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Sample records for 2-go kontura vvehr-1000

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

    PubMed

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

    2016-05-01

    A highly recoverable titanium dioxide-graphene oxide (TiO2-GO) composite was developed by a facile method of ultrasonic treatment of GO nanosheets and TiO2 nanoparticles, which should overcome the separation problem of nanosized TiO2 from treated water. Separability of the prepared samples was systematically investigated by gravity settling experiments. The samples' photocatalytic activity for stormwater disinfection was also studied under the irradiation of a solar simulator. The results demonstrated that TiO2-GO showed high efficient separability due to its accelerated settling behaviour. Zeta-potential analysis showed that the accelerated sedimentation of the catalyst was attributed to the aggregation of TiO2-GO resulting from the electrostatic attraction between TiO2 and GO. The TiO2-GO composite with a mass ratio of 100:2 (TiO2-2%GO) achieved both higher separability and good photocatalytic activity for stormwater disinfection. Its suspension became clear (turbidity < 50 NTU) after 8 h of sedimentation, while 99.5% of E.coli were deactivated in 90 min. The TiO2-GO composite exhibited excellent durability; no apparent change in the separability of TiO2-2%GO was observed after 10 treatment cycles (15 h in total), while only slight decrease in the photocatalytic activity was noted. In conclusion, the developed TiO2-GO composite showed promising results for stormwater disinfection. PMID:26991482

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. 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.

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

    ERIC Educational Resources Information Center

    Brennan, Patricia L.

    2010-01-01

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

  5. Synthesis of functional SiO₂-coated graphene oxide nanosheets decorated with Ag nanoparticles for H₂O₂ and glucose detection.

    PubMed

    Lu, Wenbo; Luo, Yonglan; Chang, Guohui; Sun, Xuping

    2011-08-15

    In this paper, we report on the first preparation of well-defined SiO(2)-coated graphene oxide (GO) nanosheets (SiO(2)/GO) without prior GO functionalization by combining sonication with sol-gel technique. The functional SiO(2)/GO nanocomposites (F-SiO(2)/GO) obtained by surface functionalization with NH(2) group were subsequently employed as a support for loading Ag nanoparticles (AgNPs) to synthesize AgNP-decorated F-SiO(2)/GO nanosheets (AgNP/F-SiO(2)/GO) by two different routes: (1) direct adsorption of preformed, negatively charged AgNPs; (2) in situ chemical reduction of silver salts. The morphologies of these nanocomposites were characterized by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). It is found that the resultant AgNP/F-SiO(2)/GO exhibits remarkable catalytic performance for H(2)O(2) reduction. This H(2)O(2) sensor has a fast amperometric response time of less than 2s. The linear range is estimated to be from 1×10(-4) M to 0.26 M (r=0.998) and the detection limit is estimated to be 4 × 10(-6) M at a signal-to-noise ratio of 3, respectively. We also fabricated a glucose biosensor by immobilizing glucose oxidase (GOD) into AgNP/F-SiO(2)/GO nanocomposite-modified glassy carbon electrode (GCE) for glucose detection. Our study demonstrates that the resultant glucose biosensor can be used for the glucose detection in human blood serum. PMID:21733668

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

    PubMed

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

    2016-02-01

    As a new type of green solvent, four kinds of choline chloride (ChCl)-based deep eutectic solvents (DESs) have been synthesized, and then a core-shell structure magnetic graphene oxide (Fe3O4-NH2@GO) nanoparticles have been prepared and coated with the ChCl-based DESs. Magnetic solid-phase extraction (MSPE) based Fe3O4-NH2@GO@DES was studied for the first time for the extraction of proteins. The characteristic results of vibrating sample magnetometer (VSM), X-ray diffraction (XRD), Fourier transform infrared spectrometry (FT-IR), thermal gravimetric analysis (TGA) and field emission scanning electron microscopy (FESEM) indicated the successful preparation of Fe3O4-NH2@GO@DES. The concentrations of proteins in studies were determined by a UV-vis spectrophotometer. The advantages of Fe3O4-NH2@GO@DES in protein extraction were compared with Fe3O4-NH2@GO and Fe3O4-NH2, and Fe3O4-NH2@GO@ChCl-glycerol was selected as the suitable extraction solvent. The influence factors of the extraction process such as the pH value, the temperature, the extraction time, the concentration of protein and the amount of Fe3O4-NH2@GO@ChCl-glycerol were evaluated. Desorption experimental result showed 98.73% of BSA could be eluted from the solid extractant with 0.1 mol/L Na2HPO4 solution contained 1 mol/L NaCl. Besides, the conformation of BSA was not changed during the elution by the investigation of circular dichromism (CD) spectra. Furthermore, the analysis of real sample demonstrated that the prepared magnetic nanoparticles did have extraction ability on proteins in bovine whole blood. PMID:26653436

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  8. Density-functional calculations of the conversion of methane to methanol on platinum-decorated sheets of graphene oxide.

    PubMed

    Wu, Shiuan-Yau; Lin, Chien-Hao; Ho, Jia-Jen

    2015-10-21

    By means of calculations based on density-functional theory (DFT), we have investigated the conversion of methane on two platinum atoms supported with a graphene-oxide sheet (Pt2/GO). In our calculations, a CH4 molecule can be adsorbed around the Pt atoms of the Pt2/GO sheet with adsorption energies within -0.11 to -0.53 eV; an elongated C-H bond indicates that Pt atoms on that sheet can activate the C-H bond of a CH4 molecule. The role of the GO sheet in the activation of CH4 was identified according to an analysis of the electronic density: the GO sheet induces the d-band of Pt atoms to generate several specific dz(2) state features above the Fermi level, which enabled the activation of the C-H bond of CH4 in generating an evident area of overlap with the hydrogen s orbital of the C-H bond. Upon a dioxygen molecule being added onto the Pt2/GO sheet, this molecule can react with activated CH4 according to mechanisms of form 2CH4 + O2 [Pt2/GO]--> 2CH3OH, and restore the original Pt2/GO sheet. PMID:26381105

  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 missions); (4) "International…

  10. 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…

  11. 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...

  12. 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...

  13. 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…

  14. 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,…

  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 Teach Technology…

  16. 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…

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

    PubMed

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

    2016-03-01

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

  18. 46 CFR 131.340 - Recommended placard for emergency instructions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... INSTRUCTIONS (a) Rough weather at sea, crossing of hazardous bars, or flooding. (1) Close each watertight and weathertight door, hatch, and air-port to prevent taking water aboard or further flooding in the vessel. (2... going becomes very rough, if the vessel is about to cross a hazardous bar, if flooding begins, or...

  19. 46 CFR 131.340 - Recommended placard for emergency instructions.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... INSTRUCTIONS (a) Rough weather at sea, crossing of hazardous bars, or flooding. (1) Close each watertight and weathertight door, hatch, and air-port to prevent taking water aboard or further flooding in the vessel. (2... going becomes very rough, if the vessel is about to cross a hazardous bar, if flooding begins, or...

  20. 46 CFR 131.340 - Recommended placard for emergency instructions.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... INSTRUCTIONS (a) Rough weather at sea, crossing of hazardous bars, or flooding. (1) Close each watertight and weathertight door, hatch, and air-port to prevent taking water aboard or further flooding in the vessel. (2... going becomes very rough, if the vessel is about to cross a hazardous bar, if flooding begins, or...

  1. 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…

  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 Issues in…

  3. 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

  4. 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.

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

    PubMed

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

    2016-06-01

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

  6. 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.

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

    PubMed

    Veerapandian, Murugan; Hunter, Robert; Neethirajan, Suresh

    2016-04-15

    Elevated concentrations of non-esterified fatty acids (NEFA) in biological fluids are recognized as critical biomarkers for early diagnosis of dairy cow metabolic diseases. Herein, a cost-effective, electrochemically active, and bio-friendly sensor element based on ruthenium bipyridyl complex-modified graphene oxide nanosheets ([Ru(bpy)3](2+)-GO) is proposed as a biosensor platform for NEFA detection. Electrochemical analysis demonstrates that the [Ru(bpy)3](2+)-GO electrodes exhibit superior and durable redox properties compared to the pristine carbon and GO electrodes. Target specificity is accomplished through immobilization of the enzyme, lipoxygenase, which catalyzes the production of redox active species from NEFA. Lipoxygenases retain their catalytic ability upon immobilization and exhibit changes to amperometric signals upon interaction with various concentrations of standard NEFA and serum samples. Our study demonstrates that the [Ru(bpy)3](2+)-GO electrode has the potential to serve as a biosensor platform for developing a field deployable, rapid, and user-friendly detection tool for on-farm monitoring of dairy cow metabolic diseases. PMID:26623509

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

    PubMed Central

    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.

    2008-01-01

    We examined the clinical, molecular, and genetic features of a 16y old boy (XP2GO) with xeroderma pigmentosum (XP) and progressive neurologic symptoms. The parents are not consanguineous. Increased sun sensitivity led to the diagnosis of XP at 2y 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 (TTD) (brittle hair with a tiger-tail banding pattern on polarized microscopy) or Cockayne syndrome (CS) (cachectic dwarfism, cataracts, pigmentary retinopathy, and spasticity) were absent. XP2GO fibroblasts showed reduced post-UV cell survival (D37=3.8 J/m2), 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 neurologic degeneration, early diagnosis and rigorous sun protection can result in minimal skin disease without cancer in XP patients. PMID:18637129

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

    PubMed

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

    2014-07-23

    There is a great interest in the utilization of silicon-based anodes for lithium-ion batteries. However, its poor cycling stability, which is caused by a dramatic volume change during lithium-ion intercalation, and intrinsic low electric conductivity hamper its industrial applications. A facile strategy is reported here to fabricate graphene oxide-immobilized NH2-terminated silicon nanoparticles (NPs) negative electrode (Si@NH2/GO) directed by hydrogen bonding and cross-linked interactions to enhance the capacity retention of the anode. The NH2-modified Si NPs first form strong hydrogen bonds and covalent bonds with GO. The Si@NH2/GO composite further forms hydrogen bonds and covalent bonds with sodium alginate, which acts as a binder, to yield a stable composite negative electrode. These two chemical cross-linked/hydrogen bonding interactions-one between NH2-modified Si NPs and GO, and another between the GO and sodium alginate-along with highly mechanically flexible graphene oxide, produced a robust network in the negative electrode system to stabilize the electrode during discharge and charge cycles. The as-prepared Si@NH2/GO electrode exhibits an outstanding capacity retention capability and good rate performance, delivering a reversible capacity of 1000 mAh g(-1) after 400 cycles at a current of 420 mA g(-1) with almost 100% capacity retention. The results indicated the importance of system-level strategy for fabricating stable electrodes with improved electrochemical performance. PMID:24922522

  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. PMID:25441340

  11. An amplified electrochemical immunosensor based on in situ-produced 1-naphthol as electroactive substance and graphene oxide and Pt nanoparticles functionalized CeO2 nanocomposites as signal enhancer.

    PubMed

    Yang, Zhe-Han; Zhuo, Ying; Yuan, Ruo; Chai, Ya-Qin

    2015-07-15

    In this work, an amplified electrochemical immunosensor based on 1-naphthol as electroactive substance and Pt/CeO2/GO composites as catalytic amplifier was constructed for sensitive detection influenza. Through "sandwich" reaction, the Pt/CeO2/GO functionalized bioconjugates were captured on electrode surface and the electrochemical signal directly originated from 1-naphthol, which was in situ produced with high local concentration though the hydrolysis of 1-naphthyl phosphate catalyzed by ALP. Then, 1-naphthol as new reactant was oxidized by Pt/CeO2/GO composites with outstanding catalytic performance, resulting in detection signal amplification. In addition, as compared to label electroactive substance to antibodies, a simplified preparative step of immunosensor could be achieved because the signal probe get rid of introducation other electroactive substances. The proposed immunosensor achieved a linear range of 1.0×10(-3)-1.0ngmL(-1) and 5.0 to 1.0×10(2)ngmL(-1) with a detection limit of 0.43pgmL(-1) (defined as S/N=3). PMID:25791337

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

    NASA Astrophysics Data System (ADS)

    Dong, Xufeng; Huo, Shuang; Qi, Min

    2016-01-01

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

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

    PubMed

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

    2013-08-01

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

  14. 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

  15. 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

  16. 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.

  17. Functional prediction of hypothetical proteins in human adenoviruses.

    PubMed

    Dorden, Shane; Mahadevan, Padmanabhan

    2015-01-01

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

  18. 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.

  19. 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. PMID:22738305

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

    PubMed

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

    2016-12-01

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

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

    SciTech Connect

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

    2011-01-06

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

  2. 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). PMID:26850098

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

    PubMed

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

    2012-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  5. Recent advances in graphene-based biosensors.

    PubMed

    Kuila, Tapas; Bose, Saswata; Khanra, Partha; Mishra, Ananta Kumar; Kim, Nam Hoon; Lee, Joong Hee

    2011-08-15

    A detailed overview towards the advancement of graphene based biosensors has been reviewed. The large surface area and excellent electrical conductivity of graphene allow it to act as an "electron wire" between the redox centers of an enzyme or protein and an electrode's surface. Rapid electron transfer facilitates accurate and selective detection of biomolecules. This review discusses the application of graphene for the detection of glucose, Cyt-c, NADH, Hb, cholesterol, AA, UA, DA, and H(2)O(2). GO and RGO have been used for the fabrication of heavy metal ion sensors, gas sensors, and DNA sensors. Graphene based FETs have also been discussed in details. In all these cases, the biosensors performed well with low working potentials, high sensitivities, low detection limits, and long-term stabilities. PMID:21683572

  6. Origin of hole and electron traps in graphene oxide

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  7. 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

  8. 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.

  9. 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.

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

    PubMed

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

    2012-01-01

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

  11. 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

  12. G alpha selectivity and inhibitor function of the multiple GoLoco motif protein GPSM2/LGN.

    PubMed

    McCudden, Christopher R; Willard, Francis S; Kimple, Randall J; Johnston, Christopher A; Hains, Melinda D; Jones, Miller B; Siderovski, David P

    2005-09-10

    GPSM2 (G-protein signalling modulator 2; also known as LGN or mammalian Pins) is a protein that regulates mitotic spindle organization and cell division. GPSM2 contains seven tetratricopeptide repeats (TPR) and four Galpha(i/o)-Loco (GoLoco) motifs. GPSM2 has guanine nucleotide dissociation inhibitor (GDI) activity towards both Galpha(o)- and Galpha(i)-subunits; however, a systematic analysis of its individual GoLoco motifs has not been described. We analyzed each of the four individual GoLoco motifs from GPSM2, assessing their relative binding affinities and GDI potencies for Galpha(i1), Galpha(i2), and Galpha(i3) and Galpha(o). Each of the four GPSM2 GoLoco motifs (36-43 amino acids in length) was expressed in bacteria as a GST-fusion protein and purified to homogeneity. The binding of each of the four GST-GoLoco motifs to Galpha(i1)-, Galpha(o)-, and Galpha(s)-subunits was assessed by surface plasmon resonance; all of the motifs bound Galpha(i1), but exhibited low affinity towards Galpha(o). GDI activity was assessed by a fluorescence-based nucleotide-binding assay, revealing that all four GoLoco motifs are functional as GDIs for Galpha(i1), Galpha(i2), and Galpha(i3). Consistent with our binding studies, the GDI activity of GPSM2 GoLoco motifs on Galpha(o) was significantly lower than that toward Galpha(i1), suggesting that the in vivo targets of GPSM2 are most likely to be Galpha(i)-subunits. PMID:15946753

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

    PubMed

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

    2016-06-01

    A class of novel, environmental friendly ionic liquids (ILs) were synthesized by on-fiber preparation strategy and modified on graphene oxide (GO)-coated stainless steel wire, which was used as a solid-phase microextraction (SPME) fiber for efficient enrichment of polycyclic aromatic hydrocarbons (PAHs) and phthalate esters (PAEs). Surface characteristic of the ILs and polymeric-ILs (PILs) fibers with the wave-structure were inspected by scanning electron microscope. The successfully synthesis of bis(trifluoromethanesulfonyl)imide (NTf2(-))-based ILs were also characterized by energy dispersive spectrometer analysis. Through the chromatograms of the proposed two ILs (1-aminoethyl-3-methylimidazolium bromide (C2NH2MIm(+)Br(-)), C2NH2MIm(+)NTf2(-)) and two PILs (polymeric 1-vinyl-3-hexylimidazolium bromide (poly(VHIm(+)Br(-))), poly(VHIm(+)NTf2(-)))-GO-coated fibers for the extraction of analytes, NTf2(-)-based PIL demonstrated higher extraction capacity for hydrophobic compounds than other as-prepared ILs. Analytical performances of the proposed fibers were investigated under the optimized extraction and desorption conditions coupled with gas chromatography (GC). Compared with the poly(VHIm(+)Br(-))-GO fiber, the poly(VHIm(+)NTf2(-))-GO SPME fiber brought wider linear ranges for analytes with correlation coefficient in the range of 0.9852-0.9989 and lower limits of detection ranging from 0.015-0.025μgL(-1). The obtained results indicated that the newly prepared PILs-GO coating was a feasible, selective and green microextraction medium, which could be suitable for extraction and determination of PAHs and PAEs in potatoes and food-wrap sample, respectively. PMID:27130133

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Aerospike nozzle contour design and its performance validation

    NASA Astrophysics Data System (ADS)

    Wang, Chang-Hui; Liu, Yu; Qin, Li-Zi

    2009-06-01

    A simplified design and optimization method of aerospike nozzle contour and the results of tests and numerical simulation of aerospike nozzles are presented. The primary nozzle contour is approximated by two circular arcs and a parabola; the plug contour is approximated by a parabola and a third-order polynomial. The maximum total impulse from sea level to design altitude is adopted as objective to optimize the aerospike nozzle contour. Experimental studies were performed on a 6-cell tile-shaped aerospike nozzle, a 1-cell linear aerospike nozzle and a 3-cell aerospike nozzle with round-to-rectangle (RTR) primary nozzles designed by method proposed in present paper. Three aerospike nozzles achieved good altitude compensation capacities in the tests and still had better performance at off-design altitudes compared with that of the bell-shaped nozzle. In cold-flow tests, 6-cell tile-shaped aerospike nozzle and 1-cell linear aerospike nozzle obtained high thrust efficiency at design altitude. Employing gas H 2/gas O 2 (GH 2/GO 2) as propellants, hot-firing tests were carried out on a 3-cell aerospike nozzle engine with RTR primary nozzles. The performance was obtained under two nozzle pressure ratios (NPR) lower than design altitude. Efficiency reached 92.0-93.5% and 95.0-96.0%, respectively. Pressure distribution along plug ramp was measured and the effects of variation in the amount of base bleed on performance were also examined in the tests.

  20. Carbon dioxide within Venus and the earth

    NASA Technical Reports Server (NTRS)

    Ahrens, T. J.

    1981-01-01

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

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

    PubMed

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

    2015-09-01

    Dientamoeba fragilis is a human bowel parasite with a worldwide distribution. Dientamoeba was once described as a rare and harmless commensal though recent reports suggest it is common and potentially pathogenic. Molecular data on Dientamoeba is scarce which limits our understanding of this parasite. To address this, sequencing of the Dientamoeba transcriptome was performed. Messenger RNA was extracted from cultured Dientamoeba trophozoites originating from clinical stool specimens, and sequenced using Roche GS FLX and Illumina HiSeq technologies. In total 6,595 Dientamoeba transcripts were identified. These sequences were analysed using the BLAST2GO software suite and via BLAST comparisons to sequences available from TrichDB, GenBank, MEROPS and kinase.com. Several novel KEGG pathway maps were generated and gene ontology analysis was also performed. These results are thoroughly discussed guided by knowledge available for other related protozoa. Attention is paid to the novel biological insights afforded by this data including peptidases and kinases of Dientamoeba, as well as its metabolism, novel chemotherapeutics and possible mechanisms of pathogenicity. Currently, this work represents the largest contribution to our understanding of Dientamoeba molecular biology and also represents a major contribution to our understanding of the trichomonads generally, many of which are important pathogens of humans and animals. PMID:26188431

  2. 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

  3. 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.

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

    PubMed

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

    2014-11-25

    The excellent physical and semiconducting properties of transition metal dichalcogenide (TMDC) monolayers make them promising materials for many applications. The TMDC monolayer MoS2 has gained significant attention as a channel material for next-generation transistors. However, while n-type single-layer MoS2 devices can be made with relative ease, fabrication of p-type transistors remains a challenge as the Fermi-level of elemental metals used as contacts are pinned close to the conduction band leading to large p-type Schottky barrier heights (SBH). Here, we propose the utilization of graphene oxide (GO) as an efficient hole injection layer for single-layer MoS2-based electronic and optoelectronic devices. Using first-principles computations, we demonstrate that GO forms a p-type contact with monolayer MoS2, and that the p-type SBH can be made smaller by increasing the oxygen concentration and the fraction of epoxy functional groups in GO. Our analysis shows that this is possible due to the high work function of GO and the relatively weak Fermi-level pinning at the MoS2/GO interfaces compared to traditional MoS2/metal systems (common metals are Ag, Al, Au, Ir, Pd, Pt). The combination of easy-to-fabricate and inexpensive GO with MoS2 could be promising for the development of hybrid all-2D p-type electronic and optoelectronic devices on flexible substrates. PMID:25347209

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

    PubMed

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

    2015-01-01

    Wool is produced via synthetic processes of wool follicles, which are embedded in the skin of sheep. The development of new-generation sequencing and RNA sequencing provides new approaches that may elucidate the molecular regulation mechanism of wool follicle development and facilitate enhanced selection for wool traits through gene-assisted selection or targeted gene manipulation. We performed de novo transcriptome sequencing of skin using the Illumina Hiseq 2000 sequencing system in sheep (Ovis aries). Transcriptome de novo assembly was carried out via short-read assembly programs, including SOAPdenovo and ESTScan. The protein function, clusters of orthologous group function, gene ontology function, metabolic pathway analysis, and protein coding region prediction of unigenes were annotated by BLASTx, BLAST2GO, and ESTScan. More than 26,266,670 clean reads were collected and assembled into 79,741 unigene sequences, with a final assembly length of 35,447,962 nucleotides. A total of 22,164 unigenes were annotated, accounting for 36.27% of the total number of unigenes, which were divided into 25 classes belonging to 218 signaling pathways. Among them, there were 17 signal paths related to hair follicle development. Based on mass sequencing data of sheepskin obtained by RNA-Seq, many unigenes were identified and annotated, which provides an excellent platform for future sheep genetic and functional genomic research. The data could be used for improving wool quality and as a model for human hair follicle development or disease prevention. PMID:25730076

  6. In silico prediction of drug targets in Vibrio cholerae.

    PubMed

    Katara, Pramod; Grover, Atul; Kuntal, Himani; Sharma, Vinay

    2011-10-01

    Identification of potential drug targets is the first step in the process of modern drug discovery, subjected to their validation and drug development. Whole genome sequences of a number of organisms allow prediction of potential drug targets using sequence comparison approaches. Here, we present a subtractive approach exploiting the knowledge of global gene expression along with sequence comparisons to predict the potential drug targets more efficiently. Based on the knowledge of 155 known virulence and their coexpressed genes mined from microarray database in the public domain, 357 coexpressed probable virulence genes for Vibrio cholerae were predicted. Based on screening of Database of Essential Genes using blastn, a total of 102 genes out of these 357 were enlisted as vitally essential genes, and hence good putative drug targets. As the effective drug target is a protein which is only present in the pathogen, similarity search of these 102 essential genes against human genome sequence led to subtraction of 66 genes, thus leaving behind a subset of 36 genes whose products have been called as potential drug targets. The gene ontology analysis using Blast2GO of these 36 genes revealed their roles in important metabolic pathways of V. cholerae or on the surface of the pathogen. Thus, we propose that the products of these genes be evaluated as target sites of drugs against V. cholerae in future investigations. PMID:21174131

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

    PubMed

    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

  8. The General Practitioner's Consultation Approaches to Medically Unexplained Symptoms: A Qualitative Study.

    PubMed

    Hansen, Henriette Schou; Rosendal, Marianne; Fink, Per; Risør, Mette Bech

    2013-01-01

    Background. The prevalence of medically unexplained symptoms (MUSs) in primary care is about 10-15%. The definition of MUS is descriptive and there are no specific diagnostic criteria for MUS in primary care. Furthermore, a general practitioner's (GP's) categorisation of patients with MUS shows large variation. The aim of the present study is to investigate how GPs employ the definition of MUS and how they manage patients with MUS in daily practice. Methods. With a grounded theory approach five focus group interviews with GPs were performed. The interviews addressed how GPs managed MUS and their reflections on the course and prognosis for MUS patients. Results. Consultations about MUS develop around the individual patient and usually include several appointments. We identified three different types of consultations: (1) "searching for a disease," (2) "going by the routine," and (3) "following various paths." These types of consultations spanned from a biomedical approach to an approach where multiple explanations were offered to explain the patient's problem. The choice of consultation types was influenced by the GP, the patient and contextual factors which, in turn, affected the diagnostic process. Conclusions. A diagnosis of MUS is contextually embedded and the diagnostic process is shaped by the consultation. PMID:24967320

  9. 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.

  10. 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.

  11. 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

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

    PubMed Central

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

    2016-01-01

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

  13. 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

  14. High-throughput sequencing of black pepper root transcriptome

    PubMed Central

    2012-01-01

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

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

    PubMed

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

    2016-08-01

    The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata. PMID:26971316

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

    PubMed

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

    2014-09-28

    A quaternary nanocomposite Fe3O4@SiO2@TiO2/graphene oxide (GO) was for the first time successfully synthesized in this work for the repeated use in simultaneous adsorption and photocatalytic degradation of aromatically structured chemical pollutants. The resulting sample was characterized by TEM, XRD, FTIR, TG-DTG, XPS, PL, and VSM. Its photocatalytic activity was evaluated in the photocatalytic degradation of rhodamine B (RhB) under high-pressure mercury lamp irradiation. The results showed that about 63% of RhB was absorbed onto the prepared Fe3O4@SiO2@TiO2/GO nanocomposites by just 30 minute mixing, and after 120 min high-pressure mercury lamp irradiation, about 92.03% of RhB was converted. The photocatalytic degradation followed pseudo first-order reaction with an apparent rate constant of 0.0136 min(-1). Compared with the Fe3O4@SiO2@TiO2 nanoparticles, it exhibits an excellent ability to adsorb aromatic compounds via π-π stacking and a higher photocatalytic activity due to the presence of GO. In addition, the synthesized nanomaterial exhibited good magnetic response and the reusability study suggested that the prepared nanocomposites were stable enough and maintained high degradation rate and catalyst recovery even after five cycles, verifying their potential application in water purification. PMID:25087943

  17. 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.

  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. PMID:24755346

  19. 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

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

    PubMed 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

  1. 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

  2. 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. PMID:27080912

  3. 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

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

    PubMed

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

    2016-06-01

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

  5. Auxiliary propulsion technology for advanced Earth-to-orbit vehicles

    NASA Technical Reports Server (NTRS)

    Schneider, Steven J.

    1987-01-01

    The payload which can be delivered to orbit by advanced Earth-to-Orbit vehicles is significantly increased by advanced subsystem technology. Any weight which can be saved by advanced subsystem design can be converted to payload at Main Engine Cut Off (MECO) given the same launch vehicle performance. The auxiliary propulsion subsystem and the impetus for the current hydrogen/oxygen technology program is examined. A review of the auxiliary propulsion requirements of advanced Earth-to-Orbit (ETO) vehicles and their proposed missions is given first. Then the performance benefits of hydrogen/oxygen auxiliary propulsion are illustrated using current shuttle data. The proposed auxiliary propulsion subsystem implementation includes liquid hydrogen/liquid oxygen (LH2/LO2) primary Reaction Control System (RCS) engines and gaseous hydrogen/gaseous oxygen (GH2/GO2) vernier RCS engines. A distribution system for the liquid cryogens to the engines is outlined. The possibility of providing one dual-phase engine that can operate on either liquid or gaseous propellants is being explored, as well as the simultaneous firing of redundant primary RCS thrusters to provide Orbital Maneuvering System (OMS) level impulse. Scavenging of propellants from integral main engine tankage is proposed to utilize main engine tank residuals and to combine launch vehicle and subsystem reserves.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Tarnas, Jesse; Redfield, Seth

    2016-01-01

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

  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. PMID:26684618

  9. 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

  10. 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

  11. 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.

  12. 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

    2016-01-01

    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

  13. 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.

  14. A label-free colorimetric sensor for Pb2+ detection based on the acceleration of gold leaching by graphene oxide.

    PubMed

    Shi, Xinhao; Gu, Wei; Zhang, Cuiling; Zhao, Longyun; Peng, Weidong; Xian, Yuezhong

    2015-03-14

    In this work, we developed a novel, label-free, colorimetric sensor for Pb(2+) detection based on the acceleration of gold leaching by graphene oxide (GO) at room temperature. Gold nanoparticles (AuNPs) can be dissolved in a thiosulfate (S2O3(2-)) aqueous environment in the presence of oxygen; however, the leaching rate is very slow due to the high activation energy (27.99 kJ mol(-1)). In order to enhance the reaction rate, some accelerators should be added. In comparison with the traditional accelerators (metal ions or middle ligands), we found that GO could efficiently accelerate the gold leaching reaction. Kinetic data demonstrate that the dissolution rate of gold in the Pb(2+)-S2O3(2-)-GO system is 5 times faster than that without GO at room temperature. In addition, the effects of surface modification and the nanoparticle size on the etching of AuNPs were investigated. Based on the GO-accelerated concentration-dependent colour changes of AuNPs, a colorimetric sensor for Pb(2+) detection was developed with a linear range from 0.1 to 20 μM and the limit of detection (LOD) was evaluated to be 0.05 μM. This colorimetric assay is simple, low-cost, label-free, and has numerous potential applications in the field of environmental chemistry. PMID:25656247

  15. Quantitative assessment of protein function prediction programs.

    PubMed

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

    2015-01-01

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

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

    PubMed

    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

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

    PubMed

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

    2011-03-15

    Graphene oxide (GO) obtained from chemical oxidation of flake graphite was derivatized with sulfonic groups to form sulfonic-functionalized GO (GO-SO(3)(-)) through four sulfonation routes: through amide formation between the carboxylic group of GO and amine of sulfanilic acid (AA-GO-SO(3)(-)), aryl diazonium reaction of sulfanilic acid (AD-GO-SO(3)(-)), amide formation between the carboxylic group of GO and amine of cysteamine and oxidation by H(2)O(2) (CA-GO-SO(3)(-)), and alkyl diazonium reaction of cysteamine and oxidation by H(2)O(2) (CD-GO-SO(3)(-)). Results of Fourier transform infrared spectroscopy and X-ray photoelectrospectrocopy showed that -SO(3)(-) groups were attached onto GO. Thermo gravimetric analysis showed that derivatization with sulfonic groups improved thermo stability of GO. X-ray diffraction results indicated that GO-SO(3)(-) had more ordered π-π stacking structure than the original GO. GO-SO(3)(-) and cationic polyelectrote, poly (diallyldimethylammoniumchloride) (PDDA) were adsorbed at indium tin oxide (ITO) glass surface through layer-by-layer assembling to form (GO-SO(3)(-)/PDDA)(n)/ITO multilayers. After tris-(2,2'-bipyridyl) ruthenium (II) dichloride (Ru(bpy)(3)(2+)) was incorporated into the multilayers, the obtained Ru(bpy)(3)(2+)/(GO-SO(3)(-)/PDDA)(n)/ITO electrodes can be used as electrochemiluminescence sensors for detection of organic amine with high sensitivity (limit of detection of 1 nM) and stability. PMID:21211958

  18. AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects

    PubMed Central

    Zhang, Qingrun; Long, Quan; Ott, Jurg

    2014-01-01

    Identifying gene-gene interaction is a hot topic in genome wide association studies. Two fundamental challenges are: (1) how to smartly identify combinations of variants that may be associated with the trait from astronomical number of all possible combinations; and (2) how to test epistatic interaction when all potential combinations are available. We developed AprioriGWAS, which brings two innovations. (1) Based on Apriori, a successful method in field of Frequent Itemset Mining (FIM) in which a pattern growth strategy is leveraged to effectively and accurately reduce search space, AprioriGWAS can efficiently identify genetically associated genotype patterns. (2) To test the hypotheses of epistasis, we adopt a new conditional permutation procedure to obtain reliable statistical inference of Pearson's chi-square test for the contingency table generated by associated variants. By applying AprioriGWAS to age-related macular degeneration (AMD) data, we found that: (1) angiopoietin 1 (ANGPT1) and four retinal genes interact with Complement Factor H (CFH). (2) GO term “glycosaminoglycan biosynthetic process” was enriched in AMD interacting genes. The epistatic interactions newly found by AprioriGWAS on AMD data are likely true interactions, since genes interacting with CFH are retinal genes, and GO term enrichment also verified that interaction between glycosaminoglycans (GAGs) and CFH plays an important role in disease pathology of AMD. By applying AprioriGWAS on Bipolar disorder in WTCCC data, we found variants without marginal effect show significant interactions. For example, multiple-SNP genotype patterns inside gene GABRB2 and GRIA1 (AMPA subunit 1 receptor gene). AMPARs are found in many parts of the brain and are the most commonly found receptor in the nervous system. The GABRB2 mediates the fastest inhibitory synaptic transmission in the central nervous system. GRIA1 and GABRB2 are relevant to mental disorders supported by multiple evidences. PMID:24901472

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

    PubMed

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

    2015-01-01

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

  20. 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/. PMID:22641428

  1. 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

  2. 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

    2016-01-01

    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

  3. 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. PMID:24718369

  4. 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

  5. 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

  6. 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

  7. Targeting impulsive processes of eating behavior via the internet. Effects on body weight.

    PubMed

    Veling, Harm; van Koningsbruggen, Guido M; Aarts, Henk; Stroebe, Wolfgang

    2014-07-01

    Because eating behavior can take on an impulsive nature many people experience difficulty with dieting to lose weight. Therefore, an experiment was conducted to test the effectiveness of two interventions targeting impulsive processes of eating behavior to facilitate weight loss: Implementation intentions to remind people about dieting versus a go/no-go task to change impulses toward palatable foods. Dieters performed an online training program (four times in 4 weeks) in which they were randomly assigned to a 2 (implementation intention condition: dieting versus control) × 2 (go/no-go task condition: food versus control) design. They formed either dieting implementation intentions (e.g., If I open the fridge I will think of dieting!) or control implementation intentions. Furthermore, they received either a go/no-go task in which behavioral stop signals were presented upon presentation of palatable foods (food go/no-go task), or upon control stimuli. Participants' weight was measured in the laboratory before and after the intervention. Strength of participants' dieting goal and their Body Mass Index (BMI; as a proxy for impulsiveness toward food) were examined as moderators. Results showed that both dieting implementation intentions and the food go/no-go task facilitated weight loss. Moreover, dieting implementation intentions facilitated weight loss particularly among people with a strong current dieting goal, whereas the food go/no-go task facilitated weight loss independent of this factor. Instead, the food go/no-go task, but not formation of dieting implementation intentions, was primarily effective among dieters with a relatively high BMI. These results provide the first preliminary evidence that interventions aimed at targeting impulsive eating-related processes via the internet can facilitate weight loss. PMID:24675683

  8. 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.

  9. 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.

  10. Synthesis and adsorption performance of Mg(OH)2 hexagonal nanosheet-graphene oxide composites

    NASA Astrophysics Data System (ADS)

    Liu, Mengdi; Xu, Jing; Cheng, Bei; Ho, Wingkei; Yu, Jiaguo

    2015-03-01

    A series of Mg(OH)2 hexagonal nanosheet-graphene oxide (GO) composites were synthesized through a simple hydrothermal method using magnesium nitrate and GO as precursors, sodium nitrate and sodium oxalate as additives, and sodium hydroxide and ammonia as precipitants. The as-prepared samples were characterized by X-ray diffraction, nitrogen adsorption-desorption isotherms, Raman spectroscopy, zeta potential analysis, and scanning electron microscopy (SEM). The adsorption affinity of the as-prepared samples toward congo red (CR) in water was analyzed and investigated. Results indicated that GO addition influenced the thickness, morphology, and adsorption performance of Mg(OH)2 hexagonal nanosheets. As GO concentration increased, the thickness decreased. Especially at high GO concentration (1 wt%), Mg(OH)2 hexagonal nanosheets changed into aggregated flower-like spheres. Addition of small amounts of GO also increased the adsorption capacity of Mg(OH)2. The equilibrium adsorption data of CR on the composite were further investigated by Langmuir and Freundlich models, indicating that the Langmuir model was much more suitable for the experimental data. The sample prepared with 0.5 wt% GO showed the highest adsorption capacity with 118 mg g-1. The experimental data were then fitted using pseudo-second order kinetics, suggesting that pseudo-second order kinetics could well describe the adsorption of CR on composites. Adsorption thermodynamics analysis showed that the adsorption activation energy was 29.2 kJ mol-1, suggesting that the adsorption of CR onto the samples was physical adsorption. Adsorption between the samples and CR was mainly due to the strong electrostatic attraction between them because they had opposite charges. These findings indicated that Mg(OH)2-GO composite was an effective adsorbent for the removal of CR in water.

  11. Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea.

    PubMed

    Gaur, Rashmi; Bhatia, Sabhyata; Gupta, Meetu

    2014-07-01

    Chickpea is the world's third most important legume crop and belongs to Fabaceae family but suffered from severe yield loss due to various biotic and abiotic stresses. Development of modern genomic tools such as molecular markers and identification of resistant genes associated with these stresses facilitate improvement in chickpea breeding towards abiotic stress tolerance. In this study, 1597 high-quality expressed sequence tags (ESTs) were generated from a cDNA library of variety Pusa 1105 root tissue after cadmium (Cd) treatment. Assembly of ESTs resulted in a total of 914 unigenes of which putative homology was obtained for 38.8 % of unigenes after BLASTX search. In terms of species distribution, majority of sequences found similarity with Medicago truncatula followed by Glycine max, Vitis vinifera and Populus trichocarpa and Pisum sativum sequences. Functional annotation was assigned using Blast2Go, and the Gene Ontology (GO) terms were categorized into biological process, molecular function and cellular component. Approximately 10.83 % of unigenes were assigned at least one GO term. Moreover, in the distribution of transcripts into various biological pathways, 20 of the annotated transcripts were assigned to ten pathways in KEGG database. A majority of the genes were found to be involved in sulphur and nitrogen metabolism. In the quantitative real-time PCR analysis, five of the transcription factors and three of the transporter genes were found to be highly expressed after Cd treatment. Besides, the utility of ESTs was demonstrated by exploiting them for the development of 83 genic molecular markers including EST-simple sequence repeats and intron targeted polymorphism that would assist in tagging of genes related to metal stress for future prospects. PMID:24414095

  12. Proteomic analysis of mature Lagenaria siceraria seed.

    PubMed

    Kumari, Neha; Tajmul, Md; Yadav, Savita

    2015-04-01

    Lagenaria siceraria (bottle gourd) class belongs to Magnoliopsida family curcurbitaceae that is a traditionally used medicinal plant. Fruit of this plant are widely used as a therapeutic vegetable in various diseases, all over the Asia and Africa. Various parts of this plant like fruit, seed, leaf and root are used as alternative medicine. In the present study, primarily, we have focused on proteomic analysis of L. siceraria seed using phenol extraction method for protein isolation. Twenty-four colloidal coomassie blue stained protein spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) after resolving on two-dimensional gel electrophoresis. Out of 24 identified protein spots, four were grouped as unidentified proteins which clearly suggest that less work has been done in the direction of plant seed proteomics. These proteins have been found to implicate in various functions such as biosynthesis of plant cell wall polysaccharides and glycoproteins, serine/threonine kinase activity, plant disease resistance and transferase activity against insects by means of insecticidal and larval growth inhibitory, anti-HIV, antihelmintic and antimicrobial properties. By Blast2GO annotation analysis, amongst the identified proteins of L. siceraria, molecular function for majority of proteins has indispensable role in catalytic activity, few in binding activity and antioxidant activity; it is mostly distributed in cell, organelle, membrane and macromolecular complex. Most of them involved in biological process such as metabolic process, cellular process, response to stimulus, single organism process, signalling, biological recognition, cellular component organization or biogenesis and localization. PMID:25672325

  13. ZERO EMISSION COAL POWER, A NEW CONCEPT

    SciTech Connect

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

    2001-04-01

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

  14. 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

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

    PubMed

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

    2016-01-01

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

  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. Short-read sequencing for genomic analysis of the brown rot fungus Fibroporia radiculosa.

    PubMed

    Tang, Juliet D; Perkins, Andy D; Sonstegard, Tad S; Schroeder, Steven G; Burgess, Shane C; Diehl, Susan V

    2012-04-01

    The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and then assembling each data set with Velvet. A simple approach was devised to determine which filter stringency was "best." Venn diagrams identified the regions containing reads that were used in an assembly but were of a low-enough quality to be removed by a filter. By plotting base quality histograms of reads in this region, we judged whether a filter was too stringent or not stringent enough. Our best assembly had a genome size of 33.6 Mb, an N50 of 65.8 kb for a k-mer of 51, and a maximum contig length of 347 kb. Using GeneMark, 9,262 genes were predicted. TargetP and SignalP analyses showed that among the 1,213 genes with secreted products, 986 had motifs for signal peptides and 227 had motifs for signal anchors. Blast2GO analysis provided functional annotation for 5,407 genes. We identified 29 genes with putative roles in copper tolerance and 73 genes for lignocellulose degradation. A search for homologs of these 102 genes showed that F. radiculosa exhibited more similarity to Postia placenta than Serpula lacrymans. Notable differences were found, however, and their involvements in copper tolerance and wood decay are discussed. PMID:22247176

  18. 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

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

    PubMed Central

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

    2016-01-01

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

  20. Genome-wide analysis of differential mRNA expression of Amsacta moorei entomopoxvirus, mediated by the gene encoding a viral protein kinase (AMV197).

    PubMed

    Muratoglu, Hacer; Nalcacioglu, Remziye; Arif, Basil M; Demirbag, Zihni

    2016-04-01

    Insect-born entomopoxviruses (Fam: Poxviridae) are potentially important bio-pesticide against insect pests and expression vectors as well as vectors for transient human gene therapies including recombinant viral vaccines. For these reasons, it is necessary to understand the regulatory genes functions to improve its biotechnological potential. Here, we focused on the characterization of serine/threonine (Ser/Thr; ORF AMV197) protein kinase gene from the Amsacta moorei entomopoxvirus (AMEV), the type species of the genus Betaentomopoxvirus. Transcription of the parental and an amv197-null recombinant AMEV was compared by whole-genome gene expression microarray analysis. Blast2GO analysis reflected a broad diversity of upregulated and downregulated genes. Results showed that expression levels of 102 genes (45%) out of 226 tested genes changed significantly in the recombinant AMEV infected cells. Of these transcripts, 72 (70.58%) were upregulated and 30 (29.41%) were downregulated throughout the infection period. Genes involved in DNA repair, replication and nucleotide metabolism, transcription and RNA modification, and protein modification were mostly upregulated at different times in cells infected with the recombinant virus. Furthermore, transcription of all studied cellular genes including metabolism of apoptosis (Nedd2-like caspase, hemolin and elongation factor-1 alpha (ef1a) gene) was downregulated in the absence of amv197. Quantitative real time reverse transcription-PCR confirmed viral transcriptional changes obtained by microarray. The results of this study indicated that the product of amv197 appears to affect the transcriptional regulation of most viral and many cellular genes. Further investigations are, however, needed to narrow down the role of AMV197 throughout the infection process. PMID:26820433

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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. PMID:24554848

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

    PubMed

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

    2016-07-01

    Copepods-which include freshwater and marine species-represent the most abundant group of aquatic invertebrates. Among them, the calanoid copepod Eurytemora affinis is widely represented in the northern hemisphere estuaries and has become a species of interest in ecotoxicology. Like other non-target organisms, E. affinis may be exposed to a wide range of chemicals such as endocrine disruptors (EDs). This study investigated the gene expression variation in E. affinis after exposure to ED pesticides-chosen as model EDs-in order to (i) improve the knowledge on their effects in crustaceans, and (ii) highlight relevant transcripts for further development of potential biomarkers of ED exposure/effect. The study focused on the reproduction function in response to ED. Copepods were exposed to sublethal concentrations of pyriproxyfen (PXF) and chlordecone (CLD) separately. After 48h, males and females (400 individuals each) were sorted for RNA extraction. Their transcriptome was pyrosequenced using the Illumina(®) technology. Contigs were blasted and functionally annotated using Blast2GO(®). The differential expression analysis between ED- and acetone-exposed organisms was performed according to sexes and contaminants. Half of the 19,721 contigs provided by pyrosequencing were annotated, mostly (80%) from arthropod sequences. Overall, 2,566 different genes were differentially expressed after ED exposures in comparison with controls. As many genes were differentially expressed after PXF exposure as after CLD exposure. In contrast, more genes were differentially expressed in males than in females after both exposures. Ninety-seven genes overlapped in all conditions. Finally, 31 transcripts involved in reproduction, growth and development, and changed in both chemical exposures were selected as potential candidates for future development of biomarkers. PMID:27111276

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

    PubMed

    Bhattacharya, Anindya; Cui, Yan

    2016-01-01

    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. PMID:26578591

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

    PubMed Central

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

    2012-01-01

    Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. The structural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studies and are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capable of degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses the ability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows the cell to grow on MBA, a highly toxic and mutagenic environmental pollutant. For the structural and functional analysis, a 346 amino acid encoding protein sequence of haloacid dehalogenase is retrieve from NCBI data base. Primary and secondary structure analysis suggested that the high percentage of helices in the structure makes the protein more flexible for folding, which might increase protein interactions. The consensus protein sub-cellular localization predictions suggest that dehalogenase protein is a periplasmic protein 3D2GO server, suggesting that it is mainly employed in metabolic process followed by hydrolase activity and catalytic activity. The tertiary structure of protein was predicted by homology modeling. The result suggests that the protein is an unstable protein which is also an important characteristic of active enzyme enabling them to bind various cofactors and substrate for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and RMSD score. This predicted information will help in better understanding of mechanism underlying haloacid dehalogenase encoding protein and its evolutionary relationship. PMID:23251046

  9. 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. PMID:26880158

  10. 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

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

    PubMed

    Ammer, H; Schulz, R

    1994-04-01

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

  12. 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

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

    PubMed

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

    2016-08-01

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

  14. 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

  15. Supercritical Carbon Dioxide Brayton Power Conversion Cycle Design for Optimized Battery-Type Integral Reactor System

    SciTech Connect

    Kim, Won J.; Kim, Tae W.; Sohn, Myoung S.; Suh, Kune Y.

    2006-07-01

    Supercritical carbon dioxide (SCO{sub 2}) promises a high power conversion efficiency of the recompression Brayton cycle due to its excellent compressibility reducing the compression work at the bottom of the cycle and to a higher density than helium or steam decreasing the component size. Therefore, the high SCO{sub 2} Brayton cycle efficiency as high as 45 % furnishes small sized nuclear reactors with economical benefits on the plant construction and maintenance. A 23 MWth BORIS (Battery Optimized Reactor Integral System) is being developed as a multipurpose reactor. BORIS, an integral-type optimized fast reactor with an ultra long life core, is coupled to the SCO{sub 2} Brayton cycle needing less room relative to the Rankine steam cycle because of its smaller components. The SCO{sub 2} Brayton cycle of BORIS consists of a 16 MW turbine, a 32 MW high temperature recuperator, a 14 MW low temperature recuperator, an 11 MW pre-cooler and 2 and 2.8 MW compressors. Entering six heat exchangers between primary and secondary system at 19.9 MPa and 663 K, the SCO{sub 2} leaves the heat exchangers at 19.9 MPa and 823 K. The promising secondary system efficiency of 45 % was calculated by a theoretical method in which the main parameters include pressure, temperature, heater power, the turbine's, recuperators' and compressors' efficiencies, and the flow split ratio of SCO{sub 2} going out from the low temperature recuperator. Test loop SOLOS (Shell-and-tube Overall Layout Optimization Study) is utilized to develop advanced techniques needed to adopt the shell-and-tube type heat exchanger in the secondary loop of BORIS by studying the SCO{sub 2} behavior from both thermal and hydrodynamic points of view. Concurrently, a computational fluid dynamics (CFD) code analysis is being conducted to develop an optimal analytical method of the SCO{sub 2} turbine efficiency having the parameters of flow characteristics of SCO{sub 2} passing through buckets of the turbine. These

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

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

    PubMed

    Mahpishanian, Shokouh; Sereshti, Hassan; Baghdadi, Majid

    2015-08-01

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

  4. 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

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

    PubMed

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

    2008-07-01

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

  6. 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

  7. 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).

  8. 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

  9. 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

  10. 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

  11. 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

  12. Computational annotation of genes differentially expressed along olive fruit development

    PubMed Central

    Galla, Giulio; Barcaccia, Gianni; Ramina, Angelo; Collani, Silvio; Alagna, Fiammetta; Baldoni, Luciana; Cultrera, Nicolò GM; Martinelli, Federico; Sebastiani, Luca; Tonutti, Pietro

    2009-01-01

    Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1), completed pit hardening (stage 2) and veraison (stage 3)] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B), and 2 and 3 (libraries C and D). All sequenced clones (1,132 in total) were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO): cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was used to query all

  13. 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

  14. 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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Before the large people influx and development of the central part of Brazil in the sixties, due to new capital Brasília, Cerrado, a typical Brazilian savanna-type vegetation, used to occupy about 2 million km2, going from the Amazon tropical forest, in the north, to the edges of what used to be the Atlantic forest in the southeast. Today, somewhat 50% of this area has given place to agriculture, pasture and managed forests. Understanding how Cerrado interacts with the atmosphere and how this interaction will be modified with this land-use change is a crucial step towards improving predictions of future climate-change scenarios. Cerrado is a vegetation adapted to a climate characterized by two distinct seasons, a wet season (Nov-Mar) and dry season (May-Ago), with April and October being transitions between seasons. Typically, 75% of precipitation happens in the wet-season months and only 5% during dry-season. In this study, it is investigated the potential impacts of the substitution of Cerrado to the eco-hydrological characteristics of the region. The focus here is Eucalyptus plantation which have increased substantially in the last decade due to government incentives. Two eddy-covariance (EC) systems were installed, one in an undisturbed Cerrado Stricto area and other in a recently-established Eucalyptus plantation. The two areas are 1,400m apart and are subjected to the same meteorology and similar edaphic conditions. Besides instrumentation typical of EC towers, a soil-moisture profiling system were installed in each site. Data from the towers will be used to parameterized a Soil-Vegetation-Atmosphere (SVAT) model to simulate hydrological and atmospheric boundary layer (ABL) processes in order to understand how the two vegetation cover modulates the exchange of mass and energy between the biosphere and atmosphere. Simulations of 30-day dry down from saturation to complete water stress were performed and were analyzed on how ABL respond to soil moisture

  17. 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

  18. 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

  19. 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

  20. The role of density gradient in liquid rocket engine combustion instability

    NASA Astrophysics Data System (ADS)

    Ghosh, Amardip

    Experimental and analytical studies were conducted to investigate key physical mechanisms responsible for flame-acoustic coupling during the onset of acoustically driven combustion instabilities in liquid rocket engines (LREs). Controlled experiments were conducted in which a turbulent Hydrogen-Oxygen (GH2-GO2) diffusion flame, established downstream of a two-dimensional model shear coaxial injector was acoustically forced by a compression driver unit mounted in a transverse direction and excited through a broad range of frequencies (200Hz-2000Hz) and amplitudes. Characteristic interactions between flame and acoustics visualized through OH* and CH* chemiluminescence imaging and dynamic pressure measurements obtained using high frequency dynamic pressure transducers indicated that small acoustic disturbances could be amplified by flame-acoustic coupling under certain conditions leading to substantial modulation in spatial heat release fluctuations. Density gradient between fuel and oxidizer was found to significantly affect the way acoustic waves interacted with density stratified flame fronts. The particular case of an asymmetric flame front oscillation under transverse acoustic forcing indicated that baroclinic vorticity, generated by the interactions between misaligned pressure gradient (across the acoustic wave) and density gradient (across the fuel oxidizer interface) could further amplify flame front distortions. Asymmetric interaction between flame and acoustics is shown to occur preferentially on flame fronts where controlled waves from the compression driver travel from lighter fluid to denser fluid and the amount of interaction between flame and acoustics is shown to depend strongly on the density ratio between the fluids on either sides of the flame front. This observation is in agreement with the baroclinic vorticity mechanism and a variant of the classical Rayleigh-Taylor instability mechanism. The results provide the first known experimental evidence

  1. 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.

  2. 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

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

    NASA Astrophysics Data System (ADS)

    Kang, Namhyun

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