution pH of 2, sorption of CIP destabilized GO suspension to form aggregates. Results obtained from this work demonstrated that GO can be used as an effective adsorbents to removal antibiotics from water. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Prime Contract Awards Alphabetically by Contractor, by State or Country, and Place, FY 88. Part 14. (Monarch Engineering-Ogie Trinidad, Inc.)

    DTIC Science & Technology

    1988-01-01

    zz zzzz Co to 2 Go to coca z ’(.0Co I "NC04 C4-4-4M4 4 -4 .4 Nl -4 4 N. I()0- 1 4 NC4 NN4 C4.4. Nl N4 N1 N* eN4 . U00L 1 4 --4 .4 -4 Sn Ln 4 4 -4...0ൌ . . " N oN C4 O I coca ) I ~ x &- 04 IN UY 0 C I 00 1 1 a 1 0 200 0 0 0 0 0 I00.- I U U 0 0 0 0 0 0. . 0 4- 40M0-4 I4 a . 0 . 00 04 0 0. 14 ’. i...8217I ’U C I > I < 𔃺 � 𔃾Cc00C4 ’ coLA (014 (0 -IN (D( (0D (04 (0( CDv ot 4 " (m104 (1(0A(00-l"NW-a( I1-0ON 1 00 C’ C0 0 00(0(0 00O COW0 0000

  20. Tensor interaction contributions to single-particle energies

    SciTech Connect

    Brown, B. A.; Duguet, T.; Otsuka, T.; Abe, D.; Suzuki, T.

    2006-12-15

    We calculate the contribution of the nucleon-nucleon tensor interaction to single-particle energies with finite-range G-matrix potentials and with zero-range Skyrme potentials. The Skx Skyrme parameters including the zero-range tensor terms with strengths calibrated to the finite-range results are refitted to nuclear properties. The fit allows the zero-range proton-neutron tensor interaction as calibrated to the finite-range potential results which gives the observed change in the single-particle gap {epsilon}(h{sub 11/2})-{epsilon}(g{sub 7/2}) going from {sup 114}Sn to {sup 132}Sn. However, the experimental l dependence of the spin-orbit splittings in {sup 132}Sn and {sup 208}Pb is not well described when the tensor is added, owing to a change in the radial dependence of the total spin-orbit potential. The gap shift and a good fit to the l dependence can be recovered when the like-particle tensor interaction is opposite in sign to that required for the G matrix.

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

    PubMed

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

    2016-06-27

    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.

  2. 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.

  3. Small rocket flowfield diagnostic chambers

    NASA Technical Reports Server (NTRS)

    Morren, Sybil; Reed, Brian

    1993-01-01

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

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

    PubMed

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

    2017-01-01

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

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

    PubMed

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

    2017-01-07

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

  6. A Lumped-Parameter Interior Ballistic Computer Code Using the TTCP (The Technical Cooperation Program) Model

    DTIC Science & Technology

    1988-11-01

    jam (nchpts) if(chdist(l) .ne.0.0)write(3,45,err=-30) 45 forinat(lx,’ # points ? ’) 15 chdist (1) -0. 0 p13-pi/3 .0 b1-0. 0 b2 -0. 0 b^Z -). 0 b4-0. 0...D+P) *(D-P-4 .*X) -4 .*D1SQ)/4./D1/PP2X A1=ATAN(SQRT(1. -B1*Bl)/B1) IF(Al.GT.0.)GO TO 610 Al=PI+Al 610 B2 =( (D+P)* (D-.P-4.*X)+4.*D1SQ)/4./D1,/Lt2X...A2=ATAN(SQRT(1 .- B2 * B2 )/ B2 ) 1 * (2. *Y-P-TW.OX) *(2 .*Y-D+TWOJX)) L1=U42X* (A1*PP2X+A2*tt42X, 650 IF(X.GT.W/2.)GO TO 690 SURF-SO+12 .*(F1+F2+F3) -6

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  9. 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.

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

    PubMed

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

    2017-12-01

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

  11. 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.

  12. 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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2013-06-01

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

  15. 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.

  16. 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.

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

    PubMed Central

    2011-01-01

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

  18. [Antimalarial guidelines and therapy practices of the population of Bouake, Ivory Coast].

    PubMed

    Dossou-Yovo, J; Amalaman, K; Carnevale, P

    2001-01-01

    This survey of 162 households in the city of Bouaké, Côte d'Ivoire was undertaken to study the behavior of the population in diagnosing and treating malaria. Findings indicate that awareness of symptoms and ability to evaluate the severity of malaria is high. In most cases, mild malaria is treated at home. In case of presumptive diagnosis of malaria, 87.6% of households undertake self-treatment, 9.3% seek institutional healthcare, 1.2% go to traditional healers, and 1.9% use traditional remedies. The most frequent drug for primary treatment is chloroquine (68.3%) which is generally obtained from pharmacies (98.8%). However, proper dosages are rarely used. If primary treatment fails, behavior is complex depending on the estimated severity of disease. Although many causes of malaria are mentioned, most people implicate mosquitoes (75.6%). In 95.1% of households surveyed, chloroquine prophylaxis was used for newborns. Most households (89.5%) practice mosquito bite protection but use of mosquito nets is low (4.9%). These results showing the preference for family-based management suggest that informational campaigns are needed to promote effective and consistent home treatment. Education is also needed to increase knowledge about mosquito nets and insecticides.

  19. Nanobubble water's promotion effect of barley (Hordeum vulgare L.) sprouts supported by RNA-Seq analysis.

    PubMed

    Liu, Shu; Oshita, Seiichi; Kawabata, Saneyuki; Thuyet, Dang Quoc

    2017-10-01

    The physiological promotion effect of nanobubble (NB) water on living organism is a still poorly understood phenomenon which was discovered one decade ago. Here, we analysed the barley (Hordeum vulgare L.) embryo transcriptome following exposure to NB water and low concentration hydrogen peroxide (H2O2) using RNA-Seq. We found that 349 genes were differentially expressed in response to 24-h exposure of NB water, and 97 genes were differentially expressed after exposure to H2O2. GO enrichment and cluster analyses revealed that NB water-induced expression of genes related to cell division and cell wall loosening. RNA-Seq, quantitative real-time polymerase chain reaction (qPCR), and enzyme activity measurements all pointed to genes encoding peroxidases as a major factor responsible for the effects of physiological enhancement due to NB water. The exogenous hydroxyl radical (•OH) produced by NB water significantly increased expression of genes related to peroxidase and NADPH, thus leading to an increased endogenous superoxide anion (O2•-) inside the barley seed. Appropriately low concentrations of exogenously added reactive oxygen species (ROS) and endogenous ROS played important roles in plant growth and development. When ROS levels were low, the endogenous ROS was eliminated by ascorbate peroxidase (APX) and other peroxidases instead of activating the catalase (CAT) and superoxidase dismutase (SOD). This dataset will serve as the foundation for a system biology approach to understand NB water's physiological promoting effects on living organisms.

  20. 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.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

    Shelby, Kent S.

    2013-01-01

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

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

    PubMed

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

    2016-08-01

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

  4. Transcriptome analyses of a Chinese hazelnut species Corylus mandshurica

    PubMed Central

    2013-01-01

    Background Corylus was renowned for its production of hazelnut and taxol. To understand the local adaptation of Chinese species and speed up breeding efforts in China, we analyzed the leaf transcriptome of Corylus mandshurica, which had a high tolerance to fungal infections and cold. Results A total of 12,255,030 clean pair-end reads were generated and then assembled into 37,846 Expressed Sequence Tag (EST) sequences. During functional annotation, 26,565 ESTs were annotated with Gene Ontology (GO) terms using Blast2go and 11,056 ESTs were grouped into the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using KEGG Automatic Annotation Server (KAAS). We identified 45 ESTs that were homologous to enzymes and transcription factors responsible for taxol synthesis. The most differentiated orthologs between C. mandshurica and a European congener, C. avellana, were enriched in stress tolerance to fungal resistance and cold. Conclusions In this study, we detected a set of genes related to taxol synthesis in a taxol-producing angiosperm species for the first time and found a close relationship between most differentiated genes and different adaptations to fungal infection and cold in C. mandshurica and C. avellana. These findings provided tools to improve our understanding of local adaptation, genetic breeding and taxol production in hazelnut. PMID:24093758

  5. Transcriptome analyses of a Chinese hazelnut species Corylus mandshurica.

    PubMed

    Ma, Hui; Lu, Zhiqiang; Liu, Bingbing; Qiu, Qiang; Liu, Jianquan

    2013-10-05

    Corylus was renowned for its production of hazelnut and taxol. To understand the local adaptation of Chinese species and speed up breeding efforts in China, we analyzed the leaf transcriptome of Corylus mandshurica, which had a high tolerance to fungal infections and cold. A total of 12,255,030 clean pair-end reads were generated and then assembled into 37,846 Expressed Sequence Tag (EST) sequences. During functional annotation, 26,565 ESTs were annotated with Gene Ontology (GO) terms using Blast2go and 11,056 ESTs were grouped into the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using KEGG Automatic Annotation Server (KAAS). We identified 45 ESTs that were homologous to enzymes and transcription factors responsible for taxol synthesis. The most differentiated orthologs between C. mandshurica and a European congener, C. avellana, were enriched in stress tolerance to fungal resistance and cold. In this study, we detected a set of genes related to taxol synthesis in a taxol-producing angiosperm species for the first time and found a close relationship between most differentiated genes and different adaptations to fungal infection and cold in C. mandshurica and C. avellana. These findings provided tools to improve our understanding of local adaptation, genetic breeding and taxol production in hazelnut.

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

    NASA Astrophysics Data System (ADS)

    Ostovari, Fatemeh; Abdi, Yaser; Ghasemi, Foad

    2012-12-01

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

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

    PubMed

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

    2016-03-09

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

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

    PubMed

    Li, Haiyan; Smigocki, Ann C

    2016-10-03

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

  9. Identification of the secreted watery saliva proteins of the rice brown planthopper, Nilaparvata lugens (Stål) by transcriptome and Shotgun LC-MS/MS approach.

    PubMed

    Liu, Xiaoqing; Zhou, Hanyu; Zhao, Jing; Hua, Hongxia; He, Yueping

    2016-06-01

    The rice brown planthopper, Nilaparvata lugens (Stål), a major rice insect pest in Asia, is a vascular bundle-feeder that ejects gelling and watery saliva during the feeding process. Although major proteins in the salivary glands of N. lugens have been identified using 2D PAGE, very little is known about the secreted saliva of this insect. In this study, we identified the major proteins in the secreted watery saliva of N. lugens, via collecting from a sucrose diet that adult planthoppers had fed upon through a membrane of stretched parafilm, and using shotgun LC-MS/MS analysis with reference to transcriptome database of salivary glands of N. lugens. A total of 107 proteins were identified in the watery saliva of N. lugens, over 80% of which showed significant similarity to known proteins. When annotated by the Blast2GO suite, 29 proteins had catalytic activity and 24 proteins were binding proteins. The saliva enzymes included oxidoreductases, hydrolases, phosphatases, peptidases (proteases), kinases, transferases, and lyases. Binding proteins in N. lugens watery saliva included ATP-binding, lipophorin, calcium-binding, actin-binding and DNA-, RNA-, and chromatin-binding proteins. Other non-enzymatic proteins, such as ubiquitins, heat shock proteins, ribosomal proteins, and immunoglobulin proteins were also found in N. lugens watery saliva. This is the first study to identify, characterize and list the proteins in watery saliva of N. lugens, which might be involved in planthopper-rice interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2013-12-01

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

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

    PubMed

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

    2011-03-01

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

  12. 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

  13. 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.

  14. In vivo nanotoxicological profile of graphene oxide

    NASA Astrophysics Data System (ADS)

    Durán, Marcela; Durán, Nelson; Fávaro, Wagner J.

    2017-06-01

    Graphene oxide, a widely studied nano materials, exhibits numerous beneficial effects in medical devices. The graphene sample Graphene oxide (GO):Single-layer graphene oxide, purity 99%, thickness 0.7-1.2 nm (AFM); ~300-800nm X&Y dimensions is the standard size <450 nm & 1-20 µm lateral dimensions from Cheap Tubes Inc., Bratleboro, USA was selected for this study. Characterization of GO and stability were previously studied. All the assays were carried out at a concentration of 1 mg/mL (stock suspension by ultrasonication)(stable 10 days). In this study the first parameter evaluated was in animal toxicity in acute and chronic responses. The second one was to observe the morphology and histological changes on major organs, like signs of inflammatory areas. A total of 25 rats (Fischer 344) were divide in 5 groups (n = 5 animals): negative control group (NCT); Positive cancer control group (PCCT); GO group-1 (GO 1); GO group-2 (GO 2) and GO group-3 (GO 3), with different concentrations of graphene oxide. All the groups were treated by via intra peritoneal (i.p) administration. Biochemical and histopathology results of acute toxicity showed no alterations. In the chronic toxicity was found deposit sections and morphology alterations in different tissues (inflammations). Genotoxicity was dose dependent of GO. This study gave us the limit concentrations of GO free for any biological study.

  15. 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.

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

    PubMed

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

    2013-09-01

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

  18. Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray

    PubMed Central

    Lenz, Petra H.; Unal, Ebru; Hassett, R. Patrick; Smith, Christine M.; Bucklin, Ann; Christie, Andrew E.; Towle, David W.

    2012-01-01

    The copepod, Calanus finmarchicus is a keystone species for the North Atlantic. Because of recent changes in the geographic distribution of this species, there are questions as to how this organism responds physiologically to environmental cues. Molecular techniques allow for examination and new understanding of these physiological changes. Here, we describe the development of a microarray for high-throughput studies of the physiological ecology of C. finmarchicus. An EST database was generated for this species using a normalized cDNA library derived from adult and sub-adult individuals. Sequence data were clustered into contigs and annotated using Blastx. Target transcripts were selected, and unique, 50 base-pair, oligomer probes were generated for 995 genes. Blast2GO processing provided detailed information on gene function. The selected targets included broad representation of biological processes, cellular components, and molecular functions. The microarray was tested in two sets of comparisons: adult females maintained at different food concentrations and field-caught sub-adults showing differences in lipid storage. Up-regulated and down-regulated transcripts were identified for both comparisons. Only a small subset of the genes up-regulated in low food individuals were also up-regulated in lipid-poor animals; no overlap was seen between the genes down-regulated in the two comparisons. PMID:22277925

  19. High-throughput sequencing of black pepper root transcriptome.

    PubMed

    Gordo, Sheila M C; Pinheiro, Daniel G; Moreira, Edith C O; Rodrigues, Simone M; Poltronieri, Marli C; de Lemos, Oriel F; da Silva, Israel Tojal; Ramos, Rommel T J; Silva, Artur; Schneider, Horacio; Silva, Wilson A; Sampaio, Iracilda; Darnet, Sylvain

    2012-09-17

    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. 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. 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.

  20. Strain hardening and ductility of iron: axisymmetric vs plane strain elongation. Technical progress report

    SciTech Connect

    Langford, G.

    1980-05-01

    The strain hardening of iron at high strains in plane strain elongation (strip drawing) is shown to fall increasingly below that of drawn iron wires at true strains above 2, going through zero strain hardening at epsilon = 3.0, and becoming strongly negative thereafter, at least up to epsilon = 4.1. High resolution selected area electron diffraction has been used to map the size, shape and crystallographic orientations of a group of about 50 contiguous cells centered around an incipient shear band in an edge section of a strip drawn to epsilon = 1.8. This map shows no textural instability or change in orientation associated with the shear band, although it does show substantial misorientations throughout the group of cells, the axis of these misorientations lying in the same direction as the trace of the shear band. No other large misorientations (i.e. 5/sup 0/ or so) are present. The only instability seen in this shear band is microstructural: the slip distances in the two primary slip directions are quite anisotropic, being much longer along the trace of the shear band. Note that this shear band has appeared during the linear hardening portion of the high-strain hardening curve of the drawn strip. It is therefore considered a direct weakening mechanism rather than a result of another weakening effect. Further such orientation maps have been or are being prepared for more highly deformed strip, and for wire and pure-shear specimens as well.

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed

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

    2015-02-13

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

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

    PubMed

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

    2017-02-01

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

  4. SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

    PubMed Central

    Arnold, Roland; Goldenberg, Florian; Mewes, Hans-Werner; Rattei, Thomas

    2014-01-01

    The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith–Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads. PMID:24165881

  5. Graphene oxide as electron shuttle for increased redox conversion of contaminants under methanogenic and sulfate-reducing conditions.

    PubMed

    Colunga, Alejandra; Rangel-Mendez, J Rene; Celis, Lourdes B; Cervantes, Francisco J

    2015-01-01

    Graphene oxide (GO) is reported for the first time as electron shuttle to increase the redox conversion of the azo compound, reactive red 2 (RR2, 0.5mM), and the nitroaromatic, 3-chloronitrobenzene (3CNB, 0.5mM). GO (5mgL(-1)) increased 10-fold and 7.6-fold the reduction rate of RR2 and 3CNB, respectively, in abiotic incubations with sulfide (2.6mM) as electron donor. GO also increased by 2-fold and 3.6-fold, the microbial reduction rate of RR2 by anaerobic sludge under methanogenic and sulfate-reducing conditions, respectively. Deep characterization of GO showed that it has a proper size distribution (predominantly between 450 and 700nm) and redox potential (+50.8mV) to promote the reduction of RR2 and 3CNB. Further analysis revealed that biogenic sulfide plays a major role on the GO-mediated reduction of RR2. GO is proposed as an electron shuttle to accelerate the redox conversion of recalcitrant pollutants, such as nitro-benzenes and azo dyes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. 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

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

    PubMed

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

    2016-01-01

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

  8. 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.

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

    PubMed Central

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

    2016-01-01

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

  10. Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes.

    PubMed

    Freitas, Robert Cardoso de; Odisi, Estácio Jussie; Kato, Chiaki; da Silva, Marcus Adonai Castro; Lima, André Oliveira de Souza

    2017-07-22

    Deep-sea bacteria can produce various biotechnologically relevant enzymes due to their adaptations to high pressures and low temperatures. To identify such enzymes, we have sequenced the genome of the polycaprolactone-degrading bacterium Moritella sp. JT01, isolated from sediment samples from Japan Trench (6957 m depth), using a Illumina HiSeq2000 sequencer (12.1 million paired-end reads) and CLC Genomics Workbench (version 6.5.1) for the assembly, resulting in a 4.83-Mb genome (42 scaffolds). The genome was annotated using Rapid Annotation using Subsystem Technology (RAST), Protein Homology/analogY Recognition Engine V 2.0 (PHYRE2), and BLAST2Go, revealing 4439 protein coding sequences and 101 RNAs. Gene products with industrial relevance, such as lipases (three) and esterases (four), were identified and are related to bacterium's ability to degrade polycaprolactone. The annotation revealed proteins related to deep-sea survival, such as cold-shock proteins (six) and desaturases (three). The presence of secondary metabolite biosynthetic gene clusters suggests that this bacterium could produce nonribosomal peptides, polyunsaturated fatty acids, and bacteriocins. To demonstrate the potential of this genome, a lipase was cloned an introduced into Escherichia coli. The lipase was purified and characterized, showing activity over a wide temperature range (over 50% at 20-60 °C) and pH range (over 80% at pH 6.3 to 9). This enzyme has tolerance to the surfactant action of sodium dodecyl sulfate and shows 30% increased activity when subjected to a working pressure of 200 MPa. The genomic characterization of Moritella sp. JT01 reveals traits associated with survival in the deep-sea and their potential uses in biotechnology, as exemplified by the characterized lipase.

  11. HIV/AIDS in older adults: a case report and literature review.

    PubMed

    Inelman, Emine Meral; Gasparini, Giulia; Enzi, Giuliano

    2005-09-01

    A 75-year-old man presented in May 2003 with suspected drop attack (atonic seizure). He reported falling over and losing consciousness. He was a retired, single ex-smoker, who lived alone in an apartment that was in a poor state of repair with precarious hygienic conditions. Over the course of 2 years he had unintentionally lost more than 10 kg (22 lbs) in weight. He had been diagnosed with diabetes approximately 10 years prior, and was receiving treatment with oral hypoglycemic therapy (fenformin/ glibenclamide, 25/2.5 mg, bid). He had been hospitalized for pneumonia in 2000. In recent months, he had gone to the emergency department several times (about once every 2 weeks) due to his weight loss and asthenia, without obtaining a definite diagnosis. On physical examination, his cognitive status was normal, but his nutritional status was deteriorated. Other clinical findings were negative. Blood chemistry tests revealed hypoalbuminemia (26.00 g/L). His personal hygiene was precarious and the apartment was completely neglected despite assistance by social support networks. In conversation with the social support worker, it was revealed that the patient was homosexual; with the patient's informed consent, he was tested and found positive for HIV. He was consequently transferred to the Infectious Diseases Department where further biochemical tests revealed: HIV-RNA Quantitative > 100.000 copies/ML COBAS Amplicor, antibodies anti-HIV 1-2 reactive sample (Enzygnost HIV Integral and Axsym HIV 1/2 GO [Abbott] EIA method, antibodies anti-HIV 1 positive (Western Blot). The patient's serum also tested positive for syphilis (TPHA positive 1:320). The patient refused any specific treatment, left the hospital, and was lost to follow-up.

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

    PubMed Central

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

    2016-01-01

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

  13. Expression of CD33 is a predictive factor for effect of gemtuzumab ozogamicin at different doses in adult acute myeloid leukaemia.

    PubMed

    Khan, N; Hills, R K; Virgo, P; Couzens, S; Clark, N; Gilkes, A; Richardson, P; Knapper, S; Grimwade, D; Russell, N H; Burnett, A K; Freeman, S D

    2017-05-01

    It remains unclear in adult acute myeloid leukaemia (AML) whether leukaemic expression of CD33, the target antigen for gemtuzumab ozogamicin (GO), adds prognostic information on GO effectiveness at different doses. CD33 expression quantified in 1583 patients recruited to UK-NCRI-AML17 (younger adults) and UK-NCRI-AML16 (older adults) trials was correlated with clinical outcomes and benefit from GO including a dose randomisation. CD33 expression associated with genetic subgroups, including lower levels in both adverse karyotype and core-binding factor (CBF)-AML, but was not independently prognostic. When comparing GO versus no GO (n=393, CBF-AMLs excluded) by stratified subgroup-adjusted analysis, patients with lowest quartile (Q1) %CD33-positivity had no benefit from GO (relapse risk, HR 2.41 (1.27-4.56), P=0.009 for trend; overall survival, HR 1.52 (0.92-2.52)). However, from the dose randomisation (NCRI-AML17, n=464, CBF-AMLs included), 6 mg/m(2) GO only had a relapse benefit without increased early mortality in CD33-low (Q1) patients (relapse risk HR 0.64 (0.36-1.12) versus 1.70 (0.99-2.92) for CD33-high, P=0.007 for trend). Thus CD33 expression is a predictive factor for GO effect in adult AML; although GO does not appear to benefit the non-CBF AML patients with lowest CD33 expression a higher GO dose may be more effective for CD33-low but not CD33-high younger adults.

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

    PubMed

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

    2017-01-01

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

  15. 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.

  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. Simple Synthesis of Molybdenum Disulfide/Reduced Graphene Oxide Composite Hollow Microspheres as Supercapacitor Electrode Material

    PubMed Central

    Xiao, Wei; Zhou, Wenjie; Feng, Tong; Zhang, Yanhua; Liu, Hongdong; Tian, Liangliang

    2016-01-01

    MoS2/RGO composite hollow microspheres were hydrothermally synthesized by using SiO2/GO microspheres as a template, which were obtained via the sonication-assisted interfacial self-assembly of tiny GO sheets on positively charged SiO2 microspheres. The structure, morphology, phase, and chemical composition of MoS2/RGO hollow microspheres were systematically investigated by a series of techniques such as FE-SEM, TEM, XRD, TGA, BET, and Raman characterizations, meanwhile, their electrochemical properties were carefully evaluated by CV, GCD, and EIS measurements. It was found that MoS2/RGO hollow microspheres possessed unique porous hollow architecture with high-level hierarchy and large specific surface area up to 63.7 m2·g−1. When used as supercapacitor electrode material, MoS2/RGO hollow microspheres delivered a maximum specific capacitance of 218.1 F·g−1 at the current density of 1 A·g−1, which was much higher than that of contrastive bare MoS2 microspheres developed in the present work and most of other reported MoS2-based materials. The enhancement of supercapacitive behaviors of MoS2/RGO hollow microspheres was likely due to the improved conductivity together with their distinct structure and morphology, which not only promoted the charge transport but also facilitated the electrolyte diffusion. Moreover, MoS2/RGO hollow microsphere electrode displayed satisfactory long-term stability with 91.8% retention of the initial capacitance after 1000 charge/discharge cycles at the current density of 3 A·g−1, showing excellent application potential. PMID:28773904

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

    PubMed Central

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

    2016-01-01

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

  19. RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing.

    PubMed

    Gupta, Vikas; Estrada, April D; Blakley, Ivory; Reid, Rob; Patel, Ketan; Meyer, Mason D; Andersen, Stig Uggerhøj; Brown, Allan F; Lila, Mary Ann; Loraine, Ann E

    2015-01-01

    Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits. Toward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3' end formation. We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.

  20. Effect of hydroxypropyl cellulose (HPC), polyvinylpyrrolidone (PVP) and polyethylene glycol (PEG) on Nd-TiO2/graphene oxide nanocomposite for removal of lead(II) and copper(II) from aquatic media.

    PubMed

    Samadi, Susan; Mirseyfifard, Sayed Mohammad Hosain; Assari, Mina; Hassannejad, Marzieh

    2017-07-01

    In order to investigate the effect of hydroxypropyl cellulose (HPC), polyvinylpyrrolidone (PVP) and polyethylene glycol (PEG) on adsorbing capacity of nanosorbent Nd-TiO2/GO, Nd-TiO2/HPC/GO, Nd-TiO2/PVP/GO and Nd-TiO2/PEG/GO nanocomposites were synthesized. Studies by Fourier transform infrared spectroscopy confirmed the expected structure and X-ray diffraction results confirmed the formation of crystalline phase of anatase titania and also graphene oxide (GO). Scanning electron microscopy pictures and energy dispersive X-ray spectroscopy analysis showed the formation of Nd-TiO2 nanoparticles. These nanocomposites were used for removal of lead(II) and copper(II) from water and the effective factors on removal were optimized. The results showed that the maximum removal for all three nanocomposites was at pH = 7. The amount of adsorbent and contact time for Nd-TiO2/HPC/GO and Nd-TiO2/PVP/GO nanocomposites was equal to 0.02 g and 20 minutes respectively, but they were equal to 0.01 g and 15 minutes for Nd-TiO2/PEG/GO nanocomposite. Investigating the effect of interfering ions showed they had no considerable effect on removal efficiency. In order to investigate the effect of photocatalytic activity in optimal conditions and in the presence of visible-ultraviolet light, the removal process was performed. The results showed an increase in removal efficiency. Furthermore, the ability of synthesized nanosorbents to decompose organic compounds available in water was confirmed and their energy band gaps were calculated.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. iTRAQ-based Protein Profiling and Fruit Quality Changes at Different Development Stages of Oriental Melon.

    PubMed

    Guo, Xiaoou; Xu, Jingjing; Cui, Xiaohui; Chen, Hao; Qi, Hongyan

    2017-01-28

    Oriental melon is one of the most popular crops for its nutritional and flavour quality. Components that determine melon quality, such as sugar, colour, texture, flavour and aroma, among other factors, accumulate in different developmental stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in the oriental melon is very important for advancing our understanding of oriental melon quality in the ripening processes. iTRAQ-based protein profiling was conducted on 'YuMeiren' oriental melon fruit at different developmental stages. Physiological quality indices, including firmness, rind colour, soluble solids content (SSC), ethylene production, sugar content and volatile compounds were also characterized during four maturity periods of the melon, including 5, 15, 25 and 35 days after anthesis (DAA). A principal component analysis (PCA) revealed that the aroma volatiles at 5 DAA and 15 DAA were similar and separated from that of 35 DAA. More than 5835 proteins were identified and quantified in the two biological repeats and divided into 4 clusters by hierarchical cluster analysis. A functional analysis was performed using Blast2GO software based on the enrichment of a GO analysis for biological process, molecular function and cellular components. The main KEGG pathways, such as glycolysis, α-linolenic acid and starch and sucrose metabolism, were analyzed. The gene family members corresponding to differentially expressed proteins, including lipoxygenase (CmLOX01-18) and alcohol acetyltransferase (CmAAT1-4) involved in the α-linolenic acid metabolic pathway, were verified with real-time qPCR. The results showed that the expression patterns of 64.7% of the genes were consistent with the expression patterns of the corresponding proteins. This study combined the variation of the quality index and differentially expressed proteins of oriental melon at different developmental stages that laid the foundation for the

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

    PubMed

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

    2017-03-01

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

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

    PubMed

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

    2017-03-15

    Fluoxetine (Flx) is the principal treatment for depression; however, the precise mechanisms of its actions remain elusive. Our aim was to identify protein expression changes within rat hippocampus regulated by chronic Flx treatment versus vehicle-controls using proteomics. Fluoxetine-hydrohloride (15mg/kg) was administered daily to adult male Wistar rats for 3weeks, and cytosolic and nonsynaptic mitochondrial hippocampal proteomes were analyzed. All differentially expressed proteins were functionally annotated according to biological process and molecular function using Uniprot and Blast2GO. Our comparative study revealed that in cytosolic and nonsynaptic mitochondrial fractions, 60 and 3 proteins respectively, were down-regulated, and 23 and 60 proteins, respectively, were up-regulated. Proteins differentially regulated in cytosolic and nonsynaptic mitochondrial fractions were primarily related to cellular and metabolic processes. Of the identified proteins, the expressions of calretinin and parvalbumine were confirmed. The predominant molecular functions of differentially expressed proteins in both cell hippocampal fractions were binding and catalytic activity. Most differentially expressed proteins in nonsynaptic mitochondria were catalytic enzymes involved in the pyruvate metabolism, citric acid cycle, oxidative phosphorylation, ATP synthesis, ATP transduction and glutamate metabolism. Results indicate that chronic Flx treatment may influence proteins involved in calcium signaling, cytoskeletal structure, chaperone system and stimulates energy metabolism via the upregulation of GAPDH expression in cytoplasm, as well as directing energy metabolism toward the citric acid cycle and oxidative phosphorylation in nonsynaptic mitochondria. This approach provides new insight into the chronic effects of Flx treatment on protein expression in a key brain region associated with stress response and memory. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. 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.

  9. Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.)

    PubMed Central

    2011-01-01

    Background Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310) and two resistant yam genotypes (TDa 87-01091, TDa 95-0328) challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species. PMID:21303556

  10. Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.).

    PubMed

    Narina, Satya S; Buyyarapu, Ramesh; Kottapalli, Kameswara Rao; Sartie, Alieu M; Ali, Mohamed I; Robert, Asiedu; Hodeba, Mignouna J D; Sayre, Brian L; Scheffler, Brian E

    2011-02-09

    Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310) and two resistant yam genotypes (TDa 87-01091, TDa 95-0328) challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species.

  11. 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.

  12. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    2013-01-01

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

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

    PubMed

    Vieira, Pabline Marinho; Coelho, Alexandre Siqueira Guedes; Steindorff, Andrei Stecca; de Siqueira, Saulo José Linhares; Silva, Roberto do Nascimento; Ulhoa, Cirano José

    2013-03-15

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

  16. 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.

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

    PubMed

    Falda, Marco; Toppo, Stefano; Pescarolo, Alessandro; Lavezzo, Enrico; Di Camillo, Barbara; Facchinetti, Andrea; Cilia, Elisa; Velasco, Riccardo; Fontana, Paolo

    2012-03-28

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

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

    PubMed

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

    2016-12-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  1. Synthesis of size-tunable anatase TiO₂ nanospindles and their assembly into anatase@titanium oxynitride/titanium nitride-graphene nanocomposites for rechargeable lithium ion batteries with high cycling performance.

    PubMed

    Qiu, Yongcai; Yan, Keyou; Yang, Shihe; Jin, Limin; Deng, Hong; Li, Weishan

    2010-11-23

    This paper embarks upon three levels of undertaking ranging from nanomaterials synthesis to assembly and functionalization. First, we have prepared size-tunable anatase TiO(2) nanospindles via a hydrothermal process by using tubular titanates as self-sacrificing precursors. Second, we have densely dispersed the TiO(2) nanospindles onto functional graphene oxides (GO) via a spontaneous self-assembly process. After annealing of the TiO(2)/GO hybrid nanocomposite in an NH(3) gas flow, the TiO(2) surface was effectively nitridated and the GO was reduced to graphene sheets (GS) in order to further fortify the electronic functionality of the nanocomposite. Third, the anatase@oxynitride/titanium nitride-GS (TiO(2)@TiO(x)N(y)/TiN-GS) hybrid nanocomposite was studied as an anode material for lithium-ion batteries (LIBs), showing excellent rate capability and cycling performance compared to the pure TiO(2) nanospindles. Our systematic studies have revealed that the TiO(2)@TiO(x)N(y)/TiN-GS nanocomposites with graphene nanosheets covered with the TiO(2)@TiO(x)N(y)/TiN nanospindles on both sides provide a promising solution to the problems of poor electron transport and severe aggregation of TiO(2) nanoparticles by enhancing both electron transport through the conductive matrix and Li-ion accessibility to the active material from the liquid electrolyte. More generally, the size-tunable TiO(2) nanospindles with their unique (101) outer surface planes provide an archetype for the in depth investigation of their surface-specific and size-dependent physicochemical properties.

  2. 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

    2015-03-20

    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.

  3. Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam].

    PubMed

    Tao, Xiang; Gu, Ying-Hong; Wang, Hai-Yan; Zheng, Wen; Li, Xiao; Zhao, Chuan-Wu; Zhang, Yi-Zheng

    2012-01-01

    Sweet potato (Ipomoea batatas L. [Lam.]) ranks among the top six most important food crops in the world. It is widely grown throughout the world with high and stable yield, strong adaptability, rich nutrient content, and multiple uses. However, little is known about the molecular biology of this important non-model organism due to lack of genomic resources. Hence, studies based on high-throughput sequencing technologies are needed to get a comprehensive and integrated genomic resource and better understanding of gene expression patterns in different tissues and at various developmental stages. Illumina paired-end (PE) RNA-Sequencing was performed, and generated 48.7 million of 75 bp PE reads. These reads were de novo assembled into 128,052 transcripts (≥ 100 bp), which correspond to 41.1 million base pairs, by using a combined assembly strategy. Transcripts were annotated by Blast2GO and 51,763 transcripts got BLASTX hits, in which 39,677 transcripts have GO terms and 14,117 have ECs that are associated with 147 KEGG pathways. Furthermore, transcriptome differences of seven tissues were analyzed by using Illumina digital gene expression (DGE) tag profiling and numerous differentially and specifically expressed transcripts were identified. Moreover, the expression characteristics of genes involved in viral genomes, starch metabolism and potential stress tolerance and insect resistance were also identified. The combined de novo transcriptome assembly strategy can be applied to other organisms whose reference genomes are not available. The data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest in sweet potato. Characterization of sweet potato transcriptome provides an effective tool for better understanding the molecular mechanisms of cellular processes including development of leaves and storage roots, tissue-specific gene expression, potential biotic and abiotic stress response in sweet

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

    PubMed

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

    2012-01-15

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

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

    PubMed

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

    2009-03-14

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

  6. 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/.

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

    PubMed Central

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

    2017-01-01

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

  8. 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

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

    PubMed

    Garzón-Martínez, Gina A; Zhu, Z Iris; Landsman, David; Barrero, Luz S; Mariño-Ramírez, Leonardo

    2012-04-25

    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. 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. 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 Solanaceae family members, S

  10. Chemical and structural properties of Pd nanoparticle-decorated graphene-Electron spectroscopic methods and QUASES

    NASA Astrophysics Data System (ADS)

    Lesiak, B.; Jiricek, P.; Bieloshapka, I.

    2017-05-01

    Graphite (Gr) and carbon nanomaterials such as graphene oxide (GO) and reduced graphene oxide (RGO) and those decorated with Pd nanoparticles were investigated by photoelectron spectroscopy (XPS) aided with Quantitative Analysis of Surfaces by Electron Spectroscopy (QUASES) and reflected electron energy loss spectroscopy (REELS). Oxidation of Gr decreased the C/O ratio from 10 (Gr) to 2.2 (GO), whereas reduction of GO by N2H4 increased this ratio to 6.6 (RGO) due to decreasing number of oxygen groups (hydroxyl, epoxy, carbonyl and hydroxyl). Graphene materials and those after Pd decoration had 6-11 average number of layers in stacked nanostructures. Pd decoration using NaBH4-reducing agents formed nanoparticles of size 6.9 nm (Pd/Gr) > 5.3 nm (Pd/RGO) > 4.25 nm (Pd/GO), with PdOx overlayer thickness of 2.20 nm (Pd/GO) > 1.42 nm (Pd/Gr) > 1.20 nm (Pd/RGO), decreased number of oxygen groups and average number of layers. Smaller Pd nanoparticles of larger PdOx overlayer thickness were observed on highly hydrophilic substrates (functional oxygen groups content). Decoration accompanied by reduction using NaBH4 led to the removal of water attached by hydrogen bonding to graphene interplanes and the formation of PdOx overlayer from oxygen functional groups. Nanoparticle size obtained from QUASES was confirmed by Pd 3d5/2 spectra binding energy and full-width at half maximum. Various chemistry and mechanisms of graphene reduction using N2H4 and NaBH4 were observed, where NaBH4 was more efficient to remove water bonded by hydrogen bonding to oxygen groups and thus further graphene exfoliation. A substantial influence of substrate, functional group content on nanoparticle coverage, size and Pd oxide overlayer thickness was observed.

  11. Nickel-iron battery system safety. Final report

    SciTech Connect

    Saltat, R.

    1984-06-01

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

  12. Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers.

    PubMed

    Grover, Atul; Kumari, Maya; Singh, Sadhana; Rathode, Shivender Singh; Gupta, Sanjay Mohan; Pandey, Pankaj; Gilotra, Sween; Kumar, Devender; Arif, Mohommad; Ahmed, Zakwan

    2014-01-01

    Oil-rich seeds of Jatropha curcas are being focussed as a source of bio-diesel. However, prior to its industrial use, a lot of crop improvement efforts are required in Jatropha. Availability of a large number of EST sequences of Jatropha in public domain allow identification of candidate genes for several agronomic characters including oil content in seeds. Here, we have analysed 42,477 ESTs of Jatropha spanning 22.9 Mbp for microsatellites and fatty acid metabolism related sequences. Unigene sequences were built using CAP 3 programme resulted in 12,358 contigs and 5,730 singlets. Nearly, 8 % unigenes showed presence of microsatellites, slightly over-represented compared to their occurrence in ESTs. Most of the microsatellites were either di- or tri-nucleotide repeats, while other categories of tetra-, penta- and hexa-nucleotide repeats together constituted ~4 % of total microsatellites. Assessment of functional relevance of unigenes was carried out using Blast2GO using its default settings. The overall sequence similarity level against sequences in 'nr' database was >80 %. A total of 931 sequences that participated in any of the pathways related to fatty acid or lipid metabolism were found at GO level 6. Among these, GO terms "Fatty acid metabolic process" and "Fatty acid biosynthetic process" were most over-represented. Overall, our work has due relevance in identifying molecular markers for the candidate genes for oil content in Jatropha seeds, and will prove to be an important reference for further studies for identification of trait specific markers in Jatropha.

  13. 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.

  14. 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.

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

    PubMed Central

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

    2013-01-01

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

  16. 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

  17. Transcriptomics reveals tissue/organ-specific differences in gene expression in the starfish Patiria pectinifera.

    PubMed

    Kim, Chan-Hee; Go, Hye-Jin; Oh, Hye Young; Jo, Yong Hun; Elphick, Maurice R; Park, Nam Gyu

    2017-09-09

    Starfish (Phylum Echinodermata) are of interest from an evolutionary perspective because as deuterostomian invertebrates they occupy an "intermediate" phylogenetic position with respect to chordates (e.g. vertebrates) and protostomian invertebrates (e.g. Drosophila). Furthermore, starfish are model organisms for research on fertilization, embryonic development, innate immunity and tissue regeneration. However, large-scale molecular data for starfish tissues/organs are limited. To provide a comprehensive genetic resource for the starfish Patiria pectinifera, we report de novo transcriptome assemblies and global gene expression analysis for six P. pectinifera tissues/organs - body wall (BW), coelomic epithelium (CE), tube feet (TF), stomach (SM), pyloric caeca (PC) and gonad (GN). A total of 408 million high-quality reads obtained from six cDNA libraries were assembled de novo using Trinity, resulting in a total of 549,598 contigs with a mean length of 835 nucleotides (nt), an N50 of 1473nt, and GC ratio of 42.5%. A total of 126,136 contigs (22.9%) were obtained as predicted open reading frames (ORFs) by TransDecoder, of which 102,187 were annotated with NCBI non-redundant (NR) hits, and 51,075 and 10,963 were annotated with Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) using the Blast2GO program, respectively. Gene expression analysis revealed that tissues/organs are grouped into three clusters: BW/CE/TF, SM/PC, and GN, which likely reflect functional relationships. 2408, 8560, 2687, 1727, 3321, and 2667 specifically expressed genes were identified for BW, GN, PC, CE, SM and TF, respectively, using the ROKU method. This study provides a valuable transcriptome resource and novel molecular insights into the functional biology of different tissues/organs in starfish as a model organism. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Modulating Electronic Properties of Monolayer MoS2 via Electron-Withdrawing Functional Groups of Graphene Oxide.

    PubMed

    Oh, Hye Min; Jeong, Hyun; Han, Gang Hee; Kim, Hyun; Kim, Jung Ho; Lee, Si Young; Jeong, Seung Yol; Jeong, Sooyeon; Park, Doo Jae; Kim, Ki Kang; Lee, Young Hee; Jeong, Mun Seok

    2016-11-22

    Modulation of the carrier concentration and electronic type of monolayer (1L) MoS2 is highly important for applications in logic circuits, solar cells, and light-emitting diodes. Here, we demonstrate the tuning of the electronic properties of large-area 1L-MoS2 using graphene oxide (GO). GO sheets are well-known as hole injection layers since they contain electron-withdrawing groups such as carboxyl, hydroxyl, and epoxy. The optical and electronic properties of GO-treated 1L-MoS2 are dramatically changed. The photoluminescence intensity of GO-treated 1L-MoS2 is increases by more than 470% compared to the pristine sample because of the increase in neutral exciton contribution. In addition, the A1g peak in Raman spectra shifts considerably, revealing that GO treatment led to the formation of p-type doped 1L-MoS2. Moreover, the current vs voltage (I-V) curves of GO-coated 1L-MoS2 field effect transistors show that the electron concentration of 1L-MoS2 is significantly lower in comparison with pristine 1L-MoS2. Current rectification is also observed from the I-V curve of the lateral diode structure with 1L-MoS2 and 1L-MoS2/GO, indicating that the electronic structure of MoS2 is significantly modulated by the electron-withdrawing functional group of GO.

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

    PubMed

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

    2011-02-01

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

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

    PubMed

    Bhattacharya, Anindya; Cui, Yan

    2016-01-04

    SomamiR 2.0 (http://compbio.uthsc.edu/SomamiR) is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). Here, we describe the recent major updates to the SomamiR database. We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. Recently, a large number of miRNA target sites have been discovered by newly emerged high-throughput technologies for mapping the miRNA interactome. We have mapped 388 247 somatic mutations to the experimentally identified miRNA target sites. The updated database also includes a list of somatic mutations in the miRNA seed regions, which contain the most important guiding information for miRNA target recognition. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA-ceRNA interactions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette.

    PubMed

    Kenny, Nathan J; Shimeld, Sebastian M

    2012-11-01

    Recent advances in both next-generation sequencing and assembly programmes have made the low-cost construction of transcriptome datasets for non-model species feasible, capable of yielding a raft of information even from less well-transcribed genes. Here we present the results of assemblies performed on a 51-bp paired end Illumina dataset derived from a mixed larval sample of the annelid Pomatoceros lamarckii at 24, 48 and 72 h post-fertilization. We used Oases to assemble 36.5 million paired end reads with k-mer sizes from 21 to 29, followed by amalgamation of assemblies, redundancy removal with Vmatch and TGICL and removal of contigs less than 500 bp in length. This resulted in a final assembly of 50,151 contigs, with a mean length of 1,221 bp and covering 61.3 Mbp. A total of 34,846 (69.4 %) of these returned a BlastX hit above a cutoff of 1.0e (-3), and 17,967 (35.8 %) were assigned at least one GO annotation using Blast2GO. We used the assembly to identify genes belonging to the homeobox superclass and the Fox, Sox and Tbx classes, recovering 37, 16, four and three genes, respectively. This included orthologues of genes previously unidentified in lophotrochozoans and protostomes. Our study illustrates the utility of such transcriptomic assembly methods as a gene discovery tool and greatly expands our knowledge of transcription factor genes in annelids in general and in this species in particular.

  2. 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

  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. 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. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers.

    PubMed

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

    2012-01-01

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

  6. Gene expression patterns regulating embryogenesis based on the integrated de novo transcriptome assembly of the Japanese flounder.

    PubMed

    Fu, Yuanshuai; Jia, Liang; Shi, Zhiyi; Zhang, Junling; Li, Wenjuan

    2017-06-01

    The Japanese flounder (Paralichthys olivaceus) is one of the most important commercial and biological marine fishes. However, the molecular biology involved during embryogenesis and early development of the Japanese flounder remains largely unknown due to a lack of genomic resources. A comprehensive and integrated transcriptome is necessary to study the molecular mechanisms of early development and to allow for the detailed characterization of gene expression patterns during embryogenesis; this approach is critical to understanding the processes that occur prior to mesectoderm formation during early embryonic development. In this study, more than 117.8 million 100bp PE reads were generated from pooled RNA extracted from unfertilized eggs to 41dph (days post-hatching) embryos and were sequenced using Illumina pair-end sequencing technology. In total, 121,513 transcripts (≥200bp) were obtained using de novo assembly. A sequence similarity search indicated that 52,338 transcripts show significant similarity to 22,462 known proteins from the NCBI non-redundant database and the Swiss-Prot protein database and were annotated using Blast2GO. GO terms were assigned to 44,627 transcripts with 12,006 functional terms, and 10,024 transcripts were assigned to 133 KEGG pathways. Furthermore, gene expression differences between the unfertilized egg and the gastrula embryo were analysed using Illumina RNA-Seq with single-read sequencing technology, and 24,837 differentially and specifically expressed transcripts were identified and included 5,286 annotated transcripts and 19,569 non-annotated transcripts. All of the expressed transcripts in the unfertilized egg and gastrula embryo were further classified as maternal, zygotic, or maternal-zygotic transcripts, which may help us to understand the roles of these transcripts during the embryonic development of the Japanese flounder. Thus, the results will contribute to an improved understanding of the gene expression patterns and

  7. 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

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

    PubMed Central

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

    2009-01-01

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

  9. 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

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

    PubMed

    Ng, Lauren; Pitt, Veronica; Huckvale, Kit; Clavisi, Ornella; Turner, Tari; Gruen, Russell; Elliott, Julian H

    2014-10-21

    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. 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. 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. 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 performance. Cochrane Database CD001048.

  11. 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

  12. Genome sequence and comparative analysis of Avibacterium paragallinarum

    PubMed Central

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

    2013-01-01

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

  13. 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.

  14. Identification of putative fertility markers in seminal plasma of crossbred bulls through differential proteomics.

    PubMed

    Aslam, M K Muhammad; Kumaresan, A; Sharma, Vinay K; Tajmul, Md; Chhillar, Shivani; Chakravarty, A K; Manimaran, A; Mohanty, T K; Srinivasan, A; Yadav, Savita

    2014-12-01

    Sub-fertility is a major problem in crossbred bulls leading to disintegration of breeding systems and huge economic loss. Identification of some potential biomarkers to determine the latent fertility of bulls accurately has long been the interest of researchers. In this study, we analyzed the proteome of seminal plasma (SP) from bulls with varying fertility to identify the fertility-associated proteins. The proteomic profile of high- and low-fertile bulls was compared by two-dimensional difference gel electrophoresis and differentially expressed proteins were identified through matrix-assisted laser desorption/ionization-time of flight/mass spectrometry. Out of the 18 differentially expressed proteins (P < 0.05), 9 were overexpressed in SP of high-fertile bulls and 9 were overexpressed in SP of low-fertile bulls. The differential expressions ranged from 1.5- to 5.5-fold between the two groups, where protection of telomeres-1 protein (POT1) was highly overexpressed (2.9-fold) in high-fertile group and prostaglandin E2 receptor EP3 (PTGER3) was highly abundant (5.5-fold) in low-fertile group. The protein interaction network was elucidated using STRING software tool, and the functional bioinformatics analysis was done using Blast2Go software. Most of the differentially expressed proteins were found to be involved in cellular processes and biological regulation with binding and catalytic function. It is inferred that the expression of certain proteins in the SP varied with bull fertility, and concurrent appraisal of their expression along with other fertility assays may help in determining bull fertility. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Changes in the organics metabolism in the hepatopancreas induced by eyestalk ablation of the Chinese mitten crab Eriocheir sinensis determined via transcriptome and DGE analysis.

    PubMed

    Sun, Yan; Zhang, Yichen; Liu, Yichen; Xue, Shuxia; Geng, Xuyun; Hao, Tong; Sun, Jinsheng

    2014-01-01

    To understand the regulation mechanism of eyestalk ablation on the activities of hepatopancreas, Illumina RNA-Seq and digital gene expression (DGE) analyses were performed to investigate the transcriptome of the eyestalk, Y-organ, and hepatopancreas of E. sinensis and to identify the genes associated with the hepatopancreas metabolism that are differentially expressed under eyestalk ablation conditions. A total of 58,582 unigenes were constructed from 157,168 contigs with SOAPdenovo. A BlastX search against the NCBI Nr database identified 21,678 unigenes with an E-value higher than 10⁻⁵. Using the BLAST2Go and BlastAll software programs, 6,883 unigenes (11.75% of the total) were annotated to the Gene Ontology (GO) database, 7,386 (12.6%) unigenes were classified into 25 Clusters of Orthologous Groups of Proteins (COGs), 16,200 (27.7%) unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 1,846 unigenes were matched to "metabolism pathways". The DGE analysis revealed that 1,416 unigenes were significantly differentially expressed in the hepatopancreas, of which 890 unigenes were up-regulated and 526 unigenes were down-regulated. Of the differentially expressed genes, 382 unigenes were annotated and 63 were classified into metabolism pathways. The results of the real-time polymerase chain reaction (PCR) analysis of four unigenes related to carbohydrate metabolism were consistent with those obtained from the DGE analysis, which demonstrates that the sequencing data were satisfactory for further gene expression analyses. This paper reported the transcriptom of the eyestalk, Y-organ, and hepatopancreas from E. sinensis. DGE analysis provided the different expressed genes of the metabolism processes in hepatopancreas that are affected by eyestalk ablation. These findings will facilitate further investigations on the mechanisms of the metabolism of organic substances during development and reproduction in crustaceans.

  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.

  18. 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.

  19. 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

  20. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

    PubMed

    Camon, Evelyn B; Barrell, Daniel G; Dimmer, Emily C; Lee, Vivian; Magrane, Michele; Maslen, John; Binns, David; Apweiler, Rolf

    2005-01-01

    GO annotation strategies. The GOA database currently extracts GO annotation from the literature with 91 to 100% precision, and at least 72% recall. This creates a particularly high threshold for text mining systems which in BioCreAtIvE task 2 (GO annotation extraction and retrieval) initial results precisely predicted GO terms only 10 to 20% of the time. Improvements in the performance and accuracy of text mining for GO terms should be expected in the next BioCreAtIvE challenge. In the meantime the manual and electronic GO annotation strategies already employed by GOA will provide high quality annotations.

  1. Graphene-supported zinc oxide solid-phase microextraction coating with enhanced selectivity and sensitivity for the determination of sulfur volatiles in Allium species.

    PubMed

    Zhang, Suling; Du, Zhuo; Li, Gongke

    2012-10-19

    A graphene-supported zinc oxide (ZnO) solid-phase microextraction (SPME) fiber was prepared via a sol-gel approach. Graphite oxide (GO), with rich oxygen-containing groups, was selected as the starting material to anchor ZnO on its nucleation center. After being deoxidized by hydrazine, the Zn(OH)2/GO coating was dehydrated at high temperature to give the ZnO/graphene coating. Sol-gel technology could efficiently incorporate ZnO/graphene composites into the sol-gel network and provided strong chemical bonding between sol-gel polymeric SPME coating and silica fiber surface, which enhanced the durability of the fiber and allowed more than 200 replicate extractions. Results indicated that pure ZnO coated fiber did not show adsorption selectivity toward sulfur compounds, which might because the ZnO nanoparticles were enwrapped in the sol-gel network, and the strong coordination action between Zn ion and S ion was therefore blocked. The incorporation of graphene into ZnO based sol-gel network greatly enlarged the BET surface area from 1.2 m2/g to 169.4 m2/g and further increased the adsorption sites. Combining the superior properties of extraordinary surface area of graphene and the strong coordination action of ZnO to sulfur compounds, the ZnO/graphene SPME fiber showed much higher adsorption affinity to 1-octanethiol (enrichment factor, EF, 1087) than other aliphatic compounds without sulfur-containing groups (EFs<200). Also, it showed higher extraction selectivity and sensitivity toward sulfur compounds than commercial polydimethylsiloxane (PDMS) and polydimethylsiloxane/divinylbenzene (PDMS/DVB) SPME fibers. Several most abundant sulfur volatiles in Chinese chive and garlic sprout were analyzed using the ZnO/graphene SPME fiber in combination with gas chromatography-mass spectrometry (GC-MS). Their limits of detection were 0.1-0.7 μg/L. The relative standard deviation (RSD) using one fiber ranged from 3.6% to 9.1%. The fiber-to-fiber reproducibility for three

  2. 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

  3. 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

  4. 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

  5. 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

  6. [Protective effects of garlic oil on n-hexane-induced neurotoxicity in rats via inhibition of hepatic alcohol dehydrogenase activity].

    PubMed

    Bi, Ye; Chen, Jing-Jing; Yan, Jie; Zeng, Tao; Fu, Qiang-Qiang; Zhong, Zhi-Xia; Xie, Ke-Qin

    2011-08-01

    To study the protective effects of garlic oil (GO) on the peripheral nerve injuries induced by n-hexane. Male Wistar rats were randomly divided into four groups (10 rats in each group): the control, the n-hexane treatment (2000 mg/kg), the low dose GO, and the high dose GO groups. The rats in the low and high doses of GO groups were pretreated with GO (40 and 80 mg/kg) before exposure to n-hexane (2000 mg/ kg), while the animals of the n-hexane treatment group were given normal saline and then 2000 mg/ kg n-hexane. The rats were exposed to GO and n-hexane 6 times a week for 10 weeks. The gait scores and staying time on the rotating rod for all rats were detected every two weeks. The rats were sacrificed at the end of ten weeks, then the levels of alcohol dehydrogenase (ADH), maleic dialdehyde (MDA), reduced glutathione (GSH), glutathione peroxidase(GSH-Px), total antioxidation capacity(T-AOC) and the ability of inhibition of *OH in livers were examined. The gait scores increased significantly and the time staying on the rotating rod obviously decreased in rats of n-hexane treatment group, as compared with control group (P < 0.05 or P < 0.01). In the hepatic tissues of n-hexane group, the levels of MDA and ADH significantly increased, the activities of GSH-Px, T-AOC and the ability of inhibition of *OH obviously decreased, as compared to control group (P < 0.05 or P < 0.01). In 2 GO groups, the gait scores and the staying time on the rotating rod were significantly improved, the levels of MDA and ADH significantly decreased, the activities of GSH-Px, T-AOC and the ability of inhibition of *OH obviously increased, as compared with n-hexane group (P < 0.05 or P < 0.01 ). ADH could play an important role in the protective effects induced by garlic oil on the peripheral nerve injuries produced by n-hexane.

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

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  9. Consequences to precipitation regimes of replacing native Brazilian Cerrado by managed Eucalyptus

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    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 has 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 was installed in each site. Surface flux data from the eddy-covariance towers, along with daily upper air sounding profiles collected at the Brasília International Airport (located 10Km from the towers), were used to drive a simplified Atmospheric Boundary Layer (ABL) slab model in order to investigate possible consequences of a large-scale shift from Cerrado to Eucalyptus to precipitation regimes in the region. Preliminary results show that replacing Cerrado for

  10. 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

  11. GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis.

    PubMed

    Powell, Justin Andrew Christiaan

    2014-05-17

    Despite the widespread use of high throughput expression platforms and the availability of a desktop implementation of Gene Set Enrichment Analysis (GSEA) that enables non-experts to perform gene set based analyses, the availability of the necessary precompiled gene sets is rare for species other than human. A software tool (GO2MSIG) was implemented that combines data from various publicly available sources and uses the Gene Ontology (GO) project term relationships to produce GSEA compatible hierarchical GO based gene sets for all species for which association data is available. Annotation sources include the GO association database (which contains data for over 200000 species), the Entrez gene2go table, and various manufacturers' array annotation files. This enables the creation of gene sets from the most up-to-date annotation data available. Additional features include the ability to restrict by evidence code, to remap gene descriptors, to filter by set size and to speed up repeat queries by caching the GO term hierarchy. Synonymous GO terms are remapped to the version preferred by the GO ontology supplied. The tool can be used in standalone form, or via a web interface. Prebuilt gene set collections constructed from the September 2013 GO release are also available for common species including human. In contrast human GO based sets available from the Broad Institute itself date from 2008. GO2MSIG enables the bioinformatician and non-bioinformatician alike to generate gene sets required for GSEA analysis for almost any organism for which GO term association data exists. The output gene sets may be used directly within GSEA and do not require knowledge of programming languages such as Perl, R or Python. The output sets can also be used with other analysis software such as ErmineJ that accept gene sets in the same format. Source code can be downloaded and installed locally from http://www.bioinformatics.org/go2msig/releases/ or used via the web interface at http

  12. Large-scale identification of wheat genes resistant to cereal cyst nematode Heterodera avenae using comparative transcriptomic analysis.

    PubMed

    Kong, Ling-An; Wu, Du-Qing; Huang, Wen-Kun; Peng, Huan; Wang, Gao-Feng; Cui, Jiang-Kuan; Liu, Shi-Ming; Li, Zhi-Gang; Yang, Jun; Peng, De-Liang

    2015-10-16

    Cereal cyst nematode Heterodera avenae, an important soil-borne pathogen in wheat, causes numerous annual yield losses worldwide, and use of resistant cultivars is the best strategy for control. However, target genes are not readily available for breeding resistant cultivars. Therefore, comparative transcriptomic analyses were performed to identify more applicable resistance genes for cultivar breeding. The developing nematodes within roots were stained with acid fuchsin solution. Transcriptome assemblies and redundancy filteration were obtained by Trinity, TGI Clustering Tool and BLASTN, respectively. Gene Ontology annotation was yielded by Blast2GO program, and metabolic pathways of transcripts were analyzed by Path_finder. The ROS levels were determined by luminol-chemiluminescence assay. The transcriptional gene expression profiles were obtained by quantitative RT-PCR. The RNA-sequencing was performed using an incompatible wheat cultivar VP1620 and a compatible control cultivar WEN19 infected with H. avenae at 24 h, 3 d and 8 d. Infection assays showed that VP1620 failed to block penetration of H. avenae but disturbed the transition of developmental stages, leading to a significant reduction in cyst formation. Two types of expression profiles were established to predict candidate resistance genes after developing a novel strategy to generate clean RNA-seq data by removing the transcripts of H. avenae within the raw data before assembly. Using the uncoordinated expression profiles with transcript abundance as a standard, 424 candidate resistance genes were identified, including 302 overlapping genes and 122 VP1620-specific genes. Genes with similar expression patterns were further classified according to the scales of changed transcript abundances, and 182 genes were rescued as supplementary candidate resistance genes. Functional characterizations revealed that diverse defense-related pathways were responsible for wheat resistance against H. avenae. Moreover

  13. 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

  14. The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato.

    PubMed

    Herraiz, Francisco J; Blanca, José; Ziarsolo, Pello; Gramazio, Pietro; Plazas, Mariola; Anderson, Gregory J; Prohens, Jaime; Vilanova, Santiago

    2016-05-04

    Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. This study represents

  15. 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

  16. RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.

    PubMed

    Rao, Rama; Bing Zhu, Ya; Alinejad, Tahereh; Tiruvayipati, Suma; Lin Thong, Kwai; Wang, Jun; Bhassu, Subha

    2015-01-01

    The Malaysian giant freshwater prawn, Macrobrachium rosenbergii, is an economically important crustacean worldwide. However, production of this prawn is facing a serious threat from Vibriosis disease caused by Vibrio species such as Vibrio parahaemolyticus. Unfortunately, the mechanisms involved in the immune response of this species to bacterial infection are not fully understood. We therefore used a high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the hepatopancreas from this freshwater prawn infected with V. parahaemolyticus to gain an increased understanding of the molecular mechanisms underlying the species' immune response to this pathogenic bacteria. A total of 59,122,940 raw reads were obtained from the control group, and 58,385,094 reads from the Vibrio-infected group. Via de novo assembly by Trinity assembler, 59,050 control unigenes and 73,946 Vibrio-infected group unigenes were obtained. By clustering unigenes from both libraries, a total of 64,411 standard unigenes were produced. The standard unigenes were annotated against the NCBI non-redundant, Swiss-Prot, Kyoto Encyclopaedia of Genes and Genome pathway (KEGG) and Orthologous Groups of Proteins (COG) databases, with 19,799 (30.73%), 16,832 (26.13%), 14,706 (22.83%) and 7,856 (12.19%) hits respectively, giving a final total of 22,455 significant hits (34.86% of all unigenes). A Gene Ontology (GO) analysis search using the Blast2GO program resulted in 6,007 unigenes (9.32%) being categorized into 55 functional groups. A differential gene expression analysis produced a total of 14,569 unigenes aberrantly expressed, with 11,446 unigenes significantly up-regulated and 3,103 unigenes significantly down-regulated. The differentially expressed immune genes fall under various processes of the animal immune system. This study provided an insight into the antibacterial mechanism in M. rosenbergii and the role of differentially expressed immune

  17. Transcriptome of Pneumocystis carinii during Fulminate Infection: Carbohydrate Metabolism and the Concept of a Compatible Parasite

    PubMed Central

    Sesterhenn, Tom; Arnold, Jonathan; Staben, Chuck; Porollo, Aleksey; Adamczak, Rafal; Meller, Jarek

    2007-01-01

    Members of the genus Pneumocystis are fungal pathogens that cause pneumonia in a wide variety of mammals with debilitated immune systems. Little is known about their basic biological functions, including life cycle, since no species can be cultured continuously outside the mammalian lung. To better understand the pathological process, about 4500 ESTS derived from sequencing of the poly(A) tail ends of P. carinii mRNAs during fulminate infection were annotated and functionally characterized as unassembled reads, and then clustered and reduced to a unigene set with 1042 members. Because of the presence of sequences from other microbial genomes and the rat host, the analysis and compression to a unigene set was necessarily an iterative process. BLASTx analysis of the unassembled reads (UR) vs. the Uni-Prot and TREMBL databases revealed 56% had similarities to existing polypeptides at E values of≤10−6, with the remainder lacking any significant homology. The most abundant transcripts in the UR were associated with stress responses, energy production, transcription and translation. Most (70%) of the UR had similarities to proteins from filamentous fungi (e.g., Aspergillus, Neurospora) and existing P. carinii gene products. In contrast, similarities to proteins of the yeast-like fungi, Schizosaccharomyces pombe and Saccharomyces cerevisiae, predominated in the unigene set. Gene Ontology analysis using BLAST2GO revealed P. carinii dedicated most of its transcripts to cellular and physiological processes (∼80%), molecular binding and catalytic activities (∼70%), and were primarily derived from cell and organellar compartments (∼80%). KEGG Pathway mapping showed the putative P. carinii genes represented most standard metabolic pathways and cellular processes, including the tricarboxylic acid cycle, glycolysis, amino acid biosynthesis, cell cycle and mitochondrial function. Several gene homologs associated with mating, meiosis, and sterol biosynthesis in fungi were

  18. Genomic adaptation of the ISA virus to Salmo salar codon usage

    PubMed Central

    2013-01-01

    Background The ISA virus (ISAV) is an Orthomyxovirus whose genome encodes for at least 10 proteins. Low protein identity and lack of genetic tools have hampered the study of the molecular mechanism behind its virulence. It has been shown that viral codon usage controls several processes such as translational efficiency, folding, tuning of protein expression, antigenicity and virulence. Despite this, the possible role that adaptation to host codon usage plays in virulence and viral evolution has not been studied in ISAV. Methods Intergenomic adaptation between viral and host genomes was calculated using the codon adaptation index score with EMBOSS software and the Kazusa database. Classification of host genes according to GeneOnthology was performed using Blast2go. A non parametric test was applied to determine the presence of significant correlations among CAI, mortality and time. Results Using the codon adaptation index (CAI) score, we found that the encoding genes for nucleoprotein, matrix protein M1 and antagonist of Interferon I signaling (NS1) are the ISAV genes that are more adapted to host codon usage, in agreement with their requirement for production of viral particles and inactivation of antiviral responses. Comparison to host genes showed that ISAV shares CAI values with less than 0.45% of Salmo salar genes. GeneOntology classification of host genes showed that ISAV genes share CAI values with genes from less than 3% of the host biological process, far from the 14% shown by Influenza A viruses and closer to the 5% shown by Influenza B and C. As well, we identified a positive correlation (p<0.05) between CAI values of a virus and the duration of the outbreak disease in given salmon farms, as well as a weak relationship between codon adaptation values of PB1 and the mortality rates of a set of ISA viruses. Conclusions Our analysis shows that ISAV is the least adapted viral Salmo salar pathogen and Orthomyxovirus family member less adapted to host codon

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  1. 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).

  2. Interspecies gene function prediction using semantic similarity.

    PubMed

    Yu, Guoxian; Luo, Wei; Fu, Guangyuan; Wang, Jun

    2016-12-23

    Gene Ontology (GO) is a collaborative project that maintains and develops controlled vocabulary (or terms) to describe the molecular function, biological roles and cellular location of gene products in a hierarchical ontology. GO also provides GO annotations that associate genes with GO terms. GO consortium independently and collaboratively annotate terms to gene products, mainly from model organisms (or species) they are interested in. Due to experiment ethics, research interests of biologists and resources limitations, homologous genes from different species currently are annotated with different terms. These differences can be more attributed to incomplete annotations of genes than to functional difference between them. Semantic similarity between genes is derived from GO hierarchy and annotations of genes. It is positively correlated with the similarity derived from various types of biological data and has been applied to predict gene function. In this paper, we investigate whether it is possible to replenish annotations of incompletely annotated genes by using semantic similarity between genes from two species with homology. For this investigation, we utilize three representative semantic similarity metrics to compute similarity between genes from two species. Next, we determine the k nearest neighborhood genes from the two species based on the chosen metric and then use terms annotated to k neighbors of a gene to replenish annotations of that gene. We perform experiments on archived (from Jan-2014 to Jan-2016) GO annotations of four species (Human, Mouse, Danio rerio and Arabidopsis thaliana) to assess the contribution of semantic similarity between genes from different species. The experimental results demonstrate that: (1) semantic similarity between genes from homologous species contributes much more on the improved accuracy (by 53.22%) than genes from single species alone, and genes from two species with low homology; (2) GO annotations of genes from

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

    PubMed

    Liang, Yuanxue; Yuan, Yijun; Liu, Tao; Mao, Wei; Zheng, Yusheng; Li, Dongdong

    2014-08-02

    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. 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 high as 66.6%. Based on

  4. Left Parietal Activation Related to Planning, Executing and Suppressing Praxis Hand Movements

    PubMed Central

    Wheaton, Lewis; Fridman, Esteban; Bohlhalter, Stephan; Vorbach, Sherry; Hallett, Mark

    2009-01-01

    Objective We sought to investigate the activity of bilateral parietal and premotor areas during a Go/No Go paradigm involving praxis movements of the dominant hand. Methods A sentence was presented which instructed subjects on what movement to make (S1; for example, “Show me how to use a hammer.”). After an 8-s delay, “Go” or “No Go” (S2) was presented. If Go, they were instructed to make the movement described in the S1 instruction sentence as quickly as possible, and continuously until the “Rest” cue was presented 3 s later. If No Go, subjects were to simply relax until the next instruction sentence. Event-related potentials (ERP) and event-related desynchronization (ERD) in the beta band (18–22 Hz) were evaluated for three time bins: after S1, after S2, and from −2.5 to −1.5 s before the S2 period. Results Bilateral premotor ERP was greater than bilateral parietal ERP after the S2 Go compared with the No Go. Additionally, left premotor ERP was greater than that from the right premotor area. There was predominant left parietal ERD immediately after S1 for both Go and No Go, which was sustained for the duration of the interval between S1 and S2. For both S2 stimuli, predominant left parietal ERD was again seen when compared to that from the left premotor or right parietal area. However, the left parietal ERD was greater for Go than No Go. Conclusion The results suggest a dominant role in the left parietal cortex for planning, executing, and suppressing praxis movements. The ERP and ERD show different patterns of activation and may reflect distinct neural movement-related activities. Significance The data can guide further studies to determine the neurophysiological changes occurring in apraxia patients and help explain the unique error profiles seen in patients with left parietal damage. PMID:19345141

  5. 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

  6. 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

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

    PubMed Central

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

    2011-01-01

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

  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://www.cycadsys.org.

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

    PubMed Central

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

    2012-01-01

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

  10. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

    PubMed Central

    Botton, Alessandro; Galla, Giulio; Conesa, Ana; Bachem, Christian; Ramina, Angelo; Barcaccia, Gianni

    2008-01-01

    and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments. PMID:18652646

  11. Transcriptional profiling of bovine milk using RNA sequencing

    PubMed Central

    2012-01-01

    Background Cow milk is a complex bioactive fluid consumed by humans beyond infancy. Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizing the milk transcriptome. This study performs a comprehensive expression profiling of genes expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing. Milk samples were collected from Holstein cows at 15, 90 and 250 days of lactation, and RNA was extracted from the pelleted milk cells. Gene expression analysis was conducted by Illumina RNA sequencing. Sequence reads were assembled and analyzed in CLC Genomics Workbench. Gene Ontology (GO) and pathway analysis were performed using the Blast2GO program and GeneGo application of MetaCore program. Results A total of 16,892 genes were expressed in transition lactation, 19,094 genes were expressed in peak lactation and 18,070 genes were expressed in late lactation. Regardless of the lactation stage approximately 9,000 genes showed ubiquitous expression. Genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway showed higher expression in early lactation. The majority of genes in the fat metabolism pathway had high expression in transition and peak lactation milk. Most of the genes encoding for endogenous proteases and enzymes in ubiquitin-proteasome pathway showed higher expression along the course of lactation. Conclusions This is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions

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

    PubMed

    Yang, Shihui; Guarnieri, Michael T; Smolinski, Sharon; Ghirardi, Maria; Pienkos, Philip T

    2013-08-23

    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. 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. Herein, we have described a workflow using commercial

  13. 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

  14. 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

  15. 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes.

    PubMed

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

    2014-08-01

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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. Evolution of continental collision styles since the Precambrian

    NASA Astrophysics Data System (ADS)

    Sizova, Elena; Gerya, Taras; Brown, Michael

    2010-05-01

    The relevance of modern tectonics to ancient orogens is a matter of international debate. Ultrahigh-pressure (UHP) methamorphic rocks of continental origin provide evidence for subduction of the continental lithosphere to mantle depths over 100 km. While UHP eclogitic rocks and high-pressure (HP) blueschists mainly occure in Phanerozoic oregenic belts, they rarely found in Precambrian terranes. To investigate a possible change of collisional style back in time which could lead to disappearing of UHP complexes from the geological surface records we performed 2D petrological-thermomechanical numerical model (I2VIS code (Gerya and Yuen, 2003)) of oceanic-continental subduction followed by continent-continent collision. The reference model was chosen in such a way that it can produce UHP complexes during transition from oceanic-continental subduction to continent-continental collision and deliver them to the surface. Based on this model we performed series of experiments varying upper-mantle temperature (up to 250 degrees higher then present), lithosphere thickness for continental plates (100,140 and 180 km) and density of subcontinental lithospheric mantle (difference with underlying mantle 20 kg/m3 corresponds to present day; 50 kg/m3 corresponds to Proterosoic). The reference model shows continental plate subducting up to 250 km depth whereupon slab break-off occurs and continental plate starts to relax. During the relaxation stage continental crust starts to melt and partially detach from the slab. There are two ways of moving this material from high depths upwards: 1) going upwards vertically as a buoyant plume and crossing both the mantle wedge and the overriding mantle lithosphere (thanks to weakening of the lithospheric rocks by melt propagation); 2) going back along the plate as a buoyant wave and penetrating into subduction channel. Both ways can lead to HP-UHP rocks formation in the end. Increasing the upper-mantle temperature we determined sharp transition

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  4. An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications

    PubMed Central

    2012-01-01

    Background Teladorsagia circumcincta (order Strongylida) is an economically important parasitic nematode of small ruminants (including sheep and goats) in temperate climatic regions of the world. Improved insights into the molecular biology of this parasite could underpin alternative methods required to control this and related parasites, in order to circumvent major problems associated with anthelmintic resistance. The aims of the present study were to define the transcriptome of the adult stage of T. circumcincta and to infer the main pathways linked to molecules known to be expressed in this nematode. Since sheep develop acquired immunity against T. circumcincta, there is some potential for the development of a vaccine against this parasite. Hence, we infer excretory/secretory molecules for T. circumcincta as possible immunogens and vaccine candidates. Results A total of 407,357 ESTs were assembled yielding 39,852 putative gene sequences. Conceptual translation predicted 24,013 proteins, which were then subjected to detailed annotation which included pathway mapping of predicted proteins (including 112 excreted/secreted [ES] and 226 transmembrane peptides), domain analysis and GO annotation was carried out using InterProScan along with BLAST2GO. Further analysis was carried out for secretory signal peptides using SignalP and non-classical sec pathway using SecretomeP tools. For ES proteins, key pathways, including Fc epsilon RI, T cell receptor, and chemokine signalling as well as leukocyte transendothelial migration were inferred to be linked to immune responses, along with other pathways related to neurodegenerative diseases and infectious diseases, which warrant detailed future studies. KAAS could identify new and updated pathways like phagosome and protein processing in endoplasmic reticulum. Domain analysis for the assembled dataset revealed families of serine, cysteine and proteinase inhibitors which might represent targets for parasite intervention. Inter

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

    PubMed

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

    2017-03-21

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

  6. 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

  7. The Utility of a Small Pressurized Rover with Suit Ports for Lunar Exploration: A Geologist's Perspective

    NASA Technical Reports Server (NTRS)

    Kring, David A.; Bleacher, Jacob E.; Garry, W. Brent; Love, Stanley G.; Young, Kelsey E.

    2017-01-01

    crew time in a spacesuit. Additionally, the vehicle could be driven with crew locked into the suit ports. This approach could involve a driver in the cockpit with a suited crewmember in a suit port, or the vehicle could be driven from the aft deck with both crewmembers in their suit ports. This approach was used when distances between stops were short enough that vehicle ingress and egress were less efficient than remaining in the suits and driving. Utility of suit ports: The advantages of suit ports were clearly demonstrated in those field-based trade studies. To illustrate those advantages further, consider the consequences of a SPR without suit ports at the Apollo 17 landing site. At that site, the crew's second EVA was an approximately 18 km loop conducted in a UPR, called the Lunar Roving Vehicle (LRV), in 7 hr 36 min 56 s. The traverse was composed of 5 formal stations, plus 8 additional LRV stations where crew made brief scientific stops. In a scenario involving a SPR without suit ports, crew would go EVA through an airlock and probably be limited to a single EVA per day. In that case, crew could drive the SPR 9 km from the landing site to station 2, go EVA, and complete station 2 tasks. However, to conduct station 3 tasks, the crew would then need to walk approximately 3 km to station 3, while ground control in Houston tele-robotically drives the LER to station 3. A walk of approximately 3 km is possible, as that is what the Apollo 14 crew did before LRVs were deployed, but it is a lengthy and potentially grueling EVA. Assuming crew completes station 3 tasks, they would likely need to re-enter the SPR, ending the day's EVA, and return to the landing site. They would not be able to walk the additional distances to stations 4 and 5 (the latter being about 6 km from station 3). Thus, crew in an SPR without suit ports would require two days to accomplish the same tasks Apollo 17 crew completed in a single day. If a future crew is involved in long duration traverses