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Sample records for higher eukaryote photochemical

  1. Enzymes from Higher Eukaryotes for Industrial Biocatalysis

    Directory of Open Access Journals (Sweden)

    Zhibin Liu

    2004-01-01

    Full Text Available The industrial production of fine chemicals, feed and food ingredients, pharmaceuticals, agrochemicals and their respective intermediates relies on an increasing application of biocatalysis, i.e. on enzyme or whole-cell catalyzed conversions of molecules. Simple procedures for discovery, cloning and over-expression as well as fast growth favour fungi, yeasts and especially bacteria as sources of biocatalysts. Higher eukaryotes also harbour an almost unlimited number of potential biocatalysts, although to date the limited supply of enzymes, the high heterogeneity of enzyme preparations and the hazard of infectious contaminants keep some interesting candidates out of reach for industrial bioprocesses. In the past only a few animal and plant enzymes from agricultural waste materials were employed in food processing. The use of bacterial expression strains or non-conventional yeasts for the heterologous production of efficient eukaryotic enzymes can overcome the bottleneck in enzyme supply and provide sufficient amounts of homogenous enzyme preparations for reliable and economically feasible applications at large scale. Ideal enzymatic processes represent an environmentally friendly, »near-to-completion« conversion of (mostly non-natural substrates to pure products. Recent developments demonstrate the commercial feasibility of large-scale biocatalytic processes employing enzymes from higher eukaryotes (e.g. plants, animals and also their usefulness in some small-scale industrial applications.

  2. Repair of DNA DSB in higher eukaryotes

    International Nuclear Information System (INIS)

    Wang, H.; Perrault, A.R.; Takeda, Y.; Iliakis, G.

    2003-01-01

    Cells of higher eukaryotes process within minutes double strand breaks (DSBs) in their genome using a NHEJ apparatus that engages DNA-PKcs, Ku, DNA ligase IV, XRCC4, and other as of yet unidentified factors. Although chemical inhibition, or mutation, in any of these factors delays processing, cells ultimately remove the majority of DNA DSBs using an alternative pathway operating with slower kinetics. This alternative pathway is active in mutants deficient in genes of the RAD52 epistasis group. We proposed, therefore, that it reflects an alternative form of NHEJ that operates as a backup (B-NHEJ) to the DNA-PK- dependent (D-NHEJ) pathway, rather than homology directed repair of DSBs. We studied the role of Ku and DNA-PKcs in the coordination of these pathways using as a model end joining of restriction endonuclease linearized plasmid DNA in whole cell extracts. Efficient error-free endjoining observed in such in-vitro reactions is strongly inhibited by anti-Ku antibodies. The inhibition requires DNA-PKcs, despite that fact that Ku efficiently binds DNA ends in the presence of antibodies, or in the absence of DNA-PKcs. Strong inhibition of DNA endjoining is also mediated by wortmannin, an inhibitor of DNA-PKcs, in the presence but not in the absence of Ku, and this inhibition can be rescued by pre-incubating the reaction with double stranded oligonucleotides. The results are compatible with a role of Ku in directing endjoining to a DNA-PK dependent pathway, mediated by efficient end binding and productive interactions with DNA-PKcs. On the other hand, efficient end joining is observed in extracts of cells lacking DNA-PKcs, as well as in Ku-depleted extracts sugggesting the operation of alternative pathways. Extracts depleted of Ku and DNA-PKcs rejoin blunt ends, as well as homologous ends with 3' or 5' protruding single strands with similar efficiency, but addition of Ku suppresses joining of blunt ends and homologous ends with 3' overhangs. We propose that the

  3. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

  4. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

    Science.gov (United States)

    Klionsky, Daniel J.; Abeliovich, Hagai; Agostinis, Patrizia; Agrawal, Devendra K.; Aliev, Gjumrakch; Askew, David S.; Baba, Misuzu; Baehrecke, Eric H.; Bahr, Ben A.; Ballabio, Andrea; Bamber, Bruce A.; Bassham, Diane C.; Bergamini, Ettore; Bi, Xiaoning; Biard-Piechaczyk, Martine; Blum, Janice S.; Bredesen, Dale E.; Brodsky, Jeffrey L.; Brumell, John H.; Brunk, Ulf T.; Bursch, Wilfried; Camougrand, Nadine; Cebollero, Eduardo; Cecconi, Francesco; Chen, Yingyu; Chin, Lih-Shen; Choi, Augustine; Chu, Charleen T.; Chung, Jongkyeong; Clarke, Peter G.H.; Clark, Robert S.B.; Clarke, Steven G.; Clavé, Corinne; Cleveland, John L.; Codogno, Patrice; Colombo, María I.; Coto-Montes, Ana; Cregg, James M.; Cuervo, Ana Maria; Debnath, Jayanta; Demarchi, Francesca; Dennis, Patrick B.; Dennis, Phillip A.; Deretic, Vojo; Devenish, Rodney J.; Di Sano, Federica; Dice, J. Fred; DiFiglia, Marian; Dinesh-Kumar, Savithramma; Distelhorst, Clark W.; Djavaheri-Mergny, Mojgan; Dorsey, Frank C.; Dröge, Wulf; Dron, Michel; Dunn, William A.; Duszenko, Michael; Eissa, N. Tony; Elazar, Zvulun; Esclatine, Audrey; Eskelinen, Eeva-Liisa; Fésüs, László; Finley, Kim D.; Fuentes, José M.; Fueyo, Juan; Fujisaki, Kozo; Galliot, Brigitte; Gao, Fen-Biao; Gewirtz, David A.; Gibson, Spencer B.; Gohla, Antje; Goldberg, Alfred L.; Gonzalez, Ramon; González-Estévez, Cristina; Gorski, Sharon; Gottlieb, Roberta A.; Häussinger, Dieter; He, You-Wen; Heidenreich, Kim; Hill, Joseph A.; Høyer-Hansen, Maria; Hu, Xun; Huang, Wei-Pang; Iwasaki, Akiko; Jäättelä, Marja; Jackson, William T.; Jiang, Xuejun; Jin, Shengkan; Johansen, Terje; Jung, Jae U.; Kadowaki, Motoni; Kang, Chanhee; Kelekar, Ameeta; Kessel, David H.; Kiel, Jan A.K.W.; Kim, Hong Pyo; Kimchi, Adi; Kinsella, Timothy J.; Kiselyov, Kirill; Kitamoto, Katsuhiko; Knecht, Erwin; Komatsu, Masaaki; Kominami, Eiki; Kondo, Seiji; Kovács, Attila L.; Kroemer, Guido; Kuan, Chia-Yi; Kumar, Rakesh; Kundu, Mondira; Landry, Jacques; Laporte, Marianne; Le, Weidong; Lei, Huan-Yao; Lenardo, Michael J.; Levine, Beth; Lieberman, Andrew; Lim, Kah-Leong; Lin, Fu-Cheng; Liou, Willisa; Liu, Leroy F.; Lopez-Berestein, Gabriel; López-Otín, Carlos; Lu, Bo; Macleod, Kay F.; Malorni, Walter; Martinet, Wim; Matsuoka, Ken; Mautner, Josef; Meijer, Alfred J.; Meléndez, Alicia; Michels, Paul; Miotto, Giovanni; Mistiaen, Wilhelm P.; Mizushima, Noboru; Mograbi, Baharia; Monastyrska, Iryna; Moore, Michael N.; Moreira, Paula I.; Moriyasu, Yuji; Motyl, Tomasz; Münz, Christian; Murphy, Leon O.; Naqvi, Naweed I.; Neufeld, Thomas P.; Nishino, Ichizo; Nixon, Ralph A.; Noda, Takeshi; Nürnberg, Bernd; Ogawa, Michinaga; Oleinick, Nancy L.; Olsen, Laura J.; Ozpolat, Bulent; Paglin, Shoshana; Palmer, Glen E.; Papassideri, Issidora; Parkes, Miles; Perlmutter, David H.; Perry, George; Piacentini, Mauro; Pinkas-Kramarski, Ronit; Prescott, Mark; Proikas-Cezanne, Tassula; Raben, Nina; Rami, Abdelhaq; Reggiori, Fulvio; Rohrer, Bärbel; Rubinsztein, David C.; Ryan, Kevin M.; Sadoshima, Junichi; Sakagami, Hiroshi; Sakai, Yasuyoshi; Sandri, Marco; Sasakawa, Chihiro; Sass, Miklós; Schneider, Claudio; Seglen, Per O.; Seleverstov, Oleksandr; Settleman, Jeffrey; Shacka, John J.; Shapiro, Irving M.; Sibirny, Andrei; Silva-Zacarin, Elaine C.M.; Simon, Hans-Uwe; Simone, Cristiano; Simonsen, Anne; Smith, Mark A.; Spanel-Borowski, Katharina; Srinivas, Vickram; Steeves, Meredith; Stenmark, Harald; Stromhaug, Per E.; Subauste, Carlos S.; Sugimoto, Seiichiro; Sulzer, David; Suzuki, Toshihiko; Swanson, Michele S.; Tabas, Ira; Takeshita, Fumihiko; Talbot, Nicholas J.; Tallóczy, Zsolt; Tanaka, Keiji; Tanaka, Kozo; Tanida, Isei; Taylor, Graham S.; Taylor, J. Paul; Terman, Alexei; Tettamanti, Gianluca; Thompson, Craig B.; Thumm, Michael; Tolkovsky, Aviva M.; Tooze, Sharon A.; Truant, Ray; Tumanovska, Lesya V.; Uchiyama, Yasuo; Ueno, Takashi; Uzcátegui, Néstor L.; van der Klei, Ida; Vaquero, Eva C.; Vellai, Tibor; Vogel, Michael W.; Wang, Hong-Gang; Webster, Paul; Wiley, John W.; Xi, Zhijun; Xiao, Gutian; Yahalom, Joachim; Yang, Jin-Ming; Yap, George; Yin, Xiao-Ming; Yoshimori, Tamotsu; Yu, Li; Yue, Zhenyu; Yuzaki, Michisuke; Zabirnyk, Olga; Zheng, Xiaoxiang; Zhu, Xiongwei; Deter, Russell L.

    2009-01-01

    Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response. PMID:18188003

  5. Backup pathways of NHEJ in cells of higher eukaryotes: Cell cycle dependence

    International Nuclear Information System (INIS)

    Iliakis, George

    2009-01-01

    DNA double-strand breaks (DSBs) induced by ionizing radiation (IR) in cells of higher eukaryotes are predominantly repaired by a pathway of non-homologous end joining (NHEJ) utilizing Ku, DNA-PKcs, DNA ligase IV, XRCC4 and XLF/Cernunnos (D-NHEJ) as central components. Work carried out in our laboratory and elsewhere shows that when this pathway is chemically or genetically compromised, cells do not shunt DSBs to homologous recombination repair (HRR) but instead use another form of NHEJ operating as a backup (B-NHEJ). Here I review our efforts to characterize this repair pathway and discuss its dependence on the cell cycle as well as on the growth conditions. I present evidence that B-NHEJ utilizes ligase III, PARP-1 and histone H1. When B-NHEJ is examined throughout the cell cycle, significantly higher activity is observed in G2 phase that cannot be attributed to HRR. Furthermore, the activity of B-NHEJ is compromised when cells enter the plateau phase of growth. Together, these observations uncover a repair pathway with unexpected biochemical constitution and interesting cell cycle and growth factor regulation. They generate a framework for investigating the mechanistic basis of HRR contribution to DSB repair.

  6. The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

    Science.gov (United States)

    SINA M. ADL; ALASTAIR G. B. SIMPSON; MARK A. FARMER; ROBERT A. ANDERSEN; O. ROGER ANDERSON; JOHN R. BARTA; SAMUEL S. BOWSER; GUY BRUGEROLLE; ROBERT A. FENSOME; SUZANNE FREDERICQ; TIMOTHY Y. JAMES; SERGEI KARPOV; PAUL KUGRENS; JOHN KRUG; CHRISTOPHER E. LANE; LOUISE A. LEWIS; JEAN LODGE; DENIS H. LYNN; DAVID G. MANN; RICHARD M. MCCOURT; LEONEL MENDOZA; ØJVIND MOESTRUP; SHARON E. MOZLEY-STANDRIDGE; THOMAS A. NERAD; CAROL A. SHEARER; ALEXEY V. SMIRNOV; FREDERICK W. SPIEGEL; MAX F.J.R. TAYLOR

    2005-01-01

    This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic...

  7. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

    Science.gov (United States)

    Sina M. Adl; Alastair G.B. Simpson; Mark A. Farmer; Robert A. Andersen; O. Roger Anderson; John R. Barta; Samuel S. Bowser; Guy Brugerolle; Robert A. Fensome; Suzanne Fredericq; Timothy Y. James; Sergei Karpov; Paul Kugrens; John Krug; Christopher E. Lane; Louise A. Lewis; Jean Lodge; Denis H. Lynn; David G. Mann; Richard M. McCourt; Leonel Mendoza; Ojvind Moestrup; Sharon E. Mozley-Standridge; Thomas A. Nerad; Carol A. Shearer; Alexey V. Smirnov; Frederick W. Speigel; Max F.J.R. Taylor

    2005-01-01

    This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic...

  8. Higher order structure in the 3'-minor domain of small subunit ribosomal RNAs from a gram negative bacterium, a gram positive bacterium and a eukaryote

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1983-01-01

    of additional higher order structure in the renatured free RNA. It can be concluded that a high level of conservation of higher order structure has occurred during the evolution of the gram negative and gram positive eubacteria and the eukaryote in both the double helical regions and the "unstructured" regions...

  9. Photosensory transduction in unicellular eukaryotes: a comparison between related ciliates Blepharisma japonicum and Stentor coeruleus and photoreceptor cells of higher organisms.

    Science.gov (United States)

    Sobierajska, Katarzyna; Fabczak, Hanna; Fabczak, Stanisław

    2006-06-01

    Blepharisma japonicum and Stentor coeruleus are related ciliates, conspicuous by their photosensitivity. They are capable of avoiding illuminated areas in the surrounding medium, gathering exclusively in most shaded places (photodispersal). Such behaviour results mainly from motile photophobic response occurring in ciliates. This light-avoiding response is observed during a relatively rapid increase in illumination intensity (light stimulus) and consists of cessation of cell movement, a period of backward movement (ciliary reversal), followed by a forward swimming, usually in a new direction. The photosensitivity of ciliates is ascribed to their photoreceptor system, composed of pigment granules, containing the endogenous photoreceptor -- blepharismin in Blepharisma japonicum, and stentorin in Stentor coeruleus. A light stimulus, applied to both ciliates activates specific stimulus transduction processes leading to the electrical changes at the plasma membrane, correlated with a ciliary reversal during photophobic response. These data indicate that both ciliates Blepharisma japonicum and Stentor coeruleus, the lower eukaryotes, are capable of transducing the perceived light stimuli in a manner taking place in some photoreceptor cells of higher eukaryotes. Similarities and differences concerning particular stages of light transduction in eukaryotes at different evolutional levels are discussed in this article.

  10. Photochemical air pollution

    International Nuclear Information System (INIS)

    Te Winkel, B.H.

    1992-01-01

    During periods of severe photochemical air pollution (smog) the industry in the Netherlands is recommended by the Dutch government to strongly reduce the emissions of air pollutants. For the electric power generating companies it is important to investigate the adequacy of this policy. The purpose of this investigation is to determine the contribution of electric power plants to photochemical air pollution and to assess the efficacy of emission reducing measures. A literature survey on the development of photochemical air pollution was carried out and modelled calculations concerning the share of the electric power plants to the photochemical air pollution were executed

  11. Photochemical effects of sunlight.

    Science.gov (United States)

    Daniels, F

    1972-07-01

    The importance of sunlight in bringing about not only photosynthesis in plants, but also other photochemical effects, is reviewed. More effort should be devoted to photochemical storage of the sun's energy without the living plant. There is no theoretical reason to believe that such reactions are impossible. Ground rules for searching for suitable solar photochemical reactions are given, and a few attempts are described, but nothing successful has yet been found. Future possibilities are suggested. Photogalvanic cells which convert sunlight into electricity deserve further research. Eugene Rabinowitch has been an active pioneer in these fields.

  12. Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes.

    Science.gov (United States)

    Crepin, Thibaut; Shalak, Vyacheslav F; Yaremchuk, Anna D; Vlasenko, Dmytro O; McCarthy, Andrew; Negrutskii, Boris S; Tukalo, Michail A; El'skaya, Anna V

    2014-11-10

    Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon-anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the 'GTP'- and 'GDP'-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Photochemical hydrogen production system

    International Nuclear Information System (INIS)

    Copeland, R.J.

    1990-01-01

    Both technical and economic factors affect the cost of producing hydrogen by photochemical processes. Technical factors include the efficiency and the capital and operating costs of the renewable hydrogen conversion system; economic factors include discount rates, economic life, credit for co-product oxygen, and the value of the energy produced. This paper presents technical and economic data for a system that generates on-peak electric power form photochemically produced hydrogen

  14. Photochemical decomposition of catecholamines

    International Nuclear Information System (INIS)

    Mol, N.J. de; Henegouwen, G.M.J.B. van; Gerritsma, K.W.

    1979-01-01

    During photochemical decomposition (lambda=254 nm) adrenaline, isoprenaline and noradrenaline in aqueous solution were converted to the corresponding aminochrome for 65, 56 and 35% respectively. In determining this conversion, photochemical instability of the aminochromes was taken into account. Irradiations were performed in such dilute solutions that the neglect of the inner filter effect is permissible. Furthermore, quantum yields for the decomposition of the aminochromes in aqueous solution are given. (Author)

  15. Autophagy in unicellular eukaryotes

    NARCIS (Netherlands)

    Kiel, J.A.K.W.

    2010-01-01

    Cells need a constant supply of precursors to enable the production of macromolecules to sustain growth and survival. Unlike metazoans, unicellular eukaryotes depend exclusively on the extracellular medium for this supply. When environmental nutrients become depleted, existing cytoplasmic components

  16. Photochemical smog and plants

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, T.

    1974-07-01

    Surveys of plant damage due to photochemical smog are summarized. The components of smog which appear to be responsible for plant damage include ozone and peroxyacyl nitrates. Their phytotoxic effects are much greater than those due to sulfur oxides. Damage surveys since 1970 reveal the following symptoms appearing on herbaceous plants (morning glory, cocks comb, dahlia, knotweed, petunia, chickweed, Welsh onion, spinach, Chinese cabbage, chard, taro): yellowish-white leaf discoloration, white and brown spots on matured leaves, and silvering of the lower surfaces of young leaves. Symptoms which appear on arboraceous plants such as zelkova, poplar, ginkgo, planetree, rose mallow, magnolia, pine tree, and rhododendron include early yellowing and reddening, white or brown spots, and untimely leaf-fall. The above plants are now utilized as indicator plants of photochemical smog. Surveys covering a broad area of Tokyo and three other prefectures indicate that plant damage due to photochemical smog extends to relatively unpolluted areas.

  17. How natural a kind is "eukaryote?".

    Science.gov (United States)

    Doolittle, W Ford

    2014-06-02

    Systematics balances uneasily between realism and nominalism, uncommitted as to whether biological taxa are discoveries or inventions. If the former, they might be taken as natural kinds. I briefly review some philosophers' concepts of natural kinds and then argue that several of these apply well enough to "eukaryote." Although there are some sticky issues around genomic chimerism and when eukaryotes first appeared, if we allow for degrees in the naturalness of kinds, existing eukaryotes rank highly, higher than prokaryotes. Most biologists feel this intuitively: All I attempt to do here is provide some conceptual justification. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  18. Investigation of the non-photochemical processes in photosynthetic bacteria and higher plants using interference of coherent radiation - a new approach

    Czech Academy of Sciences Publication Activity Database

    Roháček, Karel; Kloz, M.; Bína, David; Batysta, F.; Vácha, František

    2007-01-01

    Roč. 91, 2-3 (2007), s. 301 ISSN 0166-8595. [International Congress of Photosynthesis/14./. 22.07.2007-27.07.2007, Glasgow] Institutional research plan: CEZ:AV0Z50510513 Keywords : Photosynthesis * higher plants Subject RIV: CE - Biochemistry

  19. Iron oxides photochemical dissolution

    International Nuclear Information System (INIS)

    Blesa, M.A.; Litter, M.I.

    1987-01-01

    This work was intended to study the light irradiation influence of diverse wave-lengths on iron oxides dissolution in aqueous solutions. The objectives of this work were: the exploration of photochemical processes with the aim of its eventual application in: a) decontamination and chemical cleaning under special conditions; b) materials for solar energy conversion. (Author)

  20. Interaction of tRNA with Eukaryotic Ribosome

    Directory of Open Access Journals (Sweden)

    Dmitri Graifer

    2015-03-01

    Full Text Available This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.

  1. PsbS-specific zeaxanthin-independent changes in fluorescence emission spectrum as a signature of energy-dependent non-photochemical quenching in higher plants.

    Science.gov (United States)

    Zulfugarov, Ismayil S; Tovuu, Altanzaya; Dogsom, Bolormaa; Lee, Chung Yeol; Lee, Choon-Hwan

    2010-05-01

    The PsbS protein of photosystem II is necessary for the development of energy-dependent quenching of chlorophyll (Chl) fluorescence (qE), and PsbS-deficient Arabidopsis plant leaves failed to show qE-specific changes in the steady-state 77 K fluorescence emission spectra observed in wild-type leaves. The difference spectrum between the quenched and un-quenched states showed a negative peak at 682 nm. Although the level of qE development in the zeaxanthin-less npq1-2 mutant plants, which lacked violaxanthin de-epoxidase enzyme, was only half that of wild type, there were no noticeable changes in this qE-dependent difference spectrum. This zeaxanthin-independent DeltaF682 signal was not dependent on state transition, and the signal was not due to photobleaching of pigments either. These results suggest that DeltaF682 signal is formed due to PsbS-specific conformational changes in the quenching site of qE and is a new signature of qE generation in higher plants.

  2. Eukaryotic Cell Panorama

    Science.gov (United States)

    Goodsell, David S.

    2011-01-01

    Diverse biological data may be used to create illustrations of molecules in their cellular context. This report describes the scientific results that support an illustration of a eukaryotic cell, enlarged by one million times to show the distribution and arrangement of macromolecules. The panoramic cross section includes eight panels that extend…

  3. Eukaryotic cell flattening

    Science.gov (United States)

    Bae, Albert; Westendorf, Christian; Erlenkamper, Christoph; Galland, Edouard; Franck, Carl; Bodenschatz, Eberhard; Beta, Carsten

    2010-03-01

    Eukaryotic cell flattening is valuable for improving microscopic observations, ranging from bright field to total internal reflection fluorescence microscopy. In this talk, we will discuss traditional overlay techniques, and more modern, microfluidic based flattening, which provides a greater level of control. We demonstrate these techniques on the social amoebae Dictyostelium discoideum, comparing the advantages and disadvantages of each method.

  4. Comparative Genomics of Eukaryotes.

    NARCIS (Netherlands)

    Noort, V. van

    2007-01-01

    This thesis focuses on developing comparative genomics methods in eukaryotes, with an emphasis on applications for gene function prediction and regulatory element detection. In the past, methods have been developed to predict functional associations between gene pairs in prokaryotes. The challenge

  5. Photochemical Assessment Monitoring Stations (PAMS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — Photochemical Assessment Monitoring Stations (PAMS). This file provides information on the numbers and distribution (latitude/longitude) of air monitoring sites...

  6. Tropospheric Ozone and Photochemical Smog

    Science.gov (United States)

    Sillman, S.

    2003-12-01

    The question of air quality in polluted regions represents one of the issues of geochemistry with direct implications for human well-being. Human health and well-being, along with the well-being of plants, animals, and agricultural crops, are dependent on the quality of air we breathe. Since the start of the industrial era, air quality has become a matter of major importance, especially in large cities or urbanized regions with heavy automobile traffic and industrial activity.Concern over air quality existed as far back as the 1600s. Originally, polluted air in cities resulted from the burning of wood or coal, largely as a source of heat. The industrial revolution in England saw a great increase in the use of coal in rapidly growing cities, both for industrial use and domestic heating. London suffered from devastating pollution events during the late 1800s and early 1900s, with thousands of excess deaths attributed to air pollution (Brimblecombe, 1987). With increasing use of coal, other instances also occurred in continental Europe and the USA. These events were caused by directly emitted pollutants (primary pollutants), including sulfur dioxide (SO2), carbon monoxide (CO), and particulates. They were especially acute in cities with northerly locations during fall and winter when sunlight is at a minimum. These original pollution events gave rise to the term "smog" (a combination of smoke and fog). Events of this type have become much less severe since the 1950s in Western Europe and the US, as natural gas replaced coal as the primary source of home heating, industrial smokestacks were designed to emit at higher altitudes (where dispersion is more rapid), and industries were required to install pollution control equipment.Beginning in the 1950s, a new type of pollution, photochemical smog, became a major concern. Photochemical smog consists of ozone (O3) and other closely related species ("secondary pollutants") that are produced photochemically from directly

  7. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  8. Photochemically Synthesized Polyimides

    Science.gov (United States)

    Meador, Michael A.; Tyson, Daniel S.

    2008-01-01

    An alternative to the conventional approach to synthesis of polyimides involves the use of single monomers that are amenable to photopolymerization. Heretofore, the synthesis of polyimides has involved multiple-monomer formulations and heating to temperatures that often exceed 250 C. The present alternative approach enables synthesis under relatively mild conditions that can include room temperature. The main disadvantages of the conventional approach are the following: Elevated production temperatures can lead to high production costs and can impart thermal stresses to the final products. If the proportions of the multiple monomeric ingredients in a given batch are not exactly correct, the molecular weight and other physical properties of the final material could be reduced from their optimum or desired values. To be useful in the alternative approach, a monomer must have a molecular structure tailored to exploit Diels-Alder trapping of a photochemically generated ortho-quinodimethane. (In a Diels-Alder reaction, a diene combines with a dienophile to form molecules that contain six-membered rings.) In particular, a suitable monomer (see figure) contains ortho-methylbenzophenone connected to a dienophile (in this case, a maleimide) through a generic spacer group. Irradiation with ultraviolet light gives rise to a photochemical intermediate the aforementioned ortho-quinodimethane from the ortho-methylbenzophenone. This group may react with the dienophile on another such monomer molecule to produce an oligomer that, in turn may react in a stepgrowth manner to produce a polyimide. This approach offers several advantages in addition to those mentioned above: The monomer can be stored for a long time because it remains unreactive until exposed to light. Because the monomer is the only active starting ingredient, there is no need for mixing, no concern for ensuring correct proportions of monomers, and the purity of the final product material is inherently high. The use

  9. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.; Oke, Muse; Hamdan, Samir

    2014-01-01

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  10. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.

    2014-11-21

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  11. Research opportunities in photochemical sciences

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-07-01

    The workshop entitled {open_quotes}Research Opportunities in Photochemical Sciences{close_quotes} was initiated by the U.S. Department of Energy (DOE), Office of Energy Research (ER), Office of Basic Energy Sciences (BES), Division of Chemical Sciences. The National Renewable Energy Laboratory (NREL) in Golden, Colorado was requested by ER to host the workshop. It was held February 5-8, 1996 at the Estes Park Conference Center, Estes Park, CO, and attended by about 115 leading scientists and engineers from the U.S., Japan, and Europe; program managers for the DOE ER and Energy Efficiency and Renewable Energy (EERE) programs also attended. The purpose of the workshop was to bridge the communication gap between the practioneers and supporters of basic research in photochemical science and the practioneers and supporters of applied research and development in technologies related to photochemical science. For the purposes of the workshop the definition of the term {open_quotes}photochemical science{close_quotes} was broadened to include homogeneous photochemistry, heterogeneous photochemistry, photoelectrochemistry, photocatalysis, photobiology (for example, the light-driven processes of biological photosynthesis and proton pumping), artificial photosynthesis, solid state photochemistry, and solar photochemistry. The technologies under development through DOE support that are most closely related to photochemical science, as defined above, are the renewable energy technologies of photovoltaics, biofuels, hydrogen energy, carbon dioxide reduction and utilization, and photocatalysis for environmental cleanup of water and air. Individual papers were processed separately for the United states Department of Energy databases.

  12. Photochemical reactions of actinide ions

    International Nuclear Information System (INIS)

    Tomiyasu, Hiroshi

    1995-01-01

    This paper reviews the results of photochemical studies of actinide ions, which have been performed in our research group for past several years as follows: I) behavior of the excited uranyl(VI) ion; II) photo-reductions of the uranyl ion with organic and inorganic compounds; III) photo-oxidations of uranium(IV) and plutonium(III) in nitric acid solutions. (author)

  13. Trapping Dynamics in Photosystem I-Light Harvesting Complex I of Higher Plants Is Governed by the Competition Between Excited State Diffusion from Low Energy States and Photochemical Charge Separation.

    Science.gov (United States)

    Molotokaite, Egle; Remelli, William; Casazza, Anna Paola; Zucchelli, Giuseppe; Polli, Dario; Cerullo, Giulio; Santabarbara, Stefano

    2017-10-26

    The dynamics of excited state equilibration and primary photochemical trapping have been investigated in the photosystem I-light harvesting complex I isolated from spinach, by the complementary time-resolved fluorescence and transient absorption approaches. The combined analysis of the experimental data indicates that the excited state decay is described by lifetimes in the ranges of 12-16 ps, 32-36 ps, and 64-77 ps, for both detection methods, whereas faster components, having lifetimes of 550-780 fs and 4.2-5.2 ps, are resolved only by transient absorption. A unified model capable of describing both the fluorescence and the absorption dynamics has been developed. From this model it appears that the majority of excited state equilibration between the bulk of the antenna pigments and the reaction center occurs in less than 2 ps, that the primary charge separated state is populated in ∼4 ps, and that the charge stabilization by electron transfer is completed in ∼70 ps. Energy equilibration dynamics associated with the long wavelength absorbing/emitting forms harbored by the PSI external antenna are also characterized by a time mean lifetime of ∼75 ps, thus overlapping with radical pair charge stabilization reactions. Even in the presence of a kinetic bottleneck for energy equilibration, the excited state dynamics are shown to be principally trap-limited. However, direct excitation of the low energy chlorophyll forms is predicted to lengthen significantly (∼2-folds) the average trapping time.

  14. Photochemical degradation of alachlor in water

    Directory of Open Access Journals (Sweden)

    Tajana Đurkić

    2017-01-01

    Full Text Available This study investigates the photochemical degradation of alachlor, a chloroacetanilide herbicide. All experiments were conducted in ultra-pure deionized water (ASTM Type I quality using direct ultraviolet (UV photolysis and the UV/H2O2 advanced oxidation process. The direct UV photolysis and UV/H2O2 experiments were conducted in a commercial photochemical reactor with a quartz reaction vessel equipped with a 253.7 nm UV low pressure mercury lamp (Philips TUV 16 W. The experimental results demonstrate that UV photolysis was very effective for alachlor degradation (up to 97% removal using a high UV fluence of 4200 mJ/cm2. The UV/H2O2 process promoted alachlor degradation compared to UV photolysis alone, with a high degree of decomposition (97% achieved at a significantly lower UV fluence of 600 mJ/cm2 when combined with 1 mg H2O2/L. The application of UV photolysis alone with a UV fluence of 600 mJ/cm2 gave a negligible 4% alachlor degradation. The photo degradation of alachlor, in both direct UV photolysis and the UV/H2O2 process, followed pseudo first-order kinetics. The degradation rate constant was about 6 times higher for the UV/H2O2 process than for UV photolysis alone.

  15. Photochemical heavy-atom effects

    International Nuclear Information System (INIS)

    Koziar, J.C.; Cowan, D.O.

    1978-01-01

    The effects of halogenated solvents such as n-butyl chloride, n-propyl bromide, and ethyl iodide, on the photochemistry of several aromatic compounds are reviewed. Dimerization of acenaphthylene is discussed in terms of spin -orbit coupling induced by the solvents. Appropriate wave functions are given for both the solvents and the compound. Cycloaddition reactions, electrocyclic rearrangements, and photochemical cis-trans isomerization are also considered

  16. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

    2014-03-14

    Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

  17. Gonococcal attachment to eukaryotic cells

    International Nuclear Information System (INIS)

    James, J.F.; Lammel, C.J.; Draper, D.L.; Brown, D.A.; Sweet, R.L.; Brooks, G.F.

    1983-01-01

    The attachment of Neisseria gonorrhoeae to eukaryotic cells grown in tissue culture was analyzed by use of light and electron microscopy and by labeling of the bacteria with [ 3 H]- and [ 14 C]adenine. Isogenic piliated and nonpiliated N. gonorrhoeae from opaque and transparent colonies were studied. The results of light microscopy studies showed that the gonococci attached to cells of human origin, including Flow 2000, HeLa 229, and HEp 2. Studies using radiolabeled gonococci gave comparable results. Piliated N. gonorrhoeae usually attached in larger numbers than nonpiliated organisms, and those from opaque colonies attached more often than isogenic variants from transparent colonies. Day-to-day variation in rate of attachment was observed. Scanning electron microscopy studies showed the gonococcal attachment to be specific for microvilli of the host cells. It is concluded that more N. gonorrhoeae from opaque colonies, as compared with isogenic variants from transparent colonies, attach to eukaryotic cells grown in tissue culture

  18. Defensins: antifungal lessons from eukaryotes

    Directory of Open Access Journals (Sweden)

    Patrícia M. Silva

    2014-03-01

    Full Text Available Over the last years, antimicrobial peptides (AMPs have been the focus of intense research towards the finding of a viable alternative to current antifungal drugs. Defensins are one of the major families of AMPs and the most represented among all eukaryotic groups, providing an important first line of host defense against pathogenic microorganisms. Several of these cysteine-stabilized peptides present a relevant effect against fungi. Defensins are the AMPs with the broader distribution across all eukaryotic kingdoms, namely, Fungi, Plantæ and Animalia, and were recently shown to have an ancestor in a bacterial organism. As a part of the host defense, defensins act as an important vehicle of information between innate and adaptive immune system and have a role in immunomodulation. This multidimensionality represents a powerful host shield, hard for microorganisms to overcome using single approach resistance strategies. Pathogenic fungi resistance to conventional antimycotic drugs is becoming a major problem. Defensins, as other AMPs, have shown to be an effective alternative to the current antimycotic therapies, demonstrating potential as novel therapeutic agents or drug leads. In this review, we summarize the current knowledge on some eukaryotic defensins with antifungal action. An overview of the main targets in the fungal cell and the mechanism of action of these AMPs (namely, the selectivity for some fungal membrane components are presented. Additionally, recent works on antifungal defensins structure, activity and citotoxicity are also reviewed.

  19. Mitochondrial uncoupling proteins in unicellular eukaryotes.

    Science.gov (United States)

    Jarmuszkiewicz, Wieslawa; Woyda-Ploszczyca, Andrzej; Antos-Krzeminska, Nina; Sluse, Francis E

    2010-01-01

    Uncoupling proteins (UCPs) are members of the mitochondrial anion carrier protein family that are present in the mitochondrial inner membrane and mediate free fatty acid (FFA)-activated, purine nucleotide (PN)-inhibited proton conductance. Since 1999, the presence of UCPs has been demonstrated in some non-photosynthesising unicellular eukaryotes, including amoeboid and parasite protists, as well as in non-fermentative yeast and filamentous fungi. In the mitochondria of these organisms, UCP activity is revealed upon FFA-induced, PN-inhibited stimulation of resting respiration and a decrease in membrane potential, which are accompanied by a decrease in membranous ubiquinone (Q) reduction level. UCPs in unicellular eukaryotes are able to divert energy from oxidative phosphorylation and thus compete for a proton electrochemical gradient with ATP synthase. Our recent work indicates that membranous Q is a metabolic sensor that might utilise its redox state to release the PN inhibition of UCP-mediated mitochondrial uncoupling under conditions of phosphorylation and resting respiration. The action of reduced Q (QH2) could allow higher or complete activation of UCP. As this regulatory feature was demonstrated for microorganism UCPs (A. castellanii UCP), plant and mammalian UCP1 analogues, and UCP1 in brown adipose tissue, the process could involve all UCPs. Here, we discuss the functional connection and physiological role of UCP and alternative oxidase, two main energy-dissipating systems in the plant-type mitochondrial respiratory chain of unicellular eukaryotes, including the control of cellular energy balance as well as preventive action against the production of reactive oxygen species. Copyright © 2009 Elsevier B.V. All rights reserved.

  20. [MiRNA system in unicellular eukaryotes and its evolutionary implications].

    Science.gov (United States)

    Zhang, Yan-Qiong; Wen, Jian-Fan

    2010-02-01

    microRNAs (miRNAs) in higher multicellular eukaryotes have been extensively studied in recent years. Great progresses have also been achieved for miRNAs in unicellular eukaryotes. All these studies not only enrich our knowledge about the complex expression regulation system in diverse organisms, but also have evolutionary significance for understanding the origin of this system. In this review, Authors summarize the recent advance in the studies of miRNA in unicellular eukaryotes, including that on the most primitive unicellular eukaryote--Giardia. The origin and evolution of miRNA system is also discussed.

  1. Cold-acclimation limits low temperature induced photoinhibition by promoting a higher photochemical quantum yield and a more effective PSII restoration in darkness in the Antarctic rather than the Andean ecotype of Colobanthus quitensis Kunt Bartl (Cariophyllaceae

    Directory of Open Access Journals (Sweden)

    Bascuñán-Godoy Luisa

    2012-07-01

    Full Text Available Abstract Background Ecotypes of Colobanthus quitensis Kunt Bartl (Cariophyllaceae from Andes Mountains and Maritime Antarctic grow under contrasting photoinhibitory conditions, reaching differential cold tolerance upon cold acclimation. Photoinhibition depends on the extent of photodamage and recovery capability. We propose that cold acclimation increases resistance to low-temperature-induced photoinhibition, limiting photodamage and promoting recovery under cold. Therefore, the Antarctic ecotype (cold hardiest should be less photoinhibited and have better recovery from low-temperature-induced photoinhibition than the Andean ecotype. Both ecotypes were exposed to cold induced photoinhibitory treatment (PhT. Photoinhibition and recovery of photosystem II (PSII was followed by fluorescence, CO2 exchange, and immunoblotting analyses. Results The same reduction (25% in maximum PSII efficiency (Fv/Fm was observed in both cold-acclimated (CA and non-acclimated (NA plants under PhT. A full recovery was observed in CA plants of both ecotypes under dark conditions, but CA Antarctic plants recover faster than the Andean ecotype. Under PhT, CA plants maintain their quantum yield of PSII, while NA plants reduced it strongly (50% and 73% for Andean and Antarctic plants respectively. Cold acclimation induced the maintenance of PsaA and Cyt b6/f and reduced a 41% the excitation pressure in Antarctic plants, exhibiting the lowest level under PhT. xCold acclimation decreased significantly NPQs in both ecotypes, and reduced chlorophylls and D1 degradation in Andean plants under PhT. NA and CA plants were able to fully restore their normal photosynthesis, while CA Antarctic plants reached 50% higher photosynthetic rates after recovery, which was associated to electron fluxes maintenance under photoinhibitory conditions. Conclusions Cold acclimation has a greater importance on the recovery process than on limiting photodamage. Cold acclimation determined the

  2. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.

    Directory of Open Access Journals (Sweden)

    Yubo Hou

    Full Text Available The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10-transformed protein-coding gene number (Y' versus log(10-transformed genome size (X', genome size in kbp were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91. Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1% compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%. The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6 kbp contains 38,188 protein-coding (40,086 total genes and the largest (245x10(6 kbp 87,688 protein-coding (92,013 total genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.

  3. Southern Africa - a giant natural photochemical reactor

    CSIR Research Space (South Africa)

    Diab, RD

    2006-04-01

    Full Text Available photochemical reactor’ are abundant sources of ozone precursors (biomass burning, lightning, biogenic and urban-industrial sources), and meteorological conditions that promote anticyclonic recirculation on a subhemispheric scale....

  4. HANDBOOK ON ADVANCED PHOTOCHEMICAL OXIDATION ...

    Science.gov (United States)

    This handbook summarizes commercial-scale system performance and cost data for advanced photochemical oxidation (APO) treatment of contaminated water, air, and solids. Similar information from pilot- and bench-scale evaluations of APO processes is also included to supplement the commercial-scale data. Performance and cost data is summarized for various APO processes, including vacuum ultraviolet (VUV) photolysis, ultraviolet (UV)/oxidation, photo-Fenton, and dye- or semiconductor-sensitized APO processes. This handbook is intended to assist engineering practitioners in evaluating the applicability of APO processes and in selecting one or more such processes for site-specific evaluation.APO has been shown to be effective in treating contaminated water and air. Regarding contaminated water treatment, UV/oxidation has been evaluated for the most contaminants, while VUV photolysis has been evaluated for the fewest. Regarding contaminated air treatment, the sensitized APO processes have been evaluated for the most contaminants, while VUV photolysis has been evaluated for the fewest.APO processes for treating contaminated solids generally involve treatment of contaminated slurry or leachate generated using an extraction process such as soil washing. APO has been shown to be effective in treating contaminated solids, primarily at the bench-scale level. Information

  5. Photochemical reduction of uranyl nitrate

    Energy Technology Data Exchange (ETDEWEB)

    Duerksen, W.K.

    1993-10-20

    The photochemical reduction of uranyl nitrate solutions to tetravalent uranium was investigated as a means of producing uranium dioxide feed for the saltless direct oxide reduction (SDOR) process. At high uranium concentrations, reoxidation of U{sup +4} occurs rapidly. The kinetics of the nitric oxidation of tetravalent uranium depend on the concentrations of hydrogen ion, nitrate ion, nitrous acid, and tetravalent uranium in the same manner as was reported elsewhere for the nitrate oxidation of PU{sup +3}. Reaction rate data were successfully correlated with a mechanism in which nitrogen dioxide is the reactive intermediate. Addition of a nitrous acid scavenger suppresses the reoxidation reaction. An immersion reactor employing a mercury vapor lamp gave reduction times fast enough for routine production usage. Precipitation techniques for conversion of aqueous U(NO{sub 3}){sub 4} to hydrous UO{sub 2} were evaluated. Prolonged dewatering times tended to make the process time consuming. Use of 3- to 4-M aqueous NaOH gave the best dewatering times observed. Reoxidation of the UO{sub 2} by water of hydration was encountered, which required the drying process to be carried out under a reducing atmosphere.

  6. Conservation of RNA sequence and cross-linking ability in ribosomes from a higher eukaryote: photochemical cross-linking of the anticodon of P site bound tRNA to the penultimate cytidine of the UACACACG sequence in Artemia salina 18S rRNA

    International Nuclear Information System (INIS)

    Ciesiolka, J.; Nurse, K.; Klein, J.; Ofengand, J.

    1985-01-01

    The complex of Artemia salina ribosomes and Escherichia coli acetylvalyl-tRNA could be cross-linked by irradiation with near-UV light. Cross-linking required the presence of the codon GUU, GUA being ineffective. The acetylvalyl group could be released from the cross-linked tRNA by treatment with puromycin, demonstrating that cross-linking had occurred at the P site. This was true both for pGUU- and also for poly(U2,G)-dependent cross-linking. All of the cross-linking was to the 18S rRNA of the small ribosomal subunit. Photolysis of the cross-link at 254 nm occurred with the same kinetics as that for the known cyclobutane dimer between this tRNA and Escherichia coli 16S rRNA. T1 RNase digestion of the cross-linked tRNA yielded an oligonucleotide larger in molecular weight than any from un-cross-linked rRNA or tRNA or from a prephotolyzed complex. Extended electrophoresis showed this material to consist of two oligomers of similar mobility, a faster one-third component and a slower two-thirds component. Each oligomer yielded two components on 254-nm photolysis. The slower band from each was the tRNA T1 oligomer CACCUCCCUVACAAGp, which includes the anticodon. The faster band was the rRNA 9-mer UACACACCGp and its derivative UACACACUG. Unexpectedly, the dephosphorylated and slower moving 9-mer was derived from the faster moving dimer. Deamination of the penultimate C to U is probably due to cyclobutane dimer formation and was evidence for that nucleotide being the site of cross-linking. Direct confirmation of the cross-linking site was obtained by Z-gel analysis

  7. Arabinogalactan proteins have deep roots in eukaryotes

    DEFF Research Database (Denmark)

    Hervé, Cécile; Siméon, Amandine; Jam, Murielle

    2016-01-01

    Arabinogalactan proteins (AGPs) are highly glycosylated, hydroxyproline-rich proteins found at the cell surface of plants, where they play key roles in developmental processes. Brown algae are marine, multicellular, photosynthetic eukaryotes. They belong to the phylum Stramenopiles, which...

  8. Photochemical dynamics of surface oriented molecules

    International Nuclear Information System (INIS)

    Ho, W.

    1992-01-01

    The period 8/01/91-7/31/92 is the first year of a new project titled ''Photochemical Dynamics of Surface Oriented Molecules'', initiated with DOE Support. The main objective of this project is to understand the dynamics of elementary chemical reactions by studying photochemical dynamics of surface-oriented molecules. In addition, the mechanisms of photon-surface interactions need to be elucidated. The strategy is to carry out experiments to measure the translational energy distribution, as a function of the angle from the surface normal, of the photoproducts by time-of-flight (TOF) technique by varying the photon wavelength, intensity, polarization, and pulse duration. By choosing adsorbates with different bonding configuration, the effects of adsorbate orientation on surface photochemical dynamics can be studied

  9. Photochemical reduction of uranyl ion with triphenylphosphine

    International Nuclear Information System (INIS)

    Brar, A.S.; Sidhu, M.S.; Sandhu, S.S.

    1981-01-01

    Photochemical reduction of uranyl ion with triphenylphosphine has been studied in acetone-water medium in the presence of sulphuric acid at 346nm, 400nm and 434nm wavelengths. The photochemical reduction is of second order and increases with increase in hydrogen ion concentration. Absorption spectra of uranyl ion in acidic medium and uranyl ion with triphenylphosphine do not show any ground state complex formation. The value of quantum yield increases with the wavelength of the radiation increase from 346 to 434nm. Plots of reciprocal of quantum yield for the formation of U(IV) versus reciprocal [triphenylphosphine] are linear. Products characterized by UV and visible, IR and TLC show the formation of U(IV) and triphenylphosphine oxide. On the basis of above observations mechanism of the photochemical reduction has been proposed. (author)

  10. Transfer of DNA from Bacteria to Eukaryotes

    Directory of Open Access Journals (Sweden)

    Benoît Lacroix

    2016-07-01

    Full Text Available Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen, Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium, or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs, the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer.

  11. Trace organic removal by photochemical oxidation

    International Nuclear Information System (INIS)

    Gupta, S.K. Sen; Peori, R.G.; Wickware, S.L.

    1995-02-01

    Photochemical oxidation methods can be used for the destruction of dissolved organic contaminants in most process effluent streams, including those originating from the nuclear power sector. Evaporators can be used to separate organic contaminants from the aqueous phase if they are non volatile, but a large volume of secondary waste (concentrate) is produced, and the technology is capital-intensive. This paper describes two different types of photochemical oxidation technologies used to destroy trace organics in wastewater containing oil and grease. (author). 9 refs., 4 figs

  12. Photochemical and other pollution in South Holland

    Energy Technology Data Exchange (ETDEWEB)

    Posthumus, A.C.

    1976-01-01

    At the same 15 places as in 1974, regularly distributed over the industrial area west of Rotterdam, indicator plants for air pollution were set out in the open and were cultivated by the same standard method. Tulip and gladiolus were used as indicators for HF, during spring and summer, respectively. Both indicated that the same two sites, at Vlaardingen and Spijkenisse, had maximum HF concentration. In general, the mean leaf-tip injury at all sites was somewhat heavier than in 1974. Lucerne, as an indicator for SO2, sometimes showed more injury north of the New Waterway than south of it in June. Spinach, an indicator for O3/SO2, showed maximum injury in three different periods in June, July and mostly in August. The frequency and the measure of the injury to tobacco Bel W3 by O3 was maximum during some periods in August and September, the mean injury being heavier than in 1974. Urtica urens and Poa annua too, indicator plants for photochemical air pollution by peroxyacetyl nitrate and O3, showed more frequent injury in 1975, specially in some weeks in June and most of it in August. Petunia too indicated more influence of ethylene than in 1974, mostly in the second half of June. This year again the effect of air pollution on growth and yield of tulip Blue Parrot, tobacco Bel W3 and tomato extase plants was studied at the same six sites as last year by the mouth of the Rhine, with filtered and unfiltered greenhouses. Tulips in the unfiltered greenhouses showed a heavier leaf injury than those in the filtered greenhouses, except at the site in The Hague. These injured plants had a significantly lower average fresh and dry weight of the stems and leaves and of the bulbs too. Tobacco and tomato plants had a higher average dry weight of stems and leaves in the filtered greenhouses than in the unfiltered ones.

  13. EMERGING TECHNOLOGY PROJECT BULLETIN: LASER INDUCED PHOTOCHEMICAL OXIDATIVE DESTRUCTION

    Science.gov (United States)

    The process developed by Energy and Environmental Engineering, Incorporated, is designed to photochemically oxidize organic compounds in wastewater by applying ultraviolet radiation using an Excimer laser. The photochemical reactor can destroy low to moderate concentrations...

  14. Photochemical synthesis of UO2 nanoparticles

    International Nuclear Information System (INIS)

    Rath, M.C.; Keny, Sangeeta; Naik, D.B.

    2014-01-01

    UO 2 nanoparticles have been recently synthesized by us from aqueous solutions of uranyl nitrate through radiolytic method on high-energy electron beam irradiation. In this study, the synthesis of UO 2 nanoparticles through photochemical method is reported which is a complementary route to radiation chemical method

  15. Atypical mitochondrial inheritance patterns in eukaryotes.

    Science.gov (United States)

    Breton, Sophie; Stewart, Donald T

    2015-10-01

    Mitochondrial DNA (mtDNA) is predominantly maternally inherited in eukaryotes. Diverse molecular mechanisms underlying the phenomenon of strict maternal inheritance (SMI) of mtDNA have been described, but the evolutionary forces responsible for its predominance in eukaryotes remain to be elucidated. Exceptions to SMI have been reported in diverse eukaryotic taxa, leading to the prediction that several distinct molecular mechanisms controlling mtDNA transmission are present among the eukaryotes. We propose that these mechanisms will be better understood by studying the deviations from the predominating pattern of SMI. This minireview summarizes studies on eukaryote species with unusual or rare mitochondrial inheritance patterns, i.e., other than the predominant SMI pattern, such as maternal inheritance of stable heteroplasmy, paternal leakage of mtDNA, biparental and strictly paternal inheritance, and doubly uniparental inheritance of mtDNA. The potential genes and mechanisms involved in controlling mitochondrial inheritance in these organisms are discussed. The linkage between mitochondrial inheritance and sex determination is also discussed, given that the atypical systems of mtDNA inheritance examined in this minireview are frequently found in organisms with uncommon sexual systems such as gynodioecy, monoecy, or andromonoecy. The potential of deviations from SMI for facilitating a better understanding of a number of fundamental questions in biology, such as the evolution of mtDNA inheritance, the coevolution of nuclear and mitochondrial genomes, and, perhaps, the role of mitochondria in sex determination, is considerable.

  16. Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Lykidis, Athanasios

    2006-12-01

    Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

  17. Gene Transfer in Eukaryotic Cells Using Activated Dendrimers

    Science.gov (United States)

    Dennig, Jörg

    Gene transfer into eukaryotic cells plays an important role in cell biology. Over the last 30 years a number of transfection methods have been developed to mediate gene transfer into eukaryotic cells. Classical methods include co-precipitation of DNA with calcium phosphate, charge-dependent precipitation of DNA with DEAE-dextran, electroporation of nucleic acids, and formation of transfection complexes between DNA and cationic liposomes. Gene transfer technologies based on activated PAMAM-dendrimers provide another class of transfection reagents. PAMAM-dendrimers are highly branched, spherical molecules. Activation of newly synthesized dendrimers involves hydrolytic removal of some of the branches, and results in a molecule with a higher degree of flexibility. Activated dendrimers assemble DNA into compact structures via charge interactions. Activated dendrimer - DNA complexes bind to the cell membrane of eukaryotic cells, and are transported into the cell by non-specific endocytosis. A structural model of the activated dendrimer - DNA complex and a potential mechanism for its uptake into cells will be discussed.

  18. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

    Energy Technology Data Exchange (ETDEWEB)

    Parfrey, Laura Wegener; Walters, William A.; Lauber, Christian L.; Clemente, Jose C.; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A.; Knight, Rob

    2014-06-19

    Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across

  19. Photochemical versus biological production of methyl iodide during Meteor 55

    Science.gov (United States)

    Richter, U.; Wallace, D.

    2003-04-01

    The flux of methyl iodide from sea to air represents the largest flux of iodine from the ocean to the atmosphere. Surface water concentrations and hence fluxes are particularly high in tropical regions. This flux may be responsible for the enrichment of iodine in the marine aerosol and may contribute to important processes in the marine boundary layer, including particle formation. Methyl iodide is commonly referred to as a biogenic gas, with both macroalgae and phytoplankton identified as important sources. On the other hand experimental and field data have shown the importance of photochemical production that is not necessarily associated directly with biological activity. During the Meteor cruise 55 along 11°N in the tropical Atlantic Ocean, a series of experiments were conducted to examine the biological vs. photochemical production of methyl iodide. A total of eight separate experiments were conducted. Production of CH3I in quartz glass flasks during 24 hour incubations (dark and natural sunlight) was measured under three experimental treatments: untreated seawater, filtered seawater (0.1 um pore size filter to exclude most phytoplankton and bacteria), and seawater that was poisoned with mercuric chloride. There were two clear findings from these experiments: (1) methyl iodide production was significantly higher in all the incubations that were exposed to the light than in the dark incubations; (2) there was no significant difference between CH3I production under the three experimental treatments. These results argue very strongly for the primary importance of photochemical production of CH3I as opposed to biogenic production at least for the tropical open ocean surface waters. Further experiments are required to investigate the reactants involved, their sources, the wavelength and depth dependence of production, etc. as well as (possibly related) sink processes.

  20. Eukaryotes first: how could that be?

    Science.gov (United States)

    Mariscal, Carlos; Doolittle, W Ford

    2015-09-26

    In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such 'eukaryotes first' (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier 'progenotic' period or RNA world. Bacteria and Archaea thus must have lost these complex features secondarily, through 'streamlining'. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic. We ask what this means and how it might be tested. © 2015 The Author(s).

  1. Reproduction, symbiosis, and the eukaryotic cell

    Science.gov (United States)

    Godfrey-Smith, Peter

    2015-01-01

    This paper develops a conceptual framework for addressing questions about reproduction, individuality, and the units of selection in symbiotic associations, with special attention to the origin of the eukaryotic cell. Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction. The sequence of changes seen in this “egalitarian” evolutionary transition is compared with those that apply in “fraternal” transitions, such as the evolution of multicellularity in animals. PMID:26286983

  2. The origin of the eukaryotic cell

    Science.gov (United States)

    Hartman, H.

    1984-01-01

    The endosymbiotic hypothesis for the origin of the eukaryotic cell has been applied to the origin of the mitochondria and chloroplasts. However as has been pointed out by Mereschowsky in 1905, it should also be applied to the nucleus as well. If the nucleus, mitochondria and chloroplasts are endosymbionts, then it is likely that the organism that did the engulfing was not a DNA-based organism. In fact, it is useful to postulate that this organism was a primitive RNA-based organism. This hypothesis would explain the preponderance of RNA viruses found in eukaryotic cells. The centriole and basal body do not have a double membrane or DNA. Like all MTOCs (microtubule organising centres), they have a structural or morphic RNA implicated in their formation. This would argue for their origin in the early RNA-based organism rather than in an endosymbiotic event involving bacteria. Finally, the eukaryotic cell uses RNA in ways quite unlike bacteria, thus pointing to a greater emphasis of RNA in both control and structure in the cell. The origin of the eukaryotic cell may tell us why it rather than its prokaryotic relative evolved into the metazoans who are reading this paper.

  3. Eukaryotic acquisition of a bacterial operon

    Science.gov (United States)

    The yeast Saccharomyces cerevisiae is one of the champions of basic biomedical research due to its compact eukaryotic genome and ease of experimental manipulation. Despite these immense strengths, its impact on understanding the genetic basis of natural phenotypic variation has been limited by strai...

  4. PHOTOCHEMICAL HEATING OF DENSE MOLECULAR GAS

    Energy Technology Data Exchange (ETDEWEB)

    Glassgold, A. E. [Astronomy Department, University of California, Berkeley, CA 94720 (United States); Najita, J. R. [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States)

    2015-09-10

    Photochemical heating is analyzed with an emphasis on the heating generated by chemical reactions initiated by the products of photodissociation and photoionization. The immediate products are slowed down by collisions with the ambient gas and then heat the gas. In addition to this direct process, heating is also produced by the subsequent chemical reactions initiated by these products. Some of this chemical heating comes from the kinetic energy of the reaction products and the rest from collisional de-excitation of the product atoms and molecules. In considering dense gas dominated by molecular hydrogen, we find that the chemical heating is sometimes as large, if not much larger than, the direct heating. In very dense gas, the total photochemical heating approaches 10 eV per photodissociation (or photoionization), competitive with other ways of heating molecular gas.

  5. Photochemical reduction of uranyl ion by acetonitrile and propionitrile

    International Nuclear Information System (INIS)

    Brar, A.S.; Chander, R.; Sandhu, S.S.

    1979-01-01

    The photochemical reduction of uranyl ion by acetonitrile, propionitrile, benzonitrile, phenylacetonitrile, cyanoacetic acid and malononitrile in aqueous or aq. acetone medium using radiations >= 400 nm from a medium pressure mercury vapour lamp has been investigated. Except acetonitrile and propionitrile all other nitriles fail to bring about the reduction of uranyl ion. The reduction with aceto- and propionitriles has been found to obey pseudo-first order kinetics. The magnitude of rate of reduction with propionitrile is higher than that with acetonitrile. The pseudo-first order rate constants and quenching constant have been calculated from the kinetic data. It has been found that physical and chemical quenching compete with each other. The plot of reciprocal of quantum yield versus reciprocal (nitrile) is linear with a small intercept on the ordinate axis. Absorption spectra of uranyl ion in pure water, in the presence of acid and in the presence of acid+nitrile reveal that there is no ground state interaction between uranyl ion and the nitrile. A mechanism of photochemical reduction of uranyl ion based on α-hydrogen abstraction from the nitrile has been proposed. (auth.)

  6. Photochemical stability of electrochromic polymers and devices

    DEFF Research Database (Denmark)

    Jensen, Jacob; Madsen, Morten Vesterager; Krebs, Frederik C

    2013-01-01

    The stability of fully printed flexible organic electrochromics based on 11 different conjugated polymers is explored from the fundamental chemical degradation level to the operational device level. The photochemical stability of the electrochromic polymers (ECPs) is studied enabling an analysis ...... based on flexible barrier substrates exhibit increased stability and are indeed viable in devices such as shading elements, light management systems, displays with low switching speed requirements and signage. © 2013 The Royal Society of Chemistry....

  7. Photochemical reaction products in air pollution

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, E R; Darley, E F; Taylor, O C; Scott, W E

    1961-01-01

    Isolation and purification of peroxyacetyl nitrate (PAN) from artificial photochemical reaction of olefins and NO/sub x/ in air are analyzed. Olefin splits at the double bond, one end forming carbonyl compound and the other yielding PAN, among others. At concentrations below 1 ppM, PAN causes plant damage. At a concentration of about 1 ppM, PAN is a strong eye irritant.

  8. Anaerobic energy metabolism in unicellular photosynthetic eukaryotes.

    Science.gov (United States)

    Atteia, Ariane; van Lis, Robert; Tielens, Aloysius G M; Martin, William F

    2013-02-01

    Anaerobic metabolic pathways allow unicellular organisms to tolerate or colonize anoxic environments. Over the past ten years, genome sequencing projects have brought a new light on the extent of anaerobic metabolism in eukaryotes. A surprising development has been that free-living unicellular algae capable of photoautotrophic lifestyle are, in terms of their enzymatic repertoire, among the best equipped eukaryotes known when it comes to anaerobic energy metabolism. Some of these algae are marine organisms, common in the oceans, others are more typically soil inhabitants. All these species are important from the ecological (O(2)/CO(2) budget), biotechnological, and evolutionary perspectives. In the unicellular algae surveyed here, mixed-acid type fermentations are widespread while anaerobic respiration, which is more typical of eukaryotic heterotrophs, appears to be rare. The presence of a core anaerobic metabolism among the algae provides insights into its evolutionary origin, which traces to the eukaryote common ancestor. The predicted fermentative enzymes often exhibit an amino acid extension at the N-terminus, suggesting that these proteins might be compartmentalized in the cell, likely in the chloroplast or the mitochondrion. The green algae Chlamydomonas reinhardtii and Chlorella NC64 have the most extended set of fermentative enzymes reported so far. Among the eukaryotes with secondary plastids, the diatom Thalassiosira pseudonana has the most pronounced anaerobic capabilities as yet. From the standpoints of genomic, transcriptomic, and biochemical studies, anaerobic energy metabolism in C. reinhardtii remains the best characterized among photosynthetic protists. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Photochemical reactions of neptunium in nitric acid solution containing photocatalyst

    International Nuclear Information System (INIS)

    Fukasawa, Tetsuo; Kawamura, Fumio

    1991-01-01

    Photochemical oxidation and reduction behaviors of neptunium were preliminarily investigated in 3 mol/l nitric acid solution. Nitric acid of 3 mol/l simulated the high level waste solution from a spent fuel reprocessing process. Concentrations of Np(V), Np(VI) and nitrous acid were determined with a photospectrometer, and solution potential with an electrode. Without additives, Np(VI) was reduced to Np(V) by nitrous acid which was photolytically generated from nitric acid. With a scavenger for nitrous acid, Np(V) was oxidized to extractable Np(VI) by a photolytically generated oxidizing reagent which were predicted by the solution potential measurement. The reduction rate was higher than the oxidation rate because of the larger quantity and higher reactivity of nitrous acid than an oxidizing reagent. Photocatalyst was proved to be effective for the oxidation of Np(V) to Np(VI). (author)

  10. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  11. WATER DEFICIT ENSURES THE PHOTOCHEMICAL EFFICIENCY OF Copaifera langsdorffii Desf1

    Directory of Open Access Journals (Sweden)

    Angélica Lino Rodrigues

    2017-02-01

    Full Text Available ABSTRACT The intensity and frequency of drought periods has increased according to climate change predictions. The fast overcome and recovery are important adaptive features for plant species found in regions presenting water shortage periods. Copaifera langsdorffii is a neotropical species that has developed leaves presenting physiological mechanisms and morphological adaptations that allow its survival under seasonal water stress. We aimed in this work to observe substantial physiological responses for water saving and damage representative to the photochemical reaction after exposed plants to water stress and to subsequent recovery. We found in plants mechanisms to control water loss through the lower stomatal conductance, even after rehydration. It goes against the rapid recovery of leaves, indicated by the relative water content values restored to previously unstressed plants. Stomatal conductance was the only variable presenting high plasticity index. In photochemical activity, the species presented higher photochemical quenching, electron transport rate and effective quantum yield of photosystem II when they were subjected to rehydration after water stress period. Our results suggest that C. langsdorffii presented rapid rehydration and higher photochemical efficiency even after water restriction. These data demonstrate that this species can be used as a model for physiological studies due to the adjustment developed in response to different environmental schemes.

  12. Symbiosis and the origin of eukaryotic motility

    Science.gov (United States)

    Margulis, L.; Hinkle, G.

    1991-01-01

    Ongoing work to test the hypothesis of the origin of eukaryotic cell organelles by microbial symbioses is discussed. Because of the widespread acceptance of the serial endosymbiotic theory (SET) of the origin of plastids and mitochondria, the idea of the symbiotic origin of the centrioles and axonemes for spirochete bacteria motility symbiosis was tested. Intracellular microtubular systems are purported to derive from symbiotic associations between ancestral eukaryotic cells and motile bacteria. Four lines of approach to this problem are being pursued: (1) cloning the gene of a tubulin-like protein discovered in Spirocheata bajacaliforniesis; (2) seeking axoneme proteins in spirochets by antibody cross-reaction; (3) attempting to cultivate larger, free-living spirochetes; and (4) studying in detail spirochetes (e.g., Cristispira) symbiotic with marine animals. Other aspects of the investigation are presented.

  13. Towards New Antifolates Targeting Eukaryotic Opportunistic Infections

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Bolstad, D; Bolstad, E; Wright, D; Anderson, A

    2009-01-01

    Trimethoprim, an antifolate commonly prescribed in combination with sulfamethoxazole, potently inhibits several prokaryotic species of dihydrofolate reductase (DHFR). However, several eukaryotic pathogenic organisms are resistant to trimethoprim, preventing its effective use as a therapeutic for those infections. We have been building a program to reengineer trimethoprim to more potently and selectively inhibit eukaryotic species of DHFR as a viable strategy for new drug discovery targeting several opportunistic pathogens. We have developed a series of compounds that exhibit potent and selective inhibition of DHFR from the parasitic protozoa Cryptosporidium and Toxoplasma as well as the fungus Candida glabrata. A comparison of the structures of DHFR from the fungal species Candida glabrata and Pneumocystis suggests that the compounds may also potently inhibit Pneumocystis DHFR.

  14. Inorganic phosphate uptake in unicellular eukaryotes.

    Science.gov (United States)

    Dick, Claudia F; Dos-Santos, André L A; Meyer-Fernandes, José R

    2014-07-01

    Inorganic phosphate (Pi) is an essential nutrient for all organisms. The route of Pi utilization begins with Pi transport across the plasma membrane. Here, we analyzed the gene sequences and compared the biochemical profiles, including kinetic and modulator parameters, of Pi transporters in unicellular eukaryotes. The objective of this review is to evaluate the recent findings regarding Pi uptake mechanisms in microorganisms, such as the fungi Neurospora crassa and Saccharomyces cerevisiae and the parasite protozoans Trypanosoma cruzi, Trypanosoma rangeli, Leishmania infantum and Plasmodium falciparum. Pi uptake is the key step of Pi homeostasis and in the subsequent signaling event in eukaryotic microorganisms. Biochemical and structural studies are important for clarifying mechanisms of Pi homeostasis, as well as Pi sensor and downstream pathways, and raise possibilities for future studies in this field. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Comparative radiobiology of genetic loci of eukaryots as the basis of the general theory of mutations

    International Nuclear Information System (INIS)

    Aleksandrov, I.D.

    1983-01-01

    One of the fundamental problems of modern molecular cellular radiobiology is to reveal general and peculiar processes of the formation of gene mutations and chromosome aberrations in each stage of their formation in the irradiated genome of the higher eukaryots. The solution of the problems depends on the development of research within the framework of comparative radiobiology of genetic loci of the higher eukaryots that makes it possible to study quantitative regularities in the formation of gene (point) mutations and chromosome aberrations in one object and in the same experiment

  16. Utility of Photochemical Traits as Diagnostics of Thermal Tolerance amongst Great Barrier Reef Corals

    Directory of Open Access Journals (Sweden)

    Matthew R. Nitschke

    2018-02-01

    Full Text Available Light availability is considered a key factor regulating the thermal sensitivity of reef building corals, where excessive excitation of photosystem II (PSII further exacerbates pressure on photochemical pathways already compromised by heat stress. Coral symbionts acclimate to changes in light availability (photoacclimation by continually fine-tuning the photochemical operating efficiency of PSII. However, how this process adjusts throughout the warmest months in naturally heat-tolerant or sensitive species is unknown, and whether this influences the capacity to tolerate transient heat stress is untested. We therefore examined the PSII photophysiology of 10 coral species (with known thermal tolerances from shallow reef environments at Heron Island (Great Barrier Reef, Australia, in spring (October-November, 2015 vs. summer (February-March, 2016. Corals were maintained in flow-through aquaria and rapid light curve (RLC protocols using pulse amplitude modulated (PAM fluorometry captured changes in the PSII photoacclimation strategy, characterized as the minimum saturating irradiance (Ek, and the extent of photochemical ([1 – C], operating efficiency vs. non-photochemical ([1 – Q] energy dissipation. Values of Ek across species were >2-fold higher in all coral species in spring, consistent with a climate of higher overall light exposure (i.e., higher PAR from lower cloud cover, rainfall and wind speed compared with summer. Summer decreases in Ek were combined with a shift toward preferential photochemical quenching in all species. All coral species were subsequently subjected to thermal stress assays. An equivalent temperature-ramping profile of 1°C increase per day and then maintenance at 32°C was applied in each season. Despite the significant seasonal photoacclimation, the species hierarchy of thermal tolerance [maximum quantum yields of PSII (Fv/Fm, monitored at dawn and dusk] did not shift between seasons, except for Pocillopora

  17. Arsenic and Antimony Transporters in Eukaryotes

    Directory of Open Access Journals (Sweden)

    Ewa Maciaszczyk-Dziubinska

    2012-03-01

    Full Text Available Arsenic and antimony are toxic metalloids, naturally present in the environment and all organisms have developed pathways for their detoxification. The most effective metalloid tolerance systems in eukaryotes include downregulation of metalloid uptake, efflux out of the cell, and complexation with phytochelatin or glutathione followed by sequestration into the vacuole. Understanding of arsenic and antimony transport system is of high importance due to the increasing usage of arsenic-based drugs in the treatment of certain types of cancer and diseases caused by protozoan parasites as well as for the development of bio- and phytoremediation strategies for metalloid polluted areas. However, in contrast to prokaryotes, the knowledge about specific transporters of arsenic and antimony and the mechanisms of metalloid transport in eukaryotes has been very limited for a long time. Here, we review the recent advances in understanding of arsenic and antimony transport pathways in eukaryotes, including a dual role of aquaglyceroporins in uptake and efflux of metalloids, elucidation of arsenic transport mechanism by the yeast Acr3 transporter and its role in arsenic hyperaccumulation in ferns, identification of vacuolar transporters of arsenic-phytochelatin complexes in plants and forms of arsenic substrates recognized by mammalian ABC transporters.

  18. Arsenic and Antimony Transporters in Eukaryotes

    Science.gov (United States)

    Maciaszczyk-Dziubinska, Ewa; Wawrzycka, Donata; Wysocki, Robert

    2012-01-01

    Arsenic and antimony are toxic metalloids, naturally present in the environment and all organisms have developed pathways for their detoxification. The most effective metalloid tolerance systems in eukaryotes include downregulation of metalloid uptake, efflux out of the cell, and complexation with phytochelatin or glutathione followed by sequestration into the vacuole. Understanding of arsenic and antimony transport system is of high importance due to the increasing usage of arsenic-based drugs in the treatment of certain types of cancer and diseases caused by protozoan parasites as well as for the development of bio- and phytoremediation strategies for metalloid polluted areas. However, in contrast to prokaryotes, the knowledge about specific transporters of arsenic and antimony and the mechanisms of metalloid transport in eukaryotes has been very limited for a long time. Here, we review the recent advances in understanding of arsenic and antimony transport pathways in eukaryotes, including a dual role of aquaglyceroporins in uptake and efflux of metalloids, elucidation of arsenic transport mechanism by the yeast Acr3 transporter and its role in arsenic hyperaccumulation in ferns, identification of vacuolar transporters of arsenic-phytochelatin complexes in plants and forms of arsenic substrates recognized by mammalian ABC transporters. PMID:22489166

  19. Thermo-cleavable polymers: Materials with enhanced photochemical stability

    DEFF Research Database (Denmark)

    Manceau, Matthieu; Petersen, Martin Helgesen; Krebs, Frederik C

    2010-01-01

    Photochemical stability of three thermo-cleavable polymers was investigated as thin films under atmospheric conditions. A significant increase in lifetime was observed once the side-chain was cleaved emphasizing the detrimental effect of solubilizing groups on the photochemical stability of conju......Photochemical stability of three thermo-cleavable polymers was investigated as thin films under atmospheric conditions. A significant increase in lifetime was observed once the side-chain was cleaved emphasizing the detrimental effect of solubilizing groups on the photochemical stability...... of conjugated polymers. In addition to their ease of processing, thermo-cleavable polymers thus also offer a greater intrinsic stability under illumination....

  20. Photochemical smog incident on June 30, 1973

    Energy Technology Data Exchange (ETDEWEB)

    Hata, S

    1973-01-01

    The first photochemical smog incident in Shizuoka prefecture (June 30, 1973) started in Hamamatsu and extended 100 km northeast as far as Fujinomiya city. This not only involved an extraordinarily large area, but the type of smog was different from that in Tokyo and Osaka. The victims were all pupils exercising at the time in the playgrounds. In Hamamatsu, 1050 children were involved and complained of eye irritation and pain, throat pain, coughs, and headaches between 2 and 3 pm, but there were no serious effects. The damages to agricultural produce were extensive and 70% of the total rice fields (1656 hectares), and 40 hectares of green scallions were affected. In Shizuoka, 716 children were affected about 5:30 pm, but in Fujinomiya, which is located further northeast, 16 children were affected about 4 pm. The movement of the damages, the locations, the extent of damages, and the direction of the wind, were puzzling in the light of the normal pattern of photochemical smogs, and the pollution sources could not be the coastal industrial area or automobile exhaust gases. Meteorological factors were similar to the usual photochemical smog conditions, but the locations of the cities involved and the wind direction from the sea suggested that the pollution source was the Pacific Ocean. Since the wind above 1000 m was northeast, circulation of industrial pollutants by the sea breeze is a possible explanation. The maximum concentration of oxidants was about 0.2 ppm in all areas except for Hamamatsu, where it was a little over 0.2 ppm.

  1. Photochemical reactions of aqueous plutonium systems

    International Nuclear Information System (INIS)

    Friedman, H.A.; Toth, L.M.; Bell, J.T.

    1977-01-01

    The photochemical shift of the Pu 4+ disproportionation equilibrium in aqueous perchloric acid solutions has been measured and shown to be reversible. Ratios of equilibrium quotients between light and dark conditions have been measured for 0.01 M Pu ion concentrations in 0.53 to 1.24 N acid solutions exposed to 0.5 Watt of UV light. The photodecomposition of time- and temperature-aged Pu(IV) polymers in perchloric and nitric acid solutions have been examined as a function of aging conditions. Effects similar to those seen previously for fresh polymers have been observed in the aged perchloric acid solutions. (author)

  2. Photochemical synthesis of biomolecules under anoxic conditions

    Science.gov (United States)

    Folsome, C.; Brittain, A.; Zelko, M.

    1983-01-01

    The long-wavelength UV anoxic photosynthesis of uracil, various sugars (including deoxyribose and glycoaldehyde), amino acids, and other organic photoproducts is reported. The reactions were conducted in a mixture of water, calcium carbonate, hydrazine, and formaldehyde which were subjected to 24 hr or 72 hr radiation. Product yields were greatest when the hydrazine/formaldehyde ratio was one, and when the reactant concentrations were low. These data suggest that organic products can be formed in variety from those amounts of formaldehyde and hydazine precursors which are themselves formed under anoxic UV photochemical conditions.

  3. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

    DEFF Research Database (Denmark)

    Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas

    2013-01-01

    BACKGROUND: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have...... approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers...... indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. RESULTS: We used a phylogenomic...

  4. Trends in photochemical smog in the Cape Peninsula and the ...

    African Journals Online (AJOL)

    There has been growing public concern over reports of increasing air pollution in the Cape Peninsula. Attention has been focused on the 'brown haze' and on photochemical smog. Because of deficiencies in the monitoring equipment, information on trends in photochemical smog levels over the past decade is limited.

  5. Prokaryotes versus Eukaryotes: Who is hosting whom?

    Directory of Open Access Journals (Sweden)

    Guillermo eTellez

    2014-10-01

    Full Text Available Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals’ actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a ‘forgotten organ’, functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short chain fatty acids, a process which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system,. Despite these important effects, the mechanisms by which the gut microbial community influences the host’s biology remains almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes which encourage us to postulate: Who is

  6. The evolution of photochemical smog in a power plant plume

    Science.gov (United States)

    Luria, Menachem; Valente, Ralph J.; Tanner, Roger L.; Gillani, Noor V.; Imhoff, Robert E.; Mueller, Stephen F.; Olszyna, Kenneth J.; Meagher, James F. Present address: Aeronomy Laboratory, NOAA, 325 Broadway, Boulder CO 80303, USA.)

    The evolution of photochemical smog in a plant plume was investigated with the aid of an instrumented helicopter. Air samples were taken in the plume of the Cumberland Power Plant, located in central Tennessee, during the afternoon of 16 July 1995 as part of the Southern Oxidants Study - Nashville Middle Tennessee Ozone Study. Twelve cross-wind air sampling traverses were made at six distance groups from 35 to 116 km from the source. During the sampling period the winds were from the west-northwest and the plume drifted towards the city of Nashville TN. Ten of the traverses were made upwind of the city, where the power plant plume was isolated, and two traverses downwind of the city when the plumes were possibly mixed. The results revealed that even six hours after the release, excess ozone production was limited to the edges of the plume. Only when the plume was sufficiently dispersed, but still upwind of Nashville, was excess ozone (up to 109 ppbv, 50-60 ppbv above background levels) produced in the center of the plume. The concentrations image of the plume and a Lagrangian particle model suggests that portions of the power plant plume mixed with the urban plume. The mixed urban power plant plume began to regenerate O 3 that peaked at 120 ppbv at a short distance (15-25 km) downwind of Nashville. Ozone productivity (the ratio of excess O 3 to NO y and NO z) in the isolated plume was significantly lower compared with that found in the city plume. The production of nitrate, a chain termination product, was significantly higher in the power plant plume compared to the mixed plume, indicating shorter chain length of the photochemical smog chain reaction mechanism.

  7. The evolution of photochemical smog in a power plant plume

    International Nuclear Information System (INIS)

    Luria, M.; The Hebrew University, Jerusalem; Valente, R.J.; Tanner, R.L.; Imhoff, R.E.; Mueller, S.F.; Olszyna, K.J.; Meagher, J.F.; Gillani, N.V.; University of Alabama, Huntsville, AL

    1999-01-01

    The evolution of photochemical smog in a plant plume was investigated with the aid of an instrumented helicopter. Air samples were taken in the plume of the Cumberland Power Plant, located in central Tennessee, during the afternoon of 16 July 1995 as part of the Southern Oxidants Study - Nashville Middle Tennessee Ozone Study. Twelve cross-wind air sampling traverses were made at six distance groups from 35 to 116 km from the source. During the sampling period the winds were from the west-northwest and the plume drifted towards the city of Nashville TN. Ten of the traverses were made upwind of the city, where the power plant plume was isolated, and two traverses downwind of the city when the plumes were possibly mixed. The results revealed that even six hours after the release, excess ozone production was limited to the edges of the plume. Only when the plume was sufficiently dispersed, but still upwind of Nashville, was excess ozone (up to 109 ppbv, 50-60 ppbv above background levels) produced in the center of the plume. The concentrations image of the plume and a Lagrangian particle model suggests that portions of the power plant plume mixed with the urban plume. The mixed urban power plant plume began to regenerate O 3 that peaked at 120 ppbv at a short distance (15-25 km) downwind of Nashville. Ozone productivity (the ratio of excess O 3 to NO y and NO z ) in the isolated plume was significantly lower compared with that found in the city plume. The production of nitrate, a chain termination product, was significantly higher in the power plant plume compared to the mixed plume, indicating shorter chain length of the photochemical smog chain reaction mechanism. (author)

  8. Intraspecific variation in Pinus pinaster PSII photochemical efficiency in response to winter stress and freezing temperatures.

    Science.gov (United States)

    Corcuera, Leyre; Gil-Pelegrin, Eustaquio; Notivol, Eduardo

    2011-01-01

    As part of a program to select maritime pine (Pinus pinaster Ait.) genotypes for resistance to low winter temperatures, we examined variation in photosystem II activity by chlorophyll fluorescence. Populations and families within populations from contrasting climates were tested during two consecutive winters through two progeny trials, one located at a continental and xeric site and one at a mesic site with Atlantic influence. We also obtained the LT₅₀, or the temperature that causes 50% damage, by controlled freezing and the subsequent analysis of chlorophyll fluorescence in needles and stems that were collected from populations at the continental trial site.P. pinaster showed sensitivity to winter stress at the continental site, during the colder winter. The combination of low temperatures, high solar irradiation and low precipitation caused sustained decreases in maximal photochemical efficiency (F(v)/F(m)), quantum yield of non-cyclic electron transport (Φ(PSII)) and photochemical quenching (qP). The variation in photochemical parameters was larger among families than among populations, and population differences appeared only under the harshest conditions at the continental site. As expected, the environmental effects (winter and site) on the photochemical parameters were much larger than the genotypic effects (population or family). LT₅₀ was closely related to the minimum winter temperatures of the population's range. The dark-adapted F(v)/F(m) ratio discriminated clearly between interior and coastal populations.In conclusion, variations in F(v)/F(m), Φ(PSII), qP and non-photochemical quenching (NPQ) in response to winter stress were primarily due to the differences between the winter conditions and the sites and secondarily due to the differences among families and their interactions with the environment. Populations from continental climates showed higher frost tolerance (LT₅₀) than coastal populations that typically experience mild winters

  9. Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2012-01-01

    in proteins is currently lacking. We have therefore analyzed the occurrence and occupancy of phosphorylated sites (~ 100,281) in a large set of eukaryotic proteins (~ 22,995). Phosphorylation probability was found to be much higher in both the  termini of protein sequences and this is much pronounced...... maximum randomness. An analysis of phosphorylation motifs indicated that just 40 motifs and a much lower number of associated kinases might account for nearly 50% of the known phosphorylations in eukaryotic proteins. Our results provide a broad picture of the phosphorylation sites in eukaryotic proteins.......Many recent high throughput technologies have enabled large-scale discoveries of new phosphorylation sites and phosphoproteins. Although they have provided a number of insights into protein phosphorylation and the related processes, an inclusive analysis on the nature of phosphorylated sites...

  10. Consistent mutational paths predict eukaryotic thermostability

    Directory of Open Access Journals (Sweden)

    van Noort Vera

    2013-01-01

    Full Text Available Abstract Background Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. Results Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1, we could also characterise the molecular consequences of some of these mutations. Conclusions The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.

  11. Strong eukaryotic IRESs have weak secondary structure.

    Directory of Open Access Journals (Sweden)

    Xuhua Xia

    Full Text Available BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. CONCLUSIONS: We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5'-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.

  12. RNA Export through the NPC in Eukaryotes.

    Science.gov (United States)

    Okamura, Masumi; Inose, Haruko; Masuda, Seiji

    2015-03-20

    In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC.

  13. Photochemically induced oscillations of aromatic pentazadienes

    Energy Technology Data Exchange (ETDEWEB)

    Kunz, T; Hahn, C; Wokaun, A [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    Aromatic pentazadienes are used to enhance the laser induced ablation of standard polymers with low absorption in the UV. Therefore the photochemistry of substituted 1,5-diaryl-3-alkyl-1,4-pentazadiene monomers was studied with a pulsed excimer laser as irradiation source. The net photochemical reaction proceeds in an overall one-step pathway A{yields}B. Quantum yields for the laser decomposition were determined to be up to 10%. An oscillating behaviour of the absorption was found during the dark period following the irradiation. The temperature dependence of this dark reaction has been studied. An attempt to model this behaviour in terms of a non-linear coupling between heat released, heat transfer, and reaction kinetics will be described. (author) 4 figs., 4 refs.

  14. Engineering photochemical smog through convection towers

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, S.; Prueitt, M.L.; Bossert, J.E.; Mroz, E.J.; Krakowski, R.A.; Miller, R.L. [Los Alamos National Lab., NM (United States); Jacobson, M.Z.; Turco, R.P. [Los Alamos National Lab., NM (United States)]|[Univ. of California, Los Angeles, CA (United States). Atmospheric Sciences Dept.

    1995-02-01

    Reverse convection towers have attracted attention as a medium for cleansing modern cities. Evaporation of an aqueous mist injected at the tower opening could generate electrical power by creating descent, and simultaneously scavenge unsightly and unhealthful particulates. The study offered here assesses the influence to tower water droplets on the photochemical component of Los Angeles type smog. The primary radical chain initiator OH is likely removed into aqueous phases well within the residence time of air in the tower, and then reacts away rapidly. Organics do not dissolve, but nighttime hydrolysis of N{sub 2}O{sub 5} depletes the nitrogen oxides. A lack of HOx would slow hydrocarbon oxidation and so also ozone production. Lowering of NOx would also alter ozone production rates, but the direction is uncertain. SO{sub 2} is available in sufficient quantities in some urban areas to react with stable oxidants, and if seawater were the source of the mist, the high pH would lead to fast sulfur oxidation kinetics. With an accommodation coefficient of 10{sup {minus}3}, however, ozone may not enter the aqueous phase efficiently. Even if ozone is destroyed or its production suppressed, photochemical recovery times are on the order of hours, so that tower processing must be centered on a narrow midday time window. The cost of building the number of structures necessary for this brief turnover could be prohibitive. The increase in humidity accompanying mist evaporation could be controlled with condensers, but might otherwise counteract visibility enhancements by recreating aqueous aerosols. Quantification of the divergent forcings convection towers must exert upon the cityscape would call for coupled three dimensional modeling of transport, microphysics, and photochemistry. 112 refs.

  15. Origin and evolution of SINEs in eukaryotic genomes.

    Science.gov (United States)

    Kramerov, D A; Vassetzky, N S

    2011-12-01

    Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements.

  16. The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

    Energy Technology Data Exchange (ETDEWEB)

    Fritz-Laylin, Lillian K.; Prochnik, Simon E.; Ginger, Michael L.; Dacks, Joel; Carpenter, Meredith L.; Field, Mark C.; Kuo, Alan; Paredez, Alex; Chapman, Jarrod; Pham, Jonathan; Shu, Shengqiang; Neupane, Rochak; Cipriano, Michael; Mancuso, Joel; Tu, Hank; Salamov, Asaf; Lindquist, Erika; Shapiro, Harris; Lucas, Susan; Grigoriev, Igor V.; Cande, W. Zacheus; Fulton, Chandler; Rokhsar, Daniel S.; Dawson, Scott C.

    2010-03-01

    Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.

  17. Photochemical epoxidation of olefins by visible light in a redox system involving Sb(V) tetraphenylporphyrin and water

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, Haruo; Hida, Mitsuhiko (Tokyo Metropolitan Univ. (Japan))

    1989-03-25

    The authors explore electron donors from the viewpoint of solar energy storage. Much attention has been focused on how a water molecule can be incorporated into electron donor system. In this paper, the authors describe a photochemical epoxidation of alkene sensitized by Sb(V)-, P(V)-, Sn(IV)-, Ge(IV)- tetraphenylporphyrin (TPP) with higher oxidation potential than 1.0 Volts vs. NHE in redox systems with a water molecule as an electron donor. The water molecule acts as an electron donor, and alkene acts as an oxygen atom acceptor in this photoredox system. Epoxidation of alkenes usually requires strong oxidizing agents either by the thermal or photochemical method. This is the first example of the photochemical epoxide formation from alkene and water without any strong oxidizing agent. 1 fig.

  18. Ultrastructural diversity between centrioles of eukaryotes.

    Science.gov (United States)

    Gupta, Akshari; Kitagawa, Daiju

    2018-02-16

    Several decades of centriole research have revealed the beautiful symmetry present in these microtubule-based organelles, which are required to form centrosomes, cilia, and flagella in many eukaryotes. Centriole architecture is largely conserved across most organisms, however, individual centriolar features such as the central cartwheel or microtubule walls exhibit considerable variability when examined with finer resolution. Here, we review the ultrastructural characteristics of centrioles in commonly studied organisms, highlighting the subtle and not-so-subtle differences between specific structural components of these centrioles. Additionally, we survey some non-canonical centriole structures that have been discovered in various species, from the coaxial bicentrioles of protists and lower land plants to the giant irregular centrioles of the fungus gnat Sciara. Finally, we speculate on the functional significance of these differences between centrioles, and the contribution of individual structural elements such as the cartwheel or microtubules towards the stability of centrioles.Centriole structure, cartwheel, triplet microtubules, SAS-6, centrosome.

  19. Protein splicing and its evolution in eukaryotes

    Directory of Open Access Journals (Sweden)

    Starokadomskyy P. L.

    2010-02-01

    Full Text Available Inteins, or protein introns, are parts of protein sequences that are post-translationally excised, their flanking regions (exteins being spliced together. This process was called protein splicing. Originally inteins were found in prokaryotic or unicellular eukaryotic organisms. But the general principles of post-translation protein rearrangement are evolving yielding different post-translation modification of proteins in multicellular organisms. For clarity, these non-intein mediated events call either protein rearrangements or protein editing. The most intriguing example of protein editing is proteasome-mediated splicing of antigens in vertebrates that may play important role in antigen presentation. Other examples of protein rearrangements are maturation of Hg-proteins (critical receptors in embryogenesis as well as maturation of several metabolic enzymes. Despite a lack of experimental data we try to analyze some intriguing examples of protein splicing evolution.

  20. Redox characteristics of the eukaryotic cytosol

    DEFF Research Database (Denmark)

    López-Mirabal, H Reynaldo; Winther, Jakob R

    2007-01-01

    The eukaryotic cytoplasm has long been regarded as a cellular compartment in which the reduced state of protein cysteines is largely favored. Under normal conditions, the cytosolic low-molecular weight redox buffer, comprising primarily of glutathione, is highly reducing and reactive oxygen species...... (ROS) and glutathionylated proteins are maintained at very low levels. In the present review, recent progress in the understanding of the cytosolic thiol-disulfide redox metabolism and novel analytical approaches to studying cytosolic redox properties are discussed. We will focus on the yeast model...... organism, Saccharomyces cerevisiae, where the combination of genetic and biochemical approaches has brought us furthest in understanding the mechanisms underlying cellular redox regulation. It has been shown in yeast that, in addition to the enzyme glutathione reductase, other mechanisms may exist...

  1. Bacterial proteins pinpoint a single eukaryotic root

    Czech Academy of Sciences Publication Activity Database

    Derelle, R.; Torruella, G.; Klimeš, V.; Brinkmann, H.; Kim, E.; Vlček, Čestmír; Lang, B.F.; Eliáš, M.

    2015-01-01

    Roč. 112, č. 7 (2015), E693-E699 ISSN 0027-8424 R&D Projects: GA ČR GA13-24983S Grant - others:GA MŠk(CZ) ED2.1.00/03.0100; Howard Hughes Medical Institute International Early Career Scientist Program(US) 55007424; Spanish Ministry of Economy and Competitiveness, European Molecular Biology Organization Young Investigator Program(ES) BFU2012-31329; Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa" - European Regional Development Fund(ES) Sev-2012-0208, BES-2013-064004 Institutional support: RVO:68378050 Keywords : eukaryote phylogeny * phylogenomics * Opimoda * Diphoda * LECA Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.423, year: 2015

  2. The COG database: an updated version includes eukaryotes

    Directory of Open Access Journals (Sweden)

    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  3. Photochemical degradation of PCBs in snow.

    Science.gov (United States)

    Matykiewiczová, Nina; Klánová, Jana; Klán, Petr

    2007-12-15

    This work represents the first laboratory study known to the authors describing photochemical behavior of persistent organic pollutants in snow at environmentally relevant concentrations. The snow samples were prepared by shock freezing of the corresponding aqueous solutions in liquid nitrogen and were UV-irradiated in a photochemical cold chamber reactor at -25 degrees C, in which simultaneous monitoring of snow-air exchange processeswas also possible. The main photodegradation pathway of two model snow contaminants, PCB-7 and PCB-153 (c approximately 100 ng kg(-1)), was found to be reductive dehalogenation. Possible involvement of the water molecules of snow in this reaction has been excluded by performing the photolyses in D2O snow. Instead, trace amounts of volatile organic compounds have been proposed to be the major source of hydrogen atom in the reduction, and this hypothesis was confirmed by the experiments with deuterated organic cocontaminants, such as d6-ethanol or d8-tetrahydrofuran. It is argued that bimolecular photoreduction of PCBs was more efficient or feasible than any other phototransformations under the experimental conditions used, including the coupling reactions. The photodegradation of PCBs, however, competed with a desorption process responsible for the pollutant loss from the snow samples, especially in case of lower molecular-mass congeners. Organic compounds, apparently largely located or photoproduced on the surface of snow crystals, had a predisposition to be released to the air but, at the same time, to react with other species in the gas phase. It is concluded that physicochemical properties of the contaminants and trace co-contaminants, their location and local concentrations in the matrix, and the wavelength and intensity of radiation are the most important factors in the evaluation of organic contaminants' lifetime in snow. Based on the results, it has been estimated that the average lifetime of PCBs in surface snow, connected

  4. Photochemical oxidation: A solution for the mixed waste dilemma

    Energy Technology Data Exchange (ETDEWEB)

    Prellberg, J.W.; Thornton, L.M.; Cheuvront, D.A. [Vulcan Peroxidation Systems, Inc., Tucson, AZ (United States)] [and others

    1995-12-31

    Numerous technologies are available to remove organic contamination from water or wastewater. A variety of techniques also exist that are used to neutralize radioactive waste. However, few technologies can satisfactorily address the treatment of mixed organic/radioactive waste without creating unacceptable secondary waste products or resulting in extremely high treatment costs. An innovative solution to the mixed waste problem is on-site photochemical oxidation. Liquid-phase photochemical oxidation has a long- standing history of successful application to the destruction of organic compounds. By using photochemical oxidation, the organic contaminants are destroyed on-site leaving the water, with radionuclides, that can be reused or disposed of as appropriate. This technology offers advantages that include zero air emissions, no solid or liquid waste formation, and relatively low treatment cost. Discussion of the photochemical process will be described, and several case histories from recent design testing, including cost analyses for the resulting full-scale installations, will be presented as examples.

  5. Method of making gold thiolate and photochemically functionalized microcantilevers

    Science.gov (United States)

    Boiadjiev, Vassil I [Knoxville, TN; Brown, Gilbert M [Knoxville, TN; Pinnaduwage, Lal A [Knoxville, TN; Thundat, Thomas G [Knoxville, TN; Bonnesen, Peter V [Knoxville, TN; Goretzki, Gudrun [Nottingham, GB

    2009-08-25

    Highly sensitive sensor platforms for the detection of specific reagents, such as chromate, gasoline and biological species, using microcantilevers and other microelectromechanical systems (MEMS) whose surfaces have been modified with photochemically attached organic monolayers, such as self-assembled monolayers (SAM), or gold-thiol surface linkage are taught. The microcantilever sensors use photochemical hydrosilylation to modify silicon surfaces and gold-thiol chemistry to modify metallic surfaces thereby enabling individual microcantilevers in multicantilever array chips to be modified separately. Terminal vinyl substituted hydrocarbons with a variety of molecular recognition sites can be attached to the surface of silicon via the photochemical hydrosilylation process. By focusing the activating UV light sequentially on selected silicon or silicon nitride hydrogen terminated surfaces and soaking or spotting selected metallic surfaces with organic thiols, sulfides, or disulfides, the microcantilevers are functionalized. The device and photochemical method are intended to be integrated into systems for detecting specific agents including chromate groundwater contamination, gasoline, and biological species.

  6. DNA to DNA transcription might exist in eukaryotic cells

    OpenAIRE

    Li, Gao-De

    2016-01-01

    Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the functions of certain noncoding DNA in the human and other eukaryotic genomes.

  7. Study of the photochemical isomerization of ergosterol

    International Nuclear Information System (INIS)

    Mermet-Bouvier, Rene

    1972-01-01

    The photochemical reaction scheme of Ergosterol-Vitamin D 2 was studied. The schemes proposed in published literature are described together with earlier methods used for the analysis and determination. The method used is then discussed. In the first part, the factors concerning the changes occurring in molecular systems exposed to radiation, and the formalism used, are examined. Investigations of linear molecular systems and their applications to the reaction scheme of Ergosterol-Vitamin D 2 are discussed. The properties which enable the last three reaction schemes proposed in the literature to be distinguished are described. In the second part, the experimental analytical methods and the determinations made of the different isomers formed are presented. Chromatographic techniques (thin films, columns, gaseous phase) suitable for separating the various isomeric species are used. The existence of 8 isomers was established as well as a transformation occurring in one of them. The ultraviolet and infrared spectra were obtained. A reaction scheme is proposed (in which all the quantum yield values are given) from comparisons between the calculated and experimental values of the eigenvalue of the absolute minimum value λ m and the eigenvector corresponding to V m . (author) [fr

  8. Photochemically enhanced microbial degradation of environmental pollutants

    International Nuclear Information System (INIS)

    Katayama, A.; Matsumura, F.

    1991-01-01

    Biodegradation of persistent halogenated organic pollutants is of great interest from the viewpoint of its potential use to cleanup the contaminated sites and industrial waste streams on-site (i.e., in situ remediation). Recent studies have shown that lignin-degrading white rot fungi possess capabilities to degrade a variety of highly recalcitrant and toxic compounds. On the other hand, photodegradation by sunlight or ultraviolet light (UV) has not been considered as a potential technology to detoxify the contaminated sites, in spite of the availability of extensive research data, because of its limited reaching ability to subsurface locations. In view of the urgent needs for the development of technology to deal with mounting problems of toxic wastes, the authors have decided to experiment with the ideas of combining photochemical and microbial technologies. The main obstacle in developing such simultaneous combination systems has been the susceptibilities of microorganisms in general to UV irradiation. To overcome this problem, the authors have developed an ultraviolet- and fungicide-resistant strain of white rot fungus and now report their results

  9. Decomposition of oxalate precipitates by photochemical reaction

    International Nuclear Information System (INIS)

    Yoo, J.H.; Kim, E.H.

    1998-01-01

    A photo-radiation method was applied to decompose oxalate precipitates so that it can be dissolved into dilute nitric acid. This work has been studied as a part of partitioning of minor actinides. Minor actinides can be recovered from high-level wastes as oxalate precipitates, but they tend to be coprecipitated together with lanthanide oxalates. This requires another partitioning step for mutual separation of actinide and lanthanide groups. In this study, therefore, the photochemical decomposition mechanism of oxalates in the presence of nitric acid was elucidated by experimental work. The decomposition of oxalates was proved to be dominated by the reaction with hydroxyl radical generated from the nitric acid, rather than with nitrite ion also formed from nitrate ion. The decomposition rate of neodymium oxalate, which was chosen as a stand-in compound representing minor actinide and lanthanide oxalates, was found to be 0.003 M/hr at the conditions of 0.5 M HNO 3 and room temperature when a mercury lamp was used as a light source. (author)

  10. Decomposition of oxalate precipitates by photochemical reaction

    International Nuclear Information System (INIS)

    Jae-Hyung Yoo; Eung-Ho Kim

    1999-01-01

    A photo-radiation method was applied to decompose oxalate precipitates so that it can be dissolved into dilute nitric acid. This work has been studied as a part of partitioning of minor actinides. Minor actinides can be recovered from high-level wastes as oxalate precipitates, but they tend to be coprecipitated together with lanthanide oxalates. This requires another partitioning step for mutual separation of actinide and lanthanide groups. In this study, therefore, some experimental work of photochemical decomposition of oxalate was carried out to prove its feasibility as a step of partitioning process. The decomposition of oxalic acid in the presence of nitric acid was performed in advance in order to understand the mechanistic behaviour of oxalate destruction, and then the decomposition of neodymium oxalate, which was chosen as a stand-in compound representing minor actinide and lanthanide oxalates, was examined. The decomposition rate of neodymium oxalate was found as 0.003 mole/hr at the conditions of 0.5 M HNO 3 and room temperature when a mercury lamp was used as a light source. (author)

  11. Photochemical organonitrate formation in wet aerosols

    Science.gov (United States)

    Lim, Yong Bin; Kim, Hwajin; Kim, Jin Young; Turpin, Barbara J.

    2016-10-01

    Water is the most abundant component of atmospheric fine aerosol. However, despite rapid progress, multiphase chemistry involving wet aerosols is still poorly understood. In this work, we report results from smog chamber photooxidation of glyoxal- and OH-containing ammonium sulfate or sulfuric acid particles in the presence of NOx and O3 at high and low relative humidity. Particles were analyzed using ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). During the 3 h irradiation, OH oxidation products of glyoxal that are also produced in dilute aqueous solutions (e.g., oxalic acids and tartaric acids) were formed in both ammonium sulfate (AS) aerosols and sulfuric acid (SA) aerosols. However, the major products were organonitrogens (CHNO), organosulfates (CHOS), and organonitrogen sulfates (CHNOS). These were also the dominant products formed in the dark chamber, indicating non-radical formation. In the humid chamber (> 70 % relative humidity, RH), two main products for both AS and SA aerosols were organonitrates, which appeared at m / z- 147 and 226. They were formed in the aqueous phase via non-radical reactions of glyoxal and nitric acid, and their formation was enhanced by photochemistry because of the photochemical formation of nitric acid via reactions of peroxy radicals, NOx and OH during the irradiation.

  12. Photochemical oxidants: state of the science.

    Science.gov (United States)

    Kley, D; Kleinmann, M; Sanderman, H; Krupa, S

    1999-01-01

    Atmospheric photochemical processes resulting in the production of tropospheric ozone (O(3)) and other oxidants are described. The spatial and temporal variabilities in the occurrence of surface level oxidants and their relationships to air pollution meteorology are discussed. Models of photooxidant formation are reviewed in the context of control strategies and comparisons are provided of the air concentrations of O(3) at select geographic locations around the world. This overall oxidant (O(3)) climatology is coupled to human health and ecological effects. The discussion of the effects includes both acute and chronic responses, mechanisms of action, human epidemiological and plant population studies and briefly, efforts to establish cause-effect relationships through numerical modeling. A short synopsis is provided of the interactive effects of O(3) with other abiotic and biotic factors. The overall emphasis of the paper is on identifying the current uncertainties and gaps in our understanding of the state of the science and some suggestions as to how they may be addressed.

  13. Photochemical reduction of uranyl ion with amides

    International Nuclear Information System (INIS)

    Brar, A.S.; Chander, R.; Sandhu, S.S.

    1981-01-01

    The photochemical reduction of uranyl ion by formamide, acetamide, propionamide, butyramide, iso butyramids, n-methylformamide, N, N-dimethylformamide and N, N-diethylformamide in aqueous medium using radiation >= 380 nm from a medium pressure mercury vapour lamp has been investigated. The reduction with the said amides has been found to obey pseudo first order kinetics. The magnitude of the rate of reduction for the simple amides has been found to follow the following order formamide > isobutyramide approx. butyramide > propionamide > acetamide while the rate order for N-alkylformamides compared with that of the formamide has been found to be formamide > N-methylformamide > N,N-diethylformamide approx. N,N-dimethylformamide. The pseudo first order rate constants and quenching constants have been found from the kinetic data. It has been found that physical and chemical quenching compete with each other. Plots of reciprocal of quantum yields versus reciprocal [amide] have been found to be linear with intercepts on the ordinate axis. Absorption spectra of uranyl ion in doubly distilled water, in the presence of acid and in the presence of acid and amide reveal that there is no ground state interaction between uranyl ion and the amide. A mechanism of photoreduction of uranyl ion with amides has been proposed. (author)

  14. Morphological and ecological complexity in early eukaryotic ecosystems.

    Science.gov (United States)

    Javaux, E J; Knoll, A H; Walter, M R

    2001-07-05

    Molecular phylogeny and biogeochemistry indicate that eukaryotes differentiated early in Earth history. Sequence comparisons of small-subunit ribosomal RNA genes suggest a deep evolutionary divergence of Eukarya and Archaea; C27-C29 steranes (derived from sterols synthesized by eukaryotes) and strong depletion of 13C (a biogeochemical signature of methanogenic Archaea) in 2,700 Myr old kerogens independently place a minimum age on this split. Steranes, large spheroidal microfossils, and rare macrofossils of possible eukaryotic origin occur in Palaeoproterozoic rocks. Until now, however, evidence for morphological and taxonomic diversification within the domain has generally been restricted to very late Mesoproterozoic and Neoproterozoic successions. Here we show that the cytoskeletal and ecological prerequisites for eukaryotic diversification were already established in eukaryotic microorganisms fossilized nearly 1,500 Myr ago in shales of the early Mesoproterozoic Roper Group in northern Australia.

  15. Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water.

    Science.gov (United States)

    Aguilar, Maria; Richardson, Elisabeth; Tan, BoonFei; Walker, Giselle; Dunfield, Peter F; Bass, David; Nesbø, Camilla; Foght, Julia; Dacks, Joel B

    2016-11-01

    Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  16. Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding

    Directory of Open Access Journals (Sweden)

    Corbo Laura

    2001-11-01

    Full Text Available Abstract Background The yeast yCCR4 factor belongs to the CCR4-NOT transcriptional regulatory complex, in which it interacts, through its leucine-rich repeat (LRR motif with yPOP2. Recently, yCCR4 was shown to be a component of the major cytoplasmic mRNA deadenylase complex, and to contain a fold related to the Mg2+-dependent endonuclease core. Results Here, we report the identification of nineteen yCCR4-related proteins in eukaryotes (including yeast, plants and animals, which all contain the yCCR4 endonuclease-like fold, with highly conserved CCR4-specific residues. Phylogenetic and genomic analyses show that they form four distinct families, one of which contains the yCCR4 orthologs. The orthologs in animals possess a leucine-rich repeat domain. We show, using two-hybrid and far-Western assays, that the human member binds to the human yPOP2 homologs, i.e. hCAF1 and hPOP2, in a LRR-dependent manner. Conclusions We have identified the mammalian orthologs of yCCR4 and have shown that the human member binds to the human yPOP2 homologs, thus strongly suggesting conservation of the CCR4-NOT complex from yeast to human. All members of the four identified yCCR4-related protein families show stricking conservation of the endonuclease-like catalytic motifs of the yCCR4 C-terminal domain and therefore constitute a new family of potential deadenylases in mammals.

  17. Genomic impact of eukaryotic transposable elements.

    Science.gov (United States)

    Arkhipova, Irina R; Batzer, Mark A; Brosius, Juergen; Feschotte, Cédric; Moran, John V; Schmitz, Jürgen; Jurka, Jerzy

    2012-11-21

    The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.

  18. Genomic impact of eukaryotic transposable elements

    Directory of Open Access Journals (Sweden)

    Arkhipova Irina R

    2012-11-01

    Full Text Available Abstract The third international conference on the genomic impact of eukaryotic transposable elements (TEs was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.

  19. Do lipids shape the eukaryotic cell cycle?

    Science.gov (United States)

    Furse, Samuel; Shearman, Gemma C

    2018-01-01

    Successful passage through the cell cycle presents a number of structural challenges to the cell. Inceptive studies carried out in the last five years have produced clear evidence of modulations in the lipid profile (sometimes referred to as the lipidome) of eukaryotes as a function of the cell cycle. This mounting body of evidence indicates that lipids play key roles in the structural transformations seen across the cycle. The accumulation of this evidence coincides with a revolution in our understanding of how lipid composition regulates a plethora of biological processes ranging from protein activity through to cellular signalling and membrane compartmentalisation. In this review, we discuss evidence from biological, chemical and physical studies of the lipid fraction across the cell cycle that demonstrate that lipids are well-developed cellular components at the heart of the biological machinery responsible for managing progress through the cell cycle. Furthermore, we discuss the mechanisms by which this careful control is exercised. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  20. Origins and evolution of viruses of eukaryotes: The ultimate modularity

    International Nuclear Information System (INIS)

    Koonin, Eugene V.; Dolja, Valerian V.; Krupovic, Mart

    2015-01-01

    Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources

  1. Origins and evolution of viruses of eukaryotes: The ultimate modularity

    Energy Technology Data Exchange (ETDEWEB)

    Koonin, Eugene V., E-mail: koonin@ncbi.nlm.nih.gov [National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 (United States); Dolja, Valerian V., E-mail: doljav@science.oregonstate.edu [Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 (United States); Krupovic, Mart, E-mail: krupovic@pasteur.fr [Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015 (France)

    2015-05-15

    Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources

  2. Photochemical internalization enhanced macrophage delivered chemotherapy.

    Science.gov (United States)

    Shin, Diane; Christie, Catherine; Ju, David; Nair, Rohit Kumar; Molina, Stephanie; Berg, Kristian; Krasieva, Tatiana B; Madsen, Steen J; Hirschberg, Henry

    2018-03-01

    Macrophage (Ma) vectorization of chemotherapeutic drugs has the advantage for cancer therapy in that it can actively target and maintain an elevated concentration of drugs at the tumor site, preventing their spread into healthy tissue. A potential drawback is the inability to deliver a sufficient number of drug-loaded Ma into the tumor, thus limiting the amount of active drug delivered. This study examined the ability of photochemical internalization (PCI) to enhance the efficacy of released drug by Ma transport. Tumor spheroids consisting of either F98 rat glioma cells or F98 cells combined with a subpopulation of empty or doxorubicin (DOX)-loaded mouse Ma (RAW264.7) were used as in vitro tumor models. PCI was performed with the photosensitizer AlPcS 2a and laser irradiation at 670 nm. RAW264.7 Ma pulsed with DOX released the majority of the incorporated DOX within two hours of incubation. PCI significantly increased the toxicity of DOX either as pure drug or derived from monolayers of DOX-loaded Ma. Significant growth inhibition of hybrid spheroids was also observed with PCI even at subpopulations of DOX-loaded Ma as low as 11% of the total initial hybrid spheroid cell number. Results show that RAW264.7 Ma, pulsed with DOX, could effectively incorporate and release DOX. PCI significantly increased the ability of both free and Ma-released DOX to inhibit the growth of tumor spheroids in vitro. The growth of F98 + DOX loaded Ma hybrid spheroids were synergistically reduced by PCI, compared to either photodynamic therapy or released DOX acting alone. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Instantaneous global nitrous oxide photochemical rates

    International Nuclear Information System (INIS)

    Johnston, H.S.; Serang, O.; Podolske, J.

    1979-01-01

    In recent years, vertical profiles of nitrous oxide have been measured by balloon up to midstratosphere at several latitudes between 63 0 N and 73 0 S, including one profile in the tropical zone at 9 0 N. Two rocket flights measured nitrous oxide mixing ratios at 44 and 49 km. From these experimental data plus a large amount of interpolation and extrapolation, we have estimated a global distribution of nitrous oxide up to the altitude of 50 km. With standard global distributions of oxygen and ozone we carried out instantaneous, three-dimensional, global photochemical calculations, using recently measured temperature-dependent cross sections for nitrous oxide. The altitude of maximum photolysis rate of N 2 O is about 30 km at all latitudes, and the rate of photolysis is a maximum in tropical latitudes. The altitude of maximum rate of formation of nitric oxide is latitude dependent, about 26 km at the equator, about 23 km over temperate zones, and 20 km at the summer pole. The global rate of N 2 O destruction is 6.2 x 10 27 molecules s -1 , and the global rate of formation of NO from N 2 O is 1.4 x 10 27 molecules s -1 . The global N 2 O inventory divided by the stratospheric loss rate gives a residence time of about 175 years with respect to this loss process. From the global average N 2 O profile a vertical eddy diffusion profile was derived, and this profile agrees very closely with that of Stewart and Hoffert

  4. Genome-reconstruction for eukaryotes from complex natural microbial communities.

    Science.gov (United States)

    West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

    2018-04-01

    Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae.

    Science.gov (United States)

    Wijffels, René H; Kruse, Olaf; Hellingwerf, Klaas J

    2013-06-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments. Cyanobacteria are promising host organisms for the production of small molecules that can be secreted such as ethanol, butanol, fatty acids and other organic acids. Eukaryotic microalgae are interesting for products for which cellular storage is important such as proteins, lipids, starch and alkanes. For the development of new and promising lines of production, strains of both cyanobacteria and eukaryotic microalgae have to be improved. Transformation systems have been much better developed in cyanobacteria. However, several products would be preferably produced with eukaryotic microalgae. In the case of cyanobacteria a synthetic-systems biology approach has a great potential to exploit cyanobacteria as cell factories. For eukaryotic microalgae transformation systems need to be further developed. A promising strategy is transformation of heterologous (prokaryotic and eukaryotic) genes in established eukaryotic hosts such as Chlamydomonas reinhardtii. Experimental outdoor pilots under containment for the production of genetically modified cyanobacteria and microalgae are in progress. For full scale production risks of release of genetically modified organisms need to be assessed. Copyright © 2013. Published by Elsevier Ltd.

  6. Functions and structures of eukaryotic recombination proteins

    International Nuclear Information System (INIS)

    Ogawa, Tomoko

    1994-01-01

    We have found that Rad51 and RecA Proteins form strikingly similar structures together with dsDNA and ATP. Their right handed helical nucleoprotein filaments extend the B-form DNA double helixes to 1.5 times in length and wind the helix. The similarity and uniqueness of their structures must reflect functional homologies between these proteins. Therefore, it is highly probable that similar recombination proteins are present in various organisms of different evolutional states. We have succeeded to clone RAD51 genes from human, mouse, chicken and fission yeast genes, and found that the homologues are widely distributed in eukaryotes. The HsRad51 and MmRad51 or ChRad51 proteins consist of 339 amino acids differing only by 4 or 12 amino acids, respectively, and highly homologous to both yeast proteins, but less so to Dmcl. All of these proteins are homologous to the region from residues 33 to 240 of RecA which was named ''homologous core. The homologous core is likely to be responsible for functions common for all of them, such as the formation of helical nucleoprotein filament that is considered to be involved in homologous pairing in the recombination reaction. The mouse gene is transcribed at a high level in thymus, spleen, testis, and ovary, at lower level in brain and at a further lower level in some other tissues. It is transcribed efficiently in recombination active tissues. A clear functional difference of Rad51 homologues from RecA was suggested by the failure of heterologous genes to complement the deficiency of Scrad51 mutants. This failure seems to reflect the absence of a compatible partner, such as ScRad52 protein in the case of ScRad51 protein, between different species. Thus, these discoveries play a role of the starting point to understand the fundamental gene targeting in mammalian cells and in gene therapy. (J.P.N.)

  7. HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus

    Directory of Open Access Journals (Sweden)

    Santiago Guerrero

    2015-01-01

    Full Text Available Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1 uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.

  8. AUG is the only initiation codon in eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Sherman, F; McKnight, G; Stewart, J W

    1980-01-01

    An analysis of mutants of the yeast Saccharomyces cerevisiae indicates that AUG is the sole codon capable of initiating translation of iso-1-cytochrome c. This result with yeast and the sequence results of numerous eukaryotic genes indicate that AUG is the only initiation codon in eukaryotes; in contrast, results with Escherichia colia and bacteriophages indicate that both AUG and GUG are initiation codons in prokaryotes. The difference can be explained by the lack of the t/sup 6/ A hypermodified nucleoside (N-(9-(..beta..-D-ribofuranosyl)purin-6-ylcarbamoyl)threonine) in prokaryotic initiator tRNA and its presence in eukaryotic initiator tRNA.

  9. David and Goliath: chemical perturbation of eukaryotes by bacteria.

    Science.gov (United States)

    Ho, Louis K; Nodwell, Justin R

    2016-03-01

    Environmental microbes produce biologically active small molecules that have been mined extensively as antibiotics and a smaller number of drugs that act on eukaryotic cells. It is known that there are additional bioactives to be discovered from this source. While the discovery of new antibiotics is challenged by the frequent discovery of known compounds, we contend that the eukaryote-active compounds may be less saturated. Indeed, despite there being far fewer eukaryotic-active natural products these molecules interact with a far richer diversity of molecular and cellular targets.

  10. Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

    Science.gov (United States)

    Filker, Sabine; Sommaruga, Ruben; Vila, Irma; Stoeck, Thorsten

    2016-05-01

    Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures. © 2016 John Wiley & Sons Ltd.

  11. Counterintuitive effect of fall mixed layer deepening on eukaryotic new production in the Sargasso Sea

    Science.gov (United States)

    Fawcett, S. E.; Lomas, M. W.; Ward, B. B.; Sigman, D. M.

    2012-12-01

    The Sargasso Sea is characterized by a short period of deep vertical mixing in the late winter and early spring, followed by strong thermal stratification during the summer. Stratification persists into the fall, impeding the upward flux of nitrate from depth so that recycled forms of nitrogen (N) such as ammonium are thought to support most primary production. We collected particles from surface waters during March, July, October, and December, used flow cytometry to separate the prokaryotic and eukaryotic phytoplankton, and analyzed their respective 15N/14N. In all months, the 15N/14N of the prokaryotic genera, Prochlorococcus and Synechococcus, was low, indicative of reliance on recycled N throughout the year. In July, the 15N/14N of eukaryotic phytoplankton was variable but consistently higher than that of the prokaryotes, reflecting eukaryotic consumption of subsurface nitrate. Two eukaryotic profiles from October and December were similar to those from July. In three other fall profiles, the eukaryotes had a 15N/14N similar to that of the prokaryotes, suggesting a switch toward greater reliance on recycled N. This change in the dominant N source supporting eukaryotic production appears to be driven by the density structure of the upper water column. The very shallow low-density surface "mixed layer" (≤20 m) that develops in early-to-mid summer does not contribute to stratification at the base of the euphotic zone, and subsurface nitrate can mix up into the lower euphotic zone, facilitating continued production. The deepening of the mixed layer into the fall, typically taken as an indication of weaker overall stratification, actually strengthens the isolation of the euphotic zone as a whole, reducing the upward supply of nitrate to the photosynthetically active layer. The same counterintuitive dynamic explains the latitudinal patterns in a set of three October depth profiles. Two northern stations (32°N and 27°N) were characterized by a thick, low

  12. Photochemical Transformation Processes in Sunlit Surface Waters

    Science.gov (United States)

    Vione, D.

    2012-12-01

    Photochemical reactions are major processes in the transformation of hardly biodegradable xenobiotics in surface waters. They are usually classified into direct photolysis and indirect or sensitised degradation. Direct photolysis requires xenobiotic compounds to absorb sunlight, and to get transformed as a consequence. Sensitised transformation involves reaction with transient species (e.g. °OH, CO3-°, 1O2 and triplet states of chromophoric dissolved organic matter, 3CDOM*), photogenerated by so-called photosensitisers (nitrate, nitrite and CDOM). CDOM is a major photosensitiser: is it on average the main source of °OH (and of CO3-° as a consequence, which is mainly produced upon oxidation by °OH of carbonate and bicarbonate) and the only important source of 1O2 and 3CDOM* [1, 2]. CDOM origin plays a key role in sensitised processes: allochthonous CDOM derived from soil runoff and rich in fulvic and humic substances is usually more photoactive than autochthonous CDOM (produced by in-water biological processes and mainly consisting of protein-like material) or of CDOM derived from atmospheric deposition. An interesting gradual evolution of CDOM origin and photochemistry can be found in mountain lakes across the treeline, which afford a gradual transition of allochthonous- autochtonous - atmopheric CDOM when passing from trees to alpine meadows to exposed rocks [3]. Another important issue is the sites of reactive species photoproduction in CDOM. While there is evidence that smaller molecular weight fractions are more photoactive, some studies have reported considerable 1O2 reactivity in CDOM hydrophobic sites and inside particles [4]. We have recently addressed the problem and found that dissolved species in standard humic acids (hydrodynamic diameter pollutants to be assessed and modelled. For instance, it is possible to predict pollutant half-life times by knowing absorption spectrum, direct photolysis quantum yield and reaction rate constants with °OH, CO3

  13. Intraspecific variation in Pinus pinaster PSII photochemical efficiency in response to winter stress and freezing temperatures.

    Directory of Open Access Journals (Sweden)

    Leyre Corcuera

    Full Text Available As part of a program to select maritime pine (Pinus pinaster Ait. genotypes for resistance to low winter temperatures, we examined variation in photosystem II activity by chlorophyll fluorescence. Populations and families within populations from contrasting climates were tested during two consecutive winters through two progeny trials, one located at a continental and xeric site and one at a mesic site with Atlantic influence. We also obtained the LT₅₀, or the temperature that causes 50% damage, by controlled freezing and the subsequent analysis of chlorophyll fluorescence in needles and stems that were collected from populations at the continental trial site.P. pinaster showed sensitivity to winter stress at the continental site, during the colder winter. The combination of low temperatures, high solar irradiation and low precipitation caused sustained decreases in maximal photochemical efficiency (F(v/F(m, quantum yield of non-cyclic electron transport (Φ(PSII and photochemical quenching (qP. The variation in photochemical parameters was larger among families than among populations, and population differences appeared only under the harshest conditions at the continental site. As expected, the environmental effects (winter and site on the photochemical parameters were much larger than the genotypic effects (population or family. LT₅₀ was closely related to the minimum winter temperatures of the population's range. The dark-adapted F(v/F(m ratio discriminated clearly between interior and coastal populations.In conclusion, variations in F(v/F(m, Φ(PSII, qP and non-photochemical quenching (NPQ in response to winter stress were primarily due to the differences between the winter conditions and the sites and secondarily due to the differences among families and their interactions with the environment. Populations from continental climates showed higher frost tolerance (LT₅₀ than coastal populations that typically experience mild

  14. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae.

    NARCIS (Netherlands)

    Wijffels, R.H.; Kruse, O.; Hellingwerf, K.J.

    2013-01-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments. Cyanobacteria are promising host organisms

  15. Conservation and Variability of Meiosis Across the Eukaryotes.

    Science.gov (United States)

    Loidl, Josef

    2016-11-23

    Comparisons among a variety of eukaryotes have revealed considerable variability in the structures and processes involved in their meiosis. Nevertheless, conventional forms of meiosis occur in all major groups of eukaryotes, including early-branching protists. This finding confirms that meiosis originated in the common ancestor of all eukaryotes and suggests that primordial meiosis may have had many characteristics in common with conventional extant meiosis. However, it is possible that the synaptonemal complex and the delicate crossover control related to its presence were later acquisitions. Later still, modifications to meiotic processes occurred within different groups of eukaryotes. Better knowledge on the spectrum of derived and uncommon forms of meiosis will improve our understanding of many still mysterious aspects of the meiotic process and help to explain the evolutionary basis of functional adaptations to the meiotic program.

  16. DNA mismatch repair and its many roles in eukaryotic cells

    DEFF Research Database (Denmark)

    Liu, Dekang; Keijzers, Guido; Rasmussen, Lene Juel

    2017-01-01

    in the clinic, and as a biomarker of cancer susceptibility in animal model systems. Prokaryotic MMR is well-characterized at the molecular and mechanistic level; however, MMR is considerably more complex in eukaryotic cells than in prokaryotic cells, and in recent years, it has become evident that MMR plays...... novel roles in eukaryotic cells, several of which are not yet well-defined or understood. Many MMR-deficient human cancer cells lack mutations in known human MMR genes, which strongly suggests that essential eukaryotic MMR components/cofactors remain unidentified and uncharacterized. Furthermore......, the mechanism by which the eukaryotic MMR machinery discriminates between the parental (template) and the daughter (nascent) DNA strand is incompletely understood and how cells choose between the EXO1-dependent and the EXO1–independent subpathways of MMR is not known. This review summarizes recent literature...

  17. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils

    2015-01-01

    The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly......, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations....... and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate...

  18. Blocking Modification of Eukaryotic Initiation 5A2 Antagonizes Cervical Carcinoma via Inhibition of RhoA/ROCK Signal Transduction Pathway.

    Science.gov (United States)

    Liu, Xiaojun; Chen, Dong; Liu, Jiamei; Chu, Zhangtao; Liu, Dongli

    2017-10-01

    Cervical carcinoma is one of the leading causes of cancer-related death for female worldwide. Eukaryotic initiation factor 5A2 belongs to the eukaryotic initiation factor 5A family and is proposed to be a key factor involved in the development of diverse cancers. In the current study, a series of in vivo and in vitro investigations were performed to characterize the role of eukaryotic initiation factor 5A2 in oncogenesis and metastasis of cervical carcinoma. The expression status of eukaryotic initiation factor 5A2 in 15 cervical carcinoma patients was quantified. Then, the effect of eukaryotic initiation factor 5A2 knockdown on in vivo tumorigenicity ability, cell proliferation, cell cycle distribution, and cell mobility of HeLa cells was measured. To uncover the mechanism driving the function of eukaryotic initiation factor 5A2 in cervical carcinoma, expression of members within RhoA/ROCK pathway was detected, and the results were further verified with an RhoA overexpression modification. The level of eukaryotic initiation factor 5A2 in cervical carcinoma samples was significantly higher than that in paired paratumor tissues ( P cycle arrest ( P ROCK I, and ROCK II were downregulated. The above-mentioned changes in eukaryotic initiation factor 5A2 knockdown cells were alleviated by the overexpression of RhoA. The major findings outlined in the current study confirmed the potential of eukaryotic initiation factor 5A2 as a promising prognosis predictor and therapeutic target for cervical carcinoma treatment. Also, our data inferred that eukaryotic initiation factor 5A2 might function in carcinogenesis of cervical carcinoma through an RhoA/ROCK-dependent manner.

  19. Photochemical Approaches to Complex Chemotypes: Applications in Natural Product Synthesis

    Science.gov (United States)

    2016-01-01

    The use of photochemical transformations is a powerful strategy that allows for the formation of a high degree of molecular complexity from relatively simple building blocks in a single step. A central feature of all light-promoted transformations is the involvement of electronically excited states, generated upon absorption of photons. This produces transient reactive intermediates and significantly alters the reactivity of a chemical compound. The input of energy provided by light thus offers a means to produce strained and unique target compounds that cannot be assembled using thermal protocols. This review aims at highlighting photochemical transformations as a tool for rapidly accessing structurally and stereochemically diverse scaffolds. Synthetic designs based on photochemical transformations have the potential to afford complex polycyclic carbon skeletons with impressive efficiency, which are of high value in total synthesis. PMID:27120289

  20. Inheritance of photochemical air pollution tolerance in petunias

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, G.P.; Addis, D.H.; Thorne, L.

    1976-12-01

    Seven commercial inbred lines of pink flowered multiflora petunia (Petunia hybrida Vilm.) which differed widely in degrees of tolerance to photochemical oxidants were crossed in all possible combinations to yield a complete diallel cross. Sibling representatives of all 49 possible hybrids were then separately subjected to ozone (O/sub 3/), peroxyacetyl nitrate (PAN), and ambient oxidants at Arcadia, California. The seedlings were scored for tolerance to each pollutant and the inheritance of tolerance to each pollutant was studied. At the ambient levels of photochemical oxidants encountered, PAN more severely injured the petunias than did the O/sub 3/ component. Hybrids tolerant to one oxidant were not necessarily tolerant to the other. The genes which contributed photochemical oxidant tolerance in petunia acted primarily in an additive manner with some indication of partial dominance for tolerance. Gene interaction was evident in the expression of petunia sensitivity to PAN.

  1. Structure and Mechanism of a Eukaryotic FMN Adenylyltransferase

    OpenAIRE

    Huerta, Carlos; Borek, Dominika; Machius, Mischa; Grishin, Nick V.; Zhang, Hong

    2009-01-01

    Flavin mononucleotide adenylyltransferase (FMNAT) catalyzes the formation of the essential flavocoenzyme FAD and plays an important role in flavocoenzyme homeostasis regulation. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different set of active site residues to accomplish the same chemistry. Here we report the first structural characterization of a eukaryotic FMNAT from a pathogenic yeast Candida glabrata...

  2. Massive expansion of the calpain gene family in unicellular eukaryotes

    Directory of Open Access Journals (Sweden)

    Zhao Sen

    2012-09-01

    Full Text Available Abstract Background Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists. Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. Conclusions The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.

  3. Massive expansion of the calpain gene family in unicellular eukaryotes.

    Science.gov (United States)

    Zhao, Sen; Liang, Zhe; Demko, Viktor; Wilson, Robert; Johansen, Wenche; Olsen, Odd-Arne; Shalchian-Tabrizi, Kamran

    2012-09-29

    Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists). Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.

  4. Chemical characteristics of fulvic acids from Arctic surface waters: Microbial contributions and photochemical transformations

    Science.gov (United States)

    Cory, Rose M.; McKnight, Diane M.; Chin, Yu-Ping; Miller, Penney; Jaros, Chris L.

    2007-12-01

    Dissolved organic matter (DOM) originating from the extensive Arctic tundra is an important source of organic material to the Arctic Ocean. Chemical characteristics of whole water dissolved organic matter (DOM) and the fulvic acid fraction of DOM were studied from nine surface waters in the Arctic region of Alaska to gain insight into the extent of microbial and photochemical transformation of this DOM. All the fulvic acids had a strong terrestrial/higher plant signature, with uniformly depleted δ13C values of -28‰, and low fluorescence indices around 1.3. Several of the measured chemical characteristics of the Arctic fulvic acids were related to water residence time, a measure of environmental exposure to sunlight and microbial activity. For example, fulvic acids from Arctic streams had higher aromatic contents, higher specific absorbance values, lower nitrogen content, lower amino acid-like fluorescence and were more depleted in δ15N relative to fulvic acids isolated from lake and coastal surface waters. The differences in the nitrogen signature between the lake and coastal fulvic acids compared to the stream fulvic acids indicated that microbial contributions to the fulvic acid pool increased with increasing water residence time. The photo-lability of the fulvic acids was positively correlated with water residence time, suggesting that the fulvic acids isolated from source waters with larger water residence times (i.e., lakes and coastal waters) have experienced greater photochemical degradation than the stream fulvic acids. In addition, many of the initial differences in fulvic acid chemical characteristics across the gradient of water residence times were consistent with changes observed in fulvic acid photolysis experiments. Taken together, results from this study suggest that photochemical processes predominantly control the chemical character of fulvic acids in Arctic surface waters. Our findings show that hydrologic transport in addition to

  5. Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins

    Directory of Open Access Journals (Sweden)

    Lek Monkol

    2010-07-01

    Full Text Available Abstract Background The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the fundamental function of this gene family, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease. The availability of genome sequences from a wide range of species makes it possible to explore the evolution of the ferlin family, providing contextual insight into characteristic features that define the ferlin gene family in its present form in humans. Results Ferlin genes were detected from all species of representative phyla, with two ferlin subgroups partitioned within the ferlin phylogenetic tree based on the presence or absence of a DysF domain. Invertebrates generally possessed two ferlin genes (one with DysF and one without, with six ferlin genes in most vertebrates (three DysF, three non-DysF. Expansion of the ferlin gene family is evident between the divergence of lamprey (jawless vertebrates and shark (cartilaginous fish. Common to almost all ferlins is an N-terminal C2-FerI-C2 sandwich, a FerB motif, and two C-terminal C2 domains (C2E and C2F adjacent to the transmembrane domain. Preservation of these structural elements throughout eukaryotic evolution suggests a fundamental role of these motifs for ferlin function. In contrast, DysF, C2DE, and FerA are optional, giving rise to subtle differences in domain topologies of ferlin genes. Despite conservation of multiple C2 domains in all ferlins, the C-terminal C2 domains (C2E and C2F displayed higher sequence conservation and greater conservation of putative calcium binding residues across paralogs and orthologs. Interestingly, the two most studied non-mammalian ferlins (Fer-1 and Misfire in model organisms C. elegans and D. melanogaster, present as outgroups in the phylogenetic analysis, with results suggesting

  6. Biosurfactant gene clusters in eukaryotes: regulation and biotechnological potential.

    Science.gov (United States)

    Roelants, Sophie L K W; De Maeseneire, Sofie L; Ciesielska, Katarzyna; Van Bogaert, Inge N A; Soetaert, Wim

    2014-04-01

    Biosurfactants (BSs) are a class of secondary metabolites representing a wide variety of structures that can be produced from renewable feedstock by a wide variety of micro-organisms. They have (potential) applications in the medical world, personal care sector, mining processes, food industry, cosmetics, crop protection, pharmaceuticals, bio-remediation, household detergents, paper and pulp industry, textiles, paint industries, etc. Especially glycolipid BSs like sophorolipids (SLs), rhamnolipids (RLs), mannosylerythritol lipids (MELs) and cellobioselipids (CBLs) have been described to provide significant opportunities to (partially) replace chemical surfactants. The major two factors currently limiting the penetration of BSs into the market are firstly the limited structural variety and secondly the rather high production price linked with the productivity. One of the keys to resolve the above mentioned bottlenecks can be found in the genetic engineering of natural producers. This could not only result in more efficient (economical) recombinant producers, but also in a diversification of the spectrum of available BSs as such resolving both limiting factors at once. Unraveling the genetics behind the biosynthesis of these interesting biological compounds is indispensable for the tinkering, fine tuning and rearrangement of these biological pathways with the aim of obtaining higher yields and a more extensive structural variety. Therefore, this review focuses on recent developments in the investigation of the biosynthesis, genetics and regulation of some important members of the family of the eukaryotic glycolipid BSs (MELs, CBLs and SLs). Moreover, recent biotechnological achievements and the industrial potential of engineered strains are discussed.

  7. On the Diversification of the Translation Apparatus across Eukaryotes

    Directory of Open Access Journals (Sweden)

    Greco Hernández

    2012-01-01

    Full Text Available Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

  8. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Directory of Open Access Journals (Sweden)

    Neil W. Blackstone

    2016-04-01

    Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  9. Compositional patterns in the genomes of unicellular eukaryotes.

    Science.gov (United States)

    Costantini, Maria; Alvarez-Valin, Fernando; Costantini, Susan; Cammarano, Rosalia; Bernardi, Giorgio

    2013-11-05

    The genomes of multicellular eukaryotes are compartmentalized in mosaics of isochores, large and fairly homogeneous stretches of DNA that belong to a small number of families characterized by different average GC levels, by different gene concentration (that increase with GC), different chromatin structures, different replication timing in the cell cycle, and other different properties. A question raised by these basic results concerns how far back in evolution the compartmentalized organization of the eukaryotic genomes arose. In the present work we approached this problem by studying the compositional organization of the genomes from the unicellular eukaryotes for which full sequences are available, the sample used being representative. The average GC levels of the genomes from unicellular eukaryotes cover an extremely wide range (19%-60% GC) and the compositional patterns of individual genomes are extremely different but all genomes tested show a compositional compartmentalization. The average GC range of the genomes of unicellular eukaryotes is very broad (as broad as that of prokaryotes) and individual compositional patterns cover a very broad range from very narrow to very complex. Both features are not surprising for organisms that are very far from each other both in terms of phylogenetic distances and of environmental life conditions. Most importantly, all genomes tested, a representative sample of all supergroups of unicellular eukaryotes, are compositionally compartmentalized, a major difference with prokaryotes.

  10. Approximate photochemical dynamics of azobenzene with reactive force fields

    Science.gov (United States)

    Li, Yan; Hartke, Bernd

    2013-12-01

    We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work).

  11. New electrochemical and photochemical systems for water and wastewater treatment

    International Nuclear Information System (INIS)

    Sarria, Victor M; Parra, Sandra; Rincon, Angela G; Torres, Ricardo A; Pulgarin, Cesar

    2005-01-01

    With the increasing pressure on a more effective use of water resources, the development of appropriate water treatment technologies become more and more important. Photochemical and electrochemical oxidation processes have been proposed in recent years as an attractive alternative for the treatment of contaminated water containing anthropogenic substances hardly biodegradable as well as to purify and disinfect drinking waters. The aim of this paper is to present some of our last results demonstrating that electrochemical, photochemical, and the coupling of these processes with biological systems are very promising alternatives for the improvement of the water quality

  12. Atmospheric photochemical reactivity and ozone production at two sites in Hong Kong: Application of a Master Chemical Mechanism-photochemical box model

    Science.gov (United States)

    Ling, Z. H.; Guo, H.; Lam, S. H. M.; Saunders, S. M.; Wang, T.

    2014-09-01

    A photochemical box model incorporating the Master Chemical Mechanism (v3.2), constrained with a full suite of measurements, was developed to investigate the photochemical reactivity of volatile organic compounds at a semirural site (Mount Tai Mo Shan (TMS)) and an urban site (Tsuen Wan (TW)) in Hong Kong. The levels of ozone (O3) and its precursors, and the magnitudes of the reactivity of O3 precursors, revealed significant differences in the photochemistry at the two sites. Simulated peak hydroperoxyl radical (HO2) mixing ratios were similar at TW and TMS (p = 0.05), while the simulated hydroxyl radical (OH) mixing ratios were much higher at TW (p TMS, but at TW, both HCHO and O3 photolyses were found to be major contributors. By contrast, radical-radical reactions governed HOx radical losses at TMS, while at TW, the OH + NO2 reaction was found to dominate in the morning and the radical-radical reactions at noon. Overall, the conversion of NO to NO2 by HO2 dictated the O3 production at the two sites, while O3 destruction was dominated by the OH + NO2 reaction at TW, and at TMS, O3 photolysis and the O3 + HO2 reaction were the major mechanisms. The longer OH chain length at TMS indicated that more O3 was produced for each radical that was generated at this site.

  13. The composition dependence of the photochemical reactivity of strontium barium titanate

    Science.gov (United States)

    Bhardwaj, Abhilasha

    The efficiency of particulate water photolysis catalysts is impractically low due to the recombination of intermediate species and charge carriers. The back reaction can occur easily if the oxidation and reduction sites on the surface of the catalyst are not far enough apart. It is hypothesized that it will be possible to increase the separation of the sites of the two half reactions and reduce the recombination of photogenerated charge carriers by using a ferroelectric material with permanent internal dipolar fields. This separation of the reaction sites may significantly increase the efficiency of the process. The present work compares the photochemical reactivities of ferroelectric and nonferroelectric materials (SrxBa1-xTiO 3, 0.0≤ x ≤1.0) with similar composition and structure. The reactivities are compared by measuring the color change of methylene blue dye after the aqueous dye solution reacts on the surface of ceramic sample pellets as a result of exposure to UV light. The reactivities are also compared by measuring the amount of silver that is formed when an aqueous AgNO3 solution photochemically reacts on the surface. The change in the color of the dye is measured by diffuse reflectance spectroscopy and absorbance measurements. The amount of silver is measured by atomic force microscopy. The photochemical reactivity of SrxBa1-xTiO3 shows a local maximum at the composition of the ferroelectric to non-ferroelectric transition. Also, the reactivities decrease as BaTiO3 and SrTiO3 become less pure. The dominant factors causing this trend in reactivities of SrxBa1-xTiO3 are the dielectric constant and alloy scattering. It is found that higher values of the dielectric constant increase the photochemical reactivity by enlarging the space charge region. The increase in alloy scattering in SrxBa1-xTiO 3 solid solutions as x increases from zero or decreases from 1, has adverse effect on reactivity. There are other factors such as ferroelectric polarization

  14. Photo-chemical transport modelling of tropospheric ozone: A review

    Science.gov (United States)

    Sharma, Sumit; Sharma, Prateek; Khare, Mukesh

    2017-06-01

    Ground level ozone (GLO), a secondary pollutant having adverse impact on human health, ecology, and agricultural productivity, apart from being a major contributor to global warming, has been a subject matter of several studies. In order to identify appropriate strategies to control GLO levels, accurate assessment and prediction is essential, for which elaborate simulation and modelling is required. Several studies have been undertaken in the past to simulate GLO levels at different scales and for various applications. It is important to evaluate these studies, widely spread over in literature. This paper aims to critically review various studies that have been undertaken, especially in the past 15 years (2000-15) to model GLO. The review has been done of the studies that range over different spatial scales - urban to regional and continental to global. It also includes a review of performance evaluation and sensitivity analysis of photo-chemical transport models in order to assess the extent of application of these models and their predictive capability. The review indicates following major findings: (a) models tend to over-estimate the night-time GLO concentrations due to limited titration of GLO with NO within the model; (b) dominance of contribution from far-off regional sources to average ozone concentration in the urban region and higher contribution of local sources during days of high ozone episodes; requiring strategies for controlling precursor emissions at both regional and local scales; (c) greater influence of NOx over VOC in export of ozone from urban regions due to shifting of urban plumes from VOC-sensitive regime to NOx-sensitive as they move out from city centres to neighbouring rural regions; (d) models with finer resolution inputs perform better to a certain extent, however, further improvement in resolutions (beyond 10 km) did not show improvement always; (e) future projections show an increase in GLO concentrations mainly due to rise in

  15. Photochemical and other air pollutants in South Holland

    Energy Technology Data Exchange (ETDEWEB)

    Posthumus, A.C.

    1975-01-01

    This year at fifteen places, regularly distributed over the industrial area west of Rotterdam, indicator plants for air pollution were again set out in the open. Tulip, gladiolus and freesia, indicators for HF, all demonstrated the same two sites to have maximum HF concentration. Spinach, an indicator for O/sub 3//SO/sub 2/, showed maximum injury in April and May and more south of the New Waterway than north of it. Medicago sativa, a plant species rather sensitive for SO/sub 2/ and O/sub 3/, showed little damage, and the reaction of petunia indicated a possible effect of ethylene only in a few cases. The photochemical air pollutant PAN caused in a few cases as well a slight injury to the indicator plants Urtica urens and Poa annua. The frequency of the injury to tobacco Bel W3 by O/sub 3//SO/sub 2/ was maximum during some periods in summer and autumn. This year again the effect of air pollution on growth and yield of tulips, tobacco and tomato plants was studied at six sites at the mouth of the Rhine with filtered and unfiltered greenhouses. The climatic conditions in these greenhouses were completely alike. Tulips in all the unfiltered greenhouses showed twice as heavy leaf injury as those in the filtered greenhouses. Tobacco plants had a higher average fresh and dry weight in the filtered greenhouses than in the unfiltered ones. The same usually held for tomato plants and also for the number of fruits and the average fresh and dry weight of tomato fruits.

  16. Snapshot of the Eukaryotic Gene Expression in Muskoxen Rumen—A Metatranscriptomic Approach

    Science.gov (United States)

    O'Toole, Nicholas; Barboza, Perry S.; Ungerfeld, Emilio; Leigh, Mary Beth; Selinger, L. Brent; Butler, Greg; Tsang, Adrian; McAllister, Tim A.; Forster, Robert J.

    2011-01-01

    Background Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. Methodology/Principal Findings In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus), with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. Conclusions/Significance The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes. PMID:21655220

  17. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

    Directory of Open Access Journals (Sweden)

    Meng Qi

    Full Text Available BACKGROUND: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus, with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6, GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. CONCLUSIONS/SIGNIFICANCE: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

  18. Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

    International Nuclear Information System (INIS)

    Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

    2011-01-01

    Based on the molecular architecture revealed by electron cryo-tomography, the mechanism of the bending motion of eukaryotic flagella/cilia is discussed. Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed

  19. Photochemically induced emission tuning of conductive polumers used in OLEDs

    Energy Technology Data Exchange (ETDEWEB)

    Vasilopoulou, M [NCSR ' Demokritos' , Institute of Microelectronics, POB 60228, 153 10 Agia Paraskevi, Attiki (Greece); Pistolis, G [Institute of Physical Chemistry, NCSR ' Demokritos' Athens 153 10 (Greece); Argitis, P [NCSR ' Demokritos' , Institute of Microelectronics, POB 60228, 153 10 Agia Paraskevi, Attiki (Greece)

    2005-01-01

    The present work focuses on the use of novel patterning technology schemes for the fabrication of OLED-based displays and in particular on the definition of two colour emitting pixels in one polymeric conducting layer. The approach adopted to this end is based on photochemically induced emition tuning. On the basis of this approach a novel photolithographic patterning technique was developed, aiming at the considerable simplification of the display fabrication process and on the performance improvement. We prepared electroluminescent devices that are emitting blue colour ({lambda}{sub max} 413 nm) with a turnon voltage about 12-15 V. In other devices we introduce a dispersed dye (1-[4-(dimethylamino)phenyl]-6-phenylhexatriene) and a series of photoacid generators (onium salts) in the polymeric layer and, by using an appropriate photochemical transformation through a photomask in a single layer, we were able to change the colour to desirable direction, since the parent compound and its photochemical product have distinguishable luminescence spectra (green and blue colour respectively). We were able to produce two of the three primary colours in a single layer of a conductive polymer by using a photochemical transformation based on photoacid induced emission change. A series of photoacid generators were evaluated.

  20. Photochemical processes and ozone production in Finnish conditions

    Energy Technology Data Exchange (ETDEWEB)

    Laurila, T.; Hakola, H. [Finnish Meteorological Inst., Helsinki (Finland). Air Quality Dept.

    1996-12-31

    Photochemical ozone production is observed in March-September. Highest ozone concentrations and production efficiencies are observed in spring in the northern parts and in summer in the southern parts of the country. VOC concentrations are relatively low compared to continental areas in general. During the growing season a substantial part of the total reactive mass of VOCs is of biogenic origin. Large forest areas absorb ozone substantially, decreasing the ambient ozone concentrations in central and northern parts of Finland where long-range transport of ozone is relatively important compared to local production. The aim of the work conducted at Finnish Meteorological Institute has been to characterise concentrations of photochemically active species in the boundary layer and their photochemical formation and deposition including the effects on vegetation. Also interactions between the boundary layer and free troposphere of ozone have been studied. In the future, fluxes of both biogenic species and air pollutants will be measured and the models will be further developed so that the photochemical and micrometeorological processes could be better understood

  1. Photochemical Aryl Radical Cyclizations to Give (E-3-Ylideneoxindoles

    Directory of Open Access Journals (Sweden)

    Michael Gurry

    2014-09-01

    Full Text Available (E-3-Ylideneoxindoles are prepared in methanol in reasonable to good yields, as adducts of photochemical 5-exo-trig of aryl radicals, in contrast to previously reported analogous radical cyclizations initiated by tris(trimethylsilylsilane and azo-initiators that gave reduced oxindole adducts.

  2. Photochemical processes and ozone production in Finnish conditions

    Energy Technology Data Exchange (ETDEWEB)

    Laurila, T; Hakola, H [Finnish Meteorological Inst., Helsinki (Finland). Air Quality Dept.

    1997-12-31

    Photochemical ozone production is observed in March-September. Highest ozone concentrations and production efficiencies are observed in spring in the northern parts and in summer in the southern parts of the country. VOC concentrations are relatively low compared to continental areas in general. During the growing season a substantial part of the total reactive mass of VOCs is of biogenic origin. Large forest areas absorb ozone substantially, decreasing the ambient ozone concentrations in central and northern parts of Finland where long-range transport of ozone is relatively important compared to local production. The aim of the work conducted at Finnish Meteorological Institute has been to characterise concentrations of photochemically active species in the boundary layer and their photochemical formation and deposition including the effects on vegetation. Also interactions between the boundary layer and free troposphere of ozone have been studied. In the future, fluxes of both biogenic species and air pollutants will be measured and the models will be further developed so that the photochemical and micrometeorological processes could be better understood

  3. Surface retention and photochemical reactivity of the diphenylether herbicide oxyfluorfen.

    Science.gov (United States)

    Scrano, Laura; Bufo, Sabino A; Cataldi, Tommaso R I; Albanis, Triantafyllos A

    2004-01-01

    The photochemical behavior of oxyfluorfen [2-chloro-1-(3-etoxy-4-nitrophenoxy)-4-(trifluoromethyl) benzene] on two Greek soils was investigated. Soils were sampled from Nea Malgara and Preveza regions, characterized by a different organic matter content. Soils were spiked with the diphenyl-ether herbicide and irradiation experiments were performed either in the laboratory with a solar simulator (xenon lamp) or outside, under natural sunlight irradiation; other soil samples were kept in the dark to control the retention reaction. Kinetic parameters of both retention and photochemical reactions were calculated using zero-, first- and second- (Langmuir-Hinshelwood) order equations, and best fit was checked through statistical analysis. The soil behaviors were qualitatively similar but quantitatively different, with the soil sampled from the Nea Malgara region much more sorbent as compared with Preveza soil. All studied reactions followed second-order kinetics and photochemical reactions were influenced by retaining capability of the soils. The contributions of the photochemical processes to the global dissipation rates were also calculated. Two main metabolites were identified as 2-chloro-1-(3-ethoxy-4-hydroxyphenoxy)-4-(trifluoromethyl)benzene and 2-chloro-1- (3-hydroxy-4-nitrophenoxy)-4-(trifluoromethyl)benzene.

  4. Photochemical Copper Coating on 3D Printed Thermoplastics

    Science.gov (United States)

    Yung, Winco K. C.; Sun, Bo; Huang, Junfeng; Jin, Yingdi; Meng, Zhengong; Choy, Hang Shan; Cai, Zhixiang; Li, Guijun; Ho, Cheuk Lam; Yang, Jinlong; Wong, Wai Yeung

    2016-08-01

    3D printing using thermoplastics has become very popular in recent years, however, it is challenging to provide a metal coating on 3D objects without using specialized and expensive tools. Herein, a novel acrylic paint containing malachite for coating on 3D printed objects is introduced, which can be transformed to copper via one-step laser treatment. The malachite containing pigment can be used as a commercial acrylic paint, which can be brushed onto 3D printed objects. The material properties and photochemical transformation processes have been comprehensively studied. The underlying physics of the photochemical synthesis of copper was characterized using density functional theory calculations. After laser treatment, the surface coating of the 3D printed objects was transformed to copper, which was experimentally characterized by XRD. 3D printed prototypes, including model of the Statue of Liberty covered with a copper surface coating and a robotic hand with copper interconnections, are demonstrated using this painting method. This composite material can provide a novel solution for coating metals on 3D printed objects. The photochemical reduction analysis indicates that the copper rust in malachite form can be remotely and photo-chemically reduced to pure copper with sufficient photon energy.

  5. Repair processes for photochemical damage in mammalian cells

    International Nuclear Information System (INIS)

    Cleaver, J.E.

    1974-01-01

    Repair processes for photochemical damage in cells following uv irradiation are reviewed. Cultured fibroblast cells from human patients with xeroderma pigmentosum were used as an example to illustrate aspects of repair of injuries to DNA and proteins. (250 references) (U.S.)

  6. Archaeal “Dark Matter” and the Origin of Eukaryotes

    Science.gov (United States)

    Williams, Tom A.; Embley, T. Martin

    2014-01-01

    Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis. PMID:24532674

  7. Eukaryotic systematics: a user's guide for cell biologists and parasitologists.

    Science.gov (United States)

    Walker, Giselle; Dorrell, Richard G; Schlacht, Alexander; Dacks, Joel B

    2011-11-01

    Single-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.

  8. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

    Directory of Open Access Journals (Sweden)

    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  9. Photochemical fate of beta-blockers in NOM enriched waters

    International Nuclear Information System (INIS)

    Wang, Ling; Xu, Haomin; Cooper, William J.; Song, Weihua

    2012-01-01

    Beta-blockers, prescribed for the treatment of high blood pressure and for long-term use after a heart attack, have been detected in surface and ground waters. This study examines the photochemical fate of three beta-blockers, atenolol, metoprolol, and nadolol. Hydrolysis accounted for minor losses of these beta-blockers in the pH range 4–10. The rate of direct photolysis at pH 7 in a solar simulator varied from 6.1 to 8.9 h −1 at pH 7. However, the addition of a natural organic matter (NOM) isolate enhanced the photochemical loss of all three compounds. Indirect photochemical fate, generally described by reactions with hydroxyl radical (·OH) and singlet oxygen ( 1 ΔO 2 ), and, the direct reaction with the triplet excited state, 3 NOM ⁎ , also varied but collectively appeared to be the major loss factor. Bimolecular reaction rate constants of the three beta-blockers with 1 ΔO 2 and ·OH were measured and accounted for 0.02–0.04% and 7.2–38.9% of their loss, respectively. These data suggest that the 3 NOM ⁎ contributed 50.6–85.4%. Experiments with various 3 NOM ⁎ quenchers supported the hypothesis that it was singly the most important reaction. Atenolol was chosen for more detailed investigation, with the photoproducts identified by LC–MS analysis. The results suggested that electron-transfer could be an important mechanism in photochemical fate of beta-blockers in the presence of NOM. - Highlights: ► Photochemical degradation of beta-blockers in the simulated natural waters. ► Reactive Oxygen Species play a minor role in the indirect photodegradation. ► The loss of beta-blockers results from direct reaction with 3 DOM ⁎ .

  10. EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

    Science.gov (United States)

    Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

    2017-08-01

    Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  11. Tracking the rise of eukaryotes to ecological dominance with zinc isotopes.

    Science.gov (United States)

    Isson, Terry T; Love, Gordon D; Dupont, Christopher L; Reinhard, Christopher T; Zumberge, Alex J; Asael, Dan; Gueguen, Bleuenn; McCrow, John; Gill, Ben C; Owens, Jeremy; Rainbird, Robert H; Rooney, Alan D; Zhao, Ming-Yu; Stueeken, Eva E; Konhauser, Kurt O; John, Seth G; Lyons, Timothy W; Planavsky, Noah J

    2018-06-05

    The biogeochemical cycling of zinc (Zn) is intimately coupled with organic carbon in the ocean. Based on an extensive new sedimentary Zn isotope record across Earth's history, we provide evidence for a fundamental shift in the marine Zn cycle ~800 million years ago. We discuss a wide range of potential drivers for this transition and propose that, within available constraints, a restructuring of marine ecosystems is the most parsimonious explanation for this shift. Using a global isotope mass balance approach, we show that a change in the organic Zn/C ratio is required to account for observed Zn isotope trends through time. Given the higher affinity of eukaryotes for Zn relative to prokaryotes, we suggest that a shift toward a more eukaryote-rich ecosystem could have provided a means of more efficiently sequestering organic-derived Zn. Despite the much earlier appearance of eukaryotes in the microfossil record (~1700 to 1600 million years ago), our data suggest a delayed rise to ecological prominence during the Neoproterozoic, consistent with the currently accepted organic biomarker records. © 2018 John Wiley & Sons Ltd.

  12. Photochemical and microbial alterations of DOM spectroscopic properties in the estuarine system Ria de Aveiro.

    Science.gov (United States)

    Santos, L; Santos, E B H; Dias, J M; Cunha, A; Almeida, A

    2014-08-01

    The influence of photochemical transformations of chromophoric dissolved organic matter (CDOM) on microbial communities was evaluated in the estuarine system Ria de Aveiro. Two sites, representative of the marine and brackish water zones of the estuary, were surveyed regularly in order to determine seasonal and vertical profiles of variation of CDOM properties. Optical parameters of CDOM indicative of aromaticity and molecular weight were used to establish CDOM sources, and microbial abundance and activity was characterized. Additionally, microcosm experiments were performed in order to simulate photochemical reactions of CDOM and to evaluate microbial responses to light-induced changes in CDOM composition. The CDOM of the two estuarine zones showed different spectral characteristics, with significantly higher values of the specific ultra-violet absorbance at 254 nm (SUVA254) (5.5 times) and of the absorption coefficient at 350 nm (a350) (12 times) and lower SR (S275-295/S350-400) ratio at brackish water compared with the marine zone, reflecting the different amounts and prevailing sources of organic matter, as well as distinct riverine and oceanic influences. At the marine zone, the abundance of bacteria and the activity of Leu-AMPase correlated with a350 and a254, suggesting a microbial contribution to the HMW CDOM pool. The irradiation of DOM resulted in a decrease of the values of a254 and a350 and an increase of the slope S275-295 and of the ratios E2 : E3 (a250/a365) and SR, which in turn increase its bioavailability. However, the extent of photoinduced transformations and microbial responses was dependent on the initial optical characteristics of CDOM. In Ria de Aveiro both photochemical and microbial processes yielded optical changes in CDOM and the overall results of these combined processes determine the fate of CDOM in the estuarine system and have an influence on local productivity and in adjacent coastal areas.

  13. Systems and methods for solar energy storage, transportation, and conversion utilizing photochemically active organometallic isomeric compounds and solid-state catalysts

    Science.gov (United States)

    Vollhardt, K. Peter C.; Segalman, Rachel A; Majumdar, Arunava; Meier, Steven

    2015-02-10

    A system for converting solar energy to chemical energy, and, subsequently, to thermal energy includes a light-harvesting station, a storage station, and a thermal energy release station. The system may include additional stations for converting the released thermal energy to other energy forms, e.g., to electrical energy and mechanical work. At the light-harvesting station, a photochemically active first organometallic compound, e.g., a fulvalenyl diruthenium complex, is exposed to light and is photochemically converted to a second, higher-energy organometallic compound, which is then transported to a storage station. At the storage station, the high-energy organometallic compound is stored for a desired time and/or is transported to a desired location for thermal energy release. At the thermal energy release station, the high-energy organometallic compound is catalytically converted back to the photochemically active organometallic compound by an exothermic process, while the released thermal energy is captured for subsequent use.

  14. Positive selection for unpreferred codon usage in eukaryotic genomes

    Directory of Open Access Journals (Sweden)

    Galagan James E

    2007-07-01

    Full Text Available Abstract Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral mutation and genetic drift. We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (Kp/Ku. Results Here we show that for some genes natural selection is indeed responsible for causing accelerated unpreferred codon substitution, and document the scope of this selection. In Cryptococcus and to a lesser extent Drosophila, we find many genes showing a statistically significant signal of selection for unpreferred codon usage in one or more lineages. We did not find evidence for this type of selection in Saccharomyces. The signal of positive selection observed from unpreferred synonymous codon substitutions is coincident in Cryptococcus and Drosophila with the distribution of upstream open reading frames (uORFs, another genic feature known to reduce translational efficiency. Functional enrichment analysis of genes exhibiting low Kp/Ku ratios reveals that genes in regulatory roles are particularly subject to this type of selection. Conclusion Through genome-wide scans, we find recent selection for unpreferred codon usage at approximately 1% of genetic loci in a Cryptococcus and several genes in Drosophila. Unpreferred codons can impede translation efficiency, and we find that genes with translation-impeding uORFs are enriched for this selection signal. We find that regulatory genes are particularly likely to be subject to selection for unpreferred codon usage. Given that expression noise can propagate through regulatory cascades, and that low translational efficiency can reduce expression noise, this finding supports the hypothesis that translational

  15. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

    Science.gov (United States)

    Riechmann, J L; Heard, J; Martin, G; Reuber, L; Jiang, C; Keddie, J; Adam, L; Pineda, O; Ratcliffe, O J; Samaha, R R; Creelman, R; Pilgrim, M; Broun, P; Zhang, J Z; Ghandehari, D; Sherman, B K; Yu, G

    2000-12-15

    The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

  16. Eukaryotic ribosome display with in situ DNA recovery.

    Science.gov (United States)

    He, Mingyue; Edwards, Bryan M; Kastelic, Damjana; Taussig, Michael J

    2012-01-01

    Ribosome display is a cell-free display technology for in vitro selection and optimisation of proteins from large diversified libraries. It operates through the formation of stable protein-ribosome-mRNA (PRM) complexes and selection of ligand-binding proteins, followed by DNA recovery from the selected genetic information. Both prokaryotic and eukaryotic ribosome display systems have been developed. In this chapter, we describe the eukaryotic rabbit reticulocyte method in which a distinct in situ single-primer RT-PCR procedure is used to recover DNA from the selected PRM complexes without the need for prior disruption of the ribosome.

  17. Characterization of prokaryotic and eukaryotic promoters usinghidden Markov models

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, Pierre; Brunak, Søren

    1996-01-01

    In this paper we utilize hidden Markov models (HMMs) and information theory to analyze prokaryotic and eukaryotic promoters. We perform this analysis with special emphasis on the fact that promoters are divided into a number of different classes, depending on which polymerase-associated factors...... that bind to them. We find that HMMs trained on such subclasses of Escherichia coli promoters (specifically, the so-called sigma-70 and sigma-54 classes) give an excellent classification of unknown promoters with respect to sigma-class. HMMs trained on eukaryotic sequences from human genes also model nicely...

  18. Characterization of prokaryotic and eukaryotic promoters using hidden Markov models

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, P.; Chauvin, Y.

    1996-01-01

    In this paper we utilize hidden Markov models (HMMs) and information theory to analyze prokaryotic and eukaryotic promoters. We perform this analysis with special emphasis on the fact that promoters are divided into a number of different classes, depending on which polymerase-associated factors...... that bind to them. We find that HMMs trained on such subclasses of Escherichia coli promoters (specifically, the so-called sigma 70 and sigma 54 classes) give an excellent classification of unknown promoters with respect to sigma-class. HMMs trained on eukaryotic sequences from human genes also model nicely...

  19. Unicellular eukaryotes as models in cell and molecular biology: critical appraisal of their past and future value.

    Science.gov (United States)

    Simon, Martin; Plattner, Helmut

    2014-01-01

    Unicellular eukaryotes have been appreciated as model systems for the analysis of crucial questions in cell and molecular biology. This includes Dictyostelium (chemotaxis, amoeboid movement, phagocytosis), Tetrahymena (telomere structure, telomerase function), Paramecium (variant surface antigens, exocytosis, phagocytosis cycle) or both ciliates (ciliary beat regulation, surface pattern formation), Chlamydomonas (flagellar biogenesis and beat), and yeast (S. cerevisiae) for innumerable aspects. Nowadays many problems may be tackled with "higher" eukaryotic/metazoan cells for which full genomic information as well as domain databases, etc., were available long before protozoa. Established molecular tools, commercial antibodies, and established pharmacology are additional advantages available for higher eukaryotic cells. Moreover, an increasing number of inherited genetic disturbances in humans have become elucidated and can serve as new models. Among lower eukaryotes, yeast will remain a standard model because of its peculiarities, including its reduced genome and availability in the haploid form. But do protists still have a future as models? This touches not only the basic understanding of biology but also practical aspects of research, such as fund raising. As we try to scrutinize, due to specific advantages some protozoa should and will remain favorable models for analyzing novel genes or specific aspects of cell structure and function. Outstanding examples are epigenetic phenomena-a field of rising interest. © 2014 Elsevier Inc. All rights reserved.

  20. Computational identification of candidate nucleotide cyclases in higher plants

    KAUST Repository

    Wong, Aloysius Tze; Gehring, Christoph A

    2013-01-01

    In higher plants guanylyl cyclases (GCs) and adenylyl cyclases (ACs) cannot be identified using BLAST homology searches based on annotated cyclic nucleotide cyclases (CNCs) of prokaryotes, lower eukaryotes, or animals. The reason is that CNCs

  1. An algorithm for detecting eukaryotic sequences in metagenomic ...

    Indian Academy of Sciences (India)

    species but also from accidental contamination from the genome of eukaryotic host cells. The latter scenario generally occurs in the case of host-associated metagenomes, e.g. microbes living in human gut. In such cases, one needs to identify and remove contaminating host DNA sequences, since the latter sequences will ...

  2. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae

    NARCIS (Netherlands)

    Wijffels, R.H.; Kruse, O.; Hellingwerf, K.J.

    2013-01-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments.Cyanobacteria are promising host organisms for

  3. A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

    Science.gov (United States)

    Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

    2013-01-01

    SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

  4. Eu-Detect: An algorithm for detecting eukaryotic sequences in ...

    Indian Academy of Sciences (India)

    Supplementary figure 1. Plots depicting the classification accuracy of Eu-Detect with various combinations of. 'cumulative sequence count' (40K, 50K, 60K, 70K, 80K) and 'coverage threshold' (20%, 30%, 40%, 50%, 60%, 70%,. 80%). While blue bars represent Eu-Detect's average classification accuracy with eukaryotic ...

  5. Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

    NARCIS (Netherlands)

    Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

    2010-01-01

    The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes.

  6. Modeling of photochemical air pollution in the Barcelona area with highly disaggregated anthropogenic and biogenic emissions

    International Nuclear Information System (INIS)

    Toll, I.; Baldasano, J.M.

    2000-01-01

    The city of Barcelona and its surrounding area, located in the western Mediterranean basin, can reach high levels of O 3 in spring and summertime. To study the origin of this photochemical pollution, a numerical modeling approach was adopted and the episode that took place between 3 and 5 August 1990 was chosen. The main meteorological mesoscale flows were reproduced with the meteorological non-hydrostatic mesoscale model MEMO for 5 August 1990, when weak pressure synoptic conditions took place. The emissions inventory was calculated with the EIM-LEM model, giving highly disaggregated anthropogenic and biogenic emissions in the zone studied, an 80 x 80 km 2 area around the city of Barcelona. Major sources of VOC were road traffic (51%) and vegetation (34%), while NO x were mostly emitted by road traffic (88%). However, emissions from some industrial stacks can be locally important and higher than those from road traffic. Photochemical simulation with the MARS model revealed that the combination of mesoscale wind flows and the above-mentioned local emissions is crucial in the production and transport of O 3 in the area. On the other hand, the geostrophic wind also played an important role in advecting the air masses away from the places O 3 had been generated. The model simulations were also evaluated by comparing meteorological measurements from nine surface stations and concentration measurements from five surface stations, and the results proved to be fairly satisfactory. (author)

  7. Role of nitrite in the photochemical formation of radicals in the snow.

    Science.gov (United States)

    Jacobi, Hans-Werner; Kleffmann, Jörg; Villena, Guillermo; Wiesen, Peter; King, Martin; France, James; Anastasio, Cort; Staebler, Ralf

    2014-01-01

    Photochemical reactions in snow can have an important impact on the composition of the atmosphere over snow-covered areas as well as on the composition of the snow itself. One of the major photochemical processes is the photolysis of nitrate leading to the formation of volatile nitrogen compounds. We report nitrite concentrations determined together with nitrate and hydrogen peroxide in surface snow collected at the coastal site of Barrow, Alaska. The results demonstrate that nitrite likely plays a significant role as a precursor for reactive hydroxyl radicals as well as volatile nitrogen oxides in the snow. Pollution events leading to high concentrations of nitrous acid in the atmosphere contributed to an observed increase in nitrite in the surface snow layer during nighttime. Observed daytime nitrite concentrations are much higher than values predicted from steady-state concentrations based on photolysis of nitrate and nitrite indicating that we do not fully understand the production of nitrite and nitrous acid in snow. The discrepancy between observed and expected nitrite concentrations is probably due to a combination of factors, including an incomplete understanding of the reactive environment and chemical processes in snow, and a lack of consideration of the vertical structure of snow.

  8. Molecular-beam studies of primary photochemical processes

    International Nuclear Information System (INIS)

    Lee, Y.T.

    1982-12-01

    Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser

  9. Dispersion and photochemical evolution of reactive pollutants in street canyons

    Science.gov (United States)

    Kwak, Kyung-Hwan; Baik, Jong-Jin; Lee, Kwang-Yeon

    2013-05-01

    Dispersion and photochemical evolution of reactive pollutants in street canyons with canyon aspect ratios of 1 and 2 are investigated using a computational fluid dynamics (CFD) model coupled with the carbon bond mechanism IV (CBM-IV). Photochemical ages of NOx and VOC are expressed as a function of the NO2-to-NOx and toluene-to-xylene ratios, respectively. These are found to be useful for analyzing the O3 and OH oxidation processes in the street canyons. The OH oxidation process (O3 oxidation process) is more pronounced in the upper (lower) region of the street canyon with a canyon aspect ratio of 2, which is characterized by more (less) aged air. In the upper region of the street canyon, O3 is chemically produced as well as transported downward across the roof level, whereas O3 is chemically reduced in the lower region of the street canyon. The O3 chemical production is generally favorable when the normalized photochemical ages of NOx and VOC are larger than 0.55 and 0.28, respectively. The sensitivities of O3 chemical characteristics to NOx and VOC emission rates, photolysis rate, and ambient wind speed are examined for the lower and upper regions of the street canyon with a canyon aspect ratio of 2. The O3 concentration and the O3 chemical production rate divided by the O3 concentration increase as the NOx emission rate decreases and the VOC emission rate and photolysis rate increase. The O3 concentration is less sensitive to the ambient wind speed than to other factors considered. The relative importance of the OH oxidation process compared to the O3 oxidation process increases with increasing NOx emission rate and photolysis rate and decreasing VOC emission rate. In this study, both O3 and OH oxidation processes are found to be important in street-canyon scale chemistry. The methodology of estimating the photochemical ages can potentially be adopted to neighborhood scale chemistry.

  10. Molecular-beam studies of primary photochemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T.

    1982-12-01

    Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser.

  11. Separation of the mercury isotopes by the indirect photochemical method

    International Nuclear Information System (INIS)

    Botter nee Bergheaud, F.; Scaringella nee Desnoyer, M.; Wacongne, M.

    1976-01-01

    A method of photochemical separation of the mercury isotopes by the so-called indirect route in which a gas stream of oxygen and butadiene containing a mixture of mercury isotopes is passed through one or a number of vessels placed in series. The gas stream is irradiated by a lamp containing mercury which is depleted in one or a number of the isotopes and said isotopes are recovered in a trap placed downstream of the vessel or vessels

  12. Uniting sex and eukaryote origins in an emerging oxygenic world.

    Science.gov (United States)

    Gross, Jeferson; Bhattacharya, Debashish

    2010-08-23

    Theories about eukaryote origins (eukaryogenesis) need to provide unified explanations for the emergence of diverse complex features that define this lineage. Models that propose a prokaryote-to-eukaryote transition are gridlocked between the opposing "phagocytosis first" and "mitochondria as seed" paradigms, neither of which fully explain the origins of eukaryote cell complexity. Sex (outcrossing with meiosis) is an example of an elaborate trait not yet satisfactorily addressed in theories about eukaryogenesis. The ancestral nature of meiosis and its dependence on eukaryote cell biology suggest that the emergence of sex and eukaryogenesis were simultaneous and synergic and may be explained by a common selective pressure. We propose that a local rise in oxygen levels, due to cyanobacterial photosynthesis in ancient Archean microenvironments, was highly toxic to the surrounding biota. This selective pressure drove the transformation of an archaeal (archaebacterial) lineage into the first eukaryotes. Key is that oxygen might have acted in synergy with environmental stresses such as ultraviolet (UV) radiation and/or desiccation that resulted in the accumulation of reactive oxygen species (ROS). The emergence of eukaryote features such as the endomembrane system and acquisition of the mitochondrion are posited as strategies to cope with a metabolic crisis in the cell plasma membrane and the accumulation of ROS, respectively. Selective pressure for efficient repair of ROS/UV-damaged DNA drove the evolution of sex, which required cell-cell fusions, cytoskeleton-mediated chromosome movement, and emergence of the nuclear envelope. Our model implies that evolution of sex and eukaryogenesis were inseparable processes. Several types of data can be used to test our hypothesis. These include paleontological predictions, simulation of ancient oxygenic microenvironments, and cell biological experiments with Archaea exposed to ROS and UV stresses. Studies of archaeal conjugation

  13. Patterns of intron gain and conservation in eukaryotic genes

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2007-10-01

    Full Text Available Abstract Background: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions. Results: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only ~8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs. Conclusion: We obtained robust estimates of the contribution of parallel gain to the observed

  14. A plasmaless, photochemical etch process for porous organosilicate glass films

    Science.gov (United States)

    Ryan, E. Todd; Molis, Steven E.

    2017-12-01

    A plasmaless, photochemical etch process using ultraviolet (UV) light in the presence of NH3 or O2 etched porous organosilicate glass films, also called pSiCOH films, in a two-step process. First, a UV/NH3 or UV/O2 treatment removed carbon (mostly methyl groups bonded to silicon) from a pSiCOH film by demethylation to a depth determined by the treatment exposure time. Second, aqueous HF was used to selectively remove the demethylated layer of the pSiCOH film leaving the methylated layer below. UV in the presence of inert gas or H2 did not demethylate the pSiCOH film. The depth of UV/NH3 demethylation followed diffusion limited kinetics and possible mechanisms of demethylation are presented. Unlike reactive plasma processes, which contain ions that can damage surrounding structures during nanofabrication, the photochemical etch contains no damaging ions. Feasibility of the photochemical etching was shown by comparing it to a plasma-based process to remove the pSiCOH dielectric from between Cu interconnect lines, which is a critical step during air gap fabrication. The findings also expand our understanding of UV photon interactions in pSiCOH films that may contribute to plasma-induced damage to pSiCOH films.

  15. The chitosan - Porphyrazine hybrid materials and their photochemical properties.

    Science.gov (United States)

    Chełminiak-Dudkiewicz, Dorota; Ziegler-Borowska, Marta; Stolarska, Magdalena; Sobotta, Lukasz; Falkowski, Michal; Mielcarek, Jadwiga; Goslinski, Tomasz; Kowalonek, Jolanta; Węgrzynowska-Drzymalska, Katarzyna; Kaczmarek, Halina

    2018-04-01

    Three magnesium sulfanyl porphyrazines differing in the size of peripheral substituents (3,5-dimethoxybenzylsulfanyl, (3,5-dimethoxybenzyloxy)benzylsulfanyl, 3,5-bis[(3,5-bis[(3,5-dimethoxybenzyloxy)benzyloxy]benzylsulfanyl) were exposed to visible and ultraviolet radiation (UV A + B + C) in order to determine their photochemical properties. The course of photochemical reactions in dimethylformamide solutions and the ability of the systems to generate singlet oxygen were studied by UV-Vis spectroscopy, which additionally gave information on aggregation processes. The porphyrazines were found to be stable upon visible light irradiation conditions, but when exposed to high energy UV radiation, the efficient photodegradation of these macrocycles was observed. Therefore, these three magnesium sulfanyl porphyrazines were incorporated into chitosan matrix. The obtained thin films of chitosan doped with porphyrazines were subjected to polychromatic UV-radiation and studied by spectroscopic methods (UV-Vis, FTIR), scanning electron microscopy (SEM) and atomic force microscopy (AFM). Application of chitosan as a polymer matrix for porphyrazines was found to be successful method that effectively stopped the unwelcome degradation of macrocycles, thus worth considering for their photoprotection. In addition, the surface properties of the hybrid material were determined by contact angle measurements and calculation of surface free energy. Intermolecular interactions between these novel porphyrazines and chitosan were detected. The mechanism of photochemical reactions occurring in studied systems has been discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Volatile organic compounds (VOCs) in photochemically aged air from the eastern and western Mediterranean

    Science.gov (United States)

    Derstroff, Bettina; Hüser, Imke; Bourtsoukidis, Efstratios; Crowley, John N.; Fischer, Horst; Gromov, Sergey; Harder, Hartwig; Janssen, Ruud H. H.; Kesselmeier, Jürgen; Lelieveld, Jos; Mallik, Chinmay; Martinez, Monica; Novelli, Anna; Parchatka, Uwe; Phillips, Gavin J.; Sander, Rolf; Sauvage, Carina; Schuladen, Jan; Stönner, Christof; Tomsche, Laura; Williams, Jonathan

    2017-08-01

    During the summertime CYPHEX campaign (CYprus PHotochemical EXperiment 2014) in the eastern Mediterranean, multiple volatile organic compounds (VOCs) were measured from a 650 m hilltop site in western Cyprus (34° 57' N/32° 23' E). Periodic shifts in the northerly Etesian winds resulted in the site being alternately impacted by photochemically processed emissions from western (Spain, France, Italy) and eastern (Turkey, Greece) Europe. Furthermore, the site was situated within the residual layer/free troposphere during some nights which were characterized by high ozone and low relative humidity levels. In this study we examine the temporal variation of VOCs at the site. The sparse Mediterranean scrub vegetation generated diel cycles in the reactive biogenic hydrocarbon isoprene, from very low values at night to a diurnal median level of 80-100 pptv. In contrast, the oxygenated volatile organic compounds (OVOCs) methanol and acetone exhibited weak diel cycles and were approximately an order of magnitude higher in mixing ratio (ca. 2.5-3 ppbv median level by day, range: ca. 1-8 ppbv) than the locally emitted isoprene and aromatic compounds such as benzene and toluene. Acetic acid was present at mixing ratios between 0.05 and 4 ppbv with a median level of ca. 1.2 ppbv during the daytime. When data points directly affected by the residual layer/free troposphere were excluded, the acid followed a pronounced diel cycle, which was influenced by various local effects including photochemical production and loss, direct emission, dry deposition and scavenging from advecting air in fog banks. The Lagrangian model FLEXPART was used to determine transport patterns and photochemical processing times (between 12 h and several days) of air masses originating from eastern and western Europe. Ozone and many OVOC levels were ˜ 20 and ˜ 30-60 % higher, respectively, in air arriving from the east. Using the FLEXPART calculated transport time, the contribution of photochemical

  17. Volatile organic compounds (VOCs in photochemically aged air from the eastern and western Mediterranean

    Directory of Open Access Journals (Sweden)

    B. Derstroff

    2017-08-01

    Full Text Available During the summertime CYPHEX campaign (CYprus PHotochemical EXperiment 2014 in the eastern Mediterranean, multiple volatile organic compounds (VOCs were measured from a 650 m hilltop site in western Cyprus (34° 57′ N/32° 23′ E. Periodic shifts in the northerly Etesian winds resulted in the site being alternately impacted by photochemically processed emissions from western (Spain, France, Italy and eastern (Turkey, Greece Europe. Furthermore, the site was situated within the residual layer/free troposphere during some nights which were characterized by high ozone and low relative humidity levels. In this study we examine the temporal variation of VOCs at the site. The sparse Mediterranean scrub vegetation generated diel cycles in the reactive biogenic hydrocarbon isoprene, from very low values at night to a diurnal median level of 80–100 pptv. In contrast, the oxygenated volatile organic compounds (OVOCs methanol and acetone exhibited weak diel cycles and were approximately an order of magnitude higher in mixing ratio (ca. 2.5–3 ppbv median level by day, range: ca. 1–8 ppbv than the locally emitted isoprene and aromatic compounds such as benzene and toluene. Acetic acid was present at mixing ratios between 0.05 and 4 ppbv with a median level of ca. 1.2 ppbv during the daytime. When data points directly affected by the residual layer/free troposphere were excluded, the acid followed a pronounced diel cycle, which was influenced by various local effects including photochemical production and loss, direct emission, dry deposition and scavenging from advecting air in fog banks. The Lagrangian model FLEXPART was used to determine transport patterns and photochemical processing times (between 12 h and several days of air masses originating from eastern and western Europe. Ozone and many OVOC levels were  ∼  20 and  ∼  30–60 % higher, respectively, in air arriving from the east. Using the FLEXPART

  18. Photochemical fate of beta-blockers in NOM enriched waters

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ling; Xu, Haomin; Cooper, William J. [Urban Water Research Center, Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA 92697-2175 (United States); Song, Weihua, E-mail: wsong@fudan.edu.cn [Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China)

    2012-06-01

    Beta-blockers, prescribed for the treatment of high blood pressure and for long-term use after a heart attack, have been detected in surface and ground waters. This study examines the photochemical fate of three beta-blockers, atenolol, metoprolol, and nadolol. Hydrolysis accounted for minor losses of these beta-blockers in the pH range 4-10. The rate of direct photolysis at pH 7 in a solar simulator varied from 6.1 to 8.9 h{sup -1} at pH 7. However, the addition of a natural organic matter (NOM) isolate enhanced the photochemical loss of all three compounds. Indirect photochemical fate, generally described by reactions with hydroxyl radical ({center_dot}OH) and singlet oxygen ({sup 1}{Delta}O{sub 2}), and, the direct reaction with the triplet excited state, {sup 3}NOM{sup Low-Asterisk }, also varied but collectively appeared to be the major loss factor. Bimolecular reaction rate constants of the three beta-blockers with {sup 1}{Delta}O{sub 2} and {center_dot}OH were measured and accounted for 0.02-0.04% and 7.2-38.9% of their loss, respectively. These data suggest that the {sup 3}NOM{sup Low-Asterisk} contributed 50.6-85.4%. Experiments with various {sup 3}NOM{sup Low-Asterisk} quenchers supported the hypothesis that it was singly the most important reaction. Atenolol was chosen for more detailed investigation, with the photoproducts identified by LC-MS analysis. The results suggested that electron-transfer could be an important mechanism in photochemical fate of beta-blockers in the presence of NOM. - Highlights: Black-Right-Pointing-Pointer Photochemical degradation of beta-blockers in the simulated natural waters. Black-Right-Pointing-Pointer Reactive Oxygen Species play a minor role in the indirect photodegradation. Black-Right-Pointing-Pointer The loss of beta-blockers results from direct reaction with {sup 3}DOM{sup Low-Asterisk }.

  19. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.

    Science.gov (United States)

    Amoutzias, Gregory D; Robertson, David L; Oliver, Stephen G; Bornberg-Bauer, Erich

    2004-03-01

    By combining phylogenetic, proteomic and structural information, we have elucidated the evolutionary driving forces for the gene-regulatory interaction networks of basic helix-loop-helix transcription factors. We infer that recurrent events of single-gene duplication and domain rearrangement repeatedly gave rise to distinct networks with almost identical hub-based topologies, and multiple activators and repressors. We thus provide the first empirical evidence for scale-free protein networks emerging through single-gene duplications, the dominant importance of molecular modularity in the bottom-up construction of complex biological entities, and the convergent evolution of networks.

  20. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes

    OpenAIRE

    Amoutzias, Gregory D; Robertson, David L; Oliver, Stephen G; Bornberg-Bauer, Erich

    2004-01-01

    By combining phylogenetic, proteomic and structural information, we have elucidated the evolutionary driving forces for the gene-regulatory interaction networks of basic helix–loop–helix transcription factors. We infer that recurrent events of single-gene duplication and domain rearrangement repeatedly gave rise to distinct networks with almost identical hub-based topologies, and multiple activators and repressors. We thus provide the first empirical evidence for scale-free protein networks e...

  1. Please do not recycle! Translation reinitiation in microbes and higher eukaryotes

    Czech Academy of Sciences Publication Activity Database

    Gunišová, Stanislava; Hronová, Vladislava; Mohammad, Mahabub Pasha; Hinnebusch, A.G.; Valášek, Leoš Shivaya

    2018-01-01

    Roč. 42, č. 2 (2018), s. 165-192 E-ISSN 1574-6976 R&D Projects: GA ČR GA15-10116S EU Projects: Wellcome Trust(GB) 090812/B/09/Z Institutional support: RVO:61388971 Keywords : translation reinitiation * termination-reinitiation * uORF Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology

  2. Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes

    NARCIS (Netherlands)

    Galluzzi, L.; Aaronson, S. A.; Abrams, J.; Alnemri, E. S.; Andrews, D. W.; Baehrecke, E. H.; Bazan, N. G.; Blagosklonny, M. V.; Blomgren, K.; Borner, C.; Bredesen, D. E.; Brenner, C.; Castedo, M.; Cidlowski, J. A.; Ciechanover, A.; Cohen, G. M.; de Laurenzi, V.; de Maria, R.; Deshmukh, M.; Dynlacht, B. D.; El-Deiry, W. S.; Flavell, R. A.; Fulda, S.; Garrido, C.; Golstein, P.; Gougeon, M.-L.; Green, D. R.; Gronemeyer, H.; Hajnóczky, G.; Hardwick, J. M.; Hengartner, M. O.; Ichijo, H.; Jäättelä, M.; Kepp, O.; Kimchi, A.; Klionsky, D. J.; Knight, R. A.; Kornbluth, S.; Kumar, S.; Levine, B.; Lipton, S. A.; Lugli, E.; Madeo, F.; Malorni, W.; Marine, J.-Cw; Martin, S. J.; Medema, J. P.; Mehlen, P.; Melino, G.; Moll, U. M.; Morselli, E.; Nagata, S.; Nicholson, D. W.; Nicotera, P.; Nuñez, G.; Oren, M.; Penninger, J.; Pervaiz, S.; Peter, M. E.; Piacentini, M.; Prehn, J. H. M.; Puthalakath, H.; Rabinovich, G. A.; Rizzuto, R.; Rodrigues, C. M. P.; Rubinsztein, D. C.; Rudel, T.; Scorrano, L.; Simon, H.-U.; Steller, H.; Tschopp, J.; Tsujimoto, Y.; Vandenabeele, P.; Vitale, I.; Vousden, K. H.; Youle, R. J.; Yuan, J.; Zhivotovsky, B.; Kroemer, G.

    2009-01-01

    Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous

  3. Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes.

    Science.gov (United States)

    Galluzzi, L; Aaronson, S A; Abrams, J; Alnemri, E S; Andrews, D W; Baehrecke, E H; Bazan, N G; Blagosklonny, M V; Blomgren, K; Borner, C; Bredesen, D E; Brenner, C; Castedo, M; Cidlowski, J A; Ciechanover, A; Cohen, G M; De Laurenzi, V; De Maria, R; Deshmukh, M; Dynlacht, B D; El-Deiry, W S; Flavell, R A; Fulda, S; Garrido, C; Golstein, P; Gougeon, M-L; Green, D R; Gronemeyer, H; Hajnóczky, G; Hardwick, J M; Hengartner, M O; Ichijo, H; Jäättelä, M; Kepp, O; Kimchi, A; Klionsky, D J; Knight, R A; Kornbluth, S; Kumar, S; Levine, B; Lipton, S A; Lugli, E; Madeo, F; Malomi, W; Marine, J-C W; Martin, S J; Medema, J P; Mehlen, P; Melino, G; Moll, U M; Morselli, E; Nagata, S; Nicholson, D W; Nicotera, P; Nuñez, G; Oren, M; Penninger, J; Pervaiz, S; Peter, M E; Piacentini, M; Prehn, J H M; Puthalakath, H; Rabinovich, G A; Rizzuto, R; Rodrigues, C M P; Rubinsztein, D C; Rudel, T; Scorrano, L; Simon, H-U; Steller, H; Tschopp, J; Tsujimoto, Y; Vandenabeele, P; Vitale, I; Vousden, K H; Youle, R J; Yuan, J; Zhivotovsky, B; Kroemer, G

    2009-08-01

    Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous implications for the development of novel therapeutic strategies. It is, therefore, of utmost importance to standardize the experimental procedures that identify dying and dead cells in cell cultures and/or in tissues, from model organisms and/or humans, in healthy and/or pathological scenarios. Thus far, dozens of methods have been proposed to quantify cell death-related parameters. However, no guidelines exist regarding their use and interpretation, and nobody has thoroughly annotated the experimental settings for which each of these techniques is most appropriate. Here, we provide a nonexhaustive comparison of methods to detect cell death with apoptotic or nonapoptotic morphologies, their advantages and pitfalls. These guidelines are intended for investigators who study cell death, as well as for reviewers who need to constructively critique scientific reports that deal with cellular demise. Given the difficulties in determining the exact number of cells that have passed the point-of-no-return of the signaling cascades leading to cell death, we emphasize the importance of performing multiple, methodologically unrelated assays to quantify dying and dead cells.

  4. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

    NARCIS (Netherlands)

    Klionsky, Daniel J; Abeliovich, Hagai; Agostinis, Patrizia; Agrawal, Devendra K; Aliev, Gjumrakch; Askew, David S; Baba, Misuzu; Baehrecke, Eric H; Bahr, Ben A; Ballabio, Andrea; Bamber, Bruce A; Bassham, Diane C; Bergamini, Ettore; Bi, Xiaoning; Biard-Piechaczyk, Martine; Blum, Janice S; Bredesen, Dale E; Brodsky, Jeffrey L; Brumell, John H; Brunk, Ulf T; Bursch, Wilfried; Camougrand, Nadine; Cebollero, Eduardo; Cecconi, Francesco; Chen, Yingyu; Chin, Lih-Shen; Choi, Augustine; Chu, Charleen T; Chung, Jongkyeong; Clarke, Peter G H; Clark, Robert S B; Clarke, Steven G; Clavé, Corinne; Cleveland, John L; Codogno, Patrice; Colombo, María I; Coto-Montes, Ana; Cregg, James M; Cuervo, Ana Maria; Debnath, Jayanta; Demarchi, Francesca; Dennis, Patrick B; Dennis, Phillip A; Deretic, Vojo; Devenish, Rodney J; Di Sano, Federica; Dice, J Fred; Difiglia, Marian; Dinesh-Kumar, Savithramma; Distelhorst, Clark W; Djavaheri-Mergny, Mojgan; Dorsey, Frank C; Dröge, Wulf; Dron, Michel; Dunn, William A; Duszenko, Michael; Eissa, N Tony; Elazar, Zvulun; Esclatine, Audrey; Eskelinen, Eeva-Liisa; Fésüs, László; Finley, Kim D; Fuentes, José M; Fueyo, Juan; Fujisaki, Kozo; Galliot, Brigitte; Gao, Fen-Biao; Gewirtz, David A; Gibson, Spencer B; Gohla, Antje; Goldberg, Alfred L; Gonzalez, Ramon; González-Estévez, Cristina; Gorski, Sharon; Gottlieb, Roberta A; Häussinger, Dieter; He, You-Wen; Heidenreich, Kim; Hill, Joseph A; Høyer-Hansen, Maria; Hu, Xun; Huang, Wei-Pang; Iwasaki, Akiko; Jäättelä, Marja; Jackson, William T; Jiang, Xuejun; Jin, Shengkan; Johansen, Terje; Jung, Jae U; Kadowaki, Motoni; Kang, Chanhee; Kelekar, Ameeta; Kessel, David H; Kiel, Jan A K W; Kim, Hong Pyo; Kimchi, Adi; Kinsella, Timothy J; Kiselyov, Kirill; Kitamoto, Katsuhiko; Knecht, Erwin; Komatsu, Masaaki; Kominami, Eiki; Kondo, Seiji; Kovács, Attila L; Kroemer, Guido; Kuan, Chia-Yi; Kumar, Rakesh; Kundu, Mondira; Landry, Jacques; Laporte, Marianne; Le, Weidong; Lei, Huan-Yao; Lenardo, Michael J; Levine, Beth; Lieberman, Andrew; Lim, Kah-Leong; Lin, Fu-Cheng; Liou, Willisa; Liu, Leroy F; Lopez-Berestein, Gabriel; López-Otín, Carlos; Lu, Bo; Macleod, Kay F; Malorni, Walter; Martinet, Wim; Matsuoka, Ken; Mautner, Josef; Meijer, Alfred J; Meléndez, Alicia; Michels, Paul; Miotto, Giovanni; Mistiaen, Wilhelm P; Mizushima, Noboru; Mograbi, Baharia; Monastyrska, Iryna; Moore, Michael N; Moreira, Paula I; Moriyasu, Yuji; Motyl, Tomasz; Münz, Christian; Murphy, Leon O; Naqvi, Naweed I; Neufeld, Thomas P; Nishino, Ichizo; Nixon, Ralph A; Noda, Takeshi; Nürnberg, Bernd; Ogawa, Michinaga; Oleinick, Nancy L; Olsen, Laura J; Ozpolat, Bulent; Paglin, Shoshana; Palmer, Glen E; Papassideri, Issidora; Parkes, Miles; Perlmutter, David H; Perry, George; Piacentini, Mauro; Pinkas-Kramarski, Ronit; Prescott, Mark; Proikas-Cezanne, Tassula; Raben, Nina; Rami, Abdelhaq; Reggiori, Fulvio; Rohrer, Bärbel; Rubinsztein, David C; Ryan, Kevin M; Sadoshima, Junichi; Sakagami, Hiroshi; Sakai, Yasuyoshi; Sandri, Marco; Sasakawa, Chihiro; Sass, Miklós; Schneider, Claudio; Seglen, Per O; Seleverstov, Oleksandr; Settleman, Jeffrey; Shacka, John J; Shapiro, Irving M; Sibirny, Andrei; Silva-Zacarin, Elaine C M; Simon, Hans-Uwe; Simone, Cristiano; Simonsen, Anne; Smith, Mark A; Spanel-Borowski, Katharina; Srinivas, Vickram; Steeves, Meredith; Stenmark, Harald; Stromhaug, Per E; Subauste, Carlos S; Sugimoto, Seiichiro; Sulzer, David; Suzuki, Toshihiko; Swanson, Michele S; Tabas, Ira; Takeshita, Fumihiko; Talbot, Nicholas J; Tallóczy, Zsolt; Tanaka, Keiji; Tanaka, Kozo; Tanida, Isei; Taylor, Graham S; Taylor, J Paul; Terman, Alexei; Tettamanti, Gianluca; Thompson, Craig B; Thumm, Michael; Tolkovsky, Aviva M; Tooze, Sharon A; Truant, Ray; Tumanovska, Lesya V; Uchiyama, Yasuo; Ueno, Takashi; Uzcátegui, Néstor L; van der Klei, Ida J; Vaquero, Eva C; Vellai, Tibor; Vogel, Michael W; Wang, Hong-Gang; Webster, Paul; Wiley, John W; Xi, Zhijun; Xiao, Gutian; Yahalom, Joachim; Yang, Jin-Ming; Yap, George; Yin, Xiao-Ming; Yoshimori, Tamotsu; Yu, Li; Yue, Zhenyu; Yuzaki, Michisuke; Zabirnyk, Olga; Zheng, Xiaoxiang; Zhu, Xiongwei; Deter, Russell L; Reggiori, Fulvio

    2008-01-01

    Research in autophagy continues to accelerate, and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used

  5. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

    NARCIS (Netherlands)

    Klionsky, Daniel J.; Abeliovich, Hagai; Agostinis, Patrizia; Agrawal, Devendra K.; Aliev, Giumrakch; Askew, David S.; Baba, Misuzu; Baehrecke, Eric H.; Bahr, Ben A.; Ballabio, Andrea; Bamber, Bruce A.; Bassham, Diane C.; Bergamini, Ettore; Bi, Xiaoning; Biard-Piechaczyk, Martine; Blum, Janice S.; Breclesen, Dale E.; Brodsky, Jeffrey L.; Brumell, John H.; Brunk, Ulf T.; Bursch, Wilfried; Camougrand, Nadine; Cebollero, Eduardo; Cecconi, Francesco; Chen, Yingyu; Chin, Lih-Shen; Choi, Augustine; Chu, Charleen T.; Chung, Jongkyeong; Clarke, Peter G. H.; Clark, Robert S. B.; Clarke, Steven G.; Clave, Corinne; Cleveland, John L.; Codogno, Patrice; Colombo, Maria I.; Coto-Montes, Ana; Cregg, James M.; Cuervo, Ana Maria; Debnath, Jayanta; Demarchi, Francesca; Dennis, Patrick B.; Dennis, Phillip A.; Deretic, Vojo; Devenish, Rodney J.; Di Sano, Federica; Dice, J. Fred; Difiglia, Marian; Dinesh-Kumar, Savithramma; Distelhorst, Clark W.; Djavaheri-Mergny, Mojgan; Dorsey, Frank C.; Droege, Wulf; Dron, Michel; Dunn, William A.; Duszenko, Michael; Eissa, N. Tony; Elazar, Zvulun; Esclatine, Audrey; Eskelinen, Eeva-Liisa; Fesues, Laszlo; Finley, Kim D.; Fuentes, Jose M.; Fueyo, Juan; Fujisaki, Kozo; Galliot, Brigitte; Gao, Fen-Biao; Gewirtz, David A.; Gibson, Spencer B.; Gohla, Antje; Goldberg, Alfred L.; Gonzalez, Ramon; Gonzalez-Estevez, Cristina; Gorski, Sharon; Gottlieb, Roberta A.; Haussinger, Dieter; He, You-Wen; Heidenreich, Kim; Hill, Joseph A.; Hoyer-Hansen, Maria; Hu, Xun; Huang, Wei-Pang; Iwasaki, Akiko; Jaattela, Marja; Jackson, William T.; Jiang, Xuejun; Jin, Shengkan; Johansen, Terje; Jung, Jae U.; Kadowaki, Motoni; Kang, Chanhee; Kelekar, Ameeta; Kessel, David H.; Kiel, Jan A. K. W.; Kim, Hong Pyo; Kimchi, Adi; Kinsella, Timothy J.; Kiselyov, Kirill; Kitamoto, Katsuhiko; Knecht, Erwin; Komatsu, Masaaki; Kominami, Eiki; Konclo, Seiji; Kovacs, Attila L.; Kroemer, Guido; Kuan, Chia-Yi; Kumar, Rakesh; Kundu, Mondira; Landry, Jacques; Laporte, Marianne; Le, Weidong; Lei, Huan-Yao; Lenardo, Michael J.; Levine, Beth; Lieberman, Andrew; Lim, Kah-Leong; Lin, Fu-Cheng; Liou, Willisa; Liu, Leroy F.; Lopez-Berestein, Gabriel; Lopez-Otin, Carlos; Lu, Bo; Macleod, Kay F.; Malorni, Walter; Martinet, Wim; Matsuoka, Ken; Mautner, Josef; Meijer, Alfred J.; Melendez, Alicia; Michels, Paul; Miotto, Giovanni; Mistiaen, Wilhelm P.; Mizushima, Noboru; Mograbi, Baharia; Monastyrska, Iryna; Moore, Michael N.; Moreira, Paula I.; Moriyasu, Yuji; Motyl, Tomasz; Muenz, Christian; Murphy, Leon O.; Naqvi, Naweed I.; Neufeld, Thomas P.; Nishino, Ichizo; Nixon, Ralph A.; Noda, Takeshi; Nuernberg, Bernd; Ogawa, Michinaga; Oleinick, Nancy L.; Olsen, Laura J.; Ozpolat, Bulent; Paglin, Shoshana; Palmer, Glen E.; Papassideri, Issidora; Parkes, Miles; Perlmutter, David H.; Perry, George; Piacentini, Mauro; Pinkas-Kramarski, Ronit; Prescott, Mark; Proikas-Cezanne, Tassula; Raben, Nina; Rami, Abdelhaq; Reggiori, Fulvio; Rohrer, Baerbel; Rubinsztein, David C.; Ryan, Kevin M.; Sadoshima, Junichi; Sakagami, Hiroshi; Sakai, Yasuyoshi; Sandri, Marco; Sasakawa, Chihiro; Sass, Miklos; Schneider, Claudio; Seglen, Per O.; Seleverstov, Oleksandr; Settleman, Jeffre; Shacka, John J.; Shapiro, Irving M.; Sibirny, Andrei; Silva-Zacarin, Elaine C. M.; Simon, Hans-Uwe; Simone, Cristiano; Simonsen, Anne; Smith, Mark A.; Spanel-Borowski, Katharina; Srinivas, Vickram; Steeves, Meredith; Stenmark, Harald; Stromhaug, Per E.; Subauste, Carlos S.; Sugimoto, Seiichiro; Sulzer, David; Suzuki, Toshihiko; Swanson, Michele S.; Takeshita, Fumihiko; Talbot, Nicholas. J.; Talloczy, Zsolt; Tanaka, Keiji; Tanaka, Kozo; Tanida, Isei; Taylor, Graham S.; Taylor, J. Paul; Terman, Alexei; Tettamanti, Gianluca; Thompson, Craig B.; Thumm, Michael; Tolkovsky, Aviva M.; Tooze, Sharon A.; Truant, Ray; Tumanovska, Lesya V.; Uchiyama, Yasuo; Ueno, Takashi; Uzcategui, Nestor L.; van der Klei, Ida; Vaquero, Eva C.; Vellai, Tibor; Vogel, Michael W.; Wang, Hong-Gang; Webster, Paul; Wiley, John W.; Xi, Zhijun; Xiao, Gutian; Yahalom, Joachim; Yang, Jin-Ming; Yap, George; Yin, Xiao-Min; Yoshimori, Tamotsu; Yu, Li; Yue, Zhenyu; Yuzaki, Michisuke; Zabirnyk, Olga; Zheng, Xiaoxiang; Zhu, Xiongwei; Deter, Russell L.; Tabas, Ira

    2008-01-01

    Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used

  6. [PS II photochemical efficiency in flag leaf of wheat varieties and its adaptation to strong sun- light intensity on farmland of Xiangride in Qinghai Province, Northwest China].

    Science.gov (United States)

    Shi, Sheng-Bo; Chen, Wen-Jie; Shi, Rui; Li, Miao; Zhang, Huai-Gang; Sun, Ya-Nan

    2014-09-01

    Taking four wheat varieties developed by Northwest Institute of Plateau Biology, Chinese Academy of Sciences, as test materials, with the measurement of content of photosynthetic pigments, leaf area, fresh and dry mass of flag leaf, the PS II photochemistry efficiency of abaxial and adaxial surface of flag leaf and its adaptation to strong solar radiation during the period of heading stage in Xiangride region were investigated with the pulse-modulated in-vivo chlorophyll fluorescence technique. The results indicated that flag leaf angle mainly grew in horizontal state in Gaoyuan 314, Gaoyuan 363 and Gaoyuan 584, and mainly in vertical state in Gaoyuan 913 because of its smaller leaf area and larger width. Photosynthetic pigments were different among the 4 varieties, and positively correlated with intrinsic PS II photochemistry efficiencies (Fv/Fm). In clear days, especially at noon, the photosynthetic photoinhibition was more serious in abaxial surface of flag leaf due to directly facing the solar radiation, but it could recover after reduction of sunlight intensity in the afternoon, which meant that no inactive damage happened in PS II reaction centers. There were significant differences of PS II actual and maximum photochemical efficiencies at the actinic light intensity (ΦPS II and Fv'/Fm') between abaxial and adaxial surface, and their relative variation trends were on the contrary. The photochemical and non-photochemical quenching coefficients (qP and NPQ) had a similar tendency in both abaxial and adaxial surfaces. Although ΦPS II and qP were lower in adaxial surface of flag leaf, the Fv'/Fm' was significantly higher, which indicated that the potential PS II capture efficiency of excited energy was higher. The results demonstrated that process of photochemical and non-photochemical quenching could effectively dissipate excited energy caused by strong solar radiation, and there were higher adaptation capacities in wheat varieties natively cultivated in

  7. Anionic lipids and the maintenance of membrane electrostatics in eukaryotes.

    Science.gov (United States)

    Platre, Matthieu Pierre; Jaillais, Yvon

    2017-02-01

    A wide range of signaling processes occurs at the cell surface through the reversible association of proteins from the cytosol to the plasma membrane. Some low abundant lipids are enriched at the membrane of specific compartments and thereby contribute to the identity of cell organelles by acting as biochemical landmarks. Lipids also influence membrane biophysical properties, which emerge as an important feature in specifying cellular territories. Such parameters are crucial for signal transduction and include lipid packing, membrane curvature and electrostatics. In particular, membrane electrostatics specifies the identity of the plasma membrane inner leaflet. Membrane surface charges are carried by anionic phospholipids, however the exact nature of the lipid(s) that powers the plasma membrane electrostatic field varies among eukaryotes and has been hotly debated during the last decade. Herein, we discuss the role of anionic lipids in setting up plasma membrane electrostatics and we compare similarities and differences that were found in different eukaryotic cells.

  8. Regulated eukaryotic DNA replication origin firing with purified proteins.

    Science.gov (United States)

    Yeeles, Joseph T P; Deegan, Tom D; Janska, Agnieszka; Early, Anne; Diffley, John F X

    2015-03-26

    Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric minichromosome maintenance (MCM) complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45-MCM-GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin-dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4-dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication.

  9. The MCM Helicase Motor of the Eukaryotic Replisome.

    Science.gov (United States)

    Abid Ali, Ferdos; Costa, Alessandro

    2016-05-08

    The MCM motor of the CMG helicase powers ahead of the eukaryotic replication machinery to unwind DNA, in a process that requires ATP hydrolysis. The reconstitution of DNA replication in vitro has established the succession of events that lead to replication origin activation by the MCM and recent studies have started to elucidate the structural basis of duplex DNA unwinding. Despite the exciting progress, how the MCM translocates on DNA remains a matter of debate. Copyright © 2016. Published by Elsevier Ltd.

  10. Biological Influence of Deuterium on Procariotic and Eukaryotic Cells

    OpenAIRE

    Oleg Mosin; Ignat Ignatov

    2014-01-01

    Biologic influence of deuterium (D) on cells of various taxonomic groups of prokaryotic and eukaryotic microorganisms realizing methylotrophic, chemoheterotrophic, photo-organotrophic, and photosynthetic ways of assimilation of carbon substrates are investigated at growth on media with heavy water (D2О). The method of step by step adaptation technique of cells to D2О was developed, consisting in plating of cells on 2 % agarose nutrient media containing increasing gradient of concentration of ...

  11. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    OpenAIRE

    Neil W. Blackstone

    2016-01-01

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real?the endosymbiosis that led to the mitochondrion is often described as ?non-Darwinian? because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious?all of the major fea...

  12. Gram-Negative Bacterial Sensors for Eukaryotic Signal Molecules

    Directory of Open Access Journals (Sweden)

    Olivier Lesouhaitier

    2009-09-01

    Full Text Available Ample evidence exists showing that eukaryotic signal molecules synthesized and released by the host can activate the virulence of opportunistic pathogens. The sensitivity of prokaryotes to host signal molecules requires the presence of bacterial sensors. These prokaryotic sensors, or receptors, have a double function: stereospecific recognition in a complex environment and transduction of the message in order to initiate bacterial physiological modifications. As messengers are generally unable to freely cross the bacterial membrane, they require either the presence of sensors anchored in the membrane or transporters allowing direct recognition inside the bacterial cytoplasm. Since the discovery of quorum sensing, it was established that the production of virulence factors by bacteria is tightly growth-phase regulated. It is now obvious that expression of bacterial virulence is also controlled by detection of the eukaryotic messengers released in the micro-environment as endocrine or neuro-endocrine modulators. In the presence of host physiological stress many eukaryotic factors are released and detected by Gram-negative bacteria which in return rapidly adapt their physiology. For instance, Pseudomonas aeruginosa can bind elements of the host immune system such as interferon-γ and dynorphin and then through quorum sensing circuitry enhance its virulence. Escherichia coli sensitivity to the neurohormones of the catecholamines family appears relayed by a recently identified bacterial adrenergic receptor. In the present review, we will describe the mechanisms by which various eukaryotic signal molecules produced by host may activate Gram-negative bacteria virulence. Particular attention will be paid to Pseudomonas, a genus whose representative species, P. aeruginosa, is a common opportunistic pathogen. The discussion will be particularly focused on the pivotal role played by these new types of pathogen sensors from the sensing to the transduction

  13. Replication and Transcription of Eukaryotic DNA in Esherichia coli

    Science.gov (United States)

    Morrow, John F.; Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Goodman, Howard M.; Helling, Robert B.

    1974-01-01

    Fragments of amplified Xenopus laevis DNA, coding for 18S and 28S ribosomal RNA and generated by EcoRI restriction endonuclease, have been linked in vitro to the bacterial plasmid pSC101; and the recombinant molecular species have been introduced into E. coli by transformation. These recombinant plasmids, containing both eukaryotic and prokaryotic DNA, replicate stably in E. coli. RNA isolated from E. coli minicells harboring the plasmids hybridizes to amplified X. laevis rDNA. Images PMID:4600264

  14. Extreme Diversity of Diplonemid Eukaryotes in the Ocean

    Czech Academy of Sciences Publication Activity Database

    Flegontova, Olga; Flegontov, Pavel; Malviya, S.; Audic, S.; Wincker, P.; de Vargas, C.; Bowler, C.; Lukeš, Julius; Horák, Aleš

    2016-01-01

    Roč. 26, č. 22 (2016), s. 3060-3065 ISSN 0960-9822 R&D Projects: GA ČR GPP506/12/P931; GA ČR(CZ) GA14-23986S Institutional support: RVO:60077344 Keywords : virus-sized particles * microbial eukaryotes * sea-floor * phytoplankton * communities * euglenozoa * dispersal * ecosystem Subject RIV: EG - Zoology Impact factor: 8.851, year: 2016

  15. Photochemical Cyclopolymerization of Polyimides in Ultraviolet Ridgidizing Composites for Use in Inflatable Structures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This innovation uses photochemical cyclopolymerization of polyimides to manufacture ultraviolet rigidizable composites for use in RIS (ridgidizing inflatable)...

  16. diArk – a resource for eukaryotic genome research

    Directory of Open Access Journals (Sweden)

    Kollmar Martin

    2007-04-01

    Full Text Available Abstract Background The number of completed eukaryotic genome sequences and cDNA projects has increased exponentially in the past few years although most of them have not been published yet. In addition, many microarray analyses yielded thousands of sequenced EST and cDNA clones. For the researcher interested in single gene analyses (from a phylogenetic, a structural biology or other perspective it is therefore important to have up-to-date knowledge about the various resources providing primary data. Description The database is built around 3 central tables: species, sequencing projects and publications. The species table contains commonly and alternatively used scientific names, common names and the complete taxonomic information. For projects the sequence type and links to species project web-sites and species homepages are stored. All publications are linked to projects. The web-interface provides comprehensive search modules with detailed options and three different views of the selected data. We have especially focused on developing an elaborate taxonomic tree search tool that allows the user to instantaneously identify e.g. the closest relative to the organism of interest. Conclusion We have developed a database, called diArk, to store, organize, and present the most relevant information about completed genome projects and EST/cDNA data from eukaryotes. Currently, diArk provides information about 415 eukaryotes, 823 sequencing projects, and 248 publications.

  17. Biotransformation of arsenic by a Yellowstone thermoacidophilic eukaryotic alga.

    Science.gov (United States)

    Qin, Jie; Lehr, Corinne R; Yuan, Chungang; Le, X Chris; McDermott, Timothy R; Rosen, Barry P

    2009-03-31

    Arsenic is the most common toxic substance in the environment, ranking first on the Superfund list of hazardous substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. Geothermal environments are known for their elevated arsenic content and thus provide an excellent setting in which to study microbial redox transformations of arsenic. To date, most studies of microbial communities in geothermal environments have focused on Bacteria and Archaea, with little attention to eukaryotic microorganisms. Here, we show the potential of an extremophilic eukaryotic alga of the order Cyanidiales to influence arsenic cycling at elevated temperatures. Cyanidioschyzon sp. isolate 5508 oxidized arsenite [As(III)] to arsenate [As(V)], reduced As(V) to As(III), and methylated As(III) to form trimethylarsine oxide (TMAO) and dimethylarsenate [DMAs(V)]. Two arsenic methyltransferase genes, CmarsM7 and CmarsM8, were cloned from this organism and demonstrated to confer resistance to As(III) in an arsenite hypersensitive strain of Escherichia coli. The 2 recombinant CmArsMs were purified and shown to transform As(III) into monomethylarsenite, DMAs(V), TMAO, and trimethylarsine gas, with a T(opt) of 60-70 degrees C. These studies illustrate the importance of eukaryotic microorganisms to the biogeochemical cycling of arsenic in geothermal systems, offer a molecular explanation for how these algae tolerate arsenic in their environment, and provide the characterization of algal methyltransferases.

  18. Ubiquitination dynamics in the early-branching eukaryote Giardia intestinalis

    Science.gov (United States)

    Niño, Carlos A; Chaparro, Jenny; Soffientini, Paolo; Polo, Simona; Wasserman, Moises

    2013-01-01

    Ubiquitination is a highly dynamic and versatile posttranslational modification that regulates protein function, stability, and interactions. To investigate the roles of ubiquitination in a primitive eukaryotic lineage, we utilized the early-branching eukaryote Giardia intestinalis. Using a combination of biochemical, immunofluorescence-based, and proteomics approaches, we assessed the ubiquitination status during the process of differentiation in Giardia. We observed that different types of ubiquitin modifications present specific cellular and temporal distribution throughout the Giardia life cycle from trophozoites to cyst maturation. Ubiquitin signal was detected in the wall of mature cysts, and enzymes implicated in cyst wall biogenesis were identified as substrates for ubiquitination. Interestingly, inhibition of proteasome activity did not affect trophozoite replication and differentiation, while it caused a decrease in cyst viability, arguing for proteasome involvement in cyst wall maturation. Using a proteomics approach, we identified around 200 high-confidence ubiquitinated candidates that vary their ubiquitination status during differentiation. Our results indicate that ubiquitination is critical for several cellular processes in this primitive eukaryote. PMID:23613346

  19. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes.

    Science.gov (United States)

    Moriyama, Takashi; Sato, Naoki

    2014-01-01

    Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.

  20. Mechanisms and regulation of DNA replication initiation in eukaryotes.

    Science.gov (United States)

    Parker, Matthew W; Botchan, Michael R; Berger, James M

    2017-04-01

    Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.

  1. Photochemical and Photophysical Properties of Phthalocyanines Modified with Optically Active Alcohols

    Directory of Open Access Journals (Sweden)

    Aline A. Ramos

    2015-07-01

    Full Text Available Three phthalocyanine derivatives were synthesized and characterized: one modified with a racemic mixture of 1-(4-bromophenylethanol and two other macrocycles modified with each one of the enantioenriched isomers (R-1-(4-bromophenylethanol and (S-1-(4-bromophenylethanol. The compounds were characterized by 1H-NMR spectroscopy, mass spectrometry, UV-Vis absorption, and excitation and emission spectra. Additionally, partition coefficient values and the quantum yield of the generation of oxygen reactive species were determined. Interestingly, the phthalocyanine containing a (R-1-(4-bromophenylethoxy moiety showed higher quantum yield of reactive oxygen species generation than other compounds under the same conditions. In addition, the obtained fluorescence microscopy and cell viability results have shown that these phthalocyanines have different interactions with mammary MCF-7 cells. Therefore, our results indicate that the photochemical and biological properties of phthalocyanines with chiral ligands should be evaluated separately for each enantiomeric species.

  2. The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition.

    Science.gov (United States)

    Heitlinger, Emanuel; Ferreira, Susana C M; Thierer, Dagmar; Hofer, Heribert; East, Marion L

    2017-01-01

    In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena ( Crocuta crocuta ), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes.

  3. Photochemical Reactivity of Dissolved Organic Matter in Boreal Lakes

    Science.gov (United States)

    Gu, Y.; Vuorio, K.; Tiirola, M.; Perämäki, S.; Vahatalo, A.

    2016-12-01

    Boreal lakes are rich in dissolved organic matter (DOM) that terrestrially derived from forest soil and wetland, yet little is known about potential for photochemical transformation of aquatic DOM in boreal lakes. Transformation of chromophoric dissolved organic matter (CDOM) can decrease water color and enhance microbial mineralization, affecting primary production and respiration, which both affect the CO2 balance of the lakes. We used laboratory solar radiation exposure experiments with lake water samples collected from 54 lakes located in Finland and Sweden, representing different catchment composition and watershed location to assess photochemical reactivity of DOM. The pH of water samples ranged from 5.4 to 8.3, and the concentrations of dissolved iron (Fe) were between samples received simulated solar radiation corresponding to a daily dose of sunlight, and photomineralization of dissolved organic carbon (DOC) to dissolved inorganic carbon (DIC) was measured for determination of spectral apparent quantum yields (AQY). During irradiation, photobleaching decreased the absorption coefficients of CDOM at 330 nm between 4.9 and 79 m-1 by 0.5 to 11 m-1. Irradiation generated DIC from 2.8 to 79 μmol C L-1. The AQY at 330 nm ranged between 31 and 273 ×10-6 mol C mol photons-1 h-1, which was correlated positively with concentration of dissolved Fe, and negatively with pH. Further statistical analyze indicated that the interaction between pH and Fe may explain much of the photochemical reactivity of DOM in the examined lakes, and land cover concerns main catchment areas also can have impact on the photoreaction process. This study may suggest how environmental conditions regulate DOM photomineralization in boreal lakes.

  4. How MCM loading and spreading specify eukaryotic DNA replication initiation sites [version 1; referees: 4 approved

    Directory of Open Access Journals (Sweden)

    Olivier Hyrien

    2016-08-01

    Full Text Available DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs, the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC, they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.

  5. How MCM loading and spreading specify eukaryotic DNA replication initiation sites.

    Science.gov (United States)

    Hyrien, Olivier

    2016-01-01

    DNA replication origins strikingly differ between eukaryotic species and cell types. Origins are localized and can be highly efficient in budding yeast, are randomly located in early fly and frog embryos, which do not transcribe their genomes, and are clustered in broad (10-100 kb) non-transcribed zones, frequently abutting transcribed genes, in mammalian cells. Nonetheless, in all cases, origins are established during the G1-phase of the cell cycle by the loading of double hexamers of the Mcm 2-7 proteins (MCM DHs), the core of the replicative helicase. MCM DH activation in S-phase leads to origin unwinding, polymerase recruitment, and initiation of bidirectional DNA synthesis. Although MCM DHs are initially loaded at sites defined by the binding of the origin recognition complex (ORC), they ultimately bind chromatin in much greater numbers than ORC and only a fraction are activated in any one S-phase. Data suggest that the multiplicity and functional redundancy of MCM DHs provide robustness to the replication process and affect replication time and that MCM DHs can slide along the DNA and spread over large distances around the ORC. Recent studies further show that MCM DHs are displaced along the DNA by collision with transcription complexes but remain functional for initiation after displacement. Therefore, eukaryotic DNA replication relies on intrinsically mobile and flexible origins, a strategy fundamentally different from bacteria but conserved from yeast to human. These properties of MCM DHs likely contribute to the establishment of broad, intergenic replication initiation zones in higher eukaryotes.

  6. Influence of Vitamin B Auxotrophy on Nitrogen Metabolism in Eukaryotic Phytoplankton

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    Erin M Bertrand

    2012-10-01

    Full Text Available While nitrogen availability is known to limit primary production in large parts of the ocean, vitamin starvation amongst eukaryotic phytoplankton is becoming increasingly recognized as an oceanographically relevant phenomenon. Cobalamin (B12 and thiamine (B1 auxotrophy are widespread throughout eukaryotic phytoplankton, with over 50% of cultured isolates requiring B12 and 20% requiring B1. The frequency of vitamin auxotrophy in harmful algal bloom species is even higher. Instances of colimitation between nitrogen and B vitamins have been observed in marine environments, and interactions between these nutrients have been shown to impact phytoplankton species composition. This review evaluates the potential for interactive effects of nitrogen and vitamin B12 and B1 starvation in eukaryotic phytoplankton. B12 plays essential roles in amino acid and one-carbon metabolism, while B1 is important for primary carbohydrate and amino acid metabolism and likely useful as an anti-oxidant. Here we will focus on three potential metabolic interconnections between vitamin, nitrogen and sulfur metabolism that may have ramifications for the role of vitamin and nitrogen scarcities in driving ocean productivity and species composition. These include: (1 B12, B1, and N starvation impacts on osmolyte and antioxidant production, (2 B12 and B1 starvation impacts on polyamine biosynthesis, and (3 influence of B12 and B1 starvation on the diatom urea cycle and amino acid recycling through impacts on the citric acid cycle. We evaluate evidence for these interconnections and identify oceanographic contexts in which each may impact rates of primary production and phytoplankton community composition. Major implications include that B12 and B1 deprivation may impair the ability of phytoplankton to recover from nitrogen starvation and that changes in vitamin and nitrogen availability may synergistically impact harmful algal bloom formation.

  7. Photochemical production of ozone and control strategy for Southern Taiwan

    Science.gov (United States)

    Shiu, Chein-Jung; Liu, Shaw Chen; Chang, Chih-Chung; Chen, Jen-Ping; Chou, Charles C. K.; Lin, Chuan-Yao; Young, Chea-Yuan

    An observation-based method (OBM) is developed to evaluate the ozone (O 3) production efficiency (O 3 molecules produced per NO x molecule consumed) and O 3 production rate ( P(O 3)) during a field campaign in southern Taiwan. The method can also provide an estimate of the concentration of OH. A key step in the method is to use observed concentrations of two aromatic hydrocarbons, namely ethylbenzene and m, p-xylene, to estimate the degree of photochemical processing and amounts of photochemically consumed NO x and NMHCs by OH. In addition, total oxidant (O 3+NO 2) instead of O 3 itself turns out to be very useful for representing ozone production in the OBM approach. The average O 3 production efficiency during the field campaign in Fall (2003) is found to be about 10.2±3.9. The relationship of P(O 3) with NO x is examined and compared with a one-dimensional (1D) photochemical model. Values of P(O 3) derived from the OBM are slightly lower than those calculated in the 1D model. However, OH concentrations estimated by the OBM are about a factor of 2 lower than the 1D model. Fresh emissions, which affect the degree of photochemical processing appear to be a major cause of the underestimate. We have developed a three-dimensional (3D) OBM O 3 production diagram that resembles the EKMA ozone isopleth diagram to study the relationship of the total oxidant versus O 3 precursors. The 3D OBM O 3 production diagram suggests that reducing emissions of NMHCs are more effective in controlling O 3 than reducing NO x. However, significant uncertainties remain in the OBM, and considerable more work is required to minimize these uncertainties before a definitive control strategy can be reached. The observation-based approach provides a good alternative to measuring peroxy radicals for evaluating the production of O 3 and formulating O 3 control strategy in urban and suburban environments.

  8. A Model Study of the Photochemical Fate of As(III in Paddy-Water

    Directory of Open Access Journals (Sweden)

    Luca Carena

    2017-03-01

    Full Text Available The APEX (Aqueous Photochemistry of Environmentally-occurring Xenobiotics software previously developed by one of us was used to model the photochemistry of As(III in paddy-field water, allowing a comparison with biotic processes. The model included key paddy-water variables, such as the shielding effect of the rice canopy on incident sunlight and its monthly variations, water pH, and the photochemical parameters of the chromophoric dissolved organic matter (CDOM occurring in paddy fields. The half-life times (t1/2 of As(III photooxidation to As(V would be ~20–30 days in May. In contrast, the photochemical oxidation of As(III would be much slower in June and July due to rice-canopy shading of radiation because of plant growth, despite higher sunlight irradiance. At pH < 8 the photooxidation of As(III would mainly be accounted for by reaction with transient species produced by irradiated CDOM (here represented by the excited triplet states 3CDOM*, neglecting the possibly more important reactions with poorly known species such as the phenoxy radicals and, to a lesser extent, with the hydroxyl radicals (HO•. However, the carbonate radicals (CO3•− could be key photooxidants at pH > 8.5 provided that the paddy-water 3CDOM* is sufficiently reactive toward the oxidation of CO32−. In particular, if paddy-water 3CDOM* oxidizes the carbonate anion with a second-order reaction rate constant near (or higher than 106 M−1·s−1, the photooxidation of As(III could be quite fast at pH > 8.5. Such pH conditions can be produced by elevated photosynthetic activity that consumes dissolved CO2.

  9. Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms

    Directory of Open Access Journals (Sweden)

    Jékely Gáspár

    2007-01-01

    Full Text Available Abstract Background The origin of eukaryotic cells was one of the most dramatic evolutionary transitions in the history of life. It is generally assumed that eukaryotes evolved later then prokaryotes by the transformation or fusion of prokaryotic lineages. However, as yet there is no consensus regarding the nature of the prokaryotic group(s ancestral to eukaryotes. Regardless of this, a hardly debatable fundamental novel characteristic of the last eukaryotic common ancestor was the ability to exploit prokaryotic biomass by the ingestion of entire cells, i.e. phagocytosis. The recent advances in our understanding of the social life of prokaryotes may help to explain the origin of this form of total exploitation. Presentation of the hypothesis Here I propose that eukaryotic cells originated in a social environment, a differentiated microbial mat or biofilm that was maintained by the cooperative action of its members. Cooperation was costly (e.g. the production of developmental signals or an extracellular matrix but yielded benefits that increased the overall fitness of the social group. I propose that eukaryotes originated as selfish cheaters that enjoyed the benefits of social aggregation but did not contribute to it themselves. The cheaters later evolved into predators that lysed other cells and eventually became professional phagotrophs. During several cycles of social aggregation and dispersal the number of cheaters was contained by a chicken game situation, i.e. reproductive success of cheaters was high when they were in low abundance but was reduced when they were over-represented. Radical changes in cell structure, including the loss of the rigid prokaryotic cell wall and the development of endomembranes, allowed the protoeukaryotes to avoid cheater control and to exploit nutrients more efficiently. Cellular changes were buffered by both the social benefits and the protective physico-chemical milieu of the interior of biofilms. Symbiosis

  10. Symbiont shuffling linked to differential photochemical dynamics of Symbiodinium in three Caribbean reef corals

    Science.gov (United States)

    Cunning, Ross; Silverstein, Rachel N.; Baker, Andrew C.

    2018-03-01

    Dynamic symbioses with functionally diverse dinoflagellate algae in the genus Symbiodinium may allow some reef corals to alter their phenotypes through `symbiont shuffling', or changes in symbiont community composition. In particular, corals may become more bleaching resistant by increasing the relative abundance of thermally tolerant Symbiodinium in clade D after bleaching. Despite the immediate relevance of this phenomenon to corals living in warming oceans—and to interventions aimed at boosting coral resilience—the mechanisms governing how, why, and when symbiont shuffling occurs are still poorly understood. Here, we performed controlled thermal bleaching and recovery experiments on three species of Caribbean corals hosting mixtures of D1a ( S. trenchii) and other symbionts in clades B or C. We show that the degree of symbiont shuffling is related to (1) the duration of stress exposure and (2) the difference in photochemical efficiency ( F v /F m) of co-occurring symbionts under stress (i.e., the `photochemical advantage' of one symbiont over the other). The advantage of D1a under stress was greatest in Montastraea cavernosa, intermediate in Siderastrea siderea, and lowest in Orbicella faveolata and correlated positively with the magnitude of shuffling toward D1a. In holobionts where D1a had less of an advantage over co-occurring symbionts (i.e., only slightly higher F v /F m under stress), a longer stress duration was required to elicit commensurate increases in D1a abundance. In fact, across these three coral species, 92.9% of variation in the degree of symbiont shuffling could be explained by the time-integrated photochemical advantage of D1a under heat stress. Although F v /F m is governed by numerous factors that this study is unable to resolve mechanistically, its strong empirical relationship with symbiont shuffling helps elucidate general features that govern this process in reef corals, which will help refine predictions of coral responses to

  11. Aqueous photochemical degradation of hydroxylated PAHs: Kinetics, pathways, and multivariate effects of main water constituents

    Energy Technology Data Exchange (ETDEWEB)

    Ge, Linke; Na, Guangshui [Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023 (China); Chen, Chang-Er [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom); Li, Jun [Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023 (China); College of Marine Science, Shanghai Ocean University, Shanghai 201306 (China); Ju, Maowei; Wang, Ying; Li, Kai [Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023 (China); Zhang, Peng, E-mail: pzhang@nmemc.org.cn [Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023 (China); Yao, Ziwei [Key Laboratory for Ecological Environment in Coastal Areas (SOA), National Marine Environmental Monitoring Center, Dalian 116023 (China)

    2016-03-15

    Hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) are contaminants of emerging concern in the aquatic environment, so it is of great significance to understand their environmental transformation and toxicity. This study investigated the aqueous photochemical behavior of four OH-PAHs, 9-Hydroxyfluorene (9-OHFL), 2-Hydroxyfluorene, 9-Hydroxyphenanthrene and 1-Hydroxypyrene, under simulated sunlight irradiation (λ > 290 nm). It was observed that their photodegradation followed the pseudo-first-order kinetics. Based on the determined quantum yields, their calculated solar apparent photodegradation half-lives in surface waters at 45° N latitude ranged from 0.4 min for 9-Hydroxyphenanthrene to 7.5 × 10{sup 3} min for 9-OHFL, indicating that the OH-PAHs would intrinsically photodegrade fast in sunlit surface waters. Furthermore, 9-OHFL as an example was found to undergo direct photolysis, and self-sensitized photooxidation via ·OH rather than {sup 1}O{sub 2} in pure water. The potential photoreactions involved photoinduced hydroxylation, dehydrogenation and isomerization based on product identification by GC–MS/MS. 9-OHFL photodegraded slower in natural waters than in pure water, which was attributed to the integrative effects of the most photoreactive species, such as Fe(III), NO{sub 3}{sup −}, Cl{sup −} and humic acid. The photomodified toxicity was further examined using Vibrio fischeri, and it was found that the toxicity of photolyzed 9-OHFL did not decrease significantly (p > 0.05) either in pure water or in seawater, implying the comparable or higher toxicity of some intermediates. These results are important for assessing the fate and risks of OH-PAHs in surface waters. - Graphical abstract: Aqueous photochemical behavior of 4 hydroxylated PAHs is first reported on revealing the kinetics, mechanisms, toxicity, and multivariate effects of water constituents. - Highlights: • It is first reported on aqueous photochemical behavior of 4 hydroxylated

  12. Nickel films: Nonselective and selective photochemical deposition and properties

    International Nuclear Information System (INIS)

    Smirnova, N.V.; Boitsova, T.B.; Gorbunova, V.V.; Alekseeva, L.V.; Pronin, V.P.; Kon'uhov, G.S.

    2006-01-01

    Nickel films deposited on quartz surfaces by the photochemical reduction of a chemical nickel plating solution were studied. It was found that the deposition of the films occurs after an induction period, the length of which depends on the composition of the photolyte and the light intensity. Ni particles with a mean diameter of 20-30 nm were detected initially by transmission electron microscopy. The particles then increased in size (50 nm) upon irradiation and grouped into rings consisting of 4-5 particles. Irradiation with high-intensity light produces three-dimensional films. The calculated extinction coefficient of the nickel film was found to be 4800 L mol -1 cm -1 . Electron diffraction revealed that the prepared amorphous nickel films crystallize after one day of storage. It was determined that the films exhibit catalytic activity in the process of nickel deposition from nickel plating solution. The catalytic action remains for about 5-7 min after exposure of the films to air. The processes of selective and nonselective deposition of the nickel films are discussed. The use of poly(butoxy titanium) in the process of selective photochemical deposition enables negative and positive images to be prepared on quartz surfaces

  13. Global emissions and models of photochemically active compounds

    International Nuclear Information System (INIS)

    Penner, J.E.; Atherton, C.S.; Graedel, T.E.

    1993-01-01

    Anthropogenic emissions from industrial activity, fossil fuel combustion, and biomass burning are now known to be large enough (relative to natural sources) to perturb the chemistry of vast regions of the troposphere. A goal of the IGAC Global Emissions Inventory Activity (GEIA) is to provide authoritative and reliable emissions inventories on a 1 degree x 1 degree grid. When combined with atmospheric photochemical models, these high quality emissions inventories may be used to predict the concentrations of major photochemical products. Comparison of model results with measurements of pertinent species allows us to understand whether there are major shortcomings in our understanding of tropospheric photochemistry, the budgets and transport of trace species, and their effects in the atmosphere. Through this activity, we are building the capability to make confident predictions of the future consequences of anthropogenic emissions. This paper compares IGAC recommended emissions inventories for reactive nitrogen and sulfur dioxide to those that have been in use previously. We also present results from the three-dimensional LLNL atmospheric chemistry model that show how emissions of anthropogenic nitrogen oxides might potentially affect tropospheric ozone and OH concentrations and how emissions of anthropogenic sulfur increase sulfate aerosol loadings

  14. The influence of aerosols on photochemical smog in Mexico City

    Energy Technology Data Exchange (ETDEWEB)

    Castro, T.; Mar, B. [UNAM, Mexico, Centro de Ciencias de la Atmosfera (Mexico); Madronich, S.; Rivale, S. [National Center for Atmospheric Research, Boulder, CO (United States); Muhlia, A. [UNAM, Mexico, Inst. de Geofysica (Mexico)

    2001-04-01

    Aerosols in the Mexico City atmosphere can have a non-negligible effect on the ultraviolet radiation field and hence on the formation of photochemical smog. We used estimates of aerosol optical depths from sun photometer observations in a detailed radiative transfer model, to calculate photolysis rate coefficients (J{sub NO2}) for the key reaction NO{sub 2}+h{nu}{yields}NO+O ({lambda}<430nm). The calculated values are in good agreement with previously published measurements of J{sub NO2} at two sites in Mexico City: Palacio de Mineria (19 degrees 25'59''N, 99 degrees 07'58''W, 2233masl), and IMP (19 degrees 28'48''N, 99 degrees 11'07''W, 2277masl) and in Tres Marias, a town near Mexico City (19 degrees 03'N, 99 degrees 14'W, 2810masl). In particular, the model reproduces very well the contrast between the two urban sites and the evidently much cleaner Tres Marias site. For the measurement days, reductions in surface J{sub NO2} by 10-30% could be attributed to the presence of aerosols, with considerable uncertainty due largely to lack of detailed data on aerosol optical properties at ultraviolet wavelengths (esp. the single scattering albedo). The potential impact of such large reductions in photolysis rates on surface ozone concentrations is illustrated with a simple zero-dimensional photochemical model. (Author)

  15. The photochemical reaction of hydrocarbons under extreme thermobaric conditions

    Science.gov (United States)

    Serovaiskii, Aleksandr; Kolesnikov, Anton; Mukhina, Elena; Kutcherov, Vladimir

    2017-10-01

    The photochemical reaction of hydrocarbons was found to play an important role in the experiments with the synthetic petroleum conducted in Diamond Anvil Cell (DAC). Raman spectroscopy with a green laser (514.5 nm) was used for in situ sample analysis. This photochemical effect was investigated in the pressure range of 0.7-5 GPa, in the temperature interval from the ambient conditions to 450°C. The power of laser used in these experiment series was from 0.05 W to 0.6 W. The chemical transformation was observed when the necessary threshold pressure (~2.8 GPa) was reached. This transformation correlated with the luminescence appearance on the Raman spectra and a black opaque spot in the sample was observed in the place where the laser focus was forwarded. The exposure time and laser power (at least in the 0.1-0.5 W range) did not play a role in the 0.1-0.5 GPa range.

  16. Polymers designed for laser ablation-influence of photochemical properties

    International Nuclear Information System (INIS)

    Lippert, T.; Dickinson, J.T.; Hauer, M.; Kopitkovas, G.; Langford, S.C.; Masuhara, H.; Nuyken, O.; Robert, J.; Salmio, H.; Tada, T.; Tomita, K.; Wokaun, A.

    2002-01-01

    The ablation characteristics of various polymers were studied at low and high fluences. The polymers can be divided into three groups, i.e. polymers containing triazene and ester groups, the same polymers without the triazene group, and polyimide as reference polymer. At high fluences similar ablation parameters, i.e. etch rates and effective absorption coefficients, were obtained for all polymers. The main difference is the absence of carbon deposits for the designed polymers. At low fluences (at 308 nm) very pronounced differences are detected. The polymers containing the photochemically most active group (triazene) exhibit the lowest threshold of ablation (as low as 25 mJ cm -2 ) and the highest etch rates (up to 3 μm/pulse), followed by the designed polyesters and then polyimide. The laser-induced decomposition of the designed polymers was studied by nanosecond-interferometry. Only the triazene-polymer reveals etching without any sign of surface swelling, which is observed for all other polymers. The etching of the triazene-polymer starts and ends with the laser pulse, clearly indicating photochemical etching. The triazene-polymer was also studied by time-of-flight mass spectrometry (TOF-MS). The intensities of the ablation fragments show pronounced differences between irradiation at the absorption band of the triazene group (308 nm) and irradiation at a shorter wavelength (248 nm)

  17. Photochemical and other air pollutions in the Netherlands

    Energy Technology Data Exchange (ETDEWEB)

    Floor, H.

    1975-01-01

    Together with the State Institute of Public Health and the Royal Dutch Meteorological Institute, the Institute of Phytopathological Research continued investigations on incidence of air pollution in the country. The main purpose is to measure the effects of air pollution on indicator plants and to detect over the years which components separately or perhaps together damage indicator plants. In 1974, the network of experimental fields in the Netherlands was completed. From April until October, 29 fields were inspected weekly for typical symptoms of air pollution. Just as in the preceding year O3 caused most injury of the photochemical air pollutants, as shown by Spinacia oleracea and Nicotiana tabacum. Other photochemical air pollutants like PAN, and the pollutants SO2, NO/sub x/ and ethylene caused little injury to the indicator plants Urtica urens, Poa annua, Medicago sativa, Petunia nyctaginiflora and Solanum tuberosum. Symptoms of damage on Tulipa gesneriana, Gladiolus gandavensis and Freesia refracta indicated air pollution by HF in all experimental fields, but especially in the south of the country. The F determination in the air by means of the limed paper method established the results with the indicator plants.

  18. Origin and evolution of the self-organizing cytoskeleton in the network of eukaryotic organelles.

    Science.gov (United States)

    Jékely, Gáspár

    2014-09-02

    The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing "active gel," the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  19. Radical cations of quadricyclane and norbornadiene in polar ZSM-5 matrices: Radical cation photochemical transformations without photons

    International Nuclear Information System (INIS)

    Barnabas, M.V.; Trifunac, A.D.

    1994-01-01

    Radical cations of quadricyclane (Q) and norbornadiene (NBD) are produced by γ-radiolysis in zeolites. In polar ZSM-5, only one radical cation is initially observed below 100K. Increasing the temperature above 200K gives rise to the cyclopentadiene radical cation. Higher temperatures (>360K) give rise to the cyclopenten-4-yl radical. The observation of cyclopentadiene radical cation implies the occurrence of the reverse Diels-Alder reaction. This is a thermally forbidden, photochemically allowed, process, which is made possible by the interaction of the polar zeolite matrix sites with parent NBD and Q radical cations

  20. Effects of Saponins against Clinical E. coli Strains and Eukaryotic Cell Line

    Science.gov (United States)

    Arabski, Michał; Węgierek-Ciuk, Aneta; Czerwonka, Grzegorz; Lankoff, Anna; Kaca, Wiesław

    2012-01-01

    Saponins are detergent-like substances showing antibacterial as well as anticancer potential. In this study, the effects of saponins from Quillaja saponaria were analyzed against prokaryotic and eukaryotic cells. Multidrug-resistant clinical E. coli strains were isolated from human urine. As eukaryotic cells, the CHO-K1 cell lines were applied. Antibacterial effect of ampicillin, streptomycin, and ciprofloxacin in the presence of saponins was measured by cultivation methods. Properties of saponins against CHO-K1 cells were measured by the MTT test, hemolysis assay and flow cytometry. Saponin from Quillaja saponaria has a cytotoxic effect at concentrations higher than 25 μg/mL and in the range of 12–50 μg/mL significantly increases the level of early apoptotic cells. Saponin at dose of 12 μg/mL enhances the six E. coli strains growth. We postulate that saponins increase the influx of nutrients from the medium into E. coli cells. Saponins do not have synergetic effects on antibacterial action of tested antibiotics. In contrary, in the presence of saponins and antibiotics, more CFU/mL E. coli cells were observed. This effect was similar to saponins action alone towards E. coli cells. In conclusion, saponins was cytotoxic against CHO-K1 cells, whereas against E. coli cells this effect was not observed. PMID:22500084

  1. Effects of Saponins against Clinical E. coli Strains and Eukaryotic Cell Line

    Directory of Open Access Journals (Sweden)

    Michał Arabski

    2012-01-01

    Full Text Available Saponins are detergent-like substances showing antibacterial as well as anticancer potential. In this study, the effects of saponins from Quillaja saponaria were analyzed against prokaryotic and eukaryotic cells. Multidrug-resistant clinical E. coli strains were isolated from human urine. As eukaryotic cells, the CHO-K1 cell lines were applied. Antibacterial effect of ampicillin, streptomycin, and ciprofloxacin in the presence of saponins was measured by cultivation methods. Properties of saponins against CHO-K1 cells were measured by the MTT test, hemolysis assay and flow cytometry. Saponin from Quillaja saponaria has a cytotoxic effect at concentrations higher than 25 μg/mL and in the range of 12–50 μg/mL significantly increases the level of early apoptotic cells. Saponin at dose of 12 μg/mL enhances the six E. coli strains growth. We postulate that saponins increase the influx of nutrients from the medium into E. coli cells. Saponins do not have synergetic effects on antibacterial action of tested antibiotics. In contrary, in the presence of saponins and antibiotics, more CFU/mL E. coli cells were observed. This effect was similar to saponins action alone towards E. coli cells. In conclusion, saponins was cytotoxic against CHO-K1 cells, whereas against E. coli cells this effect was not observed.

  2. Resilience of freshwater communities of small microbial eukaryotes undergoing severe drought events

    Directory of Open Access Journals (Sweden)

    Marianne eSimon

    2016-05-01

    Full Text Available Small and shallow aquatic ecosystems such as ponds and streams constitute a significant proportion of continental surface waters, especially in temperate zones. In comparison with bigger lakes and rivers, they harbor higher biodiversity but they also exhibit reduced buffering capacity face to environmental shifts, such that climate global change can affect them in a more drastic way. For instance, many temperate areas are predicted to undergo droughts with increasing frequency in the near future, which may lead to the temporal desiccation of streams and ponds. In this work, we monitored temporal dynamics of planktonic communities of microbial eukaryotes (cell size range 0.2-5 µm in one brook and one pond that experienced recurrent droughts from 1 to 5 consecutive months during a temporal survey carried out monthly for two years based on high-throughput 18S rDNA metabarcoding. During drought-induced desiccation events, protist communities present in the remaining dry sediment, though highly diverse, differed radically from their planktonic counterparts. However, after water refill, the aquatic protist assemblages recovered their original structure within a month. This rapid recovery indicates that these eukaryotic communities are resilient to droughts, most likely via the entrance in dormancy. This property is essential for the long-term survival and functional stability of small freshwater ecosystems.

  3. Seasonal photochemical transformations of nitrogen species in a forest stream and lake.

    Directory of Open Access Journals (Sweden)

    Petr Porcal

    Full Text Available The photochemical release of inorganic nitrogen from dissolved organic matter is an important source of bio-available nitrogen (N in N-limited aquatic ecosystems. We conducted photochemical experiments and used mathematical models based on pseudo-first-order reaction kinetics to quantify the photochemical transformations of individual N species and their seasonal effects on N cycling in a mountain forest stream and lake (Plešné Lake, Czech Republic. Results from laboratory experiments on photochemical changes in N speciation were compared to measured lake N budgets. Concentrations of organic nitrogen (Norg; 40-58 µmol L-1 decreased from 3 to 26% during 48-hour laboratory irradiation (an equivalent of 4-5 days of natural solar insolation due to photochemical mineralization to ammonium (NH4+ and other N forms (Nx; possibly N oxides and N2. In addition to Norg mineralization, Nx also originated from photochemical nitrate (NO3- reduction. Laboratory exposure of a first-order forest stream water samples showed a high amount of seasonality, with the maximum rates of Norg mineralization and NH4+ production in winter and spring, and the maximum NO3- reduction occurring in summer. These photochemical changes could have an ecologically significant effect on NH4+ concentrations in streams (doubling their terrestrial fluxes from soils and on concentrations of dissolved Norg in the lake. In contrast, photochemical reactions reduced NO3- fluxes by a negligible (<1% amount and had a negligible effect on the aquatic cycle of this N form.

  4. Cherenkov light as a source of photochemical reactions in irradiated solutions of nitrile of malachite green

    Energy Technology Data Exchange (ETDEWEB)

    Stuglik, Z; Grodkowski, J

    1986-10-01

    Experimental data on photochemical activity of Cherenkov light are presented. Malachite green leucocyanide was used to detect the photochemical effects. The G value of Cherenkov light from the region 200-330 nm (number of quanta formed per 100 eV absorbed energy of ionizing radiation) in ethanol was estimated to be in the range of 0.0027-0.049. 14 references.

  5. Cherenkov light as a source of photochemical reactions in irradiated solutions of nitrile of malachite green

    International Nuclear Information System (INIS)

    Stuglik, Z.; Grodkowski, J.

    1986-01-01

    Experimental data on photochemical activity of Cherenkov light are presented. Malachite green leucocyanide was used to detect the photochemical effects. The G value of Cherenkov light from the region 200-330 nm (number of quanta formed per 100 eV absorbed energy of ionizing radiation) in ethanol was estimated to be in the range of 0.0027-0.049. (author)

  6. Relationships between ozone and other photochemical products at Ll. Valby, Denmark

    DEFF Research Database (Denmark)

    Skov, H.; Egeløv, A.H.; Granby, K.

    1997-01-01

    literature results it is estimated that the non-photochemical background mixing ratio of O-3 in the Northern Hemisphere is 24+/-6 ppbv. The correlation of HCOOH and CH3COOH with Ox indicates that these acids are of photochemical origin. A high correlation of HNO3 with Ox is also found. The anti-correlation...

  7. 40 CFR 52.2426 - Photochemical Assessment Monitoring Stations (PAMS) Program.

    Science.gov (United States)

    2010-07-01

    ... Stations (PAMS) Program. 52.2426 Section 52.2426 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... § 52.2426 Photochemical Assessment Monitoring Stations (PAMS) Program. On November 23, 1994 Virginia's... Photochemical Assessment Monitoring Stations (PAMS) Program as a state implementation plan (SIP) revision, as...

  8. Sources and Potential Photochemical Roles of Formaldehyde in an Urban Atmosphere in South China

    Science.gov (United States)

    Wang, Chuan; Huang, Xiao-Feng; Han, Yu; Zhu, Bo; He, Ling-Yan

    2017-11-01

    Formaldehyde (HCHO) is an important intermediate in tropospheric photochemistry. However, study of its evolution characteristics under heavy pollution conditions in China is limited, especially for high temporal resolutions, making it difficult to analyze its sources and environmental impacts. In this study, ambient levels of HCHO were monitored using a proton-transfer reaction mass spectrometer at an urban site in the Pearl River Delta of China. Continuous monitoring campaigns were conducted in the spring, summer, fall, and winter in 2016. The highest averaged HCHO concentrations were observed in autumn (5.1 ± 3.1 ppbv) and summer (5.0 ± 4.4 ppbv), followed by winter (4.2 ± 2.2 ppbv) and spring (3.4 ± 1.6 ppbv). The daily maximum of HCHO occurs in the early afternoon and shows good correlations with O3 and the secondary organic aerosol tracer during the day, revealing close relationships between ambient HCHO and secondary formations in Shenzhen, especially in summer and autumn. The daytime HCHO is estimated to be the major contributor to O3 formation and OH radical production, indicating that HCHO plays a key role in the urban atmospheric photochemical reactions. Anthropogenic secondary formation was calculated to be the dominant source of HCHO using a photochemical age-based parameterization method, with an average proportion of 39%. The contributions of biogenic sources in summer (41%) and autumn (39%) are much higher than those in spring (26%) and winter (28%), while the contributions of anthropogenic primary sources in spring (20%) and winter (18%) are twice those in summer (9%) and autumn (9%).

  9. Physiological validation of photochemical reflectance index (PRI) as a photosynthetic parameter using Arabidopsis thaliana mutants.

    Science.gov (United States)

    Kohzuma, Kaori; Hikosaka, Kouki

    2018-03-25

    Non-photochemical quenching (NPQ) is the most important photoprotective system in higher plants. NPQ can be divided into several steps according to the timescale of relaxation of chlorophyll fluorescence after reaching a steady state (i.e., the fast phase, qE; middle phase, qZ or qT; and slow phase, qI). The dissipation of excess energy as heat during the xanthophyll cycle, a large component of NPQ, is detectable during the fast to middle phase (sec to min). Although thermal dissipation is primarily investigated using indirect methods such as chlorophyll a fluorescence measurements, such analyses require dark adaptation or the application of a saturating pulse during measurement, making it difficult to continuously monitor this process. Here, we designed an unconventional technique for real-time monitoring of changes in thylakoid lumen pH (as reflected by changes in xanthophyll pigment content) based on the photochemical reflectance index (PRI), which we estimated by measuring light-driven leaf reflectance at 531 nm. We analyzed two Arabidopsis thaliana mutants, npq1 (unable to convert violaxanthin to zeaxanthin due to inhibited violaxanthin de-epoxidase [VDE] activity) and npq4 (lacking PsbS protein), to uncover the regulator of the PRI. The PRI was variable in wild-type and npq4 plants, but not in npq1, indicating that the PRI is related to xanthophyll cycle-dependent thermal energy quenching (qZ) rather than the linear electron transport rate or NPQ. In situ lumen pH substitution using a pH-controlled buffer solution caused a shift in PRI. These results suggest that the PRI reflects only xanthophyll cycle conversion and is therefore a useful parameter for monitoring thylakoid lumen pH (reflecting VDE activity) in vivo. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  10. The susceptibility of the retina to photochemical damage from visible light

    Science.gov (United States)

    Hunter, Jennifer J; Morgan, Jessica I W; Merigan, William H; Sliney, David H; Sparrow, Janet R; Williams, David R

    2011-01-01

    The photoreceptor/RPE complex must maintain a delicate balance between maximizing the absorption of photons for vision and retinal image quality while simultaneously minimizing the risk of photodamage when exposed to bright light. We review the recent discovery of two new effects of light exposure on the photoreceptor/RPE complex in the context of current thinking about the causes of retinal phototoxicity. These effects are autofluorescence photobleaching in which exposure to bright light reduces lipofuscin autofluorescence and, at higher light levels, RPE disruption in which the pattern of autofluorescence is permanently altered following light exposure. Both effects occur following exposure to visible light at irradiances that were previously thought to be safe. Photopigment, retinoids involved in the visual cycle, and bisretinoids in lipofuscin have been implicated as possible photosensitizers for photochemical damage. The mechanism of RPE disruption may follow either of these paths. On the other hand, autofluorescence photobleaching is likely an indicator of photooxidation of lipofuscin. The permanent changes inherent in RPE disruption might require modification of the light safety standards. AF photobleaching recovers after several hours although the mechanisms by which this occurs are not yet clear. Understanding the mechanisms of phototoxicity is all the more important given the potential for increased susceptibility in the presence of ocular diseases that affect either the visual cycle and/or lipofuscin accumulation. In addition, knowledge of photochemical mechanisms can improve our understanding of some disease processes that may be influenced by light exposure, such as some forms of Leber’s congenital amaurosis, and aid in the development of new therapies. Such treatment prior to intentional light exposures, as in ophthalmic examinations or surgeries, could provide an effective preventative strategy. PMID:22085795

  11. Impacts of Combustion Conditions and Photochemical Processing on the Light Absorption of Biomass Combustion Aerosol.

    Science.gov (United States)

    Martinsson, J; Eriksson, A C; Nielsen, I Elbæk; Malmborg, V Berg; Ahlberg, E; Andersen, C; Lindgren, R; Nyström, R; Nordin, E Z; Brune, W H; Svenningsson, B; Swietlicki, E; Boman, C; Pagels, J H

    2015-12-15

    The aim was to identify relationships between combustion conditions, particle characteristics, and optical properties of fresh and photochemically processed emissions from biomass combustion. The combustion conditions included nominal and high burn rate operation and individual combustion phases from a conventional wood stove. Low temperature pyrolysis upon fuel addition resulted in "tar-ball" type particles dominated by organic aerosol with an absorption Ångström exponent (AAE) of 2.5-2.7 and estimated Brown Carbon contributions of 50-70% to absorption at the climate relevant aethalometer-wavelength (520 nm). High temperature combustion during the intermediate (flaming) phase was dominated by soot agglomerates with AAE 1.0-1.2 and 85-100% of absorption at 520 nm attributed to Black Carbon. Intense photochemical processing of high burn rate flaming combustion emissions in an oxidation flow reactor led to strong formation of Secondary Organic Aerosol, with no or weak absorption. PM1 mass emission factors (mg/kg) of fresh emissions were about an order of magnitude higher for low temperature pyrolysis compared to high temperature combustion. However, emission factors describing the absorption cross section emitted per kg of fuel consumed (m(2)/kg) were of similar magnitude at 520 nm for the diverse combustion conditions investigated in this study. These results provide a link between biomass combustion conditions, emitted particle types, and their optical properties in fresh and processed plumes which can be of value for source apportionment and balanced mitigation of biomass combustion emissions from a climate and health perspective.

  12. Insights into the Initiation of Eukaryotic DNA Replication.

    Science.gov (United States)

    Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

    2015-01-01

    The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.

  13. [Structure and evolution of the eukaryotic FANCJ-like proteins].

    Science.gov (United States)

    Wuhe, Jike; Zefeng, Wu; Sanhong, Fan; Xuguang, Xi

    2015-02-01

    The FANCJ-like protein family is a class of ATP-dependent helicases that can catalytically unwind duplex DNA along the 5'-3' direction. It is involved in the processes of DNA damage repair, homologous recombination and G-quadruplex DNA unwinding, and plays a critical role in maintaining genome integrity. In this study, we systemically analyzed FNACJ-like proteins from 47 eukaryotic species and discussed their sequences diversity, origin and evolution, motif organization patterns and spatial structure differences. Four members of FNACJ-like proteins, including XPD, CHL1, RTEL1 and FANCJ, were found in eukaryotes, but some of them were seriously deficient in most fungi and some insects. For example, the Zygomycota fungi lost RTEL1, Basidiomycota and Ascomycota fungi lost RTEL1 and FANCJ, and Diptera insect lost FANCJ. FANCJ-like proteins contain canonical motor domains HD1 and HD2, and the HD1 domain further integrates with three unique domains Fe-S, Arch and Extra-D. Fe-S and Arch domains are relatively conservative in all members of the family, but the Extra-D domain is lost in XPD and differs from one another in rest members. There are 7, 10 and 2 specific motifs found from the three unique domains respectively, while 5 and 12 specific motifs are found from HD1 and HD2 domains except the conserved motifs reported previously. By analyzing the arrangement pattern of these specific motifs, we found that RTEL1 and FANCJ are more closer and share two specific motifs Vb2 and Vc in HD2 domain, which are likely related with their G-quadruplex DNA unwinding activity. The evidence of evolution showed that FACNJ-like proteins were originated from a helicase, which has a HD1 domain inserted by extra Fe-S domain and Arch domain. By three continuous gene duplication events and followed specialization, eukaryotes finally possessed the current four members of FANCJ-like proteins.

  14. Recognition of extremophilic archaeal viruses by eukaryotic cells

    DEFF Research Database (Denmark)

    Uldahl, Kristine Buch; Wu, Linping; Hall, Arnaldur

    2016-01-01

    followed viral uptake, intracellular trafficking and cell viability in human endothelial cells of brain (hCMEC/D3 cells) and umbilical vein (HUVEC) origin. Whereas SMV1 is efficiently internalized into both types of human cells, SSV2 differentiates between HUVECs and hCMEC/D3 cells, thus opening a path......Viruses from the third domain of life, Archaea, exhibit unusual features including extreme stability that allow their survival in harsh environments. In addition, these species have never been reported to integrate into human or any other eukaryotic genomes, and could thus serve for exploration...

  15. Photochemical and Spectroscopic Effects Resulting from Excimer Laser Excitation.

    Science.gov (United States)

    Wang, Xuan Xiao

    I. Photochemical production of ozone from pure oxygen using excimer lasers. Production of ozone was observed from experiments when oxygen was under a broadband pulsed KrF laser radiation. The production process was found to be autocatalytic. Mechanisms for the ozone formation were proposed. Experimental results over a range of oxygen pressure and laser pulse energy (irradiance) provided evidences in favor of the proposed mechanisms. Experiments were also numerically modeled. Good agreement between the experimental and the numerical results were observed, which provided further evidence to support the proposed mechanisms. Cross sections for some photochemical processes in the mechanisms were estimated. Production of ozone from pure oxygen under a ArF excimer laser radiation (193 nm) was also studied and numerically modeled. Effects of ambient water vapor on ozone production were investigated. Experimental results showed a fast ozone destruction when water vapor was present in the cell. However, numerical results obtained from the well-known OH and HO _2 chain ozone destruction mechanism predicted a slower ozone destruction. Possible reasons for the discrepancy are discussed. II. Resonance-enhanced multiphoton ionization of N_2 at 193 and 248 nm detected by N_sp{2}{+} fluorescence. Using a broadband excimer laser operating at 193 and 248 nm multiphoton ionization at high pressures in air and pure nitrogen has been detected by fluorescence from N_sp{2}{+} in the B-X firstnegative system. Measurements of the fluorescence intensity as a function of beam irradiance indicate resonance in N_2 at the energy of two 193 nm photons (2 + 1 REMPI) and three 248 nm photons (3 + 1 REMPI). Possible intermediate states are discussed. III. Excimer laser-induced fluorescence from some organic solvents. Fluorescence was observed from vapor phase benzene, toluene, p-xylene, benzyl chloride, methyl benzoate, acetic anhydride, ether, methanol, ethyl acetone, acetone, and 2-butanone using

  16. In silico ionomics segregates parasitic from free-living eukaryotes.

    Science.gov (United States)

    Greganova, Eva; Steinmann, Michael; Mäser, Pascal; Fankhauser, Niklaus

    2013-01-01

    Ion transporters are fundamental to life. Due to their ancient origin and conservation in sequence, ion transporters are also particularly well suited for comparative genomics of distantly related species. Here, we perform genome-wide ion transporter profiling as a basis for comparative genomics of eukaryotes. From a given predicted proteome, we identify all bona fide ion channels, ion porters, and ion pumps. Concentrating on unicellular eukaryotes (n = 37), we demonstrate that clustering of species according to their repertoire of ion transporters segregates obligate endoparasites (n = 23) on the one hand, from free-living species and facultative parasites (n = 14) on the other hand. This surprising finding indicates strong convergent evolution of the parasites regarding the acquisition and homeostasis of inorganic ions. Random forest classification identifies transporters of ammonia, plus transporters of iron and other transition metals, as the most informative for distinguishing the obligate parasites. Thus, in silico ionomics further underscores the importance of iron in infection biology and suggests access to host sources of nitrogen and transition metals to be selective forces in the evolution of parasitism. This finding is in agreement with the phenomenon of iron withholding as a primordial antimicrobial strategy of infected mammals.

  17. Eukaryotic snoRNAs: a paradigm for gene expression flexibility.

    Science.gov (United States)

    Dieci, Giorgio; Preti, Milena; Montanini, Barbara

    2009-08-01

    Small nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs - to guide site-specific rRNA modification - is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes.

  18. Characterization of an eukaryotic peptide deformylase from Plasmodium falciparum.

    Science.gov (United States)

    Bracchi-Ricard, V; Nguyen, K T; Zhou, Y; Rajagopalan, P T; Chakrabarti, D; Pei, D

    2001-12-15

    Ribosomal protein synthesis in eubacteria and eukaryotic organelles initiates with an N-formylmethionyl-tRNA(i), resulting in N-terminal formylation of all nascent polypeptides. Peptide deformylase (PDF) catalyzes the subsequent removal of the N-terminal formyl group from the majority of bacterial proteins. Until recently, PDF has been thought as an enzyme unique to the bacterial kingdom. Searches of the genomic DNA databases identified several genes that encode proteins of high sequence homology to bacterial PDF from eukaryotic organisms. The cDNA encoding Plasmodium falciparum PDF (PfPDF) has been cloned and overexpressed in Escherichia coli. The recombinant protein is catalytically active in deformylating N-formylated peptides, shares many of the properties of bacterial PDF, and is inhibited by specific PDF inhibitors. Western blot analysis indicated expression of mature PfPDF in trophozoite, schizont, and segmenter stages of intraerythrocytic development. These results provide strong evidence that a functional PDF is present in P. falciparum. In addition, PDF inhibitors inhibited the growth of P. falciparum in the intraerythrocytic culture. (c)2001 Elsevier Science.

  19. Universal Temporal Profile of Replication Origin Activation in Eukaryotes

    Science.gov (United States)

    Goldar, Arach

    2011-03-01

    The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

  20. Marine biofilm bacteria evade eukaryotic predation by targeted chemical defense.

    Directory of Open Access Journals (Sweden)

    Carsten Matz

    Full Text Available Many plants and animals are defended from predation or herbivory by inhibitory secondary metabolites, which in the marine environment are very common among sessile organisms. Among bacteria, where there is the greatest metabolic potential, little is known about chemical defenses against bacterivorous consumers. An emerging hypothesis is that sessile bacterial communities organized as biofilms serve as bacterial refuge from predation. By testing growth and survival of two common bacterivorous nanoflagellates, we find evidence that chemically mediated resistance against protozoan predators is common among biofilm populations in a diverse set of marine bacteria. Using bioassay-guided chemical and genetic analysis, we identified one of the most effective antiprotozoal compounds as violacein, an alkaloid that we demonstrate is produced predominately within biofilm cells. Nanomolar concentrations of violacein inhibit protozoan feeding by inducing a conserved eukaryotic cell death program. Such biofilm-specific chemical defenses could contribute to the successful persistence of biofilm bacteria in various environments and provide the ecological and evolutionary context for a number of eukaryote-targeting bacterial metabolites.

  1. Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability.

    Science.gov (United States)

    Bonnet, Amandine; Grosso, Ana R; Elkaoutari, Abdessamad; Coleno, Emeline; Presle, Adrien; Sridhara, Sreerama C; Janbon, Guilhem; Géli, Vincent; de Almeida, Sérgio F; Palancade, Benoit

    2017-08-17

    Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Photochemical water splitting mediated by a C1 shuttle

    KAUST Repository

    Alderman, N. P.

    2016-10-31

    The possibility of performing photochemical water splitting in a two-stage system, separately releasing the H and O components, has been probed with two separate catalysts and in combination with a formaldehyde/formate shuttling redox couple. In the first stage, formaldehyde releases hydrogen vigorously in the presence of an Na[Fe(CN)]·10HO catalyst, selectively affording the formate anion. In the second stage, the formate anion is hydro-genated back to formaldehyde by water and in the presence of a BiWO photocatalyst whilst releasing oxygen. Both stages operate at room temperature and under visible light irradiation. The two separate photocatalysts are compatible since water splitting can also be obtained in one-pot experiments with simultaneous H/O evolution.

  3. Redox reaction in photochemical and ionizing irradiation systems

    International Nuclear Information System (INIS)

    Slama-Schwok, A.

    1985-09-01

    This work presents a basic study of electron transfer reactions which could be involved in appropriate systems for photochemical conversion and storage of solar energy. The aim was to extend the knowledge to new photosensitizers and quenchers and to compare them with the most popular photosensitizers-quenchers system, i.e. a rubidium complex. The photosensitizer studied here is an irridium complex. We studied in this work the air oxidation of bromide to Br 3 - and H 2 O 2 using the irridium complex as the sensitizer. The reducing properties of the reduced irridium complex photosensitizer were studied, using the pulse radiolysis techniques. In conclusion, the oxidation reduction properties of the irridium and its lowest excited state correspond to most of the photosensitizer for electron transfer reactions. The energy temporary present in the charge separation products can be stored using appropriate environment such as polyelectrolytes

  4. Photochemical and microbial degradation technologies to remove toxic chemicals

    International Nuclear Information System (INIS)

    Matsumura, F.; Katayama, A.

    1992-01-01

    An effort was made to apply photochemical degradation technology on biodegradation processes to increase the bioremediation potential of microbial actions. For this purpose, we have chosen Phanerochaete chrysosporium, a wood decaying white-rot fungus and a variety of chlorinated pesticides and aromatics as study materials. By using UV-irradiation and benomyl (a commonly used fungicide) as selection methods, a strain of UV-resistant P. chrysosporium was developed. This strain was found to be capable of rapidly degrading these chlorinated chemicals when they were incubated in N-deficient medium which received 1 hr/day of UV-irradiation. UV-irradiation either at 300 or 254 nm showed the beneficial effect of speeding up the rate of degradation on most of test chemicals with the exception of toxaphene and HCH (hexachlorocyclohexane). By adding fresh glucose to the medium it was possible to maintain high degradation capacity for several weeks

  5. Investigation on Surface Roughness of Inconel 718 in Photochemical Machining

    Directory of Open Access Journals (Sweden)

    Nitin D. Misal

    2017-01-01

    Full Text Available The present work is focused on estimating the optimal machining parameters required for photochemical machining (PCM of an Inconel 718 and effects of these parameters on surface topology. An experimental analysis was carried out to identify optimal values of parameters using ferric chloride (FeCl3 as an etchant. The parameters considered in this analysis are concentration of etchant, etching time, and etchant temperature. The experimental analysis shows that etching performance as well as surface topology improved by appropriate selection of etching process parameters. Temperature of the etchant found to be dominant parameter in the PCM of Inconel 718 for surface roughness. At optimal etching conditions, surface roughness was found to be 0.201 μm.

  6. Applying green chemistry to the photochemical route to artemisinin.

    Science.gov (United States)

    Amara, Zacharias; Bellamy, Jessica F B; Horvath, Raphael; Miller, Samuel J; Beeby, Andrew; Burgard, Andreas; Rossen, Kai; Poliakoff, Martyn; George, Michael W

    2015-06-01

    Artemisinin is an important antimalarial drug, but, at present, the environmental and economic costs of its semi-synthetic production are relatively high. Most of these costs lie in the final chemical steps, which follow a complex acid- and photo-catalysed route with oxygenation by both singlet and triplet oxygen. We demonstrate that applying the principles of green chemistry can lead to innovative strategies that avoid many of the problems in current photochemical processes. The first strategy combines the use of liquid CO2 as solvent and a dual-function solid acid/photocatalyst. The second strategy is an ambient-temperature reaction in aqueous mixtures of organic solvents, where the only inputs are dihydroartemisinic acid, O2 and light, and the output is pure, crystalline artemisinin. Everything else-solvents, photocatalyst and aqueous acid-can be recycled. Some aspects developed here through green chemistry are likely to have wider application in photochemistry and other reactions.

  7. Energy and Molecules from Photochemical/Photocatalytic Reactions. An Overview

    Directory of Open Access Journals (Sweden)

    Davide Ravelli

    2015-01-01

    Full Text Available Photocatalytic reactions have been defined as those processes that require both a (not consumed catalyst and light. A previous definition was whether such reactions brought a system towards or away from the (thermal equilibrium. This consideration brings in the question whether a part of the photon energy is incorporated into the photochemical reaction products. Data are provided for representative organic reactions involving or not molecular catalysts and show that energy storage occurs only when a heavily strained structure is generated, and in that case only a minor part of photon energy is actually stored (ΔG up to 25 kcal·mol−1. The green role of photochemistry/photocatalysis is rather that of forming highly reactive intermediates under mild conditions.

  8. Applying green chemistry to the photochemical route to artemisinin

    Science.gov (United States)

    Amara, Zacharias; Bellamy, Jessica F. B.; Horvath, Raphael; Miller, Samuel J.; Beeby, Andrew; Burgard, Andreas; Rossen, Kai; Poliakoff, Martyn; George, Michael W.

    2015-06-01

    Artemisinin is an important antimalarial drug, but, at present, the environmental and economic costs of its semi-synthetic production are relatively high. Most of these costs lie in the final chemical steps, which follow a complex acid- and photo-catalysed route with oxygenation by both singlet and triplet oxygen. We demonstrate that applying the principles of green chemistry can lead to innovative strategies that avoid many of the problems in current photochemical processes. The first strategy combines the use of liquid CO2 as solvent and a dual-function solid acid/photocatalyst. The second strategy is an ambient-temperature reaction in aqueous mixtures of organic solvents, where the only inputs are dihydroartemisinic acid, O2 and light, and the output is pure, crystalline artemisinin. Everything else—solvents, photocatalyst and aqueous acid—can be recycled. Some aspects developed here through green chemistry are likely to have wider application in photochemistry and other reactions.

  9. Bibliographic study of photophysical and photochemical properties of laser dyes

    International Nuclear Information System (INIS)

    Doizi, D.

    1986-06-01

    Laser isotope separation of uranium requires high power and precise wave length. This report is a bibliographic and experimental study of the photophysical and photochemical properties of seven commercial laser dyes which have an emission wavelength in the range 5500-6500 A: Rhodamine 110 or 560, rhodamine 6G or 590, rhodamine B or 610, rhodamine 101 or 640, sulforhodamine B or kiton red 620, sulforhodamine 101 or 640 and DCM or LC 6500. Absorption and emission cross section values, fluorescence lifetimes and quantum yields in various solvents are indicated. For each dye, a non exhaustive list of laboratory experiments made with two types of pump sources: Nd YAG (532) and copper vapor laser is given. When it is known, the toxicity of the dyes is mentioned [fr

  10. Photochemical water splitting mediated by a C1 shuttle

    KAUST Repository

    Alderman, N. P.; Sommers, J. M.; Viasus, C. J.; Wang, C. H T; Peneau, V.; Gambarotta, S.; Vidjayacoumar, B.; Al-Bahily, K. A.

    2016-01-01

    The possibility of performing photochemical water splitting in a two-stage system, separately releasing the H and O components, has been probed with two separate catalysts and in combination with a formaldehyde/formate shuttling redox couple. In the first stage, formaldehyde releases hydrogen vigorously in the presence of an Na[Fe(CN)]·10HO catalyst, selectively affording the formate anion. In the second stage, the formate anion is hydro-genated back to formaldehyde by water and in the presence of a BiWO photocatalyst whilst releasing oxygen. Both stages operate at room temperature and under visible light irradiation. The two separate photocatalysts are compatible since water splitting can also be obtained in one-pot experiments with simultaneous H/O evolution.

  11. Photochemical and microbial degradation technologies to remove toxic chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Matsumura, F.; Katayama, A.

    1992-07-01

    An effort was made to apply photochemical degradation technology on biodegradation processes to increase the bioremediation potential of microbial actions. For this purpose, we have chosen Phanerochaete chrysosporium, a wood decaying white-rot fungus and a variety of chlorinated pesticides and aromatics as study materials. By using UV-irradiation and benomyl (a commonly used fungicide) as selection methods, a strain of UV-resistant P. chrysosporium was developed. This strain was found to be capable of rapidly degrading these chlorinated chemicals when they were incubated in N-deficient medium which received 1 hr/day of UV-irradiation. UV-irradiation either at 300 or 254 nm showed the beneficial effect of speeding up the rate of degradation on most of test chemicals with the exception of toxaphene and HCH (hexachlorocyclohexane). By adding fresh glucose to the medium it was possible to maintain high degradation capacity for several weeks.

  12. Bioavialability of Dom Photochemically Released from Resuspended Sediments

    Science.gov (United States)

    Avery, G. B., Jr.; Rainey, D. H.; Mead, R. N.; Skrabal, S. A.; Kieber, R. J.; Felix, J. D.; Helms, J. R.

    2016-02-01

    Little is known regarding the bioavailability of dissolved organic matter (DOM) released photochemically from resuspended estuarine sediments. Sediments were collected from two sites along the Cape Fear River estuary, NC, USA, size fractionated in 0.2 µm filtered Gulf Stream seawater and exposed to simulated sunlight for six hours. Light exposed samples resulted in increases of dissolved organic carbon (DOC) (34 ± 3 µM), chromophoric dissolved organic matter (CDOM) (a300nm, 2.7 m-1), and fluorescent dissolved organic matter (FDOM) (78.6 quinine sulfate equivalents (QSE)) compared to dark controls. Ultra high resolution mass spectrometric characterization indicated the photoreleased DOM was more oxidized and condensed based upon van Kreevlan analysis. Samples were then filtered and inoculated to a final ratio of 4% with coastal water sample filtered through a100 µm net to remove larger grazing organisms and particles while keeping most of bacterial community intact. All three parameters were monitored during a 30 day-long incubation in the dark to assess biological consumption and alteration. Previously light exposed samples had double (20 vs. 9 µM) the amount of DOC consumed compared to samples not previously exposed to light and twice the loss of CDOM (a300nm, 0.6 vs. 0.3 m-1) compared to samples not previously exposed to light. Previously light exposed samples resulted in a threefold loss of FDOM (9.5 QSE) compared to samples not previously exposed to light (2.8 QSE). Results of this study are important because they demonstrate dissolved organic matter released photochemically from resuspended sediments is more bioavailable than ambient material likely fueling secondary productivity and impacting ecosystem functioning in coastal regions.

  13. Application of photochemical technologies for treatment of landfill leachate

    International Nuclear Information System (INIS)

    Meeroff, Daniel E.; Bloetscher, Frederick; Reddy, D.V.; Gasnier, François; Jain, Swapnil; McBarnette, André; Hamaguchi, Hatsuko

    2012-01-01

    Highlights: ► Photochemical iron-mediated aeration and TiO 2 photocatalysis for leachate treatment. ► Removal efficiency tested on COD, BOD 5 , color, ammonia, and lead. ► Contact times for 90% removal were 10–200 h for PIMA ► Contact times for 90% removal were 3–37 h for TiO 2 photocatalysis. ► Pre-filtration is not necessary. - Abstract: Because of widely varying practices in solid waste management, an all-inclusive solution to long-term management of landfill leachate is currently not available. There is a major technological need for sustainable, economical options for safe discharge of leachate to the environment. Two potential on-site pretreatment technologies, photochemical iron-mediated aeration (PIMA) and TiO 2 photocatalysis were compared for treatment of landfill leachate at laboratory scale. Results of bench scale testing of real landfill leachate with PIMA and TiO 2 photocatalysis showed up to 86% conversion of refractory COD to complete mineralization, up to 91% removal of lead, up to 71% removal of ammonia without pH adjustment, and up to 90% effective color removal with detention times between 4 and 6 h, in field samples. The estimated contact times for 90% removal of COD, ammonia, lead, and color were found to be on the order of 10–200 h for PIMA and 3–37 h for TiO 2 photocatalysis. Testing with actual leachate samples showed 85% TiO 2 photocatalyst recovery efficiency with no loss in performance after multiple (n > 4 uses). Pre-filtration was not found to be necessary for effective treatment using either process.

  14. Application of photochemical technologies for treatment of landfill leachate

    Energy Technology Data Exchange (ETDEWEB)

    Meeroff, Daniel E., E-mail: dmeeroff@fau.edu [Department of Civil, Environmental and Geomatics Engineering, Florida Atlantic University, Boca Raton, FL (United States); Bloetscher, Frederick; Reddy, D.V.; Gasnier, Francois; Jain, Swapnil; McBarnette, Andre; Hamaguchi, Hatsuko [Department of Civil, Environmental and Geomatics Engineering, Florida Atlantic University, Boca Raton, FL (United States)

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer Photochemical iron-mediated aeration and TiO{sub 2} photocatalysis for leachate treatment. Black-Right-Pointing-Pointer Removal efficiency tested on COD, BOD{sub 5}, color, ammonia, and lead. Black-Right-Pointing-Pointer Contact times for 90% removal were 10-200 h for PIMA Black-Right-Pointing-Pointer Contact times for 90% removal were 3-37 h for TiO{sub 2} photocatalysis. Black-Right-Pointing-Pointer Pre-filtration is not necessary. - Abstract: Because of widely varying practices in solid waste management, an all-inclusive solution to long-term management of landfill leachate is currently not available. There is a major technological need for sustainable, economical options for safe discharge of leachate to the environment. Two potential on-site pretreatment technologies, photochemical iron-mediated aeration (PIMA) and TiO{sub 2} photocatalysis were compared for treatment of landfill leachate at laboratory scale. Results of bench scale testing of real landfill leachate with PIMA and TiO{sub 2} photocatalysis showed up to 86% conversion of refractory COD to complete mineralization, up to 91% removal of lead, up to 71% removal of ammonia without pH adjustment, and up to 90% effective color removal with detention times between 4 and 6 h, in field samples. The estimated contact times for 90% removal of COD, ammonia, lead, and color were found to be on the order of 10-200 h for PIMA and 3-37 h for TiO{sub 2} photocatalysis. Testing with actual leachate samples showed 85% TiO{sub 2} photocatalyst recovery efficiency with no loss in performance after multiple (n > 4 uses). Pre-filtration was not found to be necessary for effective treatment using either process.

  15. Simulations of photochemical smog formation in complex urban areas

    Science.gov (United States)

    Muilwijk, C.; Schrijvers, P. J. C.; Wuerz, S.; Kenjereš, S.

    2016-12-01

    In the present study we numerically investigated the dispersion of photochemical reactive pollutants in complex urban areas by applying an integrated Computational Fluid Dynamics (CFD) and Computational Reaction Dynamics (CRD) approach. To model chemical reactions involved in smog generation, the Generic Reaction Set (GRS) approach is used. The GRS model was selected since it does not require detailed modeling of a large set of reactive components. Smog formation is modeled first in the case of an intensive traffic emission, subjected to low to moderate wind conditions in an idealized two-dimensional street canyon with a building aspect ratio (height/width) of one. It is found that Reactive Organic Components (ROC) play an important role in the chemistry of smog formation. In contrast to the NOx/O3 photochemical steady state model that predicts a depletion of the (ground level) ozone, the GRS model predicts generation of ozone. Secondly, the effect of direct sunlight and shadow within the street canyon on the chemical reaction dynamics is investigated for three characteristic solar angles (morning, midday and afternoon). Large differences of up to one order of magnitude are found in the ozone production for different solar angles. As a proof of concept for real urban areas, the integrated CFD/CRD approach is applied for a real scale (1 × 1 km2) complex urban area (a district of the city of Rotterdam, The Netherlands) with high traffic emissions. The predicted pollutant concentration levels give realistic values that correspond to moderate to heavy smog. It is concluded that the integrated CFD/CRD method with the GRS model of chemical reactions is both accurate and numerically robust, and can be used for modeling of smog formation in complex urban areas.

  16. Photochemical cycle of bacteriorhodopsin studied by resonance Raman spectroscopy.

    Science.gov (United States)

    Stockburger, M; Klusmann, W; Gattermann, H; Massig, G; Peters, R

    1979-10-30

    Individual species of the photochemical cycle of bacteriorhodopsin, a retinal-protein complex of Halobacteria, were studied in aqueous suspensions of the "purple membrane" at room temperature by resonance Raman (RR) spectroscopy with flow systems. Two pronounced deuterium shifts were found in the RR spectra of the all-trans complex BR-570 in H2O-D2O suspensions. The first is ascribed to C=NH+ (C=ND+) stretching vibrations of the protonated Schiff base which links retinal to opsin. The second is assigned tentatively to an "X-H" ("X-D") bending mode, where "X" is an atom which carries an exchangeable proton. A RR spectrum of the 13-cis-retinal complex "BR-548" could be deduced from spectra of the dark-adapted purple membrane. The RR spectrum of the M-412 intermediate was monitored in a double-beam pump-probe experiment. The main vibrational features of the intermediate M' in the reaction M-412 in equilibrium hv M' leads to delta BR-570 could be deduced from a photostationary mixture of M-412 and M'. Difference procedures were applied to obtain RR spectra of the L-550 intermediate and of two new long-lived species, R1'-590 and R2-550. From kinetic data it is suggested that T1'-590 links the proton-translocating cycle to the "13-cis" cycle of BR-548. The protonation and isomeric states of the different species are discussed in light of the new spectroscopic and kinetic data. It is found that conformational changes during the photochemical cycle play an important role.

  17. The photochemical stability of the Venus atmosphere against UV radiation

    International Nuclear Information System (INIS)

    Mills, F.P.; Slanger, T.G.; Allen, M.

    2004-01-01

    Full text: One unresolved question regarding the Venus atmosphere is what chemical mechanism(s) stabilize its primary constituent (CO 2 ) against UV radiation. CO 2 photolyzes on the day side into CO and O after absorbing photons at 2 rather than recombining with CO to form CO 2 , and the intense night side O 2 airglow observed quantitatively supports this. CO and O 2 are photochemically stable in an otherwise pure CO 2 atmosphere so significant abundances of CO and O 2 could accumulate on Venus if no catalytic mechanism existed to speed the reformation of CO 2 . However, the observational upper limit on ground state O 2 is equivalent to 2 from CO and O 2 . Recent laboratory work verified the existence of the ClC(O)OO catalytic mechanism that has been used in photochemical models since the early 1980s. However, there are significant uncertainties in the rates for the component steps of this catalytic mechanism. An alternative mechanism for production of CO 2 that has not previously been modeled but which could be competitive with the ClCO(O)O mechanism is the reaction CO + O 2 (c 1 Σ - u ) → CO 2 + O( 1 D) or O( 1 S), Reaction (1). A range of values for Reaction (1) will be examined in model calculations to compare with observational (UV to IR) constraints and to assess under what conditions this mechanism is competitive with the ClC(O)OO catalytic mechanism. The sensitivity of the results to uncertainties in the CO 2 UV absorption cross section also will be examined

  18. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them.

    Science.gov (United States)

    Leppek, Kathrin; Das, Rhiju; Barna, Maria

    2018-03-01

    RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.

  19. Perfluorinated carboxylic and sulphonic acids in surface water media from the regions of Tibetan Plateau: Indirect evidence on photochemical degradation?

    Science.gov (United States)

    Yamazaki, Eriko; Falandysz, Jerzy; Taniyasu, Sachi; Hui, Ge; Jurkiewicz, Gabriela; Yamashita, Nobuyoshi; Yang, Yong-Liang; Lam, Paul K S

    2016-01-01

    Perfluorinated surfactants and repellents are synthetic substances that have found numerous industrial and customer applications. Due to their persistence, at least two groups of these substances-perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs)-are diffused widely in the environment. It is hypothesized that the Tibetan Plateau, is one of few unique places on the Earth, due to its topography, specifically the vast space and high elevation above sea level, geographic location, climate, high solar radiation, lack of industry, little urbanization and general lack of significant direct sources of pollution. There it is believed possible to gain an insight into atmospheric fate (possible photochemical degradation of higher molecular mass and formation of lower molecular mass PFCAs and PFSAs) of PFASs under un-disturbed environmental conditions. Ultratrace analytical method for PFCAs and PFSAs and use of transportation and field blanks, laboratory blanks and isotopically labelled surrogates for recovery control has allowed the determination of nine perfluorinated carboxylic acids and six perfluorinated sulfonic acids at ultra-trace levels in water based samples from the alpine dimension regions of the Tibetan Plateau, the eastern slope of Minya Konka peak at the eastern edge of the Tibetan Plateau, and also from the city of Chengdu from the lowland of the Sichuan Province in China. The specific compositional pattern of PFCAs and PFSAs and low levels of pollution with those compounds were observed in the central region of the Tibetan Plateau and in the region adjacent to the peaks of Minya Konka in the Eastern Tibetan Plateau. The fingerprint of the compositional pattern of PFCAs and PFSAs in water samples in the central region of the Tibetan Plateau and in the alpine region adjacent to the peaks of Minya Konka in the Eastern Tibetan Plateau may be explained by the result of photochemical degradation with dealkylation of longer chain

  20. Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

    Directory of Open Access Journals (Sweden)

    Victoria Mesa

    2017-09-01

    Full Text Available Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain, and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria, as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi. Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles, and Opisthokonta (Fungi. Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha, whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales. Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats.

  1. Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

    Science.gov (United States)

    Mesa, Victoria; Gallego, Jose L. R.; González-Gil, Ricardo; Lauga, Béatrice; Sánchez, Jesús; Méndez-García, Celia; Peláez, Ana I.

    2017-01-01

    Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats. PMID:28955322

  2. An Interactive Exercise To Learn Eukaryotic Cell Structure and Organelle Function.

    Science.gov (United States)

    Klionsky, Daniel J.; Tomashek, John J.

    1999-01-01

    Describes a cooperative, interactive problem-solving exercise for studying eukaryotic cell structure and function. Highlights the dynamic aspects of movement through the cell. Contains 15 references. (WRM)

  3. Electro- and photochemical switching of dithienylethene self-assembled monolayers on gold electrodes

    DEFF Research Database (Denmark)

    Browne, W.R.; Kudernac, T.; Katsonis, N.

    2008-01-01

    forms of the dithienylethene SAMs is examined and found to be sensitive to the molecular structure of the switch. For the three dithienylethenes, the electrochemical behavior with respect to electrochemical ring opening/closing is retained in the SAMs. In contrast, a marked dependence on the nature...... of the anchoring group is observed upon immobilization in terms of the retention of the photochemical properties observed in solution. For the meta-thiophenol anchor both photochemical ring opening and closing are observed in the SAM, while for the thienyl-thiol-anchored switches the photochemically properties...

  4. Simulation of photoreactive transients and of photochemical transformation of organic pollutants in sunlit boreal lakes across 14 degrees of latitude: A photochemical mapping of Sweden.

    Science.gov (United States)

    Koehler, Birgit; Barsotti, Francesco; Minella, Marco; Landelius, Tomas; Minero, Claudio; Tranvik, Lars J; Vione, Davide

    2018-02-01

    Lake water constituents, such as chromophoric dissolved organic matter (CDOM) and nitrate, absorb sunlight which induces an array of photochemical reactions. Although these reactions are a substantial driver of pollutant degradation in lakes they are insufficiently understood, in particular on large scales. Here, we provide for the first time comprehensive photochemical maps covering a large geographic region. Using photochemical kinetics modeling for 1048 lakes across Sweden we simulated the steady-state concentrations of four photoreactive transient species, which are continuously produced and consumed in sunlit lake waters. We then simulated the transient-induced photochemical transformation of organic pollutants, to gain insight into the relevance of the different photoreaction pathways. We found that boreal lakes were often unfavorable environments for photoreactions mediated by hydroxyl radicals (OH) and carbonate radical anions (CO 3 - ), while photoreactions mediated by CDOM triplet states ( 3 CDOM*) and, to a lesser extent, singlet oxygen ( 1 O 2 ) were the most prevalent. These conditions promote the photodegradation of phenols, which are used as plastic, medical drug and herbicide precursors. When CDOM concentrations increase, as is currently commonly the case in boreal areas such as Sweden, 3 CDOM* will also increase, promoting its importance in photochemical pathways even more. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Automatic generation of gene finders for eukaryotic species

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Krogh, A.

    2006-01-01

    and quality of reliable gene annotation grows. Results We present a procedure, Agene, that automatically generates a species-specific gene predictor from a set of reliable mRNA sequences and a genome. We apply a Hidden Markov model (HMM) that implements explicit length distribution modelling for all gene......Background The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically generate species-specific gene finders and to re-train them as the quantity...... structure blocks using acyclic discrete phase type distributions. The state structure of the each HMM is generated dynamically from an array of sub-models to include only gene features represented in the training set. Conclusion Acyclic discrete phase type distributions are well suited to model sequence...

  6. Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers

    International Nuclear Information System (INIS)

    Teif, Vladimir B; Rippe, Karsten

    2011-01-01

    A recent study of transcription regulation in Drosophila embryonic development revealed a complex non-monotonic dependence of gene expression on the distance between binding sites of repressor and activator proteins at the corresponding enhancer cis-regulatory modules (Fakhouri et al 2010 Mol. Syst. Biol. 6 341). The repressor efficiency was high at small separations, low around 30 bp, reached a maximum at 50–60 bp, and decreased at larger distances to the activator binding sites. Here, we propose a straightforward explanation for the distance dependence of repressor activity by considering the effect of the presence of a nucleosome. Using a method that considers partial unwrapping of nucleosomal DNA from the histone octamer core, we calculated the dependence of activator binding on the repressor–activator distance and found a quantitative agreement with the distance dependence reported for the Drosophila enhancer element. In addition, the proposed model offers explanations for other distance-dependent effects at eukaryotic enhancers. (communication)

  7. The biology of eukaryotic promoter prediction - a review

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, Pierre; Chauvin, Yves

    1999-01-01

    between functional promoters has been estimated to be in the range of 30-40 kilobases. Although it is conceivable that some of these predicted promoters correspond to cryptic initiation sites that are used in vivo, it is likely that most are false positives. This suggests that it is important to carefully......Computational prediction of eukaryotic promoters from the nucleotide sequence is one of the most attractive problems in sequence analysis today, but it is also a very difficult one. Thus, current methods predict in the order of one promoter per kilobase in human DNA, while the average distance...... reconsider the biological data that forms the basis of current algorithms, and we here present a review of data that may be useful in this regard. The review covers the following topics: (1) basal transcription and core promoters, (2) activated transcription and transcription factor binding sites, (3) Cp...

  8. A general strategy to construct small molecule biosensors in eukaryotes.

    Science.gov (United States)

    Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David

    2015-12-29

    Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.

  9. Cytoplasmic Flow Enhances Organelle Dispersion in Eukaryotic Cells

    Science.gov (United States)

    Koslover, Elena; Mogre, Saurabh; Chan, Caleb; Theriot, Julie

    The cytoplasm of a living cell is an active environment through which intracellular components move and mix. We explore, using theoretical modeling coupled with microrheological measurements, the efficiency of particle dispersion via different modes of transport within this active environment. In particular, we focus on the role of cytoplasmic flow over different scales in contributing to organelle transport within two different cell types. In motile neutrophil cells, we show that bulk fluid flow associated with rapid cell deformation enhances particle transport to and from the cell periphery. In narrow fungal hyphae, localized flows due to hydrodynamic entrainment are shown to contribute to optimally efficient organelle dispersion. Our results highlight the importance of non-traditional modes of transport associated with flow of the cytoplasmic fluid in the distribution of organelles throughout eukaryotic cells.

  10. Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave

    Science.gov (United States)

    Azua-Bustos, A.; Gonzalez-Silva, C.; Mancilla, R.A.; Salas, L.; Palma, R.E.; Wynne, J.J.; McKay, C.P.; Vicuna, R.

    2009-01-01

    Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert. ?? Springer Science + Business Media, LLC 2009.

  11. Short RNA guides cleavage by eukaryotic RNase III.

    Directory of Open Access Journals (Sweden)

    Bruno Lamontagne

    Full Text Available In eukaryotes, short RNAs guide a variety of enzymatic activities that range from RNA editing to translation repression. It is hypothesized that pre-existing proteins evolved to bind and use guide RNA during evolution. However, the capacity of modern proteins to adopt new RNA guides has never been demonstrated. Here we show that Rnt1p, the yeast orthologue of the bacterial dsRNA-specific RNase III, can bind short RNA transcripts and use them as guides for sequence-specific cleavage. Target cleavage occurred at a constant distance from the Rnt1p binding site, leaving the guide RNA intact for subsequent cleavage. Our results indicate that RNase III may trigger sequence-specific RNA degradation independent of the RNAi machinery, and they open the road for a new generation of precise RNA silencing tools that do not trigger a dsRNA-mediated immune response.

  12. Synthesis of eukaryotic lipid biomarkers in the bacterial domain

    Science.gov (United States)

    Welander, P. V.; Banta, A. B.; Lee, A. K.; Wei, J. H.

    2017-12-01

    Lipid biomarkers are organic molecules preserved in sediments and sedimentary rocks that can function as geological proxies for certain microbial taxa or for specific environmental conditions. These molecular fossils provide a link between organisms and their environments in both modern and ancient settings and have afforded significant insight into ancient climatic events, mass extinctions, and various evolutionary transitions throughout Earth's history. However, the proper interpretation of lipid biomarkers is dependent on a broad understanding of their diagenetic precursors in modern systems. This includes understanding the taphonomic transformations that these molecules undergo, their biosynthetic pathways, and the ecological conditions that affect their cellular production. In this study, we focus on one group of lipid biomarkers - the sterols. These are polycyclic isoprenoidal lipids that have a high preservation potential and play a critical role in the physiology of most eukaryotes. However, the synthesis and function of these lipids in the bacterial domain has not been fully explored. Here we utilize a combination of bioinformatics, microbial genetics, and biochemistry to demonstrate that bacterial sterol producers are more prevalent in environmental metagenomic samples than in the genomic databases of cultured organisms and to identify novel proteins required to synthesize and modify sterols in bacteria. These proteins represent a distinct pathway for sterol synthesis exclusive to bacteria and indicate that sterol synthesis in bacteria may have evolved independently of eukaryotic sterol biosynthesis. Taken together, these results demonstrate how studies in extant bacteria can provide insight into the biological sources and the biosynthetic pathways of specific lipid biomarkers and in turn may allow for more robust interpretation of biomarker signatures.

  13. Potential biosignatures in super-Earth atmospheres II. Photochemical responses.

    Science.gov (United States)

    Grenfell, J L; Gebauer, S; Godolt, M; Palczynski, K; Rauer, H; Stock, J; von Paris, P; Lehmann, R; Selsis, F

    2013-05-01

    Spectral characterization of super-Earth atmospheres for planets orbiting in the habitable zone of M dwarf stars is a key focus in exoplanet science. A central challenge is to understand and predict the expected spectral signals of atmospheric biosignatures (species associated with life). Our work applies a global-mean radiative-convective-photochemical column model assuming a planet with an Earth-like biomass and planetary development. We investigated planets with gravities of 1g and 3g and a surface pressure of 1 bar around central stars with spectral classes from M0 to M7. The spectral signals of the calculated planetary scenarios have been presented by in an earlier work by Rauer and colleagues. The main motivation of the present work is to perform a deeper analysis of the chemical processes in the planetary atmospheres. We apply a diagnostic tool, the Pathway Analysis Program, to shed light on the photochemical pathways that form and destroy biosignature species. Ozone is a potential biosignature for complex life. An important result of our analysis is a shift in the ozone photochemistry from mainly Chapman production (which dominates in Earth's stratosphere) to smog-dominated ozone production for planets in the habitable zone of cooler (M5-M7)-class dwarf stars. This result is associated with a lower energy flux in the UVB wavelength range from the central star, hence slower planetary atmospheric photolysis of molecular oxygen, which slows the Chapman ozone production. This is important for future atmospheric characterization missions because it provides an indication of different chemical environments that can lead to very different responses of ozone, for example, cosmic rays. Nitrous oxide, a biosignature for simple bacterial life, is favored for low stratospheric UV conditions, that is, on planets orbiting cooler stars. Transport of this species from its surface source to the stratosphere where it is destroyed can also be a key process. Comparing 1g with

  14. RNase MRP and the RNA processing cascade in the eukaryotic ancestor.

    Science.gov (United States)

    Woodhams, Michael D; Stadler, Peter F; Penny, David; Collins, Lesley J

    2007-02-08

    Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.

  15. Integrated Science Assessment (ISA) of Ozone and Related Photochemical Oxidants (Second External Review Draft, Sep 2011)

    Science.gov (United States)

    EPA has released the Integrated Science Assessment of Ozone and Related Photochemical Oxidants (Second External Review Draft) for independent peer review and public review. This draft document represents a concise synthesis and evaluation of the most policy-relevant scienc...

  16. A review of post-column photochemical reaction systems coupled to electrochemical detection in HPLC

    International Nuclear Information System (INIS)

    Fedorowski, Jennifer; LaCourse, William R.

    2010-01-01

    Post-column photochemical reaction systems have developed into a common approach for enhancing conventional methods of detection in HPLC. Photochemical reactions as a means of 'derivatization' have a significant number of advantages over chemical reaction-based methods, and a significant effort has been demonstrated to develop an efficient photochemical reactor. When coupled to electrochemical (EC) detection, the technique allows for the sensitive and selective determination of a variety of compounds (e.g., organic nitro explosives, beta-lactam antibiotics, sulfur-containing antibiotics, pesticides and insecticides). This review will focus on developments and methods using post-column photochemical reaction systems followed by EC detection in liquid chromatography. Papers are presented in chronological order to emphasize the evolution of the approach and continued importance of the application.

  17. Diagnostic Evaluation of Ozone Production and Horizontal Transport in a Regional Photochemical Air Quality Modeling System

    Science.gov (United States)

    A diagnostic model evaluation effort has been performed to focus on photochemical ozone formation and the horizontal transport process since they strongly impact the temporal evolution and spatial distribution of ozone (O3) within the lower troposphere. Results from th...

  18. Synthesis of fluorescent metal nanoparticles in aqueous solution by photochemical reduction

    KAUST Repository

    Kshirsagar, Prakash; Sangaru, Shiv; Brunetti, Virgilio; Malvindi, Maria Ada Da; Pompa, Pier Paolo

    2014-01-01

    A facile green chemistry approach for the synthesis of sub-5 nm silver and gold nanoparticles is reported. The synthesis was achieved by a photochemical method using tyrosine as the photoreducing agent. The size of the gold and silver nanoparticles

  19. APPLICATION OF BAYESIAN MONTE CARLO ANALYSIS TO A LAGRANGIAN PHOTOCHEMICAL AIR QUALITY MODEL. (R824792)

    Science.gov (United States)

    Uncertainties in ozone concentrations predicted with a Lagrangian photochemical air quality model have been estimated using Bayesian Monte Carlo (BMC) analysis. Bayesian Monte Carlo analysis provides a means of combining subjective "prior" uncertainty estimates developed ...

  20. ITS1: a DNA barcode better than ITS2 in eukaryotes?

    Science.gov (United States)

    Wang, Xin-Cun; Liu, Chang; Huang, Liang; Bengtsson-Palme, Johan; Chen, Haimei; Zhang, Jian-Hui; Cai, Dayong; Li, Jian-Qin

    2015-05-01

    A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large-scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species. © 2014 John Wiley & Sons Ltd.

  1. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water.

    Science.gov (United States)

    Korajkic, Asja; Parfrey, Laura Wegener; McMinn, Brian R; Baeza, Yoshiki Vazquez; VanTeuren, Will; Knight, Rob; Shanks, Orin C

    2015-02-01

    Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is known about how these communities change due to mixing and subsequent decomposition of the sewage contaminant. We investigated decay of sewage in upper Mississippi River using Illumina sequencing of 16S and 18S rRNA gene hypervariable regions and qPCR for human-associated and general fecal Bacteroidales indicators. Mixtures of primary treated sewage and river water were placed in dialysis bags and incubated in situ under ambient conditions for seven days. We assessed changes in microbial community composition under two treatments in a replicated factorial design: sunlight exposure versus shaded and presence versus absence of native river microbiota. Initial diversity was higher in sewage compared to river water for 16S sequences, but the reverse was observed for 18S sequences. Both treatments significantly shifted community composition for eukaryotes and bacteria (P treatments for both 16S (R = 0.50; P > 0.001) and 18S (R = 0.91; P = 0.001) communities. A comparison of 16S sequence data and fecal indicator qPCR measurements indicated that the latter was a good predictor of overall bacterial community change over time (rho: 0.804-0.814, P = 0.001). These findings suggest that biotic interactions, such as predation by bacterivorous protozoa, can be critical factors in the decomposition of sewage in freshwater habitats and support the use of Bacteroidales genetic markers as indicators of fecal pollution. Published by Elsevier Ltd.

  2. Photochemical reactions of nucleic acids and their constituents of photobiological relevance

    International Nuclear Information System (INIS)

    Saito, I.; Sugiyama, H.; Matsuura, T.

    1983-01-01

    A review is given of the papers published from 1977 to May 1983 on the UV-induced photochemical reactions of nucleic acids and their constituents of photobiological relevance where the structures of photoproducts have been fully characterized. Among the topics discussed are photoadditions relevant to nucleic acid-protein photocrosslinking, photoreactions with psoralens and nucleic acids and photochemical reactions of polynucleotides. (U.K.)

  3. Photochemical pollution indicators; Les indicateurs de la pollution photochimique. La mesure des composes azotes

    Energy Technology Data Exchange (ETDEWEB)

    Perros, P E; Marion, T [Paris-7 Univ., 75 (France). Laboratoire Interuniversitaire des Systemes Atmospheriques

    1998-11-01

    The number of photochemical pollution is generally based on the observation of ozone and nitrogen oxides concentration levels. So, the measurement of photochemical pollution indicators becomes essential to better understand the involved phenomena, and at the end to enable its reduction control and strategy. In this paper, we focus on the measurements of nitrogen compounds (NO{sub x} PAN, HNO{sub 3}). (authors) 24 refs.

  4. International conference on the photochemical conversion and storage of solar energy

    Energy Technology Data Exchange (ETDEWEB)

    Hofman, M.Z.

    1977-01-31

    Abstracts are given for the eight formal lectures and the contributed papers from delegates which were presented in the form of posters. There were seven sessions divided by subject as follows: (1) photochemistry, (2) electron transfer mechanisms in photochemical energy conversion processes, (3) photoelectrolysis, (4) photogalvanics, (5) photochemical production of fuels in homogeneous solutions, (6) membranes for photosynthesis reactions, and (7) non-biological systems for organic molecular energy storage. (WHK)

  5. Influence of photochemical transformations upon optic-spectral characteristics of iodine cadmium crystals with copper dopant

    International Nuclear Information System (INIS)

    Novosad, S.S.

    2000-01-01

    The influence of photochemical transformations upon absorption. X-ray, photo- and thermostimulated luminescence of crystals CdI 2 :CuI, CdI 2 :CuI and CdI 2 :CuO grown by Stockbarger - Czochralski method has been studied. The photochemical reactions in crystals of iodine cadmium with the dopant of copper leads to reducing the intensity of X-ray, photo- and thermostimulated luminescence, the appearance of new luminescent centers is not observed

  6. Fabrication of self-written waveguide in photosensitive polyimide resin by controlling photochemical reaction of photosensitizer

    International Nuclear Information System (INIS)

    Yamashita, K.; Kuro, T.; Oe, K.; Mune, K.; Tagawa, K.; Naitou, R.; Mochizuki, A.

    2004-01-01

    We have investigated optical properties of photosensitive polyimide appropriating for long self-written waveguide fabrication. From systematic measurements of absorption properties, it was found that photochemical reaction of photosensitizer dissolved in the photosensitive polyimide resins relates to transparency after the exposure, which limits the length of the fabricated self-written waveguide. By controlling the photochemical reaction, in which the photosensitive polyimide resin has sufficient transparency during exposure, four times longer self-written waveguide core was fabricated

  7. Photochemical surface modification of PP for abrasion resistance

    International Nuclear Information System (INIS)

    Bahners, Thomas; Haessler, Ruediger; Gao Shanglin; Maeder, Edith; Wego, Andreas; Schollmeyer, Eckhard

    2009-01-01

    The potential of a photo-chemical approach to increase the surface hardness of polypropylene (PP) has been studied. Using a 222 nm excimer lamp, fibers and film were irradiated in the presence of multi-functional substances diallylphthalate (DAP), tetraallyloxyethane (TAE), and pentaerithritoltriacylate (PETA) and characterized with regard to the resulting effect on abrasion resistance. AFM-based methods were employed to analyze thermo-mechanical surface properties. Nanoindentation and microthermal analyses of the outermost surface layers of UV treated fibers gave clear indications of an effective cross-linking of reactive substances present during irradiation. One may assume that the reactive media polymerize on top of the surface of the PP substrate and form a thin-layer. The abrasion resistance of the PP fibers was tested by applying stress through a rotating and axially oscillating roller of defined roughness and measuring the mass loss as a function of time. The abrasion resistance was found to be remarkably improved compared to the untreated fiber. Best effects were achieved using PETA as reactive substance. The experiments clearly showed the influence of processing conditions, namely with regard to homogeneous coverage of the substrate surface with the reactive medium.

  8. Application of photochemical technologies for treatment of landfill leachate.

    Science.gov (United States)

    Meeroff, Daniel E; Bloetscher, Frederick; Reddy, D V; Gasnier, François; Jain, Swapnil; McBarnette, André; Hamaguchi, Hatsuko

    2012-03-30

    Because of widely varying practices in solid waste management, an all-inclusive solution to long-term management of landfill leachate is currently not available. There is a major technological need for sustainable, economical options for safe discharge of leachate to the environment. Two potential on-site pretreatment technologies, photochemical iron-mediated aeration (PIMA) and TiO(2) photocatalysis were compared for treatment of landfill leachate at laboratory scale. Results of bench scale testing of real landfill leachate with PIMA and TiO(2) photocatalysis showed up to 86% conversion of refractory COD to complete mineralization, up to 91% removal of lead, up to 71% removal of ammonia without pH adjustment, and up to 90% effective color removal with detention times between 4 and 6h, in field samples. The estimated contact times for 90% removal of COD, ammonia, lead, and color were found to be on the order of 10-200 h for PIMA and 3-37 h for TiO(2) photocatalysis. Testing with actual leachate samples showed 85% TiO(2) photocatalyst recovery efficiency with no loss in performance after multiple (n>4 uses). Pre-filtration was not found to be necessary for effective treatment using either process. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Laser-induced photochemical enrichment of boron isotopes

    International Nuclear Information System (INIS)

    Freund, S.M.; Ritter, J.J.

    1976-01-01

    A boron trichloride starting material containing both boron-10 isotopes and boron-11 isotopes is selectively enriched in one or the other of these isotopes by a laser-induced photochemical method involving the reaction of laser-excited boron trichloride with either H 2 S or D 2 S. The method is carried out by subjecting a low pressure gaseous mixture of boron trichloride starting material and the sulfide to infrared radiation from a carbon dioxide TE laser. The wave length of the radiation is selected so as to selectively excite one or the other of boron-10 BCl 3 molecules or boron-11 BCl 3 molecules, thereby making them preferentially more reactive with the sulfide. The laser-induced reaction produces both a boron-containing solid phase reaction product and a gaseous phase containing mostly unreacted BCl 3 and small amounts of sulfhydroboranes. Pure boron trichloride selectively enriched in one of the isotopes is recovered as the primary product of the method from the gaseous phase by a multi-step recovery procedure. Pure boron trichloride enriched in the other isotope is recovered as a secondary product of the method by the subsequent chlorination of the solid phase reaction product followed by separation of BCl 3 from the mixture of gaseous products resulting from the chlorination

  10. Photochemical ozone budget during the BIBLE A and B campaigns

    Science.gov (United States)

    Ko, Malcolm; Hu, Wenjie; Rodríguez, José M.; Kondo, Yutaka; Koike, Makoto; Kita, Kazuyuki; Kawakami, Shuji; Blake, Donald; Liu, Shaw; Ogawa, Toshihiro

    2003-02-01

    Using the measured concentrations of NO, O3, H2O, CO, CH4, and NMHCs along the flight tracks, a photochemical box model is used to calculate the concentrations of the Ox radicals, the HOx radicals, and the nitrogen species at the sampling points. The calculations make use of the measurements from radiometers to scale clear sky photolysis rates to account for cloud cover and ground albedo at the sampling time/point. The concentrations of the nitrogen species in each of the sampled air parcels are computed assuming they are in instantaneous equilibrium with the measured NO and O3. The diurnally varying species concentrations are next calculated using the box model and used to estimate the diurnally averaged production and removal rates of ozone for the sampled air parcels. Clear sky photolysis rates are used in the diurnal calculations. The campaign also provided measured concentration of NOy. The observed NO/NOy ratio is usually larger than the model calculated equilibrium value. There are several possible explanations. It could be a result of recent injection of NO into the air parcel, recent removal of HNO3 from the parcel, recent rapid transport of an air parcel from another location, or a combination of all processes. Our analyses suggest that the local production rate of O3 can be used as another indicator of recent NO injection. However, more direct studies using air trajectory analyses and other collaborative evidences are needed to ascertain the roles played by individual process.

  11. Could clinical photochemical internalisation be optimised to avoid neuronal toxicity?

    Science.gov (United States)

    O'Rourke, Caitriona; Hopper, Colin; MacRobert, Alexander J; Phillips, James B; Woodhams, Josephine H

    2017-08-07

    Photochemical Internalisation (PCI) is a novel drug delivery technology in which low dose photodynamic therapy (PDT) can selectively rupture endo/lysosomes by light activation of membrane-incorporated photosensitisers, facilitating intracellular drug release in the treatment of cancer. For PCI to be developed further, it is important to understand whether nerve damage is an impending side effect when treating cancers within or adjacent to nervous system tissue. Dorsal root ganglion (DRG) neurons and their associated satellite glia were subjected to PCI treatment in a 3D co-culture system following incubation with photosensitisers: meso-tetraphenylporphine (TPPS 2a ) or tetraphenylchlorin disulfonate (TPCS 2 a) and Bleomycin. Results from the use of 3D co-culture models demonstrate that a cancer cell line PCI30 and satellite glia were more sensitive to PCI than neurons and mixed glial cells, athough neurite length was affected. Neurons in culture survived PCI treatment under conditions sufficient to kill tumour cells, suggesting cancers within or adjacent to nervous system tissue could be treated with this novel technology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  12. Enhancing endosomal escape of transduced proteins by photochemical internalisation.

    Directory of Open Access Journals (Sweden)

    Kevin Mellert

    Full Text Available Induced internalisation of functional proteins into cultured cells has become an important aspect in a rising number of in vitro and in vivo assays. The endo-lysosomal entrapment of the transduced proteins remains the major problem in all transduction protocols. In this study we compared the efficiency, cytotoxicity and protein targeting of different commercially available transduction reagents by transducing a well-studied fluorescently labelled protein (Atto488-bovine serum albumin into cultured human sarcoma cells. The amount of internalised protein and toxicity differed between the different reagents, but the percentage of transduced cells was consistently high. Furthermore, in all protocols the signals of the transduced Atto488-BSA were predominantly punctual consistent with an endosomal localisation. To overcome the endosomal entrapment, the transduction protocols were combined with a photochemical internalisation (PCI treatment. Using this combination revealed that an endosomal disruption is highly effective in cell penetrating peptide (CPP mediated transduction, whereas lipid-mediated transductions lead to a lower signal spreading throughout the cytosol. No change in the signal distribution could be achieved in treatments using non-lipid polymers as a transduction reagent. Therefore, the combination of protein transduction protocols based on CPPs with the endosomolytic treatment PCI can facilitate protein transduction experiments in vitro.

  13. Enhancing endosomal escape of transduced proteins by photochemical internalisation.

    Science.gov (United States)

    Mellert, Kevin; Lamla, Markus; Scheffzek, Klaus; Wittig, Rainer; Kaufmann, Dieter

    2012-01-01

    Induced internalisation of functional proteins into cultured cells has become an important aspect in a rising number of in vitro and in vivo assays. The endo-lysosomal entrapment of the transduced proteins remains the major problem in all transduction protocols. In this study we compared the efficiency, cytotoxicity and protein targeting of different commercially available transduction reagents by transducing a well-studied fluorescently labelled protein (Atto488-bovine serum albumin) into cultured human sarcoma cells. The amount of internalised protein and toxicity differed between the different reagents, but the percentage of transduced cells was consistently high. Furthermore, in all protocols the signals of the transduced Atto488-BSA were predominantly punctual consistent with an endosomal localisation. To overcome the endosomal entrapment, the transduction protocols were combined with a photochemical internalisation (PCI) treatment. Using this combination revealed that an endosomal disruption is highly effective in cell penetrating peptide (CPP) mediated transduction, whereas lipid-mediated transductions lead to a lower signal spreading throughout the cytosol. No change in the signal distribution could be achieved in treatments using non-lipid polymers as a transduction reagent. Therefore, the combination of protein transduction protocols based on CPPs with the endosomolytic treatment PCI can facilitate protein transduction experiments in vitro.

  14. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert

    2010-05-01

    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  15. Methane on Mars: Thermodynamic Equilibrium and Photochemical Calculations

    Science.gov (United States)

    Levine, J. S.; Summers, M. E.; Ewell, M.

    2010-01-01

    The detection of methane (CH4) in the atmosphere of Mars by Mars Express and Earth-based spectroscopy is very surprising, very puzzling, and very intriguing. On Earth, about 90% of atmospheric ozone is produced by living systems. A major question concerning methane on Mars is its origin - biological or geological. Thermodynamic equilibrium calculations indicated that methane cannot be produced by atmospheric chemical/photochemical reactions. Thermodynamic equilibrium calculations for three gases, methane, ammonia (NH3) and nitrous oxide (N2O) in the Earth s atmosphere are summarized in Table 1. The calculations indicate that these three gases should not exist in the Earth s atmosphere. Yet they do, with methane, ammonia and nitrous oxide enhanced 139, 50 and 12 orders of magnitude above their calculated thermodynamic equilibrium concentration due to the impact of life! Thermodynamic equilibrium calculations have been performed for the same three gases in the atmosphere of Mars based on the assumed composition of the Mars atmosphere shown in Table 2. The calculated thermodynamic equilibrium concentrations of the same three gases in the atmosphere of Mars is shown in Table 3. Clearly, based on thermodynamic equilibrium calculations, methane should not be present in the atmosphere of Mars, but it is in concentrations approaching 30 ppbv from three distinct regions on Mars.

  16. Photochemical Microscale Electrophoresis Allows Fast Quantification of Biomolecule Binding.

    Science.gov (United States)

    Möller, Friederike M; Kieß, Michael; Braun, Dieter

    2016-04-27

    Intricate spatiotemporal patterns emerge when chemical reactions couple to physical transport. We induce electrophoretic transport by a confined photochemical reaction and use it to infer the binding strength of a second, biomolecular binding reaction under physiological conditions. To this end, we use the photoactive compound 2-nitrobenzaldehyde, which releases a proton upon 375 nm irradiation. The charged photoproducts locally perturb electroneutrality due to differential diffusion, giving rise to an electric potential Φ in the 100 μV range on the micrometer scale. Electrophoresis of biomolecules in this field is counterbalanced by back-diffusion within seconds. The biomolecule concentration is measured by fluorescence and settles proportionally to exp(-μ/D Φ). Typically, binding alters either the diffusion coefficient D or the electrophoretic mobility μ. Hence, the local biomolecule fluorescence directly reflects the binding state. A fit to the law of mass action reveals the dissociation constant of the binding reaction. We apply this approach to quantify the binding of the aptamer TBA15 to its protein target human-α-thrombin and to probe the hybridization of DNA. Dissociation constants in the nanomolar regime were determined and match both results in literature and in control experiments using microscale thermophoresis. As our approach is all-optical, isothermal and requires only nanoliter volumes at nanomolar concentrations, it will allow for the fast screening of biomolecule binding in low volume multiwell formats.

  17. Photochemical and other air pollutants in the Netherlands

    Energy Technology Data Exchange (ETDEWEB)

    Floor, H.

    1976-01-01

    In 1975, together with the State Institute of Public Health and the Royal Dutch Meteorological Institute, The Institute of Phytopathological Research continued investigations on incidence of air pollution throughout the Netherlands. Culture vessels with indicator plants were placed on 31 test plots of the National Air Pollution Monitoring Network. During the growing season from May until October, the indicator plants were inspected weekly for typical symptoms of air pollution. Until July, photochemical air pollution by ozone caused less injury to Spinacia oleracea than in the preceding year. On Nicotiana tabacum there was as much injury as in 1974, especially in the 33rd, 36th and 37th week, all over the country. An increasing number of injurious effects by peroxyacetyl nitrate was observed on Petunia nyctaginiflora, Poa annua and Urtica urens. Medicago sativa, Fagopyrum esculentuma nd Petunia nyctaginiflora, indicator plants for the pollutants SO2, NO/sub x/ and ethylene, showed little and Solanum tuberosum, possible indicator plant for ethylene and ozone, no injury in 1975. Finally air pollution by HG occurred on the same scale as in 1974, as shown by Tulipa gesneriana in spring and Gladiolus gandavensis in summer. These results corresponded with the figures for F from the limed paper method. As in 1974, data on injury to the plants and from the limed paper method showed a decline from south to north.

  18. Plants as indicators of photochemical oxidants in the USA

    Energy Technology Data Exchange (ETDEWEB)

    Jacobson, J.S.

    1977-01-01

    Plant indicators have been important in identifying the photochemical oxidant problem in the USA since the 1940's. They continue to serve as an inexpensive means of detecting oxidants in the atmosphere and determining the geographical extent and frequency of occurrence of oxidants. Plant indicators are particularly useful for land-use planning and in the evaluation of air pollution effects on agriculture, forestry, and native vegetation. Plant indicators are not satisfactory substitutes for chemical monitoring of the atmosphere because their responses lack specificity and are affected by climatic, edaphic, and cultural factors, as well as the concentration and frequency of occurrence of oxidants. Because they integrate many environmental variables, plant indicators may be valuable models for the response of other species but only to the extent that they respond to oxidants in the same manner as these other species. The four most important factors for the successful use of plant indicators are: genetic uniformity of plant material; standardization of cultural conditions; standardization of procedures for scoring foliar symptoms; and uniformity of climatic and edaphic factors among study sites. The species used most frequently as indicators of oxidants in the US have been Bel W-3 tobacco and Pinto bean for 0/sub 3/ and petunia for peroxyacyl nitrate. 41 references, 1 table.

  19. Photochemical chlorine and bromine activation from artificial saline snow

    Directory of Open Access Journals (Sweden)

    S. N. Wren

    2013-10-01

    Full Text Available The activation of reactive halogen species – particularly Cl2 – from sea ice and snow surfaces is not well understood. In this study, we used a photochemical snow reactor coupled to a chemical ionization mass spectrometer to investigate the production of Br2, BrCl and Cl2 from NaCl/NaBr-doped artificial snow samples. At temperatures above the NaCl-water eutectic, illumination of samples (λ > 310 nm in the presence of gas phase O3 led to the accelerated release of Br2, BrCl and the release of Cl2 in a process that was significantly enhanced by acidity, high surface area and additional gas phase Br2. Cl2 production was only observed when both light and ozone were present. The total halogen release depended on [ozone] and pre-freezing [NaCl]. Our observations support a "halogen explosion" mechanism occurring within the snowpack, which is initiated by heterogeneous oxidation and propagated by Br2 or BrCl photolysis and by recycling of HOBr and HOCl into the snowpack. Our study implicates this important role of active chemistry occurring within the interstitial air of aged (i.e. acidic snow for halogen activation at polar sunrise.

  20. What can we infer about the origin of sex in early eukaryotes?

    NARCIS (Netherlands)

    Speijer, Dave

    2016-01-01

    Current analysis shows that the last eukaryotic common ancestor (LECA) was capable of full meiotic sex. The original eukaryotic life cycle can probably be described as clonal, interrupted by episodic sex triggered by external or internal stressors. The cycle could have started in a highly flexible

  1. Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life

    NARCIS (Netherlands)

    Speijer, Dave; Lukeš, Julius; Eliáš, Marek

    2015-01-01

    Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to

  2. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

    DEFF Research Database (Denmark)

    Møller, Henrik D.; Bojsen, Rasmus Kenneth; Tachibana, Chris

    2016-01-01

    Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for d...

  3. Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes

    Directory of Open Access Journals (Sweden)

    Mia M. Bengtsson

    2017-07-01

    Full Text Available Eelgrass (Zostera marina is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome (here defined as an associated prokaryotic community which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes as well as eukaryotic epibionts in- and outside lagoons on the German Baltic Sea coast. Prokaryote microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both prokaryotic and eukaryotic community composition. The prokaryotic microbiome and eukaryotic epibiont communities were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surfaces are home to a mosaic of microbiomes of several epibiotic eukaryotes, in addition to the microbiome of the eelgrass itself. Our findings thereby underline that eukaryotic diversity should be taken into account in order to explain prokaryotic microbiome assembly and dynamics in aquatic environments.

  4. Use of prokaryotic transcriptional activators as metabolite biosensors in eukaryotic cells

    DEFF Research Database (Denmark)

    2018-01-01

    The present invention relates to the use of transcriptional activators from prokaryotic organisms for use in eukaryotic cells, such as yeast as sensors of intracellular and extracellular accumulation of a ligand or metabolite specifically activating this transcriptional activator in a eukaryot...

  5. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

    DEFF Research Database (Denmark)

    Møller, Henrik D.; Bojsen, Rasmus Kenneth; Tachibana, Chris

    2016-01-01

    Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods...

  6. An Integrative Study of Photochemical Air Pollution in Hong Kong: an Overview

    Science.gov (United States)

    Wang, T.

    2014-12-01

    Hong Kong is situated in the Pearl River delta of Southern China. This region has experienced phenomenal economic growth in the past 30 years. Emissions of large amount of pollutants from urban areas and various industries coupled with subtropical climate have led to frequent occurrences of severe photochemical air pollution. Despite the long-term control efforts of the Hong Kong government, the atmospheric levels of ozone have been increasing in the past decade. To obtain an updated and more complete understanding of photochemical smog, an integrative study has been conducted during 2010-2014. Several intensive measurement campaigns were carried out at urban, suburban and rural sites in addition to the routine observations at fourteen air quality monitoring stations in Hong Kong. Meteorological, photochemical, and chemical-transport modeling studies were conducted to investigate the causes/processes of elevated photochemical pollution . The main activities of this study were to (1) examine the situation and trends of photochemical air pollution in Hong Kong, (2) understand some underlying chemical processes in particular the poorly-understood heterogeneous processes of reactive nitrogen oxides, (3) quantify the local, regional, and super-regional contributions to the ozone pollution in Hong Kong, and (4) review the control policy and make further recommendations based on the science. This paper will give an overview of this study and present some key results on the trends and chemistry of the photochemical pollution in this polluted subtropical region.

  7. Oxygen as a factor in eukaryote evolution - Some effects of low levels of oxygen on Saccharomyces cerevisiae

    Science.gov (United States)

    Jahnke, L.; Klein, H. P.

    1979-01-01

    A comparative study of the effects of varying levels of oxygen on some of the metabolic functions of the primitive eukaryote, Saccharomyces cerevisiae, has shown that these cells are responsive to very low levels of oxygen: the level of palmitoyl-Co A desaturase was greatly enhanced by only 0.03 vol % oxygen. Similarly, an acetyl-CoA synthetase associated predominantly with anaerobic growth was stimulated by as little as 0.1% oxygen, while an isoenzyme correlated with aerobic growth was maximally active at much higher oxygen levels (greater than 1%). Closely following this latter pattern were three mitochondrial enzymes that attained maximal activity only under atmospheric levels of oxygen.

  8. On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype.

    Science.gov (United States)

    Dey, Gautam; Thattai, Mukund; Baum, Buzz

    2016-07-01

    If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although 'Loki' cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Evolutionary Pattern of N-Glycosylation Sequon Numbers  in Eukaryotic ABC Protein Superfamilies

    Directory of Open Access Journals (Sweden)

    R. Shyama Prasad Rao

    2010-02-01

    Full Text Available Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline which are the potential sites of asparagine (N linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average, but the sequon density was significantly lower owing to the increase in protein size and decrease in sequon specific amino acids. However, mammalian ABC proteins have significantly higher sequon density, and both serine and threonine containing sequons (NXS and NXT have been positively selected—against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accord- ingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective.

  10. Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology.

    Science.gov (United States)

    Liljeruhm, Josefine; Funk, Saskia K; Tietscher, Sandra; Edlund, Anders D; Jamal, Sabri; Wistrand-Yuen, Pikkei; Dyrhage, Karl; Gynnå, Arvid; Ivermark, Katarina; Lövgren, Jessica; Törnblom, Viktor; Virtanen, Anders; Lundin, Erik R; Wistrand-Yuen, Erik; Forster, Anthony C

    2018-01-01

    Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Förster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field. Most near-term applications of CPs require expression in a different domain of life: bacteria. However, it is unclear which of the eukaryotic CP genes might be suitable and how best to assay them. Here, taking advantage of codon optimization programs in 12 cases, we engineered 14 CP sequences (meffRed, eforRed, asPink, spisPink, scOrange, fwYellow, amilGFP, amajLime, cjBlue, meffBlue, aeBlue, amilCP, tsPurple and gfasPurple) into a palette of Escherichia coli BioBrick plasmids. BioBricks comply with synthetic biology's most widely used, simplified, cloning standard. Differences in color intensities, maturation times and fitness costs of expression were compared under the same conditions, and visible readout of gene expression was quantitated. A surprisingly large variation in cellular fitness costs was found, resulting in loss of color in some overnight liquid cultures of certain high-copy-plasmid-borne CPs, and cautioning the use of multiple CPs as markers in competition assays. We solved these two problems by integrating pairs of these genes into the chromosome and by engineering versions of the same CP with very different colors. Availability of 14 engineered CP genes compared in E. coli , together with chromosomal mutants suitable for competition assays, should simplify and expand CP study and applications. There was no single plasmid-borne CP that combined

  11. Photochemical decomposition of perfluorooctanoic acid mediated by iron in strongly acidic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Ohno, Masaki, E-mail: mohno@hiroshima-u.ac.jp [Environmental Research and Management Center, Hiroshima University, 1-5-3 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8513 (Japan); Ito, Masataka; Ohkura, Ryouichi [Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, 265-1, Higashijima, Akiha-ku, Niigata 956-8603 (Japan); Mino A, Esteban R. [Environmental Research and Management Center, Hiroshima University, 1-5-3 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8513 (Japan); Kose, Tomohiro [Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, 265-1, Higashijima, Akiha-ku, Niigata 956-8603 (Japan); Okuda, Tetsuji [Environmental Research and Management Center, Hiroshima University, 1-5-3 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8513 (Japan); Nakai, Satoshi [Department of Chemical Engineering, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527 (Japan); Kawata, Kuniaki [Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, 265-1, Higashijima, Akiha-ku, Niigata 956-8603 (Japan); Nishijima, Wataru [Environmental Research and Management Center, Hiroshima University, 1-5-3 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8513 (Japan)

    2014-03-01

    Highlights: • Perfluorooctanoic acid (PFOA) was decomposed based on ferric ion performance. • Complete decomposition of PFOA was confirmed in strongly acidic conditions. • Fe{sup 2+} changed to Fe{sup 3+} to restore chemical equilibrium in this condition. • Fe{sup 3+} was only produced from Fe{sup 2+} by hydroxyl radical in weakly acidic conditions. • The Fe{sup 3+} regeneration mechanisms resulted in the performance of Fe{sup 3+} for PFOA. - Abstract: The performance of a ferric ion mediated photochemical process for perfluorooctanoic acid (PFOA) decomposition in strongly acidic conditions of pH 2.0 was evaluated in comparison with those in weakly acidic conditions, pH 3.7 or pH 5.0, based on iron species composition and ferric ion regeneration. Complete decomposition of PFOA under UV irradiation was confirmed at pH 2.0, whereas perfluoroheptanoic acid (PFHpA) and other intermediates were accumulated in weakly acidic conditions. Iron states at each pH were evaluated using a chemical equilibrium model, Visual MINTEQ. The main iron species at pH 2.0 is Fe{sup 3+} ion. Although Fe{sup 3+} ion is consumed and is transformed to Fe{sup 2+} ion by photochemical decomposition of PFOA and its intermediates, the produced Fe{sup 2+} ion will change to Fe{sup 3+} ion to restore chemical equilibrium. Continuous decomposition will occur at pH 2.0. However, half of the iron cannot be dissolved at pH 3.7. The main species of dissolved iron is Fe(OH){sup 2+}. At pH 3.7 or higher pH, Fe{sup 3+} ion will only be produced from the oxidation of Fe{sup 2+} ion by hydroxyl radical produced by Fe(OH){sup 2+} under UV irradiation. These different mechanisms of Fe{sup 3+} regeneration that prevail in strongly and weakly acidic conditions will engender different performances of the ferric ion.

  12. Photochemical aging of aerosol particles in different air masses arriving at Baengnyeong Island, Korea

    Science.gov (United States)

    Kang, Eunha; Lee, Meehye; Brune, William H.; Lee, Taehyoung; Park, Taehyun; Ahn, Joonyoung; Shang, Xiaona

    2018-05-01

    Atmospheric aerosol particles are a serious health risk, especially in regions like East Asia. We investigated the photochemical aging of ambient aerosols using a potential aerosol mass (PAM) reactor at Baengnyeong Island in the Yellow Sea during 4-12 August 2011. The size distributions and chemical compositions of aerosol particles were measured alternately every 6 min from the ambient air or through the highly oxidizing environment of a potential aerosol mass (PAM) reactor. Particle size and chemical composition were measured by using the combination of a scanning mobility particle sizer (SMPS) and a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS). Inside the PAM reactor, O3 and OH levels were equivalent to 4.6 days of integrated OH exposure at typical atmospheric conditions. Two types of air masses were distinguished on the basis of the chemical composition and the degree of aging: air transported from China, which was more aged with a higher sulfate concentration and O : C ratio, and the air transported across the Korean Peninsula, which was less aged with more organics than sulfate and a lower O : C ratio. For both episodes, the particulate sulfate mass concentration increased in the 200-400 nm size range when sampled through the PAM reactor. A decrease in organics was responsible for the loss of mass concentration in 100-200 nm particles when sampled through the PAM reactor for the organics-dominated episode. This loss was especially evident for the m/z 43 component, which represents less oxidized organics. The m/z 44 component, which represents further oxidized organics, increased with a shift toward larger sizes for both episodes. It is not possible to quantify the maximum possible organic mass concentration for either episode because only one OH exposure of 4.6 days was used, but it is clear that SO2 was a primary precursor of secondary aerosol in northeast Asia, especially during long-range transport from China. In addition

  13. In situ airborne measurements of aerosol optical properties during photochemical pollution events

    Science.gov (United States)

    Mallet, M.; van Dingenen, R.; Roger, J. C.; Despiau, S.; Cachier, H.

    2005-02-01

    Dry aerosol optical properties (scattering, absorbing coefficients, and single scattering albedo) were derived from in situ airborne measurements during two photochemical pollution events (25 and 26 June) observed during the Experience sur Site pour Contraindre les Modeles de Pollution atmospherique et de Transport d'Emissions (ESCOMPTE) experiment. Two flights were carried out during daytime (one during the morning and one at noon) over a domain, allowing the investigation of how an air pollution event affects the particle optical properties. Both horizontal distribution and vertical profiles are presented. Results from the horizontal mapping show that plumes of enhanced scattering and absorption are formed in the planetary boundary layer (PBL) during the day in the sea breeze-driven outflow of the coastal urban-industrial area of Marseille-Fos de Berre. The domain-averaged scattering coefficient (at 550 nm) over land σs changes from 35 (28) Mm-1 during land breeze to 63 (43) Mm-1 during sea breeze on 25 June (26 June), with local maxima reaching > 100 Mm-1. The increase in the scattering coefficient is associated with new particle formation, indicative of secondary aerosol formation. Simultaneously, the domain-averaged absorption coefficient increases from 5.6 (3.4) Mm-1 to 9.3 (8.0) Mm-1. The pollution plume leads to strong gradients in the single scattering albedo ωo over the domain studied, with local values as low as 0.73 observed inside the pollution plume. The role of photochemistry and secondary aerosol formation during the 25 June case is shown to increase ωo and to make the aerosol more `reflecting' while the plume moves away from the sources. The lower photochemical activity, observed in the 26 June case, induces a relatively higher contribution of black carbon, making the aerosol more absorbing. Results from vertical profiles at a single near-urban location in the domain indicate that the changes in optical properties happen almost entirely within

  14. Synthesis of hydroxyl liquid polybutadiene by photochemical decomposition of hydrogen peroxide

    International Nuclear Information System (INIS)

    Moutinho, Marcus Tadeu Moura

    1995-01-01

    The synthesis of hydroxyl terminated polybutadienes (HTPB) by photochemical decomposition (λ=254 nm) of hydrogen peroxide (H 2 O 2 ) in alcoholic medium was studied. The influence of reaction time, H 2 O 2 and alcohol concentrations, type of alcohol and radiation intensity on the polymerization rate was determined. Higher polymerization rates were attained when t-butyl alcohol was used as the compatibilizing agent (19% conversion after 8 hours). The HTPBs were characterized by hydroxyl content (acetylation), functionality, IR microstructure and types of hydroxyl groups ( 1 H-NMR and 13 C-NMR), 2-vinyl cyclohexene (VCH) content and viscosity. The polymers showed molecular weights (Mn) in the range of 458 to 1,099, molecular weight distribution (Mw/Mn) in the range of 1.20 to 1.46 and functionality between 1.2 and 3.2 depending on the alcohol used. NMR results 1 H and 13 C) revealed low cis content for the polybutadienes and identified primary and secondary hydroxyl groups, depending on the alcohol employed as compatibilizing agent. The incorporation of alcohol in polymer chain ends was evidenced. The produced HTPBs presented viscosities in the range of 850 to 1,250 cP (at 25 deg C) and were VCH free. (author)

  15. The properties and Roles of Resonance-Stabilized Radicals in Photochemical Pathways in Titan's Atmosphere

    Science.gov (United States)

    Sebree, Joshua A.; Kidwell, Nathan; Zwier, Timothy

    2010-11-01

    In recent years, the Cassini satellite has been providing details about the composition of Titan's atmosphere. Recent data has shown the existence of polycyclic aromatic hydrocarbons (PAHs) at higher altitudes than previously expected including masses tentatively ascribed to naphthalene and anthracene. The formation of indene (C9H9) and naphthalene (C10H8), the simplest PAHs, and their derivatives are of great interest as similar mechanisms may lead to the formation of larger fused-ring systems. In recent years it has been proposed that resonance-stabilized radicals (RSRs) may play an important role as intermediates along these pathways. RSRs gain extra stability by delocalizing the unpaired electron through a neighboring conjugated π-system. Because of this extra stability, RSRs are able to build up in concentration, allowing for the creation of larger, more complex systems through their recombination with other RSRs. Mass-selective UV-visible spectra of two RSRs, phenylallyl and benzylallenyl radicals, have been recorded under jet-cooled conditions. These two radicals, while sharing the same radical conjugation, have unique properties. The roles these radicals may play in the formation of fused ring systems will be discussed along with recent photochemical results on reaction pathways starting from benzylallene through the benzylallenyl radical.

  16. Photochemical degradation of 1,3-dichloro-2-propanol aqueous solutions

    International Nuclear Information System (INIS)

    Nikolaki, M.D.; Philippopoulos, C.J.

    2007-01-01

    The photochemical oxidation of 1,3-dichloro-2-propanol (1,3-DCP) was studied by following the target compound degradation, the total carbon removal rate by a total organic carbon (TOC) analyzer and by identifying the oxidation products by gas chromatography-mass spectrometry (GC-MS). The reaction was performed in a batch recycle reactor, at room temperature, using UV radiation provided by a low pressure 12 W Hg lamp and H 2 O 2 as oxidant. Chloride ions, formic, acetic and chloroacetic acid were measured by ion chromatography. Apart from the chloride ions and the organic acids, the presence of 1,3-dichloro-2-propanone and chloroacetyl chloride was also detected and a possible pathway is proposed for the degradation of the parent compound. Complete degradation of 1,3-dichloro-2-propanol was achieved and the TOC removal reached as much as 80% at the end of the reaction time. The effect of the initial concentration of hydrogen peroxide was investigated and it was established that higher concentrations of H 2 O 2 slow down the reaction rate. Finally, the effect of the initial concentration of 1,3-DCP was investigated

  17. Enhanced electrical and optical properties of CdS:Na thin films by photochemical deposition

    Science.gov (United States)

    Kumar, V. Nirmal; Suriakarthick, R.; Gopalakrishnan, R.; Hayakawa, Y.

    2017-06-01

    CdS:Na thin film was deposited on a glass substrate by photochemical deposition from aqueous solution contained CdSO4.5H2O and Na2S2O3 as cation and anion sources, respectively. The anion source Na2S2O3 served as Na dopant source. The deposited film exhibited cubic phase of CdS and incorporation of Na was revealed from X-ray diffraction study. The incorporation of Na in CdS changed the surface morphology from spherical to nano rods. CdS:Na thin film showed blue shift in its absorption spectrum which was more desirable for transmitting higher energy photons (visible region) in thin film solar cells. The Raman analysis confirmed 1 LO and 2 LO process at 297 and 593 cm-1, respectively. The carrier concentration of CdS increased with the inclusion of Na and its resistivity value decreased. Both the electrical and optical properties of CdS were enhanced in CdS:Na thin films which was desirable as a window layer material for photovoltaic application.

  18. Surface-enhanced Raman scattering active gold nanostructure fabricated by photochemical reaction of synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Akinobu, E-mail: yamaguti@lasti.u-hyogo.ac.jp [Laboratory of Advance Science and Technology for Industry, University of Hyogo, 3-1-2 Koto, Kamigori, Ako, Hyogo 678-1205 (Japan); Matsumoto, Takeshi [Laboratory of Advance Science and Technology for Industry, University of Hyogo, 3-1-2 Koto, Kamigori, Ako, Hyogo 678-1205 (Japan); Okada, Ikuo; Sakurai, Ikuya [Synchrotoron Radiation Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Utsumi, Yuichi [Laboratory of Advance Science and Technology for Industry, University of Hyogo, 3-1-2 Koto, Kamigori, Ako, Hyogo 678-1205 (Japan)

    2015-06-15

    The deposition of gold nanoparticles in an electroplating solution containing gold (I) trisodium disulphite under synchrotron X-ray radiation was investigated. The nanoparticles grew and aggregated into clusters with increasing radiation time. This behavior is explained by evaluating the effect of Derjaguin-Landau-Verweyand-Overbeek (DLVO) interactions combining repulsive electrostatic and attractive van der Waals forces on the particle deposition process. The surface-enhanced Raman scattering (SERS) of 4,4′ -bipyridine (4bpy) in aqueous solution was measured using gold nanoparticles immobilized on silicon substrates under systematically-varied X-ray exposure. The substrates provided an in situ SERS spectrum for 1 nM 4bpy. This demonstration creates new opportunities for chemical and environmental analyses through simple SERS measurements. - Highlights: • Gold nanoparticles were produced by photochemical reaction of synchrotron radiation. • The gold nanoparticles grew and aggregated into the higher-order nanostructure. • The behavior is qualitatively explained by analytical estimation. • The surface-enhanced Raman spectroscopy of 4,4′-bipyridine (4bpy) was demonstrated. • The substrate fabricated in a suitable condition provides in situ SERS for 1 nM 4bpy.

  19. Disulfonated tetraphenyl chlorin (TPCS2a)-induced photochemical internalisation of bleomycin in patients with solid malignancies: a phase 1, dose-escalation, first-in-man trial.

    Science.gov (United States)

    Sultan, Ahmed A; Jerjes, Waseem; Berg, Kristian; Høgset, Anders; Mosse, Charles A; Hamoudi, Rifat; Hamdoon, Zaid; Simeon, Celia; Carnell, Dawn; Forster, Martin; Hopper, Colin

    2016-09-01

    Photochemical internalisation, a novel minimally invasive treatment, has shown promising preclinical results in enhancing and site-directing the effect of anticancer drugs by illumination, which initiates localised chemotherapy release. We assessed the safety and tolerability of a newly developed photosensitiser, disulfonated tetraphenyl chlorin (TPCS2a), in mediating photochemical internalisation of bleomycin in patients with advanced and recurrent solid malignancies. In this phase 1, dose-escalation, first-in-man trial, we recruited patients (aged ≥18 to internalisation were either local, resulting from the local inflammatory process, or systemic, mostly as a result of the skin-photosensitising effect of TPCS2a. The most common grade 3 or worse adverse events were unexpected higher transient pain response (grade 3) localised to the treatment site recorded in nine patients, and respiratory failure (grade 4) noted in two patients. One dose-limiting toxicity was reported in the 1·0 mg/kg cohort (skin photosensitivity [grade 2]). Dose-limiting toxicities were reported in two of three patients at a TPCS2a dose of 1·5 mg/kg (skin photosensitivity [grade 3] and wound infection [grade 3]); thus, the maximum tolerated dose of TPCS2a was 1·0 mg/kg. Administration of TPCS2a was found to be safe and tolerable by all patients. No deaths related to photochemical internalisation treatment occurred. TPCS2a-mediated photochemical internalisation of bleomycin is safe and tolerable. We identified TPCS2a 0·25 mg/kg as the recommended treatment dose for future trials. PCI Biotech. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Cultivation of seaweed Gracilaria lemaneiformis enhanced biodiversity in a eukaryotic plankton community as revealed via metagenomic analyses.

    Science.gov (United States)

    Chai, Zhao Yang; He, Zhi Li; Deng, Yun Yan; Yang, Yu Feng; Tang, Ying Zhong

    2018-02-01

    Plankton diversity reflects the quality and health of waters and should be monitored as a critical feature of marine ecosystems. This study applied a pair of 28S rRNA gene-specific primers and pyrosequencing to assess the effects of large-scale cultivation of the seaweed Gracilaria lemaneiformis on the biodiversity of eukaryotic plankton community in the coastal water of Guangdong, China. With 1 million sequences (2,221 operational taxonomic units [OTUs]) obtained from 51 samples, we found that the biodiversity of eukaryotic plankton community was significantly higher in the seaweed cultivation area than that in the nearby control area as reflected in OTU richness, evenness (Shannon-Wiener index) and dominance (Simpson index) for total plankton community and its four subcategories when Gracilaria biomass reached the maximum, while no such a significant difference was observed before seaweed inoculation. Our laboratory experiment using an artificial phytoplankton community of nine species observed the same effects of Gracilaria exposure. Principal component analysis and principal coordinates analysis showed the plankton community structure in cultivation area markedly differed from the control area when Gracilaria biomass reached its maximum. Redundancy analysis showed that G. lemaneiformis was the critical factor in controlling the dynamics of eukaryotic plankton communities in the studied coastal ecosystem. Our results explicitly demonstrated G. lemaneiformis cultivation could enhance biodiversity of plankton community via allelopathy, which prevents one or several plankton species from blooming and consequently maintains a relatively higher biodiversity. Our study provided further support for using large-scale G. lemaneiformis cultivation as an effective approach for improving costal ecosystem health. © 2018 John Wiley & Sons Ltd.

  1. DNA-based molecular fingerprinting of eukaryotic protists and cyanobacteria contributing to sinking particle flux at the Bermuda Atlantic time-series study

    Science.gov (United States)

    Amacher, Jessica; Neuer, Susanne; Lomas, Michael

    2013-09-01

    We used denaturing gradient gel electrophoresis (DGGE) to examine the protist and cyanobacterial communities in the euphotic zone (0-120 m) and in corresponding 150 m particle interceptor traps at the Bermuda Atlantic Time-series Study (BATS) in a two-year monthly time-series from May 2008 to April 2010. Dinoflagellates were the most commonly detected taxa in both water column and trap samples throughout the time series. Diatom sequences were found only eight times in the water column, and only four times in trap material. Small-sized eukaryotic taxa, including the prasinophyte genera Ostreococcus, Micromonas, and Bathycoccus, were present in trap samples, as were the cyanobacteria Prochlorococcus and Synechococcus. Synechococcus was usually overrepresented in trap material, whereas Prochlorococcus was underrepresented compared to the water column. Both seasonal and temporal variability affected patterns of ribosomal DNA found in sediment traps. The two years of this study were quite different hydrographically, with higher storm activity and the passing of a cyclonic eddy causing unusually deep mixing in winter 2010. This was reflected in the DGGE fingerprints of the water column, which showed greater phylotype richness of eukaryotes and a lesser richness of cyanobacteria in winter of 2010 compared with the winter of 2009. Increases in eukaryotic richness could be traced to increased diversity of prasinophytes and prymnesiophytes. The decrease in cyanobacterial richness was in turn reflected in the trap composition, but the increase in eukaryotes was not, indicating a disproportionate contribution of certain taxa to sinking particle flux.

  2. Relevance of intracellular polarity to accuracy of eukaryotic chemotaxis

    International Nuclear Information System (INIS)

    Hiraiwa, Tetsuya; Nishikawa, Masatoshi; Shibata, Tatsuo; Nagamatsu, Akihiro; Akuzawa, Naohiro

    2014-01-01

    Eukaryotic chemotaxis is usually mediated by intracellular signals that tend to localize at the front or back of the cell. Such intracellular polarities frequently require no extracellular guidance cues, indicating that spontaneous polarization occurs in the signal network. Spontaneous polarization activity is considered relevant to the persistent motions in random cell migrations and chemotaxis. In this study, we propose a theoretical model that connects spontaneous intracellular polarity and motile ability in a chemoattractant solution. We demonstrate that the intracellular polarity can enhance the accuracy of chemotaxis. Chemotactic accuracy should also depend on chemoattractant concentration through the concentration-dependent correlation time in the polarity direction. Both the polarity correlation time and the chemotactic accuracy depend on the degree of responsiveness to the chemical gradient. We show that optimally accurate chemotaxis occurs at an intermediate responsiveness of intracellular polarity. Experimentally, we find that the persistence time of randomly migrating Dictyostelium cells depends on the chemoattractant concentration, as predicted by our theory. At the optimum responsiveness, this ameboid cell can enhance its chemotactic accuracy tenfold. (paper)

  3. Graph theoretic analysis of protein interaction networks of eukaryotes

    Science.gov (United States)

    Goh, K.-I.; Kahng, B.; Kim, D.

    2005-11-01

    Owing to the recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high-throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are conserved across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interologs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interolog additions, for which we present a possible scenario through an in silico modeling.

  4. NMR comparison of prokaryotic and eukaryotic cytochromes c

    International Nuclear Information System (INIS)

    Chau, Meihing; Cai, Meng Li; Timkovich, R.

    1990-01-01

    1 H NMR spectroscopy has been used to examine ferrocytochrome c-551 from Pseudomonas aeruginosa (ATCC 19429) over the pH range 3.5-10.6 and the temperature range 4-60 degree C. Resonance assignments are proposed for main-chain and side-chain protons. Comparison of results for cytochrome c-551 to recently assigned spectra for horse cytochrome c and mutants of yeast iso-1 cytochrome reveals some unique resonances with unusual chemical shifts in all cytochromes that may serve as markers for the heme region. Results for cytochrome c-551 indicate that in the smaller prokaryotic cytochrome, all benzoid side chains are rapidly flipping on the NMR time scale. In contrast, in eukaryotic cytochromes there are some rings flipping slowly on the NMR time scale. The ferrocytochrome c-551 undergoes a transition linked to pH with a pK around 7. The pH behavior of assigned resonances provides evidence that the site of protonation is the inner or buried 17-propionic acid heme substituent (IUPAC-IUB porphyrin nomenclature). Conformational heterogeneity has been observed for segments near the inner heme propionate substituent

  5. Structural similarities between prokaryotic and eukaryotic 5S ribosomal RNAs

    International Nuclear Information System (INIS)

    Welfle, H.; Boehm, S.; Damaschun, G.; Fabian, H.; Gast, K.; Misselwitz, R.; Mueller, J.J.; Zirwer, D.; Filimonov, V.V.; Venyaminov, S.Yu.; Zalkova, T.N.

    1986-01-01

    5S RNAs from rat liver and E. coli have been studied by diffuse X-ray and dynamic light scattering and by infrared and Raman spectroscopy. Identical structures at a resolution of 1 nm can be deduced from the comparison of the experimental X-ray scattering curves and electron distance distribution functions and from the agreement of the shape parameters. A flat shape model with a compact central region and two protruding arms was derived. Double helical stems are eleven-fold helices with a mean base pair distance of 0.28 nm. The number of base pairs (26 GC, 9 AU for E. coli; 27 GC, 9 AU for rat liver) and the degree of base stacking are the same within the experimental error. A very high regularity in the ribophosphate backbone is indicated for both 5S RNAs. The observed structural similarity and the consensus secondary structure pattern derived from comparative sequence analyses suggest the conclusion that prokaryotic and eukaryotic 5S RNAs are in general very similar with respect to their fundamental structural features. (author)

  6. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity.

    Science.gov (United States)

    Das, Mitali; Singh, Sunita; Pradhan, Satyajit; Narayan, Gopeshwar

    2014-01-01

    As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM) 2-7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the "MCM paradox." Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  7. The prokaryote-eukaryote dichotomy: meanings and mythology.

    Science.gov (United States)

    Sapp, Jan

    2005-06-01

    Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the "prokaryote," in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology.

  8. The current state of eukaryotic DNA base damage and repair.

    Science.gov (United States)

    Bauer, Nicholas C; Corbett, Anita H; Doetsch, Paul W

    2015-12-02

    DNA damage is a natural hazard of life. The most common DNA lesions are base, sugar, and single-strand break damage resulting from oxidation, alkylation, deamination, and spontaneous hydrolysis. If left unrepaired, such lesions can become fixed in the genome as permanent mutations. Thus, evolution has led to the creation of several highly conserved, partially redundant pathways to repair or mitigate the effects of DNA base damage. The biochemical mechanisms of these pathways have been well characterized and the impact of this work was recently highlighted by the selection of Tomas Lindahl, Aziz Sancar and Paul Modrich as the recipients of the 2015 Nobel Prize in Chemistry for their seminal work in defining DNA repair pathways. However, how these repair pathways are regulated and interconnected is still being elucidated. This review focuses on the classical base excision repair and strand incision pathways in eukaryotes, considering both Saccharomyces cerevisiae and humans, and extends to some important questions and challenges facing the field of DNA base damage repair. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Susceptibilities to DNA Structural Transitions within Eukaryotic Genomes

    Science.gov (United States)

    Zhabinskaya, Dina; Benham, Craig; Madden, Sally

    2012-02-01

    We analyze the competitive transitions to alternate secondary DNA structures in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. We use statistical mechanics to calculate the competition among all regions within the sequence that are susceptible to transitions to alternate structures. We use an approximate numerical method since the calculation of an exact partition function is numerically cumbersome for DNA molecules of lengths longer than hundreds of base pairs. This method yields accurate results in reasonable computational times. We implement algorithms that calculate the competition between transitions to denatured states and to Z-form DNA. We analyze these transitions near the transcription start sites (TSS) of a set of eukaryotic genes. We find an enhancement of Z-forming regions upstream of the TSS and a depletion of denatured regions around the start sites. We confirm that these finding are statistically significant by comparing our results to a set of randomized genes with preserved base composition at each position relative to the gene start sites. When we study the correlation of these transitions in orthologous mouse and human genes we find a clear evolutionary conservation of both types of transitions around the TSS.

  10. Isoprenoid biosynthesis in eukaryotic phototrophs: A spotlight on algae

    Energy Technology Data Exchange (ETDEWEB)

    Lohr M.; Schwender J.; Polle, J. E. W.

    2012-04-01

    Isoprenoids are one of the largest groups of natural compounds and have a variety of important functions in the primary metabolism of land plants and algae. In recent years, our understanding of the numerous facets of isoprenoid metabolism in land plants has been rapidly increasing, while knowledge on the metabolic network of isoprenoids in algae still lags behind. Here, current views on the biochemistry and genetics of the core isoprenoid metabolism in land plants and in the major algal phyla are compared and some of the most pressing open questions are highlighted. Based on the different evolutionary histories of the various groups of eukaryotic phototrophs, we discuss the distribution and regulation of the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways in land plants and algae and the potential consequences of the loss of the MVA pathway in groups such as the green algae. For the prenyltransferases, serving as gatekeepers to the various branches of terpenoid biosynthesis in land plants and algae, we explore the minimal inventory necessary for the formation of primary isoprenoids and present a preliminary analysis of their occurrence and phylogeny in algae with primary and secondary plastids. The review concludes with some perspectives on genetic engineering of the isoprenoid metabolism in algae.

  11. The Superoxide Reductase from the Early Diverging Eukaryote Giardia Intestinalis

    International Nuclear Information System (INIS)

    Cabelli, D.E.; Testa, F.; Mastronicola, D.; Bordi, E.; Pucillo, L.P.; Sarti, P.; Saraiva, L.M.; Giuffre, A.; Teixeira, M.

    2011-01-01

    Unlike superoxide dismutases (SODs), superoxidereductases (SORs) eliminate superoxide anion (O 2 # sm b ullet# - ) not through its dismutation, but via reduction to hydrogen peroxide (H 2 O 2 ) in the presence of an electron donor. The microaerobic protist Giardia intestinalis, responsible for a common intestinal disease in humans, though lacking SOD and other canonical reactive oxygen species-detoxifying systems, is among the very few eukaryotes encoding a SOR yet identified. In this study, the recombinant SOR from Giardia (SOR Gi ) was purified and characterized by pulse radiolysis and stopped-flow spectrophotometry. The protein, isolated in the reduced state, after oxidation by superoxide or hexachloroiridate(IV), yields a resting species (T final ) with Fe 3+ ligated to glutamate or hydroxide depending on pH (apparent pK a = 8.7). Although showing negligible SOD activity, reduced SOR Gi reacts with O 2 # sm b ullet# - with a pH-independent second-order rate constant k 1 = 1.0 x 10 9 M -1 s -1 and yields the ferric-(hydro)peroxo intermediate T 1 ; this in turn rapidly decays to the T final state with pH-dependent rates, without populating other detectable intermediates. Immunoblotting assays show that SOR Gi is expressed in the disease-causing trophozoite of Giardia. We propose that the superoxide-scavenging activity of SOR in Giardia may promote the survival of this air-sensitive parasite in the fairly aerobic proximal human small intestine during infection.

  12. Specificity and evolvability in eukaryotic protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Pedro Beltrao

    2007-02-01

    Full Text Available Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10(-5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 10(3 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show significantly different link dynamics. In particular, human proteins involved in immune response, transport, and establishment of localization show signs of positive selection for change of interactions. Our analysis suggests that a small degree of molecular divergence can give rise to important changes at the network level. We propose that the power law distribution observed in protein interaction networks could be partly explained by the cell's requirement for different degrees of protein binding specificity.

  13. Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

    Science.gov (United States)

    Liu, Bernard A

    2017-01-01

    Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

  14. Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes

    Directory of Open Access Journals (Sweden)

    HUAN GAO

    2009-01-01

    Full Text Available To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia, rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

  15. Higher Education

    African Journals Online (AJOL)

    Kunle Amuwo: Higher Education Transformation: A Paradigm Shilt in South Africa? ... ty of such skills, especially at the middle management levels within the higher ... istics and virtues of differentiation and diversity. .... may be forced to close shop for lack of capacity to attract ..... necessarily lead to racial and gender equity,.

  16. Sunlight technologies for photochemical deactivation of organic pollutants in water

    Energy Technology Data Exchange (ETDEWEB)

    Acher, A.; Fischer, E.; Tornheim, R. [The Volcani Center, Inst. of Soils and Water, Bet Dagan (Israel); Manor, Y. [Sheba Medical Center, Central Virology Lab., Ramat Gan (Israel)

    1997-12-31

    Sensitized-photochemical oxidation methods aimed at use in water treatment technologies for deactivation of biotic (microorganisms) and/or of xenobiotic (pesticides) pollutants in water were developed using global solar radiation or concentrated sunlight (up to 250 suns). The solar global radiation was used either for detoxification of industrial waste water from a pesticide factory to allow their discharge into the urban sewer, or for disinfection of domestric effluents to be used in crop irrigation. The disinfection process was eventually carried out in an experimental pilot-scale plant, capable of disinfection up to 50 m{sup 3}/h of effluent supplied by an activated sludge sewage treatment plant located in Tel-Aviv area. The treated effluents did not show any regrowth of the microorganisms during 7 days. The solar concentrated radiation experiments performed using facilities of the Sun Tower of The Weizman Institute of Science, Rehovot. The concentrated sunlight was provided by different combination of several computer controlled heliostates, up to 8, that track the sun and focus the received sunlight onto the target situated on the roof of the sun-tower. The sunlight intensities measured on the target reached up to 200 kW/m{sup 2}. The experiments were performed either batch- or continuous-wise. The water-samples exposed to disinfection were the above effluent, filtered and supplemented with vaccine strain poliovirus or with different concentrations of an industrial potential pollutant (bromacil), MB 2 mg/L and two concentrations of dissolved oxygen (8.0 or 40.0 mg O{sub 2}/L). An exposure time of 2-3 seconds at 150 kW/m{sup 2} was decreased the microorganisms alive (counts) by five orders of magnitude. A comparison between the two above water treatment technologies is presented. (orig./SR)

  17. Simulation of photochemical pollutants in summer 2013 in China

    Science.gov (United States)

    Zhang, H.; Guo, H.; Hu, J.

    2016-12-01

    Rapid economic growth and associated emissions increase in China have led to severe air pollution in recent decades. Photochemical pollutants are secondary formed pollutants in the atmosphere with the existence of sunlight. Ozone (O3) is adverse to human health and ecosystems and secondary organic aerosol (SOA) is a major component of fine particulate matter (PM2.5) that affects human health, visibility, and climate. In this work, the Community Multi-scale Air Quality (CMAQ) model was used to investigate the formation of O3 and SOA in three episodes from June to August 2013. Compared with observation data, O3 performance meets the EPA criteria of mean normalized bias (MNB) within ± 0.15 in major parts of China including five megacities. The diurnal variation of O3 had similar trend with the temperature. The August episode has the highest O3 concentrations of 100 ppb in North China Plain while the July episode has the lowest concentrations of 50 ppb. SOA concentrations were up to 35-40 μgm-3 at different cities in different episodes. Biogenic SOA was the majority with the contributions from glyoxal (GLY), methylglyoxal (MGLY), isoprene epoxydiol (IEPOX) and oligomers (OLGM) of 70%. Isopleth found that NOx controls O3 concentration in most areas of China. Reducing VOC would have minor effects on O3 concentrations while reducing NOx could largely reduce O3 concentration except for urban areas such as Shanghai and Guangzhou. On the contrary, SOA was controlled by VOCs in cities such as Beijing, Shanghai, and Xi'an. This study provides valuable information for designing effective control strategies for O3 and particulate matter in China.

  18. Coupled Photochemical and Condensation Model for the Venus Atmosphere

    Science.gov (United States)

    Bierson, Carver; Zhang, Xi; Mendonca, Joao; Liang, Mao-Chang

    2017-10-01

    Ground based and Venus Express observations have provided a wealth of information on the vertical and latitudinal distribution of many chemical species in the Venus atmosphere [1,2]. Previous 1D models have focused on the chemistry of either the lower [3] or middle atmosphere [4,5]. Photochemical models focusing on the sulfur gas chemistry have also been independent from models of the sulfuric acid haze and cloud formation [6,7]. In recent years sulfur-bearing particles have become important candidates for the observed SO2 inversion above 80 km [5]. To test this hypothesis it is import to create a self-consistent model that includes photochemistry, transport, and cloud condensation.In this work we extend the domain of the 1D chemistry model of Zhang et al. (2012) [5] to encompass the region between the surface to 110 km. This model includes a simple sulfuric acid condensation scheme with gravitational settling. It simultaneously solves for the chemistry and condensation allowing for self-consistent cloud formation. We compare the resulting chemical distributions to observations at all altitudes. We have also validated our model cloud mass against pioneer Venus observations [8]. This updated full atmosphere chemistry model is also being applied in our 2D solver (altitude and altitude). With this 2D model we can model how the latitudinal distribution of chemical species depends on the meridional circulation. This allows us to use the existing chemical observations to place constraints on Venus GCMs [9-11].References: [1] Arney et al., JGR:Planets, 2014 [2] Vandaele et al., Icarus 2017 (pt. 1 & 2) [3] Krasnopolsky, Icarus, 2007 [4] Krasnopolsky, Icarus, 2012 [5] Zhang et al., Icarus 2012 [6] Gao et al., Icarus, 2014 [7] Krasnopolsky, Icarus, 2015 [8] Knollenberg and Hunten, JGR:Space Physics, 1980 [9] Lee et al., JGR:Planets, 2007 [10] Lebonnois et al., Towards Understanding the Climate of Venus, 2013 [11] Mendoncca and Read, Planetary and Space Science, 2016

  19. The independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle

    Directory of Open Access Journals (Sweden)

    Jiang Yong-Hai

    2012-10-01

    Full Text Available Abstract Background In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP and sedoheptulose-1, 7-bisphosphate (SBP are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase, while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase and sedoheptulose-1, 7-bisphosphatase (SBPase, respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario. Results Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II. Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations. Conclusions There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins

  20. Higher Education

    Science.gov (United States)

    & Development (LDRD) National Security Education Center (NSEC) Office of Science Programs Richard P Databases National Security Education Center (NSEC) Center for Nonlinear Studies Engineering Institute Scholarships STEM Education Programs Teachers (K-12) Students (K-12) Higher Education Regional Education

  1. Beyond Agrobacterium-Mediated Transformation: Horizontal Gene Transfer from Bacteria to Eukaryotes.

    Science.gov (United States)

    Lacroix, Benoît; Citovsky, Vitaly

    2018-03-03

    Besides the massive gene transfer from organelles to the nuclear genomes, which occurred during the early evolution of eukaryote lineages, the importance of horizontal gene transfer (HGT) in eukaryotes remains controversial. Yet, increasing amounts of genomic data reveal many cases of bacterium-to-eukaryote HGT that likely represent a significant force in adaptive evolution of eukaryotic species. However, DNA transfer involved in genetic transformation of plants by Agrobacterium species has traditionally been considered as the unique example of natural DNA transfer and integration into eukaryotic genomes. Recent discoveries indicate that the repertoire of donor bacterial species and of recipient eukaryotic hosts potentially are much wider than previously thought, including donor bacterial species, such as plant symbiotic nitrogen-fixing bacteria (e.g., Rhizobium etli) and animal bacterial pathogens (e.g., Bartonella henselae, Helicobacter pylori), and recipient species from virtually all eukaryotic clades. Here, we review the molecular pathways and potential mechanisms of these trans-kingdom HGT events and discuss their utilization in biotechnology and research.

  2. Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota.

    Science.gov (United States)

    Xiong, Jinbo; Yu, Weina; Dai, Wenfang; Zhang, Jinjie; Qiu, Qiongfen; Ou, Changrong

    2018-04-01

    One common notion is emerging that gut eukaryotes are commensal or beneficial, rather than detrimental. To date, however, surprisingly few studies have been taken to discern the factors that govern the assembly of gut eukaryotes, despite growing interest in the dysbiosis of gut microbiota-disease relationship. Herein, we firstly explored how the gut eukaryotic microbiotas were assembled over shrimp postlarval to adult stages and a disease progression. The gut eukaryotic communities changed markedly as healthy shrimp aged, and converged toward an adult-microbiota configuration. However, the adult-like stability was distorted by disease exacerbation. A null model untangled that the deterministic processes that governed the gut eukaryotic assembly tended to be more important over healthy shrimp development, whereas this trend was inverted as the disease progressed. After ruling out the baseline of gut eukaryotes over shrimp ages, we identified disease-discriminatory taxa (species level afforded the highest accuracy of prediction) that characteristic of shrimp health status. The profiles of these taxa contributed an overall 92.4% accuracy in predicting shrimp health status. Notably, this model can accurately diagnose the onset of shrimp disease. Interspecies interaction analysis depicted how the disease-discriminatory taxa interacted with one another in sustaining shrimp health. Taken together, our findings offer novel insights into the underlying ecological processes that govern the assembly of gut eukaryotes over shrimp postlarval to adult stages and a disease progression. Intriguingly, the established model can quantitatively and accurately predict the incidences of shrimp disease.

  3. Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2007-06-01

    Full Text Available Abstract Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. Results Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages. Conclusion A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group.

  4. The Photochemical Conversion of Surrogate Emissions for Use in Toxicological Studies: Role of Particulate- and Gas-Phase Products

    Data.gov (United States)

    U.S. Environmental Protection Agency — The production of photochemical atmospheres under controlled conditions in an irradiation chamber permits the manipulation of parameters that influence the resulting...

  5. Effects of Biological and Photochemical Degradation on the Optical Properties of CDOM Exported to Coastal Marine Environments

    National Research Council Canada - National Science Library

    Moran, Mary

    2004-01-01

    .... This project quantitatively assessed the ability of coastal ocean bacteria to degrade and produce CDOM and investigated the synergistic interactions between bacterial degradation and photochemical...

  6. Structural and biomechanical basis of mitochondrial movement in eukaryotic cells

    Directory of Open Access Journals (Sweden)

    Wu M

    2013-10-01

    Full Text Available Min Wu,1 Aruna Kalyanasundaram,2 Jie Zhu1 1Laboratory of Biomechanics and Engineering, Institute of Biophysics, College of Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; 2College of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA Abstract: Mitochondria serve as energy-producing organelles in eukaryotic cells. In addition to providing the energy supply for cells, the mitochondria are also involved in other processes, such as proliferation, differentiation, information transfer, and apoptosis, and play an important role in regulation of cell growth and the cell cycle. In order to achieve these functions, the mitochondria need to move to the corresponding location. Therefore, mitochondrial movement has a crucial role in normal physiologic activity, and any mitochondrial movement disorder will cause irreparable damage to the organism. For example, recent studies have shown that abnormal movement of the mitochondria is likely to be the reason for Charcot–Marie–Tooth disease, amyotrophic lateral sclerosis, Alzheimer's disease, Huntington's disease, Parkinson's disease, and schizophrenia. So, in the cell, especially in the particular polarized cell, the appropriate distribution of mitochondria is crucial to the function and survival of the cell. Mitochondrial movement is mainly associated with the cytoskeleton and related proteins. However, those components play different roles according to cell type. In this paper, we summarize the structural basis of mitochondrial movement, including microtubules, actin filaments, motor proteins, and adaptin, and review studies of the biomechanical mechanisms of mitochondrial movement in different types of cells. Keywords: mitochondrial movement, microtubules, actin filaments, motor proteins, adaptin

  7. MetWAMer: eukaryotic translation initiation site prediction

    Directory of Open Access Journals (Sweden)

    Brendel Volker

    2008-09-01

    Full Text Available Abstract Background Translation initiation site (TIS identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations. Results MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage. Conclusion We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.

  8. Methyl labeling and TROSY NMR spectroscopy of proteins expressed in the eukaryote Pichia pastoris

    International Nuclear Information System (INIS)

    Clark, Lindsay; Zahm, Jacob A.; Ali, Rustam; Kukula, Maciej; Bian, Liangqiao; Patrie, Steven M.; Gardner, Kevin H.; Rosen, Michael K.; Rosenbaum, Daniel M.

    2015-01-01

    13 C Methyl TROSY NMR spectroscopy has emerged as a powerful method for studying the dynamics of large systems such as macromolecular assemblies and membrane proteins. Specific 13 C labeling of aliphatic methyl groups and perdeuteration has been limited primarily to proteins expressed in E. coli, preventing studies of many eukaryotic proteins of physiological and biomedical significance. We demonstrate the feasibility of efficient 13 C isoleucine δ1-methyl labeling in a deuterated background in an established eukaryotic expression host, Pichia pastoris, and show that this method can be used to label the eukaryotic protein actin, which cannot be expressed in bacteria. This approach will enable NMR studies of previously intractable targets

  9. Enhanced Indirect Photochemical Transformation of Histidine and Histamine through Association with Chromophoric Dissolved Organic Matter.

    Science.gov (United States)

    Chu, Chiheng; Lundeen, Rachel A; Remucal, Christina K; Sander, Michael; McNeill, Kristopher

    2015-05-05

    Photochemical transformations greatly affect the stability and fate of amino acids (AAs) in sunlit aquatic ecosystems. Whereas the direct phototransformation of dissolved AAs is well investigated, their indirect photolysis in the presence of chromophoric dissolved organic matter (CDOM) is poorly understood. In aquatic systems, CDOM may act both as sorbent for AAs and as photosensitizer, creating microenvironments with high concentrations of photochemically produced reactive intermediates, such as singlet oxygen (1O2). This study provides a systematic investigation of the indirect photochemical transformation of histidine (His) and histamine by 1O2 in solutions containing CDOM as a function of solution pH. Both His and histamine showed pH-dependent enhanced phototransformation in the CDOM systems as compared to systems in which model, low-molecular-weight 1O2 sensitizers were used. Enhanced reactivity resulted from sorption of His and histamine to CDOM and thus exposure to elevated 1O2 concentrations in the CDOM microenvironment. The extent of reactivity enhancement depended on solution pH via its effects on the protonation state of His, histamine, and CDOM. Sorption-enhanced reactivity was independently supported by depressed rate enhancements in the presence of a cosorbate that competitively displaced His and histamine from CDOM. Incorporating sorption and photochemical transformation processes into a reaction rate prediction model improved the description of the abiotic photochemical transformation rates of His in the presence of CDOM.

  10. Photochemical Haze Formation in the Atmospheres of Super-Earths and Mini-Neptunes

    Science.gov (United States)

    He, Chao; Hoerst, Sarah M.; Lewis, Nikole K.; Yu, Xinting; Moses, Julianne I.; Kempton, Eliza M.- R.; Marley, Mark S.; McGuiggan, Patricia; Morley, Caroline V.; Valenti, Jeff A.; hide

    2018-01-01

    UV (ultraviolet) radiation can induce photochemical processes in the atmospheres of exoplanet and produce haze particles. Recent transmission spectra of super-Earths and mini-Neptunes have demonstrated the possibility that exoplanets have haze/cloud layers at high altitudes in their atmospheres. Haze particles play an important role in planetary atmospheres because they affect the chemistry, dynamics, and radiation flux in planetary atmospheres, and may provide a source of organic material to the surface which may impact the origin or evolution of life. However, very little information is known about photochemical processes in cool, high-metallicity exoplanetary atmospheres. We present here photochemical haze formation in laboratory simulation experiments with UV radiation; we explored temperatures ranging from 300 to 600 degrees Kelvin and a range of atmospheric metallicities (100 times, 1000 times, and 10000 times solar metallicity). We find that photochemical hazes are generated in all simulated atmospheres, but the haze production rates appear to be temperature dependent: the particles produced in each metallicity group decrease as the temperature increases. The images taken with an atomic force microscope (AFM) show that the particle size (15 nanometers to 190 nanometers) varies with temperature and metallicity. Our results provide useful laboratory data on the photochemical haze formation and particle properties, which can serve as critical inputs for exoplanet atmosphere modeling, and guide future observations of exoplanets with the Transiting Exoplanet Survey Satellite (TESS), the James Webb Space Telescope (JWST), and the Wide-Field Infrared Survey Telescope (WFIRST).

  11. Assessment of diphenylcyclopropenone for photochemically induced mutagenicity in the Ames assay

    Energy Technology Data Exchange (ETDEWEB)

    Wilkerson, M.G.; Connor, T.H.; Henkin, J.; Wilkin, J.K.; Matney, T.S.

    1987-10-01

    The photochemical conversion of diphenylcyclopropenone to diphenylacetylene has recently been reported. Diphenylcyclopropenone is used in the treatment of alopecia areata and is nonmutagenic in a limited Ames assay. We examined diphenylcyclopropenone and diphenylacetylene, as well as synthetic precursors of diphenylcyclopropenone--dibenzylketone and alpha,alpha'-dibromodibenzylketone--for mutagenicity against TA100, TA98, TA102, UTH8413, and UTH8414. All compounds were nonmutagenic except alpha,alpha'-dibromodibenzylketone, which was a potent mutagen in TA100 with and without S-9 activation. The effect of photochemical activation of diphenylcyclopropenone in the presence of bacteria demonstrated mutagenicity in UTH8413 (two times background) at 10 micrograms/plate with S-9 microsomal activation. 8-Methoxypsoralen produces a mutagenic response in TA102 at 0.1 microgram/plate with 60 seconds of exposure to 350 nm light. In vitro photochemically activated Ames assay with S-9 microsomal fraction may enhance the trapping of short-lived photochemically produced high-energy mutagenic intermediates. This technique offers exciting opportunities to trap high-energy intermediates that may play an important role in mutagenesis. This method can be applied to a variety of topically applied dermatologic agents, potentially subjected to photochemical changes in normal use.

  12. Photochemical Transformation Processes in Sunlit Surface Waters (Invited)

    Science.gov (United States)

    Vione, D.

    2013-12-01

    Photochemical reactions are major processes in the transformation of hardly biodegradable xenobiotics in surface waters. They are usually classified into direct photolysis and indirect or sensitised degradation. Direct photolysis requires xenobiotic compounds to absorb sunlight, and to get transformed as a consequence. Sensitised transformation involves reaction with transient species (e.g. °OH, CO3-°, 1O2 and triplet states of chromophoric dissolved organic matter, 3CDOM*), photogenerated by so-called photosensitisers (nitrate, nitrite and CDOM). CDOM is a major photosensitiser: is it on average the main source of °OH (and of CO3-° as a consequence, which is mainly produced upon oxidation by °OH of carbonate and bicarbonate) and the only important source of 1O2 and 3CDOM* [1, 2]. CDOM origin plays a key role in sensitised processes: allochthonous CDOM derived from soil runoff and rich in fulvic and humic substances is usually more photoactive than autochthonous CDOM (produced by in-water biological processes and mainly consisting of protein-like material) or of CDOM derived from atmospheric deposition. An interesting gradual evolution of CDOM origin and photochemistry can be found in mountain lakes across the treeline, which afford a gradual transition of allochthonous- autochtonous - atmopheric CDOM when passing from trees to alpine meadows to exposed rocks [3]. Another important issue is the sites of reactive species photoproduction in CDOM. While there is evidence that smaller molecular weight fractions are more photoactive, some studies have reported considerable 1O2 reactivity in CDOM hydrophobic sites and inside particles [4]. We have recently addressed the problem and found that dissolved species in standard humic acids (hydrodynamic diameter pollutants to be assessed and modelled. For instance, it is possible to predict pollutant half-life times by knowing absorption spectrum, direct photolysis quantum yield and reaction rate constants with °OH, CO3

  13. Higher Education.

    Science.gov (United States)

    Hendrickson, Robert M.

    This chapter reports 1982 cases involving aspects of higher education. Interesting cases noted dealt with the federal government's authority to regulate state employees' retirement and raised the questions of whether Title IX covers employment, whether financial aid makes a college a program under Title IX, and whether sex segregated mortality…

  14. Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells

    NARCIS (Netherlands)

    Ortega, Alvaro D.; Quereda, Juan J; Pucciarelli, M Graciela; García-del Portillo, Francisco

    2014-01-01

    Intracellular bacterial pathogens have evolved distinct lifestyles inside eukaryotic cells. Some pathogens coexist with the infected cell in an obligate intracellular state, whereas others transit between the extracellular and intracellular environment. Adaptation to these intracellular lifestyles

  15. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

    KAUST Repository

    Pearman, John K.; Irigoien, Xabier; Carvalho, Susana

    2015-01-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based

  16. Meeting Report: Minutes from EMBO: Ten Years of Comparative Genomics of Eukaryotic Microorganisms

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; López-García, P.; Louis, E.; Boekhout, T.

    2016-01-01

    Roč. 167, č. 3 (2016), s. 217-221 ISSN 1434-4610 Institutional support: RVO:60077344 Keywords : protist * eukaryotic microorganisms * genomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.794, year: 2016

  17. Phylogenetic analysis of P5 P-type ATPases, a eukaryotic lineage of secretory pathway pumps

    DEFF Research Database (Denmark)

    Møller, Annette; Asp, Torben; Holm, Preben Bach

    2008-01-01

    prokaryotic genome. Based on a protein alignment we could group the P5 ATPases into two subfamilies, P5A and P5B that, based on the number of negative charges in conserved trans-membrane segment 4, are likely to have different ion specificities. P5A ATPases are present in all eukaryotic genomes sequenced so......Eukaryotes encompass a remarkable variety of organisms and unresolved lineages. Different phylogenetic analyses have lead to conflicting conclusions as to the origin and associations between lineages and species. In this work, we investigated evolutionary relationship of a family of cation pumps...... exclusive for the secretory pathway of eukaryotes by combining the identification of lineage-specific genes with phylogenetic evolution of common genes. Sequences of P5 ATPases, which are regarded to be cation pumps in the endoplasmic reticulum (ER), were identified in all eukaryotic lineages but not in any...

  18. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi River water

    Science.gov (United States)

    Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is kn...

  19. Laser induced photochemical and photophysical processes in fuel reprocessing: present scenario and future prospects

    International Nuclear Information System (INIS)

    Bhowmick, G.K.; Sarkar, S.K.; Ramanujam, A.

    2001-01-01

    State-of-art lasers can meet the very stringent requirements of nuclear technology and hence find application in varied areas of nuclear fuel cycle. Here, we discuss two specific applications in nuclear fuel reprocessing namely (a) add-on photochemical modifications of PUREX process where photochemical reactors replace the chemical reactors, and (b) fast, matrix independent sensitive laser analytical techniques. The photochemical modifications based on laser induced valency adjustment offers efficient separation, easy maintenance and over all reduction in the volume of radioactive waste. The analytical technique of time resolved laser induced fluorescence (TRLIF) has several attractive features like excellent sensitivity, element selective, and capability of on line remote process monitoring. For optically opaque solutions, optical excitation is detected by its conversion into thermal energy by non-radiative relaxation processes using the photo-thermal spectroscopic techniques. (author)

  20. Photochemical reduction of CO{sub 2} to fuels and chemicals

    Energy Technology Data Exchange (ETDEWEB)

    DuBois, D. [National Renewable Energy Lab., Golden, CO (United States); Eisenberg, R. [Univ. of Rochester, NY (United States); Fujita, E. [Brookhaven National Lab., Upton, NY (United States)

    1996-09-01

    Photochemical reduction of CO{sub 2} represents a potentially useful approach to developing a sustainable source of carbon-based chemicals, fuels, and materials. In this report the present status of photochemical CO{sub 2} reduction is assessed, areas that need to be better understood for advancement are identified, and approaches to overcoming barriers are suggested. Because of the interdisciplinary nature of this field, assessments of three closely interrelated areas are given including integrated photochemical systems for catalytic CO{sub 2} reduction, thermal catalytic CO{sub 2} reactions, and electrochemical CO{sub 2} reduction. The report concludes with a summary and assessment of potential impacts of this area on chemical and energy technologies.

  1. Carrier-lifetime-controlled selective etching process for semiconductors using photochemical etching

    International Nuclear Information System (INIS)

    Ashby, C.I.H.; Myers, D.R.

    1992-01-01

    This patent describes a process for selectively photochemically etching a semiconductor material. It comprises introducing at least one impurity into at least one selected region of a semiconductor material to be etched to increase a local impurity concentration in the at least one selected region relative to an impurity concentration in regions of the semiconductor material adjacent thereto, for reducing minority carrier lifetimes within the at least one selected region relative to the adjacent regions for thereby providing a photochemical etch-inhibiting mask at the at least one selected region; and etching the semiconductor material by subjecting the surface of the semiconductor material to a carrier-driven photochemical etching reaction for selectively etching the regions of the semiconductor material adjacent the at least one selected region having the increase impurity concentration; wherein the step of introducing at least one impurity is performed so as not to produce damage to the at least one selected region before any etching is performed

  2. Molecular distributions of dicarboxylic acids, ketocarboxylic acids and α-dicarbonyls in biomass burning aerosols: implications for photochemical production and degradation in smoke layers

    Directory of Open Access Journals (Sweden)

    A. Hoffer

    2010-03-01

    Full Text Available Aerosols in the size class <2.5 μm (6 daytime and 9 nighttime samples were collected at a pasture site in Rondônia, Brazil, during the intensive biomass burning period of 16–26 September 2002 as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia – Smoke, Aerosols, Clouds, Rainfall and Climate (LBA-SMOCC. Homologous series of dicarboxylic acids (C2–C11 and related compounds (ketocarboxylic acids and α-dicarbonyls were identified using gas chromatography (GC and GC/mass spectrometry (GC/MS. Among the species detected, oxalic acid was found to be the most abundant, followed by succinic, malonic and glyoxylic acids. Average concentrations of total dicarboxylic acids, ketocarboxylic acids and α-dicarbonyls in the aerosol samples were 2180, 167 and 56 ng m−3, respectively. These are 2–8, 3–11 and 2–16 times higher, respectively, than those reported in urban aerosols, such as in 14 Chinese megacities. Higher ratios of dicarboxylic acids and related compounds to biomass burning tracers (levoglucosan and K+ were found in the daytime than in the nighttime, suggesting the importance of photochemical production. On the other hand, higher ratios of oxalic acid to other dicarboxylic acids and related compounds normalized to biomass burning tracers (levoglucosan and K+ in the daytime provide evidence for the possible degradation of dicarboxylic acids (≥C3 in this smoke-polluted environment. Assuming that these and related compounds are photo-chemically oxidized to oxalic acid in the daytime, and given their linear relationship, they could account for, on average, 77% of the formation of oxalic acid. The remaining portion of oxalic acid may have been directly emitted from biomass burning as suggested by a good correlation with the biomass burning tracers (K+, CO and ECa and organic carbon (OC. However, photochemical production from other precursors could not be excluded.

  3. Arbuscular mycorrhizal symbiosis ameliorates the optimum quantum yield of photosystem II and reduces non-photochemical quenching in rice plants subjected to salt stress.

    Science.gov (United States)

    Porcel, Rosa; Redondo-Gómez, Susana; Mateos-Naranjo, Enrique; Aroca, Ricardo; Garcia, Rosalva; Ruiz-Lozano, Juan Manuel

    2015-08-01

    Rice is the most important food crop in the world and is a primary source of food for more than half of the world population. However, salinity is considered the most common abiotic stress reducing its productivity. Soil salinity inhibits photosynthetic processes, which can induce an over-reduction of the reaction centres in photosystem II (PSII), damaging the photosynthetic machinery. The arbuscular mycorrhizal (AM) symbiosis may improve host plant tolerance to salinity, but it is not clear how the AM symbiosis affects the plant photosynthetic capacity, particularly the efficiency of PSII. This study aimed at determining the influence of the AM symbiosis on the performance of PSII in rice plants subjected to salinity. Photosynthetic activity, plant gas-exchange parameters, accumulation of photosynthetic pigments and rubisco activity and gene expression were also measured in order to analyse comprehensively the response of the photosynthetic processes to AM symbiosis and salinity. Results showed that the AM symbiosis enhanced the actual quantum yield of PSII photochemistry and reduced the quantum yield of non-photochemical quenching in rice plants subjected to salinity. AM rice plants maintained higher net photosynthetic rate, stomatal conductance and transpiration rate than nonAM plants. Thus, we propose that AM rice plants had a higher photochemical efficiency for CO2 fixation and solar energy utilization and this increases plant salt tolerance by preventing the injury to the photosystems reaction centres and by allowing a better utilization of light energy in photochemical processes. All these processes translated into higher photosynthetic and rubisco activities in AM rice plants and improved plant biomass production under salinity. Copyright © 2015 Elsevier GmbH. All rights reserved.

  4. Testing fast photochemical theory during TRACE-P based on measurements of OH, HO2, and CH2O

    Science.gov (United States)

    Olson, Jennifer R.; Crawford, J. H.; Chen, G.; Fried, A.; Evans, M. J.; Jordan, C. E.; Sandholm, S. T.; Davis, D. D.; Anderson, B. E.; Avery, M. A.; Barrick, J. D.; Blake, D. R.; Brune, W. H.; Eisele, F. L.; Flocke, F.; Harder, H.; Jacob, D. J.; Kondo, Y.; Lefer, B. L.; Martinez, M.; Mauldin, R. L.; Sachse, G. W.; Shetter, R. E.; Singh, H. B.; Talbot, R. W.; Tan, D.

    2004-08-01

    Measurements of several short-lived photochemical species (e.g., OH, HO2, and CH2O) were obtained from the DC-8 and P3-B aircraft during the NASA Transport and Chemical Evolution over the Pacific (TRACE-P) campaign. To assess fast photochemical theory over the east Asian coast and western Pacific, these measurements are compared to predictions using a photochemical time-dependent box model constrained by coincident measurements of long-lived tracers and physical parameters. Both OH and HO2 are generally overpredicted by the model throughout the troposphere, which is a different result from previous field campaigns. The calculated-to-observed ratio of OH shows an altitude trend, with OH overpredicted by 80% in the upper troposphere and by 40-60% in the middle troposphere. Boundary layer and lower tropospheric OH ratios decrease from middle tropospheric values to 1.07 for the DC-8 and to 0.70 for the P3-B. HO2 measured on the DC-8 is overpredicted by a median of 23% and shows no trend in the agreement with altitude. Three subsets of data which compose 12% of the HO2 measurements represent outliers with respect to calculated-to-observed ratios: stratospherically influenced air, upper tropospheric data with NO > 135 pptv, and data from within clouds. Pronounced underpredictions of both HO2 and OH were found for stratospherically influenced air, which is in contrast to previous studies showing good agreement of predicted and observed HOx in the stratosphere. Observational evidence of heterogeneous uptake of HO2 within low and middle tropospheric clouds is presented, though there is no indication of significant HO2 uptake within higher-altitude clouds. Model predictions of CH2O are in good agreement with observations in the median for background concentrations, but a large scatter exists. Factors contributing to this scatter are examined, including the limited availability of some important constraining measurements, particularly CH3OOH. Some high concentrations of CH2O

  5. Construction of rat beta defensin-2 eukaryotic expression vector and expression in the transfected rat corneal epithelial cell

    Directory of Open Access Journals (Sweden)

    Jing Dan

    2017-03-01

    Full Text Available AIM: To construct a recombinant eukaryotic expression vector of rat beta defensin-2(rBD-2, transfect it into the rat corneal epithelial cells with lipofection, determine the expression of target gene in the transfected cells, and discuss the potentiality of recombinant plasmid expressed in corneal epithelial cells, hoping to provide an experimental foundation for further study on the antimicrobial activity of rBD-2 in vitro and in vivo and to assess the probability of defensins as a new application for infectious corneal diseases in the future. METHODS: The synthetic rBD-2 DNA fragment was inserted between the XhoI and BamHI restriction enzyme cutting sites of eukaryotic expression vector pIRES2-ZsGreen1 to construct the recombinant plasmid pIRES2-ZsGreen1-rBD-2, then transformed it into E.coli DH5α, positive clones were screened by kanamycin and identified with restriction endonucleases and sequencing analysis. Transfection into the rat corneal epithelial cells was performed by lipofection. Then the experiment was divided into three groups: rat corneal epithelial cell was transfected with the recombinant plasmid pIRES2- ZsGreen1-rBD-2, rat corneal epithelial cell was transfected with the empty plasmid pIRES2-ZsGreen1 and the non-transfected group. The inverted fluorescence microscope was used to observe the transfection process. At last, the level of rBD-2 mRNA expressed in the transfected cells and the control groups are compared by the real-time fluoresence relative quantitative PCR. RESULTS: The recombinant eukaryotic expression vector of pIRES2-ZsGreen1-rBD-2 was successfully constructed. The level of rBD-2 mRNA in transfected cells was significantly higher than that in control groups through the real-time fluorescence relative quantitative PCR. CONCLUSION: The recombinant eukaryotic expression vector pIRES2-ZsGreen1-rBD-2 could be transfected into rat corneal epithelial cells, and exogenous rBD-2 gene could be transcripted into mRNA in

  6. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  7. Extracellular matrix assembly in extreme acidic eukaryotic biofilms and their possible implications in heavy metal adsorption

    International Nuclear Information System (INIS)

    Aguilera, Angeles; Souza-Egipsy, Virginia; San Martin-Uriz, Patxi; Amils, Ricardo

    2008-01-01

    To evaluate the importance of the extracellular matrix in relation to heavy metal binding capacity in extreme acidic environments, the extracellular polymeric substances (EPS) composition of 12 biofilms isolated from Rio Tinto (SW, Spain) was analyzed. Each biofilm was composed mainly by one or two species of eukaryotes, although other microorganisms were present. EPS ranged from 130 to 439 mg g -1 biofilm dry weight, representing between 15% and the 40% of the total biofilm dry weight (DW). Statistically significant differences (p -1 dry weight; 10% to 30% of the total biofilm dry weight. Capsular EPS ranged from 50 to 318 mg g -1 dry weight; 5% to 30% of the total biofilm dry weight. Seven of the 12 biofilms showed higher amounts of capsular than colloidal EPS (p -1 biofilm dry weight, reaching up to 16% of the total composition. In general, the heavy metal composition of the EPS extracted from the biofilms closely resembled the metal composition of the water from which the biofilms were collected

  8. Mapping and characterizing N6-methyladenine in eukaryotic genomes using single molecule real-time sequencing.

    Science.gov (United States)

    Zhu, Shijia; Beaulaurier, John; Deikus, Gintaras; Wu, Tao; Strahl, Maya; Hao, Ziyang; Luo, Guanzheng; Gregory, James A; Chess, Andrew; He, Chuan; Xiao, Andrew; Sebra, Robert; Schadt, Eric E; Fang, Gang

    2018-05-15

    N6-methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes, however, methods for high resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes. Based on these differences, we describe the first approach for mapping m6dA events using SMRT sequencing specifically designed for the study of eukaryotic genomes, and provide appropriate strategies for designing experiments and carrying out sequencing in future studies. We apply the novel approach to study two eukaryotic genomes. For green algae, we construct the first complete genome-wide map of m6dA at single nucleotide and single molecule resolution. For human lymphoblastoid cells (hLCLs), joint analyses of SMRT sequencing and independent sequencing data suggest that putative m6dA events are enriched in the promoters of young, full length LINE-1 elements (L1s). These analyses demonstrate a general method for rigorous mapping and characterization of m6dA events in eukaryotic genomes. Published by Cold Spring Harbor Laboratory Press.

  9. Photochemical technique for reduction of uranium and subsequently plutonium in the Purex process

    International Nuclear Information System (INIS)

    Goldstein, M.; Barker, J.J.; Gangwer, T.

    1976-09-01

    A photochemical modification of the Purex process is described in which a purified side stream of UO 2 ++ ion is reduced to U +4 outside the radioactive area of the reprocessing plant. The U +4 is then cycled back to step 2 of the Purex process to reduce the plutonium and effect separation within the partitioning column. This process is shown to be very energy efficient and compatible with existing conventional lamp technology. Preliminary cost estimates of the energy requirements for photon production are essentially negligible. Conceptual systems and photochemical reactor designs are presented. Potential benefits of this system are discussed

  10. A Universal Protocol for Photochemical Covalent Immobilization of Intact Carbohydrates for the Preparation of Carbohydrate Microarrays

    Science.gov (United States)

    Wang, Huibin; Zhang, Yiming; Yuan, Xun; Chen, Yi; Yan, Mingdi

    2010-01-01

    A universal photochemical method has been established for the immobilization of intact carbohydrates and their analogues, and for the fabrication of carbohydrate microarrays. The method features the use of perfluorophenyl azide (PFPA)-modified substrates and the photochemical reaction of surface azido groups with printed carbohydrates. Various aldoses, ketoses, non-reducing sugars such as alditols and their derivatives can be directly arrayed on the PFPA-modified chips. The lectin-recognition ability of arrayed mannose, glucose and their oligo- and polysaccharides were confirmed using surface plasmon resonance imaging and laser-induced fluorescence imaging. PMID:21138274

  11. Photochemical oxidant transport - Mesoscale lake breeze and synoptic-scale aspects

    Science.gov (United States)

    Lyons, W. A.; Cole, H. S.

    1976-01-01

    Data from routine ozone monitoring in southeastern Wisconsin and limited monitoring of the Milwaukee area by the Environmental Protection Agency are examined. Hourly averages as high as 30 pphm have been recorded in southeastern Wisconsin, and high readings have been reported in rural regions throughout the state. The observations indicate that photochemical oxidants and their nitrogen oxide and reactive hydrocarbon precursers advect from Chicago and northern Indiana into southeastern Wisconsin. There is evidence that synoptic-scale transport of photochemical oxidants occurs, allowing the pollution of entire anticyclones. These results cast doubt on the validity of the Air Quality Control Regions established by amendment to the Clean Air Act of 1970.

  12. Sunlight-Induced Photochemical Degradation of Methylene Blue by Water-Soluble Carbon Nanorods

    Directory of Open Access Journals (Sweden)

    Anshu Bhati

    2016-01-01

    Full Text Available Water-soluble graphitic hollow carbon nanorods (wsCNRs are exploited for their light-driven photochemical activities under outdoor sunlight. wsCNRs were synthesized by a simple pyrolysis method from castor seed oil, without using any metal catalyst or template. wsCNRs exhibited the light-induced photochemical degradation of methylene blue used as a model pollutant by the generation of singlet oxygen species. Herein, we described a possible degradation mechanism of methylene blue under the irradiation of visible photons via the singlet oxygen-superoxide anion pathway.

  13. Ammonia removal from leachate by photochemical process using H2O2

    Directory of Open Access Journals (Sweden)

    Giovani Archanjo Brota

    2010-08-01

    Full Text Available In this work, it was studied the optimization of the photochemical process using H2O2/UV in order to reduce the concentration of ammonia in leachate. It was used landfills leachate previously treated in the development of studies. A photochemical reactor with the capacity of 1.7 liters equipped with refrigeration system and recirculation of leachate was employed in the research. The influence of temperature, the light bulb power, the concentration of H2O2 and treatment time were tested during the study. A removal of 97% of ammonia was observed at 90 min.

  14. Overexpression of a eukaryotic glutathione reductase gene from Brassica campestris improved resistance to oxidative stress in Escherichia coli

    International Nuclear Information System (INIS)

    Yoon, Ho-Sung; Lee, In-Ae; Lee, Hyoshin; Lee, Byung-Hyun; Jo, Jinki

    2005-01-01

    Glutathione reductase (GR) plays an essential role in a cell's defense against reactive oxygen metabolites by sustaining the reduced status of an important antioxidant glutathione. We constructed a recombinant plasmid based on the expression vector pET-18a that overexpresses a eukaryotic GR from Brassica campestris (BcGR) in Escherichia coli. For comparative analyses, E. coli GR (EcGR) was also subcloned in the same manner. The transformed E. coli with the recombinant constructs accumulated a high level of GR transcripts upon IPTG induction. Also, Western blot analysis showed overproduction of the BcGR protein in a soluble fraction of the transformed E. coli extract. When treated with oxidative stress generating reagents such as paraquat, salicylic acid, and cadmium, the BcGR overproducing E. coli exhibited a higher level of growth and survival rate than the control E. coli strain, but it was not as high as the E. coli strain transformed with the inducible EcGR. The translated amino acid sequences of BcGR and EcGR share 37.3% identity but all the functionally known important residues are conserved. It appears that eukaryotic BcGR functions in a prokaryotic system by providing protection against oxidative damages in E. coli

  15. Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea.

    Science.gov (United States)

    Wu, Wenxue; Wang, Lei; Liao, Yu; Huang, Bangqin

    2015-10-01

    To evaluate microbial eukaryotic diversity and distribution in mesoscale processes, we investigated 18S rDNA diversity in a river plume and cyclonic eddy-influenced ecosystem in the southwestern South China Sea (SCS). Restriction fragment length polymorphism analysis was carried out using multiple primer sets. Relative to a wide range of previous similar studies, we observed a significantly higher proportion of sequences of pigmented taxa. Among the photosynthetic groups, Haptophyta accounted for 27.7% of the sequenced clones, which belonged primarily to Prymnesiophyceae. Unexpectedly, five operational taxonomic units of Cryptophyta were closely related to freshwater species. The Chlorophyta mostly fell within the Prasinophyceae, which was comprised of six clades, including Clade III, which is detected in the SCS for the first time in this study. Among the photosynthetic stramenopiles, Chrysophyceae was the most diverse taxon, which included seven clades. The majority of 18S rDNA sequences affiliated with the Dictyochophyceae, Eustigmatophyceae, and Pelagophyceae were closely related to those of pure cultures. The results of redundancy analysis and the permutation Mantel test based on unweighted UniFrac distances, conducted for spatial analyses of the Haptophyta subclades suggested that the Mekong River plume and cyclonic eddy play important roles in regulating microbial eukaryotic diversity and distribution in the southwestern SCS. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  16. Efficient Production of γ-GABA Using Recombinant E. coli Expressing Glutamate Decarboxylase (GAD) Derived from Eukaryote Saccharomyces cerevisiae.

    Science.gov (United States)

    Xiong, Qiang; Xu, Zheng; Xu, Lu; Yao, Zhong; Li, Sha; Xu, Hong

    2017-12-01

    γ-Aminobutyric acid (γ-GABA) is a non-proteinogenic amino acid, which acts as a major regulator in the central nervous system. Glutamate decarboxylase (namely GAD, EC 4.1.1.15) is known to be an ideal enzyme for γ-GABA production using L-glutamic acid as substrate. In this study, we cloned and expressed GAD gene from eukaryote Saccharomyces cerevisiae (ScGAD) in E. coli BL21(DE3). This enzyme was further purified and its optimal reaction temperature and pH were 37 °C and pH 4.2, respectively. The cofactor of ScGAD was verified to be either pyridoxal 5'-phosphate (PLP) or pyridoxal hydrochloride. The optimal concentration of either cofactor was 50 mg/L. The optimal medium for E. coli-ScGAD cultivation and expression were 10 g/L lactose, 5 g/L glycerol, 20 g/L yeast extract, and 10 g/L sodium chloride, resulting in an activity of 55 U/mL medium, three times higher than that of using Luria-Bertani (LB) medium. The maximal concentration of γ-GABA was 245 g/L whereas L-glutamic acid was near completely converted. These findings provided us a good example for bio-production of γ-GABA using recombinant E. coli expressing a GAD enzyme derived from eukaryote.

  17. Quenching of excited uranyl ion during its photochemical reduction with triphenyl-phosphine : Part IV - effect of heterocyclic molecules

    International Nuclear Information System (INIS)

    Sidhu, M.S.; Bhatia, P.V.K.

    1994-01-01

    The presence of heterocyclic compounds triggers off a competition between photophysical and photochemical annihilation of excited uranyl ion during its photochemical reduction with triphenylphosphine. This competition is used to measure Stern-Volmer constant using UV visible spectrophotometer for quenching the uranyl ion luminescence with a number of heterocyclic molecules viz., pyridine, thiophene bipyridyl, tetrahydrofuran and piperidine. (author). 7 refs., 2 figs., 1 tab

  18. Investigation of Phenol Removal in Aqueous Solutions Using Advanced Photochemical Oxidation (APO

    Directory of Open Access Journals (Sweden)

    Naser Jamshidi

    2010-01-01

    Full Text Available Most organic compounds are resistant to conven­tional chemical and biological treatments. For this reason, other methods are being studied as alter­natives to the biological and classical physico-chemical pro­cesses. In this study, advanced photochemical oxidation (APO processes (UV, UV/H2O2, UV/H2O2/Fe(II, andUV/H2O2/Fe(III were investigated in lab-scale experiments for the degradation of phenol in an aqueous solution. A medium-pressure 300 watt (UV-C mercury ultraviolet lamp was used as the radiation source and H2O2 30% as the oxidant. Phenol (initial concentration= 0.5 mmol/L was selected as the model due to its high use and application. Some important parameters such as pH, H2O2 input concentration, iron catalyst concentration, the type of iron salt, and duration of UV radiation were studied based on the standard methods. The results showed that the Photo-Fenton process was the most effective treatment under acidic conditions producing a higher rate of phenol degradation over a very short radiation time. The process accelerated the oxidation rate by 4-5 times the rate of the UV/H2O2 process. The optimum conditions were obtained at a pH value of 3, with a molar ratio of 11.61 for H2O2/Phenol and molar ratios of 0.083 and 0.067for Iron/H2O2 in the UV/H2O2/Fe (II and the UV/H2O2/Fe (III systems, respectively.

  19. Role of effluent organic matter in the photochemical degradation of compounds of wastewater origin.

    Science.gov (United States)

    Bodhipaksha, Laleen C; Sharpless, Charles M; Chin, Yu-Ping; MacKay, Allison A

    2017-03-01

    The photoreactivity of treated wastewater effluent organic matter differs from that of natural organic matter, and the indirect phototransformation rates of micropollutants originating in wastewater are expected to depend on the fractional contribution of wastewater to total stream flow. Photodegradation rates of four common compounds of wastewater origin (sulfamethoxazole, sulfadimethoxine, cimetidine and caffeine) were measured in river water, treated municipal wastewater effluent and mixtures of both to simulate various effluent-stream water mixing conditions that could occur in environmental systems. Compounds were chosen for their unique photodegradation pathways with the photochemically produced reactive intermediates, triplet-state excited organic matter ( 3 OM*), singlet oxygen ( 1 O 2 ), and hydroxyl radicals (OH). For all compounds, higher rates of photodegradation were observed in effluent relative to upstream river water. Sulfamethoxazole degraded primarily via direct photolysis, with some contribution from OH and possibly from carbonate radicals and other unidentified reactive intermediates in effluent-containing samples. Sulfadimethoxine also degraded mainly by direct photolysis, and natural organic matter appeared to inhibit this process to a greater extent than predicted by light screening. In the presence of effluent organic matter, sulfadimethoxine showed additional reactions with OH and 1 O 2 . In all water samples, cimetidine degraded by reaction with 1 O 2 (>95%) and caffeine by reaction with OH (>95%). In river water mixtures, photodegradation rate constants for all compounds increased with increasing fractions of effluent. A conservative mixing model was able to predict reaction rate constants in the case of hydroxyl radical reactions, but it overestimated rate constants in the case of 3 OM* and 1 O 2 pathways. Finally, compound degradation rate constants normalized to the rate of light absorption by water correlated with E 2 /E 3 ratios

  20. Chlorophyll fluorescence, photochemical reflective index and normalized difference vegetative index during plant senescence.

    Science.gov (United States)

    Cordon, Gabriela; Lagorio, M Gabriela; Paruelo, José M

    2016-07-20

    The relationship between the Photochemical Reflectance Index (PRI), Normalized Difference Vegetation Index (NDVI) and chlorophyll fluorescence along senescence was investigated in this work. Reflectance and radiance measurements were performed at canopy level in grass species presenting different photosynthetic metabolism: Avena sativa (C3) and Setaria italica (C4), at different stages of the natural senescence process. Sun induced-chlorophyll fluorescence at 760nm (SIF 760 ) and the apparent fluorescence yield (SIF 760 /a, with a=irradiance at time of measurement) were extracted from the radiance spectra of canopies using the Fraunhofer Line Discrimination-method. The photosynthetic parameters derived from Kautsky kinetics and pigment content were also calculated at leaf level. Whilst stand level NDVI patterns were related to changes in the structure of canopies and not in pigment content, stand level PRI patterns suggested changes both in terms of canopy and of pigment content in leaves. Both SIF 760 /a and Φ PSII decreased progressively along senescence in both species. A strong increment in NPQ was evident in A. sativa while in S. italica NPQ values were lower. Our most important finding was that two chlorophyll fluorescence signals, Φ PSII and SIF 760 /a, correlated with the canopy PRI values in the two grasses assessed, even when tissues at different ontogenic stages were present. Even though significant changes occurred in the Total Chlr/Car ratio along senescence in both studied species, significant correlations between PRI and chlorophyll fluorescence signals might indicate the usefulness of this reflectance index as a proxy of photosynthetic RUE, at least under the conditions of this study. The relationships between stand level PRI and the fluorescence estimators (Φ PSII and SIF 760 /a) were positive in both cases. Therefore, an increase in PRI values as in the fluorescence parameters would indicate higher RUE. Copyright © 2016 Elsevier GmbH. All

  1. Insights into the photochemical transformation pathways of triclosan and 2′-HO-BDE-28

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ya-nan; Xie, Qing; Chen, Jingwen, E-mail: jwchen@dlut.edu.cn; Li, Yingjie; Fu, Zhiqiang

    2015-12-30

    Highlights: • Direct photolysis of anionic HO-PXDEs occurs through excited singlet states. • Dioxin products are formed from excited singlet states of HO-PXDEs. • Self-sensitized photolysis is involved in the phototransformation of HO-PXDEs. • {sup 1} O{sub 2} and ·OH can be generated in energy or electron transfer reactions between excited HO-PXDEs and dissolved O{sub 2}. - Abstract: Hydroxylated polyhalogenated diphenyl ethers (HO-PXDEs) have been recognized as a group of widely detected emerging contaminants in natural waters. Photolysis was proved to be an important transformation pathway for these compounds and their direct phototransformation results in highly toxic dioxins. However, the roles of excited states and reactive oxygen species in the photochemical transformation of these compounds are still unclear. In this study, 2′-HO-2,4,4′-trichlorodiphenyl ether (triclosan) and 2′-HO-2,4,4′-tribromodiphenyl ether (2′-HO-BDE-28) were selected as model compounds to investigate their phototransformation processes. Results showed that the direct photolysis reactions of both triclosan and 2′-HO-BDE-28 occurred via their respective excited singlet states, leading to the generation of dioxins. In addition, the energy and electron transfer reactions between excited states of model compounds and molecular O{sub 2} can lead to the generation of {sup 1}O{sub 2} and ·OH, which results in self-sensitized photolysis. We also found that both the k, Φ dioxin yield for anionic triclosan were higher than those of anionic 2′-HO-BDE-28. This study revealed the roles of the excited states in direct photolysis and the generation pathway of reactive oxygen species in self-sensitized photolysis of HO-PXDEs, which is important for understanding the phototransformation mechanisms of HO-PXDEs.

  2. Performance analysis of a solar photochemical photovoltaic hybrid system for decolorization of Acid Red 26 (AR 26)

    International Nuclear Information System (INIS)

    Cui, Lingyun; Zhu, Li; Huang, Qunwu; Wang, Yiping; Jin, Yanchao; Sun, Yong; Cui, Yong; Chen, Miao; Fan, Jiangyang

    2017-01-01

    To reduce the power energy consumption of wastewater treatment and make full use of the solar spectrum, a new water purification system that integrated homogeneous solar photochemical (SPC) and photovoltaics (PV) was constructed to treat wastewater and generate electricity for the first time. Hydrogen peroxide (H_2O_2) and potassium persulfate (K_2S_2O_8) were chosen as oxidants in the system and have a comparative analysis. The results show that solar/K_2S_2O_8 has a higher decolorization efficiency than solar/H_2O_2, the accumulated ultraviolet energy in solar/K_2S_2O_8, needed for complete decolorization, is far lower than in solar/H_2O_2. Also temperature has a positive effect on the dark-K_2S_2O_8 processes especially in the range of 40–60 °C, and it follows pseudo-first-order kinetic relationship. Meanwhile, to investigate the influence of flow channel on PV, the short circuit current (I_s_c) and maximum output power (P_m) were monitored. It indicates that the presence of flow channel effectively decreases the working temperature of PV modules, while the I_s_c and P_m have a different degree reduce. Luckily, the impact is not big. Additionally, P_m in experiment system, though lower than reference system, is sufficient to drive the whole system. - Highlights: • The hybrid system combing homogenous photochemical with photovoltaics was firstly performed. • Solar/K_2S_2O_8 and solar/H_2O_2 is comparative analysis in the decolorization of AR 26. • K_2S_2O_8 can be activated by heat and irradiation simultaneously in the hybrid system. • The PV panel of the hybrid system could work under lower temperature. • Solar spectrum could be made full use for power generation and water purification.

  3. Ultraviolet-B irradiation of seeds affects photochemical and reproductive performance of the arid-environment ephemeral Dimorphotheca pluvialis

    International Nuclear Information System (INIS)

    Musil, C.F.

    1994-01-01

    A higher polyphenolic content and thicker sclerenchymatous cylinder in the pericarp of ray than of disc seed morphs (diaspores) of Dimorphotheca pluvialis (L.) Moench (Asteraceae) could limit possible damage to the embryo during long-term seed exposure to solar UV-B radiation. This hypothesis was tested by irradiating sun-dried disc and ray diaspores continuously for 6 weeks with four different doses of biologically effective UV radiation, viz 0.0, 0.2, 9.46 and 11.97 kj m −2 8 hr −1 of visible (> 400 nm), UV-A (320–400 nm), ambient and enhanced UV-B (280–320 nm) radiation, respectively. Total effective UV-B doses approximated those received over an 18-week period following seed dispersal at this species' northerly distribution limit (26° 38′ S), at normal ozone levels (ambient UV-B) and anticipated 20% ozone depletion (enhanced UV-B). Irradiation of diaspores with enhanced UV-B improved germination in both seed morphs. However, disc diaspores exhibited a greater fractional increase in germination than ray diaspores. Disc and ray plants grown from diaspores irradiated with enhanced UV-B exhibited decreased photochemical efficiency (reduced variable to maximal fluorescence, F v /F m ), but only disc plants showed decreased potential photosynthetic activity (reduced areas over fluorescence curves, A fd ). This was accompanied by increased diaspore production and reduced diaspore mass. Irradiation of diaspores with photoreactivating UV-A produced a contrasting response (increased F v /F m and A fd , accompanied by decreased diaspore production) in disc plants only. Altered photochemical and reproductive performance, and visibly diminished leaf pigmentation, in disc plants indicated increased sensitivity to photoinhibition, a possible consequence of UV-B induced cellular (membrane and DNA) damage in seeds. (author)

  4. Photochemical decoration of gold nanoparticles on polymer stabilized magnetic microspheres for determination of adenine by surface-enhanced Raman spectroscopy

    International Nuclear Information System (INIS)

    Alula, Melisew Tadele; Yang, Jyisy

    2015-01-01

    Magnetic microspheres decorated with gold nanoparticles (AuNPs) were prepared and used for the determination of adenine by surface-enhanced Raman scattering (SERS). Magnetic particles were first synthesized by coprecipitation of solutions containing iron(II) and iron(III) ions with ammonium hydroxide. Subsequently, the magnetic particles were suspended into a solution of poly(divinylbenzene-co-methyl methacrylate) to yield polymer-stabilized magnetic microspheres. These were further decorated with AuNPs via a new photochemical reduction method. The magnetic microspheres were characterized by XRD patterns and SEM images. They are shown to represent highly SERS-active substrates by giving an enhancement by almost 7 orders of magnitude compared to conventional Raman spectroscopy. Several factors that affect the photochemical reduction to form the AuNPs were examined. It is found that the concentration of gold ion, UV irradiation time, and citrate concentration have more impact on the reaction rate than on the morphologies of the AuNPs. The gold-decorated magnetic microspheres are highly stable in aqueous solution and capable of concentrating nucleobases. A linear response of the SERS signal to adenine in concentrations up to 10 μM is found, with a linear regression coefficient of 0.997. The detection limit is estimated to a few hundreds of nM (at an SNR of 3). Based on its specific Raman peak at 734 cm −1 , adenine can be selectively determined without interference by other nucleobases, and a recovery higher than 95 % could be obtained. (author)

  5. Seasonal variations of C1-C4 alkyl nitrates at a coastal site in Hong Kong: Influence of photochemical formation and oceanic emissions.

    Science.gov (United States)

    Song, Junwei; Zhang, Yingyi; Huang, Yu; Ho, Kin Fai; Yuan, Zibing; Ling, Zhenhao; Niu, Xiaojun; Gao, Yuan; Cui, Long; Louie, Peter K K; Lee, Shun-Cheng; Lai, Senchao

    2018-03-01

    Five C 1 -C 4 alkyl nitrates (RONO 2 ) were measured at a coastal site in Hong Kong in four selected months of 2011 and 2012. The total mixing ratios of C 1 -C 4 RONO 2 (Σ 5 RONO 2 ) ranged from 15.4 to 143.7 pptv with an average of 65.9 ± 33.0 pptv. C 3 -C 4 RONO 2 (2-butyl nitrate and 2-propyl nitrate) were the most abundant RONO 2 during the entire sampling period. The mixing ratios of C 3 -C 4 RONO 2 were higher in winter than those in summer, while the ones of methyl nitrate (MeONO 2 ) were higher in summer than those in winter. Source analysis suggests that C 2 -C 4 RONO 2 were mainly derived from photochemical formation along with biomass burning (58.3-71.6%), while ocean was a major contributor to MeONO 2 (53.8%) during the whole sampling period. The photochemical evolution of C 2 -C 4 RONO 2 was investigated, and found to be dominantly produced by the parent hydrocarbon oxidation. The notable enrichment of MeONO 2 over C 3 -C 4 RONO 2 was observed in a summer episode when the air masses originating from the South China Sea (SCS) and MeONO 2 was dominantly derived from oceanic emissions. In order to improve the accuracy of ozone (O 3 ) prediction in coastal environment, the relative contribution of RONO 2 from oceanic emissions versus photochemical formation and their coupling effects on O 3 production should be taken into account in future studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. SMOG CHAMBERS: A TOOL TO EXAMINE EFFECTS OF PHOTOCHEMICALLY AGED AIR POLLUTANTS ON BIOLOGICAL SYSTEMS

    Science.gov (United States)

    Irradiative exposure chambers or 'Smog chambers' have been used at the University of North Carolina for over 30 years to study photochemically active mixtures of volatile organic compounds and their transformation products (a significant sub-set of Hazardous Air Pollutants, HAPs)...

  7. A single exposure to photochemical smog causes airway irritation and cardiac dysrhythmia in mice

    Science.gov (United States)

    The data presented here shows that a single exposure to photochemical smog causes airway irritation and cardiac dysrhythmia in mice. Smog, which is a complex mixture of particulate matter and gaseous irritants (ozone, sulfur dioxide, reactive aldehydes), as well as components whi...

  8. Considerations on photochemical genotoxicity. II: Report of the 2009 International Workshop on Genotoxicity Testing Working Group

    NARCIS (Netherlands)

    Lynch, A.M.; Guzzie, P.J.; Bauer, D.; Gocke, E.; Itoh, S.; Jacobs, A.; Krul, C.A.M.; Schepky, A.; Tanaka, N.; Kasper, P.

    2011-01-01

    A workshop to reappraise the previous IWGT recommendations for photogenotoxicity testing [E. Gocke, L. Muller, P.J. Guzzie, S. Brendler-Schwaab, S. Bulera, C.F. Chignell, L.M. Henderson, A. Jacobs, H. Murli, R.D. Snyder, N. Tanaka, Considerations on photochemical genotoxicity: report of the

  9. The study on laser photochemical process of Diazonaphthoquinon-Cresol system

    International Nuclear Information System (INIS)

    Wei Jie; Huang Yu Li; Wang Wenke

    1999-01-01

    The kinetic process of laser photochemical reaction of diazonaphthoquinon-cresol system was studied by using laser spectrophotofluorimetry and laser induced fluorescence attenuation method. The nonlinear relationship between photodecomposition rate of the sensitizer and laser power, exposure time and concentration of solutions was discussed in detail

  10. High performance oligomers: synthesis and photochemical properties of calix(n)arene containing various photoreactive groups

    International Nuclear Information System (INIS)

    Nishikubo, T.; Kameyama, A.

    1999-01-01

    Photoreactive calix(n)arenes containing radical polymerizable (meth)acrylate groups, and catatonically polymerizable vinyl ether, propargyl ether, oxirane and oxetane groups were synthesized by certain reactions of calix(n)arenes with the corresponding (meth)acrylic acid derivatives, vinyl ether compound, epibromohydrin and oxetane derivatives, respectively. The photochemical reaction of these calix(n)arene derivatives were also examined

  11. Photochemical transformations accelerated in continuous-flow reactors: basic concepts and applications.

    Science.gov (United States)

    Su, Yuanhai; Straathof, Natan J W; Hessel, Volker; Noël, Timothy

    2014-08-18

    Continuous-flow photochemistry is used increasingly by researchers in academia and industry to facilitate photochemical processes and their subsequent scale-up. However, without detailed knowledge concerning the engineering aspects of photochemistry, it can be quite challenging to develop a suitable photochemical microreactor for a given reaction. In this review, we provide an up-to-date overview of both technological and chemical aspects associated with photochemical processes in microreactors. Important design considerations, such as light sources, material selection, and solvent constraints are discussed. In addition, a detailed description of photon and mass-transfer phenomena in microreactors is made and fundamental principles are deduced for making a judicious choice for a suitable photomicroreactor. The advantages of microreactor technology for photochemistry are described for UV and visible-light driven photochemical processes and are compared with their batch counterparts. In addition, different scale-up strategies and limitations of continuous-flow microreactors are discussed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Kinetic analyses and mathematical modeling of primary photochemical and photoelectrochemical processes in plant photosystems

    NARCIS (Netherlands)

    Vredenberg, W.J.

    2011-01-01

    In this paper the model and simulation of primary photochemical and photo-electrochemical reactions in dark-adapted intact plant leaves is presented. A descriptive algorithm has been derived from analyses of variable chlorophyll a fluorescence and P700 oxidation kinetics upon excitation with

  13. Interfacial electrochemistry of colloidal ruthenium dioxide and catalysis of the photochemical generation of hydrogen from water

    NARCIS (Netherlands)

    Kleijn, J.M.

    1987-01-01

    The formation of hydrogen from water using solar energy is a very attractive research topic, because of the potential use of hydrogen as an alternative, clean fuel. It has been shown by many workers in the field that photochemical hydrogen generation can be achieved in an aqueous system,

  14. Photochemical exchange reactions of thymine, uracil and their nucleosides with selected amino acids

    International Nuclear Information System (INIS)

    Shetlar, M.D.; Taylor, J.A.; Hom, K.

    1984-01-01

    The photoinduced exchange reactions of thymine with lysine at basic pH, using 254 nm light, have been studied. Three products have been isolated, namely, 6-amino-2-(1-thyminyl)hexanoic acid (Ia), 2-amino-6-(1-thyminyl)hexanoic acid (IIa) and 1-amino-5-(1-thyminyl)pentane (IIIa). Compound IIIa was shown to be a secondary product, produced by photochemical decarboxylation of Ia. Photochemical reaction of thymine with glycine and alanine at basic pH led, respectively, to formation of 2-(1-thyminyl)acetic acid (Ic) and 2-(1-thyminyl)propionic acid (Id). Compounds Ic and Id underwent photolysis to produce the decarboxylated secondary products 1-methylthymine and 1-ethylthymine, respectively. Thymidine reacts photochemically with glycine and alanine to produce the same products. Irradiation of DNA in the presence of lysine at basic pH led to the formation of the same products formed in the thymine-lysine system, namely Ia, IIa and IIIa. Uracil was found to undergo analogous photochemical exchange reactions with lysine to form 6-amino-2-(1-uracilyl)hexanoic acid (Ib), and 2-amino-6-(1-uracilyl)hexanoic acid (IIb). Compound Ib was found to undergo photodecarboxylation to form 1-amino-5-(1-uracilyl)pentane (IIIb), analogous to the secondary photoreaction of Ia. Photoreaction of uracil with 1,5-diaminopentane (cadaverine) likewise led to formation of IIIb. (author)

  15. 40 CFR 52.430 - Photochemical Assessment Monitoring Stations (PAMS) Program.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 3 2010-07-01 2010-07-01 false Photochemical Assessment Monitoring Stations (PAMS) Program. 52.430 Section 52.430 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Natural Resources & Environmental Control submitted a plan for the establishment and implementation of a...

  16. Chemical Kinetics and Photochemical Data for Use in Stratospheric Modeling. Evaluation No. 12

    Science.gov (United States)

    DeMore, W. B.; Sander, S. P.; Golden, D. M.; Hampson, R. F.; Kurylo, M. J.; Howard, C. J.; Ravishankara, A. R.; Kolb, C. E.; Molina, M. J.

    1997-01-01

    This is the twelfth in a series of evaluated sets of rate constants and photochemical cross sections compiled by the NASA Panel for Data Evaluation. The primary application of the data is in the modeling of stratospheric processes, with special emphasis on the ozone layer and its possible perturbation by anthropogenic and natural phenomena.

  17. Water Treatment Process Intensification by Combination of Electrochemical and Photochemical Methods

    Czech Academy of Sciences Publication Activity Database

    Krystyník, Pavel; Klusoň, Petr; Tito, D.N.

    2015-01-01

    Roč. 94, SI (2015), s. 85-92 ISSN 0255-2701 R&D Projects: GA MPO(CZ) FR-TI1/065; GA TA ČR TA03010548 Institutional support: RVO:67985858 Keywords : electrocoagulation * photochemical oxidation * TOC removal Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 2.154, year: 2015

  18. A Highly Effective Photochemical System for Complex Treatment of Heavily Contaminated Wastewaters

    Czech Academy of Sciences Publication Activity Database

    Krystyník, Pavel; Klusoň, Petr; Hejda, S.; Mašín, P.; Tito, D.N.

    2014-01-01

    Roč. 86, č. 11 (2014), s. 2212-2220 ISSN 1061-4303 R&D Projects: GA MPO(CZ) FR-TI1/065 Institutional support: RVO:67985858 Keywords : advanced oxidation processes * photochemical oxidation * wastewater treatment Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 0.865, year: 2014

  19. Enhanced cellular delivery of cell-penetrating peptide-peptide nucleic acid conjugates by photochemical internalization

    DEFF Research Database (Denmark)

    Shiraishi, Takehiko; Nielsen, Peter E

    2011-01-01

    (antisense activity) is still limited by endocytotic entrapment. We have shown that this low bioavailability can be greatly improved by combining CPP-PNA conjugate administration with a photochemical internalization technique using photosensitizers such as aluminum phthalocyanine (AlPcS(2a...

  20. 40 CFR 52.480 - Photochemical Assessment Monitoring Stations (PAMS) Program.

    Science.gov (United States)

    2010-07-01

    ... of Columbia's Department of Consumer and Regulatory Affairs submitted a plan for the establishment... 40 Protection of Environment 3 2010-07-01 2010-07-01 false Photochemical Assessment Monitoring Stations (PAMS) Program. 52.480 Section 52.480 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY...

  1. 40 CFR 52.1080 - Photochemical Assessment Monitoring Stations (PAMS) Program.

    Science.gov (United States)

    2010-07-01

    ... Stations (PAMS) Program. 52.1080 Section 52.1080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... § 52.1080 Photochemical Assessment Monitoring Stations (PAMS) Program. On March 24, 1994 Maryland's... Assessment Monitoring Stations (PAMS) Program as a state implementation plan (SIP) revision, as required by...

  2. 40 CFR 52.2035 - Photochemical Assessment Monitoring Stations (PAMS) Program.

    Science.gov (United States)

    2010-07-01

    ... Stations (PAMS) Program. 52.2035 Section 52.2035 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY...) Pennsylvania § 52.2035 Photochemical Assessment Monitoring Stations (PAMS) Program. On September 23, 1994... (PAMS) Program as a state implementation plan (SIP) revision, as required by section 182(c)(1) of the...

  3. Photochemical transformations accelerated in continuous-flow reactors : basic concepts and applications

    NARCIS (Netherlands)

    Su, Y.; Straathof, N.J.W.; Hessel, V.; Noel, T.

    2014-01-01

    Continuous-flow photochemistry is used increasingly by researchers in academia and industry to facilitate photochemical processes and their subsequent scale-up. However, without detailed knowledge concerning the engineering aspects of photochemistry, it can be quite challenging to develop a suitable

  4. Photochemical recombination of deep centers in silicon: decay of donor-acceptor pairs

    International Nuclear Information System (INIS)

    Adilov, K.A.

    1991-01-01

    Processes of photochemical recombination of deep impurity centers (DIC) in p-Si alloyed by Te, Zn and Fe occuring at 300-350 K under irradiation by super-low-energy light from δ 14 -10 17 quantum/cm 2 )Xs intensity impurity absorption range, are considered

  5. Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients.

    Directory of Open Access Journals (Sweden)

    Ibrahim Hamad

    Full Text Available Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic components from fecal samples differs significantly among DNA extraction methods. Subsequently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1 and 2 (ITS2 amplicons and real-time PCRs. Our results revealed that not only richness (Chao-1 index and alpha diversity (Shannon diversity differ between HIV-infected patients and healthy volunteers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant differences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients compared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the presence of Microsporidia, Giardia lamblia, Blastocystis

  6. Evaluation of leaf energy dissipation by the Photochemical Reflectance

    Science.gov (United States)

    Raddi, S.; Magnani, F.

    Starting from the early paper by Heber (1969), several studies have demonstrated a subtle shift in leaf spectroscopic characteristics (both absorbance and reflectance) in response to rapid changes in environmental conditions. More recent work, briefly reviewed here, has also demonstrated the existence of two components in the maked peak centered at 505-540 nm: an irreversible component, attributed to the interconversion of leaf xanthophylls, and a reversible component at slightly longer wavelengths, resulting from conformational changes induced by the buildup of a pH gradient across the thylakoid membrane associated with photosynthetic electron transport. Both processes (xanthophyll de-epoxidation and conformational changes) are known to contribute to the dissipation of excess energy in Photosystem II (PSII). Leaf spectroscopy could therefore provide a powerful non-invasive tool for the determination of leaf photosynthetic processes. This led to the development of the normalized spectral index PRI (Photochemical Reflectance Index; Gamon, Penuelas &Field 1992; Gamon, Serrano &Surfus 1997), which relates the functional signal at 531 nm to a reference signal at 570 nm. The index has been found to track diurnal changes in xanthophyll de-epoxidation state, radiation use efficiency and fluorescence in response to light, both at the leaf and more recently at the canopy level. A common relationship has also beenreported across species and functional types, although such a generality has not always been confirmed. Recent reports (Stylinski et al. 2000) have also hinted of a possible link between PRI and leaf photosynthetic potential, possibly through the correlation between xanthophyll content and electron transport machinery in the chloroplast. Such a link, if confirmed, could prove very useful for the remote sensing and modelling ofvegetation. Some of these open questions were addressed in the present study. The correlation between leaf function and reflectance was

  7. Effect of photochemical ageing on the ice nucleation properties of diesel and wood burning particles

    Directory of Open Access Journals (Sweden)

    C. Chou

    2013-01-01

    Full Text Available A measurement campaign (IMBALANCE conducted in 2009 was aimed at characterizing the physical and chemical properties of freshly emitted and photochemically aged combustion particles emitted from a log wood burner and diesel vehicles: a EURO3 Opel Astra with a diesel oxidation catalyst (DOC but no particle filter and a EURO2 Volkswagen Transporter TDI Syncro without emission aftertreatment. Ice nucleation experiments in the deposition and condensation freezing modes were conducted with the Portable Ice Nucleation Chamber (PINC at three nominal temperatures, −30 °C, −35 °C and −40 °C. Freshly emitted diesel particles showed ice formation only at −40 °C in the deposition mode at 137% relative humidity with respect to ice (RHi and 92% relative humidity with respect to water (RHw, and photochemical ageing did not play a role in modifying their ice nucleation behaviour. Only one diesel experiment where α-pinene was added for the ageing process, showed an ice nucleation enhancement at −35 °C. Wood burning particles also act as ice nuclei (IN at −40 °C in the deposition mode at the same conditions as for diesel particles and photochemical ageing also did not alter the ice formation properties of the wood burning particles. Unlike diesel particles, wood burning particles form ice via condensation freezing at −35 °C whereas no ice nucleation was observed at −30 °C. Photochemical ageing did not affect the ice nucleation ability of the diesel and wood burning particles at the three different temperatures investigated but a broader range of temperatures below −40 °C need to be investigated in order to draw an overall conclusion on the effect of photochemical ageing on deposition/condensation ice nucleation across the entire temperature range relevant to cold clouds.

  8. Photochemical Reactions of Particulate Organic Matter: Deciphering the Role of Direct and Indirect Processes

    Science.gov (United States)

    Carrasquillo, A. J.; Gelfond, C. E.; Kocar, B. D.

    2016-12-01

    Photochemical reactions of natural organic matter (NOM) represent potentially important pathways for biologically recalcitrant material to be chemically altered in aquatic systems. Irradiation can alter the physical state of organic matter by facilitating the cycling between the particulate (POM) and dissolved (DOM) pools, however, a molecular level understanding of this chemically dynamic system is currently lacking. Photochemical reactions of a target molecule proceed by the direct absorption of a photon, or through reaction with a second photolytically generated species (i.e. the hydroxyl radical, singlet oxygen, excited triplet state NOM, hydrogen peroxide, etc.). Here, we isolate the major direct and indirect photochemical reactions of a lignocellulose-rich POM material (Phragmites australis) to determine their relative importance in changing the the chemical structure of the parent POM, and in the production of DOM. We measured POM molecular structure using a combination of NMR and FTIR for bulk analyses and scanning transmission x-ray microscopy (STXM) for spatially resolved chemistry, while the chemical composition of photo-produced DOM was measured using ultra-high resolution mass spectrometry. Results are discussed in the context of the differences in chemical composition of both NOM pools resulting from the isolated photochemical pathways. All treatments result in an increase in DOM with reaction time, indicating that the larger POM matrix is likely fragmenting into smaller more soluble species. Spectroscopic measurements, on the other hand, point to functionalization reactions which increase the abundance of alcohol, acid, and carbonyl moieties in both carbon pools. This unique dataset provides new insight into how photochemical reactions alter the chemical composition of NOM while highlighting the relative importance of indirect pathways.

  9. Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord.

    Science.gov (United States)

    Vader, Anna; Laughinghouse, Haywood D; Griffiths, Colin; Jakobsen, Kjetill S; Gabrielsen, Tove M

    2018-02-01

    Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes.

    Science.gov (United States)

    Sommers, Pacifica; Darcy, John L; Gendron, Eli M S; Stanish, Lee F; Bagshaw, Elizabeth A; Porazinska, Dorota L; Schmidt, Steven K

    2018-01-01

    Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome.

    Science.gov (United States)

    Wallau, Gabriel Luz; Vieira, Cristina; Loreto, Élgion Lúcio Silva

    2018-01-01

    All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes. For some time now, it has been a scientific consensus that HT events were rare and non-relevant for evolution of eukaryotic species, but there is growing evidence supporting that HT is an important and frequent phenomenon in eukaryotes as well. Here, we will discuss the latest findings regarding HT among eukaryotes, mainly HT of transposons (HTT), establishing HTT once and for all as an important phenomenon that should be taken into consideration to fully understand eukaryotes genome evolution. In addition, we will discuss the latest development methods to detect such events in a broader scale and highlight the new approaches which should be pursued by researchers to fill the knowledge gaps regarding HTT among eukaryotes.

  12. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes.

    Science.gov (United States)

    Novák, Lukáš; Zubáčová, Zuzana; Karnkowska, Anna; Kolisko, Martin; Hroudová, Miluše; Stairs, Courtney W; Simpson, Alastair G B; Keeling, Patrick J; Roger, Andrew J; Čepička, Ivan; Hampl, Vladimír

    2016-10-06

    Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

  13. Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes

    Directory of Open Access Journals (Sweden)

    Roger Andrew J

    2003-06-01

    Full Text Available Abstract Background Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH, to evaluate and compare the patterns and rates of lateral gene transfer (LGT in prokaryotes and eukaryotes. Results We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists. Conclusion LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.

  14. Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists.

    Science.gov (United States)

    Jagus, Rosemary; Bachvaroff, Tsvetan R; Joshi, Bhavesh; Place, Allen R

    2012-01-01

    The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babesia bovis to 112,000-220,050 Mb in the dinoflagellate Prorocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in "text-book" model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.

  15. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

    Science.gov (United States)

    Leppek, Kathrin; Das, Rhiju; Barna, Maria

    2017-01-01

    RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5′ untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5′ UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms. PMID:29165424

  16. Regulation of oxidative enzyme activity and eukaryotic elongation factor 2 in human skeletal muscle: influence of gender and exercise

    DEFF Research Database (Denmark)

    Roepstorff, Carsten; Schjerling, P.; Vistisen, Bodil

    2005-01-01

    AIM: To investigate gender-related differences in the responses of oxidative enzymes and eukaryotic elongation factor-2 (eEF2) to exercise. METHODS: The influence of exercise (90 min, 60%VO(2peak)) on citrate synthase (CS) and beta-hydroxyacyl-CoA dehydrogenase (HAD) activity and mRNA content...... expression and phosphorylation were unaffected by training status (NS). CONCLUSION: Basal transcriptional, translational, and/or post-translational control of CS and HAD seems to be gender-dependent. Also, gender differences in translation and/or post-translational protein modification of CS occur during...... not differ between females and males (NS). In females only, CS activity was enhanced (P differ between UT and ET but, nevertheless, CS activity was 56% higher in ET than in UT volunteers (P

  17. Ascorbic Acid Alleviates Damage from Heat Stress in the Photosystem II of Tall Fescue in Both the Photochemical and Thermal Phases

    Directory of Open Access Journals (Sweden)

    Ke Chen

    2017-08-01

    Full Text Available L-Ascorbate (Asc plays important roles in plant development, hormone signaling, the cell cycle and cellular redox system, etc. The higher content of Asc in plant chloroplasts indicates its important role in the photosystem. The objective of this study was to study the roles of Asc in tall fescue leaves against heat stress. After a heat stress treatment, we observed a lower value of the maximum quantum yield for primary photochemistry (φPo, which reflects the inhibited activity of the photochemical phase of photosystem II (PSII. Moreover, we observed a higher value of efficiency of electron transfer from QB to photosystem I acceptors (δR0, which reflects elevated activity of the thermal phase of the photosystem of the tall fescue. The addition of Asc facilitate the behavior of the photochemical phase of the PSII by lowering the ROS content as well as that of the alternative electron donor to provide electron to the tyrosine residue of the D1 protein. Additionally, exogenous Asc reduces the activity of the thermal phase of the photosystem, which could contribute to the limitation of energy input into the photosystem in tall fescue against heat stress. Synthesis of the Asc increased under heat stress treatment. However, under heat stress this regulation does not occur at the transcription level and requires further study.

  18. Photochemical Internalization of Bleomycin Before External-Beam Radiotherapy Improves Locoregional Control in a Human Sarcoma Model

    International Nuclear Information System (INIS)

    Norum, Ole-Jacob; Bruland, Oyvind Sverre; Gorunova, Ludmila; Berg, Kristian

    2009-01-01

    Purpose: The aim of this study was to explore the tumor growth response of the combination photochemical internalization and external-beam radiotherapy. Photochemical internalization is a technology to improve the utilization of therapeutic macromolecules in cancer therapy by photochemical release of endocytosed macromolecules into the cytosol. Methods and Materials: A human sarcoma xenograft TAX-1 was inoculated subcutaneously into nude mice. The photosensitizer AlPcS 2a and bleomycin were intraperitoneally administrated 48 h and 30 min, respectively, before diode laser light exposure at 670 nm (20 J/cm 2 ). Thirty minutes or 7 days after photochemical treatment, the animals were subjected to 4 Gy of ionizing radiation. Results: Using photochemical internalization of bleomycin as an adjunct to ionizing radiation increased the time to progression for the tumors from 17 to 33 days as compared with that observed with photodynamic therapy combined with ionizing radiation as well as for radiochemotherapy with bleomycin. The side effects observed when photochemical internalization of bleomycin was given shortly before ionizing radiation were eliminated by separating the treatment modalities in time. Conclusion: Photochemical internalization of bleomycin combined with ionizing radiation increased the time to progression and showed minimal toxicity and may therefore reduce the total radiation dose necessary to obtain local tumor control while avoiding long-term sequelae from radiotherapy.

  19. Highly efficient destruction of squamous carcinoma cells of the head and neck by photochemical internalization of Ranpirnase.

    Science.gov (United States)

    Liebers, Nora; Holland-Letz, Tim; Welschof, Mona; Høgset, Anders; Jäger, Dirk; Arndt, Michaela A E; Krauss, Jürgen

    2017-11-01

    Photochemical Internalization is a novel drug delivery technology for cancer treatment based on the principle of Photodynamic Treatment. Using a photosensitizer that locates in endocytic vesicles membranes of tumor cells, Photochemical internalization enables cytosolic release of endocytosed antitumor agents in a site-specific manner. The purpose of the present in-vitro study was to explore whether Photochemical Internalization is able to enhance the efficacy of Ranpirnase, a cytotoxic amphibian ribonuclease, for eradication of squamous cell carcinoma of the head and neck. Cell viability was measured in 8 primary human cell lines of squamous cell carcinoma of the head and neck after treatment with Ranpirnase and Photochemical Internalization. For Photochemical Internalization the photosensitizer disulfonated tetraphenyl porphine was incubated with tumor cells followed by exposure to blue light (435 nm). Our study demonstrates significant enhancement of antitumor activity of Ranpirnase by Photochemical Internalization. Treatment responses were heterogeneous between the primary cancer cell lines. Combining Photochemical Internalization with Ranpirnase resulted in 4.6 to 1,940-fold increased cytotoxicity when compared with the ribonuclease alone (P Internalization in squamous cell carcinoma of the head and neck.

  20. Photochemical smog modeling for assessment of potential impacts of different management strategies on air quality of the Bangkok Metropolitan Region, Thailand.

    Science.gov (United States)

    Oanh, Nguyen Thi Kim; Zhang, Baoning

    2004-10-01

    A photochemical smog model system, the Variable-Grid Urban Airshed Model/Systems Applications International Mesoscale Model (UAM-V/SAIMM), was used to investigate photochemical pollution in the Bangkok Metropolitan Region (BMR). The model system was first applied to simulate a historical photochemical smog episode of two days (January 13-14, 1997) using the 1997 anthropogenic emission database available at the Pollution Control Department and an estimated biogenic emission. The output 1-hr ozone (O3) for BMR, however, did not meet the U.S. Environmental Protection Agency suggested performance criteria. The simulated minimum and maximum O3 values in the domain were much higher than the observations. Multiple model runs with different precursor emission reduction scenarios showed that the best model performance with the simulated 1-hr O3 meeting all the criteria was obtained when the volatile organic compound (VOC) and oxides of nitrogen (NOx) emission from mobile source reduced by 50% and carbon monoxide by 20% from the original database. Various combinations of anthropogenic and biogenic emissions in Bangkok and surrounding provinces were simulated to assess the contribution of different sources to O3 pollution in the city. O3 formation in Bangkok was found to be more VOC-sensitive than NOx-sensitive. To attain the Thailand ambient air quality standard for 1-hr O3 of 100 ppb, VOC emission in BMR should be reduced by 50-60%. Management strategies considered in the scenario study consist of Stage I, Stage II vapor control, replacement of two-stroke by four-stroke motorcycles, 100% compressed natural gas bus, 100% natural gas-fired power plants, and replacement of methyltertiarybutylether by ethanol as an additive for gasoline.

  1. Emission sources of non-methane volatile organic compounds (NMVOCs) and their contribution to photochemical ozone (O3) formation at an urban atmosphere in western India.

    Science.gov (United States)

    Yadav, R.; Sahu, L. K.; Tripathi, N.; Pal, D.

    2017-12-01

    Atmospheric non-methane volatile organic compounds (NMVOCs) were measured at a sampling site in Udaipur city of western India during 2015 to recognize their pollution levels, variation characteristics, sources and photochemical reactivity. The samples were analyzed for NMVOCs using a Gas Chromatograph equipped with Flame Ionization Detector (GC/FID) and Thermal Desorption (TD) system. The main focus on understand the sources responsible for NMVOC emissions, and evaluating the role of the identified sources towards ozone formation. Hourly variations of various NMVOC species indicate that VOCs mixing ratios were influenced by photochemical removal with OH radicals for reactive species, secondary formation for oxygenated VOCs. In general, higher mixing ratios were observed during winter/pre-monsoon and lower levels during the monsoon season due to the seasonal change in meteorological, transport path of air parcel and boundary layer conditions. The high levels of propane (C3H8) and butane (C4H10) show the dominance of LPG over the study location. The correlation coefficients of typical NMVOC pairs (ethylene/propylene, propylene/isoprene, and ethane/propane) depicted that vehicular emission and natural gas leakages were important sources for atmospheric hydrocarbons in Udaipur. Based on the annual data, PMF analysis suggest the source factors namely biomass burning/ bio-fuel, automobile exhaust, Industrial/ natural gas/power plant emissions, petrol/Diesel, gasoline evaporation, and use of liquid petroleum gas (LPG) contribute to NMVOCs loading. The propylene-equivalent and ozone formation potential of NMVOCs have also been calculated in order to find out their OH reactivity and contribution to the photochemical ozone formation.

  2. Photochemical modeling of glyoxal at a rural site: observations and analysis from BEARPEX 2007

    Directory of Open Access Journals (Sweden)

    A. J. Huisman

    2011-09-01

    Full Text Available We present roughly one month of high time-resolution, direct, in situ measurements of gas-phase glyoxal acquired during the BEARPEX 2007 field campaign. The research site, located on a ponderosa pine plantation in the Sierra Nevada mountains, is strongly influenced by biogenic volatile organic compounds (BVOCs; thus this data adds to the few existing measurements of glyoxal in BVOC-dominated areas. The short lifetime of glyoxal of ~1 h, the fact that glyoxal mixing ratios are much higher during high temperature periods, and the results of a photochemical model demonstrate that glyoxal is strongly influenced by BVOC precursors during high temperature periods.

    A zero-dimensional box model using near-explicit chemistry from the Leeds Master Chemical Mechanism v3.1 was used to investigate the processes controlling glyoxal chemistry during BEARPEX 2007. The model showed that MBO is the most important glyoxal precursor (~67 %, followed by isoprene (~26 % and methylchavicol (~6 %, a precursor previously not commonly considered for glyoxal production. The model calculated a noon lifetime for glyoxal of ~0.9 h, making glyoxal well suited as a local tracer of VOC oxidation in a forested rural environment; however, the modeled glyoxal mixing ratios over-predicted measured glyoxal by a factor 2 to 5. Loss of glyoxal to aerosol was not found to be significant, likely as a result of the very dry conditions, and could not explain the over-prediction. Although several parameters, such as an approximation for advection, were found to improve the model measurement discrepancy, reduction in OH was by far the most effective. Reducing model OH concentrations to half the measured values decreased the glyoxal over-prediction from a factor of 2.4 to 1.1, as well as the overprediction of HO2 from a factor of 1.64 to 1.14. Our analysis has shown that glyoxal is particularly sensitive to OH concentration compared to other BVOC oxidation products. This

  3. Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae

    Science.gov (United States)

    2013-01-01

    green algae and higher plants. Protein domain structures and expression analyses in green alga H. pluvialis indicate that various chy genes are in different manners response to light. The knowledge of evolution of chy genes in photosynthetic eukaryotes provided information of gene cloning and functional investigation of chy genes in algae in the future. PMID:23834441

  4. Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae.

    Science.gov (United States)

    Cui, Hongli; Yu, Xiaona; Wang, Yan; Cui, Yulin; Li, Xueqin; Liu, Zhaopu; Qin, Song

    2013-07-08

    Xanthophylls, oxygenated derivatives of carotenes, play critical roles in photosynthetic apparatus of cyanobacteria, algae, and higher plants. Although the xanthophylls biosynthetic pathway of algae is largely unknown, it is of particular interest because they have a very complicated evolutionary history. Carotenoid hydroxylase (CHY) is an important protein that plays essential roles in xanthophylls biosynthesis. With the availability of 18 sequenced algal genomes, we performed a comprehensive comparative analysis of chy genes and explored their distribution, structure, evolution, origins, and expression. Overall 60 putative chy genes were identified and classified into two major subfamilies (bch and cyp97) according to their domain structures. Genes in the bch subfamily were found in 10 green algae and 1 red alga, but absent in other algae. In the phylogenetic tree, bch genes of green algae and higher plants share a common ancestor and are of non-cyanobacterial origin, whereas that of red algae is of cyanobacteria. The homologs of cyp97a/c genes were widespread only in green algae, while cyp97b paralogs were seen in most of algae. Phylogenetic analysis on cyp97 genes supported the hypothesis that cyp97b is an ancient gene originated before the formation of extant algal groups. The cyp97a gene is more closely related to cyp97c in evolution than to cyp97b. The two cyp97 genes were isolated from the green alga Haematococcus pluvialis, and transcriptional expression profiles of chy genes were observed under high light stress of different wavelength. Green algae received a β-xanthophylls biosynthetic pathway from host organisms. Although red algae inherited the pathway from cyanobacteria during primary endosymbiosis, it remains unclear in Chromalveolates. The α-xanthophylls biosynthetic pathway is a common feature in green algae and higher plants. The origination of cyp97a/c is most likely due to gene duplication before divergence of green algae and higher plants

  5. Conservation of gene co-regulation in prokaryotes and eukaryotes.

    NARCIS (Netherlands)

    Snel, B.; Bork, P.; Huynen, M.A.

    2002-01-01

    We raise some issues in detecting the conservation (or absence thereof) of co-regulation using gene order; how we think the variations in the cellular network in various species can be studied; and how to determine and interpret the higher order structure in networks of functional relations.

  6. Insights into the diversity of eukaryotes in acid mine drainage biofilm communities.

    Science.gov (United States)

    Baker, Brett J; Tyson, Gene W; Goosherst, Lindsey; Banfield, Jillian F

    2009-04-01

    Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.

  7. A second pathway to degrade pyrimidine nucleic acid precursors in eukaryotes

    DEFF Research Database (Denmark)

    Andersen, Gorm; Bjornberg, Olof; Polakova, Silvia

    2008-01-01

    Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyv...... of the eukaryotic or prokaryotic genes involved in pyrimidine degradation described to date.......Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces......, respectively. The gene products of URC1 and URC4 are highly conserved proteins with so far unknown functions and they are present in a variety of prokaryotes and fungi. In bacteria and in some fungi, URC1 and URC4 are linked on the genome together with the gene for uracil phosphoribosyltransferase (URC6). Urc1...

  8. Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation

    DEFF Research Database (Denmark)

    Bourke, Michael F.; Marriott, Philip J.; Glud, Ronnie N.

    2017-01-01

    Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea....... Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H....../hydrogenase pathway of fermentative eukaryotic H2 production, suggesting that pathway as the source of H2 and dissolved inorganic carbon production. Metabolomic analysis showed large increases in lipid production at the onset of anoxia, consistent with documented pathways of anoxic dark fermentation in microalgae...

  9. Phagosome maturation in unicellular eukaryote Paramecium: the presence of RILP, Rab7 and LAMP-2 homologues

    Directory of Open Access Journals (Sweden)

    E Wyroba

    2009-08-01

    Full Text Available Phagosome maturation is a complex process enabling degradation of internalised particles. Our data obtained at the gene, protein and cellular level indicate that the set of components involved in this process and known up to now in mammalian cells is functioning in unicellular eukaryote. Rab7-interacting partners: homologues of its effector RILP (Rab-interacting lysosomal protein and LAMP-2 (lysosomal membrane protein 2 as well as a7 subunit of the 26S proteasome were revealed in Paramecium phagolysosomal compartment. We identified the gene/transcript fragments encoding RILP-related proteins (RILP1 and RILP2 in Paramecium by PCR/RT-PCR and sequencing. The deduced amino acid sequences of RILP1 and RILP2 show 60.5% and 58.3% similarity, respectively, to the region involved in regulating of lysosomal morphology and dynein-dynactin recruitment of human RILP. RILP colocalised with Rab7 in Paramecium lysosomes and at phagolysosomal membrane during phagocytosis of both the latex beads and bacteria. In the same compartment LAMP-2 was present and its expression during latex internalisation was 2.5-fold higher than in the control when P2 protein fractions (100 000 x g of equal load were quantified by immunoblotting. LAMP-2 crossreacting polypeptide of ~106 kDa was glycosylated as shown by fluorescent and Western analysis of the same blot preceded by PNGase F treatment. The a7 subunit of 26S proteasome was detected close to the phagosomal membrane in the small vesicles, in some of which it colocalised with Rab7. Immunoblotting confirmed presence of RILPrelated polypeptide and a7 subunit of 26S proteasome in Paramecium protein fractions. These results suggest that Rab7, RILP and LAMP-2 may be involved in phagosome maturation in Paramecium.

  10. Assessment of in vivo and in vitro genotoxicity of glibenclamide in eukaryotic cells.

    Directory of Open Access Journals (Sweden)

    Juliane Rocha de Sant'Anna

    Full Text Available Glibenclamide is an oral hypoglycemic drug commonly prescribed for the treatment of type 2 diabetes mellitus, whose anti-tumor activity has been recently described in several human cancer cells. The mutagenic potential of such an antidiabetic drug and its recombinogenic activity in eukaryotic cells were evaluated, the latter for the first time. The mutagenic potential of glibenclamide in therapeutically plasma (0.6 μM and higher concentrations (10 μM, 100 μM, 240 μM and 480 μM was assessed by the in vitro mammalian cell micronucleus test in human lymphocytes. Since the loss of heterozygosity arising from allelic recombination is an important biologically significant consequence of oxidative damage, the glibenclamide recombinogenic activity at 1 μM, 10 μM and 100 μM concentrations was evaluated by the in vivo homozygotization assay. Glibenclamide failed to alter the frequency of micronuclei between 0.6 μM and 480 μM concentrations and the cytokinesis block proliferation index between 0.6 μM and 240 μM concentrations. On the other hand, glibenclamide changed the cell-proliferation kinetics when used at 480 μM. In the homozygotization assay, the homozygotization indices for the analyzed markers were lower than 2.0 and demonstrated the lack of recombinogenic activity of glibenclamide. Data in the current study demonstrate that glibenclamide, in current experimental conditions, is devoid of significant genotoxic effects. This fact encourages further investigations on the use of this antidiabetic agent as a chemotherapeutic drug.

  11. Suicidal autointegration of sleeping beauty and piggyBac transposons in eukaryotic cells.

    Directory of Open Access Journals (Sweden)

    Yongming Wang

    2014-03-01

    Full Text Available Transposons are discrete segments of DNA that have the distinctive ability to move and replicate within genomes across the tree of life. 'Cut and paste' DNA transposition involves excision from a donor locus and reintegration into a new locus in the genome. We studied molecular events following the excision steps of two eukaryotic DNA transposons, Sleeping Beauty (SB and piggyBac (PB that are widely used for genome manipulation in vertebrate species. SB originates from fish and PB from insects; thus, by introducing these transposons to human cells we aimed to monitor the process of establishing a transposon-host relationship in a naïve cellular environment. Similarly to retroviruses, neither SB nor PB is capable of self-avoidance because a significant portion of the excised transposons integrated back into its own genome in a suicidal process called autointegration. Barrier-to-autointegration factor (BANF1, a cellular co-factor of certain retroviruses, inhibited transposon autointegration, and was detected in higher-order protein complexes containing the SB transposase. Increasing size sensitized transposition for autointegration, consistent with elevated vulnerability of larger transposons. Both SB and PB were affected similarly by the size of the transposon in three different assays: excision, autointegration and productive transposition. Prior to reintegration, SB is completely separated from the donor molecule and followed an unbiased autointegration pattern, not associated with local hopping. Self-disruptive autointegration occurred at similar frequency for both transposons, while aberrant, pseudo-transposition events were more frequently observed for PB.

  12. Redox thermodynamics of the native and alkaline forms of eukaryotic and bacterial class I cytochromes c.

    Science.gov (United States)

    Battistuzzi, G; Borsari, M; Sola, M; Francia, F

    1997-12-23

    The reduction potentials of beef heart cytochrome c and cytochromes c2 from Rhodopseudomonas palustris, Rhodobacter sphaeroides, and Rhodobacter capsulatus were measured through direct electrochemistry at a surface-modified gold electrode as a function of temperature in nonisothermal experiments carried out at neutral and alkaline pH values. The thermodynamic parameters for protein reduction (DeltaS degrees rc and DeltaH degrees rc) were determined for the native and alkaline conformers. Enthalpy and entropy terms underlying species-dependent differences in E degrees and pH- and temperature-induced E degrees changes for a given cytochrome were analyzed. The difference of about +0.1 V in E degrees between cytochromes c2 and the eukaryotic species can be separated into an enthalpic term (-DeltaDeltaH degrees rc/F) of +0.130 V and an entropic term (TDeltaDeltaS degrees rc/F) of -0.040 V. Hence, the higher potential of the bacterial species appears to be determined entirely by a greater enthalpic stabilization of the reduced state. Analogously, the much lower potential of the alkaline conformer(s) as compared to the native species is by far enthalpic in origin for both protein families, and is largely determined by the substitution of Met for Lys in axial heme ligation. Instead, the biphasic E degrees /temperature profile for the native cytochromes is due to a difference in reduction entropy between the conformers at low and high temperatures. Temperature-dependent 1H NMR experiments suggest that the temperature-induced transition also involves a change in orientation of the axial methionine ligand with respect to the heme plane.

  13. Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks

    KAUST Repository

    Umarov, Ramzan

    2017-02-03

    Accurate computational identification of promoters remains a challenge as these key DNA regulatory regions have variable structures composed of functional motifs that provide gene-specific initiation of transcription. In this paper we utilize Convolutional Neural Networks (CNN) to analyze sequence characteristics of prokaryotic and eukaryotic promoters and build their predictive models. We trained a similar CNN architecture on promoters of five distant organisms: human, mouse, plant (Arabidopsis), and two bacteria (Escherichia coli and Bacillus subtilis). We found that CNN trained on sigma70 subclass of Escherichia coli promoter gives an excellent classification of promoters and non-promoter sequences (Sn = 0.90, Sp = 0.96, CC = 0.84). The Bacillus subtilis promoters identification CNN model achieves Sn = 0.91, Sp = 0.95, and CC = 0.86. For human, mouse and Arabidopsis promoters we employed CNNs for identification of two well-known promoter classes (TATA and non-TATA promoters). CNN models nicely recognize these complex functional regions. For human promoters Sn/Sp/CC accuracy of prediction reached 0.95/0.98/0,90 on TATA and 0.90/0.98/0.89 for non-TATA promoter sequences, respectively. For Arabidopsis we observed Sn/Sp/CC 0.95/0.97/0.91 (TATA) and 0.94/0.94/0.86 (non-TATA) promoters. Thus, the developed CNN models, implemented in CNNProm program, demonstrated the ability of deep learning approach to grasp complex promoter sequence characteristics and achieve significantly higher accuracy compared to the previously developed promoter prediction programs. We also propose random substitution procedure to discover positionally conserved promoter functional elements. As the suggested approach does not require knowledge of any specific promoter features, it can be easily extended to identify promoters and other complex functional regions in sequences of many other and especially newly sequenced genomes. The CNNProm program is available to run at web server http://www.softberry.com.

  14. Extracellular matrix assembly in extreme acidic eukaryotic biofilms and their possible implications in heavy metal adsorption

    Energy Technology Data Exchange (ETDEWEB)

    Aguilera, Angeles [Centro de Astrobiologia (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejon de Ardoz, 28850 Madrid (Spain)], E-mail: aguileraba@inta.es; Souza-Egipsy, Virginia [Centro de Astrobiologia (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejon de Ardoz, 28850 Madrid (Spain); San Martin-Uriz, Patxi [Centro de Biologia Molecular (UAM-CSIC), Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Amils, Ricardo [Centro de Astrobiologia (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejon de Ardoz, 28850 Madrid (Spain); Centro de Biologia Molecular (UAM-CSIC), Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain)

    2008-07-30

    To evaluate the importance of the extracellular matrix in relation to heavy metal binding capacity in extreme acidic environments, the extracellular polymeric substances (EPS) composition of 12 biofilms isolated from Rio Tinto (SW, Spain) was analyzed. Each biofilm was composed mainly by one or two species of eukaryotes, although other microorganisms were present. EPS ranged from 130 to 439 mg g{sup -1} biofilm dry weight, representing between 15% and the 40% of the total biofilm dry weight (DW). Statistically significant differences (p < 0.05) were found in the amount of total EPS extracted from biofilms dominated by the same organism at different sampling points. The amount of EPS varied among different biofilms collected from the same sampling location. Colloidal EPS ranged from 42 to 313 mg g{sup -1} dry weight; 10% to 30% of the total biofilm dry weight. Capsular EPS ranged from 50 to 318 mg g{sup -1} dry weight; 5% to 30% of the total biofilm dry weight. Seven of the 12 biofilms showed higher amounts of capsular than colloidal EPS (p < 0.05). Total amount of EPS decreased when total cell numbers and pH increased. There was a positive correlation between EPS concentration and heavy metal concentration in the water. Observations by low temperature scanning electron microscopy (LTSEM) revealed the mineral adsorption in the matrix of EPS and onto the cell walls. EPS in all biofilms were primarily composed of carbohydrates, heavy metals and humic acid, plus small quantities of proteins and DNA. After carbohydrates, heavy metals were the second main constituents of the extracellular matrix. Their total concentrations ranged from 3 to 32 mg g{sup -1} biofilm dry weight, reaching up to 16% of the total composition. In general, the heavy metal composition of the EPS extracted from the biofilms closely resembled the metal composition of the water from which the biofilms were collected.

  15. Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

    Science.gov (United States)

    Colussi, Timothy M; Costantino, David A; Zhu, Jianyu; Donohue, John Paul; Korostelev, Andrei A; Jaafar, Zane A; Plank, Terra-Dawn M; Noller, Harry F; Kieft, Jeffrey S

    2015-03-05

    The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.

  16. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species.

    Science.gov (United States)

    Hindle, Matthew M; Martin, Sarah F; Noordally, Zeenat B; van Ooijen, Gerben; Barrios-Llerena, Martin E; Simpson, T Ian; Le Bihan, Thierry; Millar, Andrew J

    2014-08-02

    The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead to the transfer of knowledge across kingdoms. Two useful properties of a eukaryote model for signalling are (1) reduced signalling complexity, and (2) conservation of signalling components. The alga Ostreococcus tauri is described as the smallest free-living eukaryote. With less than 8,000 genes, it represents a highly constrained genomic palette. Our survey revealed 133 protein kinases and 34 protein phosphatases (1.7% and 0.4% of the proteome). We conducted phosphoproteomic experiments and constructed domain structures and phylogenies for the catalytic protein-kinases. For each of the major kinases families we review the completeness and divergence of O. tauri representatives in comparison to the well-studied kinomes of the laboratory models Arabidopsis thaliana and Saccharomyces cerevisiae, and of Homo sapiens. Many kinase clades in O. tauri were reduced to a single member, in preference to the loss of family diversity, whereas TKL and ABC1 clades were expanded. We also identified kinases that have been lost in A. thaliana but retained in O. tauri. For three, contrasting eukaryotic pathways - TOR, MAPK, and the circadian clock - we established the subset of conserved components and demonstrate conserved sites of substrate phosphorylation and kinase motifs. We conclude that O. tauri satisfies our two central requirements. Several of its kinases are more closely related to H. sapiens orthologs than S. cerevisiae is to H. sapiens. The greatly reduced kinome of O. tauri is therefore a suitable model for signalling in free-living eukaryotes.

  17. Convergent use of RhoGAP toxins by eukaryotic parasites and bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Dominique Colinet

    2007-12-01

    Full Text Available Inactivation of host Rho GTPases is a widespread strategy employed by bacterial pathogens to manipulate mammalian cellular functions and avoid immune defenses. Some bacterial toxins mimic eukaryotic Rho GTPase-activating proteins (GAPs to inactivate mammalian GTPases, probably as a result of evolutionary convergence. An intriguing question remains whether eukaryotic pathogens or parasites may use endogenous GAPs as immune-suppressive toxins to target the same key genes as bacterial pathogens. Interestingly, a RhoGAP domain-containing protein, LbGAP, was recently characterized from the parasitoid wasp Leptopilina boulardi, and shown to protect parasitoid eggs from the immune response of Drosophila host larvae. We demonstrate here that LbGAP has structural characteristics of eukaryotic RhoGAPs but that it acts similarly to bacterial RhoGAP toxins in mammals. First, we show by immunocytochemistry that LbGAP enters Drosophila immune cells, plasmatocytes and lamellocytes, and that morphological changes in lamellocytes are correlated with the quantity of LbGAP they contain. Demonstration that LbGAP displays a GAP activity and specifically interacts with the active, GTP-bound form of the two Drosophila Rho GTPases Rac1 and Rac2, both required for successful encapsulation of Leptopilina eggs, was then achieved using biochemical tests, yeast two-hybrid analysis, and GST pull-down assays. In addition, we show that the overall structure of LbGAP is similar to that of eukaryotic RhoGAP domains, and we identify distinct residues involved in its interaction with Rac GTPases. Altogether, these results show that eukaryotic parasites can use endogenous RhoGAPs as virulence factors and that despite their differences in sequence and structure, eukaryotic and bacterial RhoGAP toxins are similarly used to target the same immune pathways in insects and mammals.

  18. Eukaryotic interference with homoserine lactone mediated procaryotic signalling

    DEFF Research Database (Denmark)

    Givskov, Michael Christian; de Nys, Rocky; Gram, Lone

    1996-01-01

    Acylated homoserine lactones (AHLs) plays a widespread role in intercellular communication among bacteria. The Australian macroalga Delisea pulchra produces secondary metabolites which have structural similarities to AHL molecules. We report here that these metabolites inhibited AHL-controlled pr......-controlled processes in prokaryotes. Our results suggest that the interaction between higher organisms and their surface-associated bacteria may be mediated by interference with bacterial regulatory systems....

  19. Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response.

    Science.gov (United States)

    Horváth, Vivien; Merenciano, Miriam; González, Josefa

    2017-11-01

    A relationship between transposable elements (TEs) and the eukaryotic stress response was suggested in the first publications describing TEs. Since then, it has often been assumed that TEs are activated by stress, and that this activation is often beneficial for the organism. In recent years, the availability of new high-throughput experimental techniques has allowed further interrogation of the relationship between TEs and stress. By reviewing the recent literature, we conclude that although there is evidence for a beneficial effect of TE activation under stress conditions, the relationship between TEs and the eukaryotic stress response is quite complex. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells

    DEFF Research Database (Denmark)

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-01-01

    DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells...... prokaryotes and eukaryotes are inactivated until the next cell cycle. Furthermore, in both systems the beta-clamp of the replicative polymerase associates with enzymatic activities that contribute to the inactivation of the helicase loaders. Finally, recent studies suggest that the control mechanism...

  1. Signaling mechanisms of apoptosis-like programmed cell death in unicellular eukaryotes.

    Science.gov (United States)

    Shemarova, Irina V

    2010-04-01

    In unicellular eukaryotes, apoptosis-like cell death occurs during development, aging and reproduction, and can be induced by environmental stresses and exposure to toxic agents. The essence of the apoptotic machinery in unicellular organisms is similar to that in mammals, but the apoptotic signal network is less complex and of more ancient origin. The review summarizes current data about key apoptotic proteins and mechanisms of the transduction of apoptotic signals by caspase-like proteases and mitochondrial apoptogenic proteins in unicellular eukaryotes. The roles of receptor-dependent and receptor-independent caspase cascades are reviewed. 2010 Elsevier Inc. All rights reserved.

  2. Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family.

    Science.gov (United States)

    Krapp, S; Kelly, G; Reischl, J; Weinzierl, R O; Matthews, S

    1998-02-01

    RNA polymerase II subunit RPB8 is an essential subunit that is highly conserved throughout eukaryotic evolution and is present in all three types of nuclear RNA polymerases. We report the first high resolution structural insight into eukaryotic RNA polymerase architecture with the solution structure of RPB8 from Saccharomyces cerevisiae. It consists of an eight stranded, antiparallel beta-barrel, four short helical regions and a large, unstructured omega-loop. The strands are connected in classic Greek-key fashion. The overall topology is unusual and contains a striking C2 rotational symmetry. Furthermore, it is most likely a novel associate of the oligonucleotide/oligosaccharide (OB) binding protein class.

  3. A photochemical reactor for studies of atmospheric chemistry

    DEFF Research Database (Denmark)

    Nilsson, Elna Johanna Kristina; Eskebjerg, Carsten; Johnson, Matthew Stanley

    2009-01-01

    flanges, surrounded by UV-A, UV-C and broadband sun lamps in a temperature-controlled housing. The combination of a quartz vessel and UV-C lamps allows higher concentrations of O(1D) and OH than can be generated by similar chambers. The reactor is able to produce radical concentrations of ca. 8 1011 cm 3...

  4. Synthesis and photochemical properties of a novel iron-sulfur-nitrosyl cluster derivatized with the pendant chromophore protoporphyrin IX.

    Science.gov (United States)

    Conrado, Christa L; Wecksler, Stephen; Egler, Christian; Magde, Douglas; Ford, Peter C

    2004-09-06

    The novel Roussin red-salt ester (PPIX-RSE) with a pendant porphyrin chromophore was prepared and investigated as a precursor for the photochemical generation of nitric oxide. PPIX-RSE has the general formula Fe(2)(NO)(4)[(mu-S,mu-S')P] (where (S,S')P is the bis(2-thiolatoethyl) diester of protoporphyrin IX. The photoexcitation of PPIX-RSE with 436- or 546-nm light in an aerated chloroform solution led to the photodecomposition of the cluster with the respective quantum yields (5.2 +/- 0.7) x 10(-4) and (2.5 +/- 0.5 x 10(-4)) and the concomitant release of NO. PPIX-RSE is a significantly more effective NO generator at longer wavelength excitation than are other Fe(2)(mu-SR)(2)(NO)(4) esters for which R is a simple alkyl group such as CH(3)CH(2)- because of the much higher absorptivity of the pendant PPIX chromophore at these wavelengths and a modestly higher quantum yield. Fluorescence intensity and lifetime data indicate that the photoexcited porphyrin of PPIX-RSE is largely quenched by the energy transfer to the Fe(2)S(2)(NO)(4) cluster's core. However, a small fraction of this emission is not quenched, and it is proposed that PPIX-RSE may exist in solution as two conformers.

  5. Pt nanoparticles supported over Ce-Ti-O: the solvothermal and photochemical approaches for the preparation of catalytic materials

    International Nuclear Information System (INIS)

    Silva, Adrian M. T.; Machado, Bruno F.; Gomes, Helder T.; Figueiredo, Jose L.; Drazic, Goran; Faria, Joaquim L.

    2010-01-01

    Ce-Ti-O supports with different Ce/Ti molar ratios were synthesized by the solvothermal method using hexadecyltrimethylammonium bromide. Pt nanoparticles were then supported by photochemical deposition. The shape, size, and structure of these materials were analyzed by high-resolution transmission electron microscopy. The single CeO 2 support was also prepared, consisting of agglomerated cubic particles ranging from ∼3 to 8 nm. When titania was combined with ceria, a nanostructured architecture was produced, evidencing the strong influence of Ti in the support structure. Photodeposition of Pt nanoparticles is more efficient on Ce-Ti-O supports than in pristine CeO 2 . Crystalline Pt nanoparticles (mainly of ∼2 to 4 nm) were detected. The catalytic properties of the materials were tested in the selective hydrogenation of cinnamaldehyde to cinnamyl alcohol. It was observed that Pt supported on Ce-Ti-O is more active and selective than Pt on CeO 2 or TiO 2 separately. The catalyst with 40 mol% Ce leads to total conversion of cinnamaldehyde in a few minutes; however, higher selectivity toward the desired product (cinnamyl alcohol) was obtained with higher amounts of Ce (50 mol%).

  6. The effect of polyamines on the photochemical reactivity of DNA

    International Nuclear Information System (INIS)

    Ben-Hur, E.; Hebrew Univ., Jerusalem

    1975-01-01

    The effects of diaminopentane (cadaverine), diaminoethane and the polyamine, spermine, on the photoreactions of 4,5', 8-trimethylpsoralen with DNA were studied. Near ultraviolet (UV) light (360 nm) irradiation of psoralen with DNA results in the formation of psoralen monoadducts with pyrimidine bases and DNA interstrand crosslinks. The polyamines studied reduced the rate of both photoreactions to the same extent by a factor of 1.5-2.0. The magnitude of the effect increased with polyamine concentration. Effectiveness was in the order spermine > cadaverine > diaminoethane. This is also the same order for stabilization of the DNA double-helix. Under conditions of higher DNA stability (higher ionic strength), higher polyamine concentrations were required to obtain an effect which was smaller than at low ionic strength. It is concluded that the photoreactions of psoralen with pyrimidines in DNA require some distortion of the double-helix. This distortion is made more difficult in the presence of stabilizing agents like polyamines and therefore the rate of the reaction is reduced. If crosslinking of DNA by psoralen is a two-step reaction then it must be concluded that the second step does not require further distortion. Consistently with the above, polyamines also reduced the UV-induced dimerization of thymine in DNA, although to a lesser extent. (author)

  7. Photochemical reactivity of aqueous fullerene clusters: C{sub 60} versus C{sub 70}

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Wen-Che, E-mail: whou@mail.ncku.edu.tw; Huang, Shih-Hong

    2017-01-15

    Highlights: • Aqueous C{sub 60} and C{sub 70} clusters (nC{sub 60} and nC{sub 70}) formed through direct mixing with water adopted a face-centered cubic crystal structure. • The AQYs of nC{sub 60} were greater than those of nC{sub 70}. • Both nC{sub 60} and nC{sub 70} lost considerable organic carbon contents (>80%) after ∼8 months of outdoor sunlight irradiation. • The intermediate photoproducts of nC{sub 60} and nC{sub 70} exhibited an increased content of oxygen-containing functionalities. - Abstract: Over the past few years, there has been a strong interest in exploring the potential impact of fullerenes in the environment. Despite that both C{sub 60} and C{sub 70} have been detected in environmental matrices, the research on the impact of higher fullerenes, such as C{sub 70,} has been largely missing. This study evaluated and compared the phototransformation of aqueous C{sub 60} and C{sub 70} clusters (nC{sub 60} and nC{sub 70}) and their {sup 1}O{sub 2} production under sunlight and lamp light irradiation (315 nm, 360 nm and 420 nm). The nC{sub 60} and nC{sub 70} samples formed by direct mixing with water adopted a face-centered cubic (FCC) crystal structure. The apparent quantum yields (AQYs) of fullerene phototransformed were relatively constant over the examined wavelengths, while {sup 1}O{sub 2} production AQYs decreased with increased wavelengths. The long-term fate studies with outdoor sunlight indicated that both nC{sub 60} and nC{sub 70} lost considerable organic carbon contents (>80%) in water after ∼8 months of irradiation and that the intermediate photoproducts of nC{sub 60} and nC{sub 70} exhibited a progressively increased level of oxygen-containing functionalities. Overall, the study indicates that nC{sub 70} can be photochemically removed under sunlight conditions and that the photoreactivity of nC{sub 60} based on AQYs is greater than that of nC{sub 70}.

  8. Photochemical Cycling of Reactive Oxygen Species in Hydrothermal Springs: Impacts on Biosignature Preservation

    Science.gov (United States)

    Mave, M. A.; Hinman, N. W.; Stevens, L.

    2017-12-01

    Biosignatures can be preserved via rapid entombment by aqueous minerals in a system. Wilson et al. (2000) found that high UV flux leads to increased production of reactive oxygen species (ROS), which promote iron (Fe) oxidation, and possible accumulation on microbial surfaces, leading to detectable microfossils. Hydrogen peroxide (H2O2) is a measurable ROS that serves as proxy for less stable ROS. Overall diel cycling of H2O2 is likely controlled by changes in photoreactive speciation of Fe (McKnight et al., 1988) in Fe-rich systems. To test this hypothesis, we conducted a 48-hour photochemical field study of Elk Pool in the Norris Geyser Basin at Yellowstone National Park in July, 2017 in which we measured UVA and UVB, along with H2O2 via the scopoletin fluorescence quenching method (Holm et al., 1987). Measurements were taken every few hours, and we found that maximum ROS production occurred during maximum UV irradiation. We also ran several experiments on-site in which we collected and altered spring water to either inactivate or catalyze naturally occurring reactions as well as to isolate primary mechanisms responsible for production of H2O2. Experiments were run in UV permeable Whirlpak bags and Fisherbrand tubes. Elk Pool showed only trace Fe content (pH 4) at the time of our study, so Fe-silica coated petrographic slides were added to the tube experiments (Fe-added experiments). Both sets of experiments included filtered and unfiltered spring water to differentiate biotic from abiotic mechanisms, and both UV-exposed and dark controls to separate UV-induced mechanisms for ROS formation. UV-exposed water always had greater ROS than dark experiments. Filtered spring water had higher ROS concentrations than unfiltered water, except when Fe was added. In the Fe-added experiments, unfiltered spring water had slightly greater ROS production relative to filtered water and had the lowest pH and highest aqueous Fe content after 7 hours. All Fe-added experiments showed

  9. Implications of imprecision in kinetic rate data for photochemical model calculations

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, R W; Thompson, A M [National Aeronautics and Space Administration, Greenbelt, MD (United States). Goddard Space Flight Center

    1998-12-31

    Evaluation of uncertainties in photochemical model calculations is of great importance to scientists performing assessment modeling. A major source of uncertainty is the measurement imprecision inherent in photochemical reaction rate data that modelers rely on. A rigorous method of evaluating the impact of data imprecision on computational uncertainty is the study of error propagation using Monte Carlo techniques. There are two problems with the current implementation of the Monte Carlo method. First, there is no satisfactory way of accounting for the variation of imprecision with temperature in 1, 2, or 3D models; second, due to its computational expense, it is impractical in 3D model studies. These difficulties are discussed. (author) 4 refs.

  10. Implications of imprecision in kinetic rate data for photochemical model calculations

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, R.W.; Thompson, A.M. [National Aeronautics and Space Administration, Greenbelt, MD (United States). Goddard Space Flight Center

    1997-12-31

    Evaluation of uncertainties in photochemical model calculations is of great importance to scientists performing assessment modeling. A major source of uncertainty is the measurement imprecision inherent in photochemical reaction rate data that modelers rely on. A rigorous method of evaluating the impact of data imprecision on computational uncertainty is the study of error propagation using Monte Carlo techniques. There are two problems with the current implementation of the Monte Carlo method. First, there is no satisfactory way of accounting for the variation of imprecision with temperature in 1, 2, or 3D models; second, due to its computational expense, it is impractical in 3D model studies. These difficulties are discussed. (author) 4 refs.

  11. Interaction of light and atmospheric photochemical products (smog) within plants. [Phaseolius vulgaris; Petunia hydrida

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, O C; Dugger, W M; Cardiff, E A; Darley, E F

    1961-12-02

    Damage to plants from ozone and peroxyacetyl nitrate, two photochemically formed components of smog, has been described. However, variations in symptom expression and the degree of damage caused by a given concentration of these components, whether of synthetic or natural origin, have complicated development of an adequate biological assay method for these materials. These observed variations in symptomatology have implicated stomatal action, inorganic nutrition temperature, genetics, ascorbic acid content, physiological age of tissue and photoperiod. Plants grown under artificial illumination differ in their response to the photochemically formed pollutants as compared with plants grown in the greenhouse. Interactions between light and oxidants from the polluted atmosphere within plants, as reported here, might well explain some of the variabilities in symptomatology observed in earlier controlled experiments as well as the unexplained natural variability observed in the Los Angeles area. The results presented also emphasize the importance of standardizing plant growth conditions for future work of this nature. 10 references.

  12. A review of photochemical approaches for the treatment of a wide range of pesticides.

    Science.gov (United States)

    Reddy, P Venkata Laxma; Kim, Ki-Hyun

    2015-03-21

    Pesticides are renowned as some of the most pernicious chemicals known to humankind. Nine out of twelve most hazardous and persistent organic chemicals on planet have been identified as pesticides and their derivatives. Because of their strong recalcitrant nature, it often becomes a difficult task to treat them by conventional approaches. It is well perceived that many factors can interfere with the degradation of pesticides under ambient conditions, e.g., media, light intensity, humic content, and other biological components. However, for the effective treatment of pesticides, photochemical methods are viewed as having clear and perceivable advantages. In this article, we provide a review of the fundamental characteristics of photochemical approaches for pesticide treatment and the factors governing their capacity and potential in such a process. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Effect of latitude on the potential for formation of photochemical smog

    Energy Technology Data Exchange (ETDEWEB)

    Neiboer, H [Central Laboratorium TNO, Delft, Netherlands; Carter, W P.L.; Lloyd, A C; Pitts, Jr, J N

    1976-01-01

    The effect of latitude on the potential for the formation of photochemical smog has been assessed. Calculations suggest that at the summer solstice, the integrated sunlight intensity at Rotterdam or Fairbanks (Alaska) is very similar to that in Los Angeles. Computations carried out, assuming the same pollutant emission inventory for the three locations, showed that ozone and PAN dosages depend more on the integrated light intensity than on the nature of the light intensity distribution with time. Therefore, if factors such as emissions and meteorological conditions are equal, the potential for significant photochemical smog formation during the summer months is similar for Los Angeles (34/sup 0/N) and northern cities such as Rotterdam (52/sup 0/N) and Nome or Fairbanks, Alaska (65/sup 0/N).

  14. L-Cysteine Capped CdSe Quantum Dots Synthesized by Photochemical Route.

    Science.gov (United States)

    Singh, Avinash; Kunwar, Amit; Rath, M C

    2018-05-01

    L-cysteine capped CdSe quantum dots were synthesized via photochemical route in aqueous solution under UV photo-irradiation. The as grown CdSe quantum dots exhibit broad fluorescence at room temperature. The CdSe quantum dots were found to be formed only through the reactions of the precursors, i.e., Cd(NH3)2+4 and SeSO2-3 with the photochemically generated 1-hydroxy-2-propyl radicals, (CH3)2COH radicals, which are formed through the process of H atom abstraction by the photoexcited acetone from 2-propanol. L-Cysteine was found to act as a suitable capping agent for the CdSe quantum dots and increases their biocompatability. Cytotoxicty effects of these quantum dots were evaluated in Chinese Hamster Ovary (CHO) epithelial cells, indicated a significant lower level for the L-cysteine capped CdSe quantum dots as compare to the bare ones.

  15. Photophysical, Photochemical, and BQ Quenching Properties of Zinc Phthalocyanines with Fused or Interrupted Extended Conjugation

    Directory of Open Access Journals (Sweden)

    Gülşah Gümrükçü

    2014-01-01

    Full Text Available The effects of substituents and solvents on the photophysical and photochemical parameters of zinc(II phthalocyanines containing four Schiff’s base substituents attached directly and through phenyleneoxy-bridges on peripheral positions are reported. The group effects on peripheral position and the continual and intermittent conjugation of the phthalocyanine molecules on the photophysical and photochemical properties are also investigated. General trends are described for photodegradation, singlet oxygen, and fluorescence quantum yields of these compounds in dimethylsulfoxide (DMSO, dimethylformamide (DMF, and tetrahydrofurane (THF. Among the different substituents, phthalocyanines with cinnamaldimine moieties (1c and 2c have the highest singlet oxygen quantum yields (ΦΔ and those with nitro groups (1a and 2a have the highest fluorescence quantum yields in all the solvents used. The fluorescence of the substituted zinc(II phthalocyanine complexes is effectively quenched by 1,4-benzoquinone (BQ in these solvents.

  16. Decoupling photochemical Fe(II) oxidation from shallow-water BIF deposition

    DEFF Research Database (Denmark)

    Konhauser, Kurt; Amskold, Larry; Lalonde, Stefan

    2007-01-01

    to the rise of atmospheric oxygen and the development of a protective ozone layer, the Earth's surface was subjected to high levels of ultraviolet radiation. Bulk ocean waters that were anoxic at this time could have supported high concentrations of dissolved Fe(II). Under such conditions, dissolved ferrous...... for biology [Fran??ois, L.M., 1986, Extensive deposition of banded iron formations was possible without photosynthesis. Nature 320, 352-354]. Here, we evaluate the potential importance of photochemical oxidation using a combination of experiments and thermodynamic models. The experiments simulate......-type systems, then we are driven to conclude that oxide-facies BIF are the product of a rapid, non-photochemical oxidative process, the most likely candidates being direct or indirect biological oxidation, and that a significant fraction of BIF could have initially been deposited as ferrous minerals. ?? 2007...

  17. Heparin Assisted Photochemical Synthesis of Gold Nanoparticles and Their Performance as SERS Substrates

    Science.gov (United States)

    Rodríguez-Torres, Maria del Pilar; Díaz-Torres, Luis Armando; Romero-Servin, Sergio

    2014-01-01

    Reactive and pharmaceutical-grade heparins were used as biologically compatible reducing and stabilizing agents to photochemically synthesize colloidal gold nanoparticles. Aggregates and anisotropic shapes were obtained photochemically under UV black-light lamp irradiation (λ = 366 nm). Heparin-functionalized gold nanoparticles were characterized by Scanning Electron Microscopy and UV-Vis spectroscopy. The negatively charged colloids were used for the Surface Enhanced Raman Spectroscopy (SERS) analysis of differently charged analytes (dyes). Measurements of pH were taken to inspect how the acidity of the medium affects the colloid-analyte interaction. SERS spectra were taken by mixing the dyes and the colloidal solutions without further functionalization or addition of any aggregating agent. PMID:25342319

  18. Photochemical immobilization of anthraquinone conjugated oligonucleotides and PCR amplicons on solid surfaces

    DEFF Research Database (Denmark)

    Koch, T.; Jacobsen, N.; Fensholdt, J.

    2000-01-01

    Ligand immobilization on solid surfaces is an essential step in fields such as diagnostics, bio sensor manufacturing, and new material sciences in general. In this paper a photochemical approach based on anthraquinone as the chromophore is presented. Photochemical procedures offer special...... advantages as they are able to generate highly reactive species in an orientation specific manner. As presented here, anthraquinone (AQ) mediated covalent DNA immobilization appears to be superior to currently known procedures. A synthetic procedure providing AQ-phosphoramidites is presented. These reagents...... facilitate AQ conjugation during routine DNA synthesis, thus enabling the AQ-oligonucleotides to be immobilized in a very convenient and efficient manner. AQ-conjugated PCR primers can be used directly in PCR. When the PCR is performed in solution, the amplicons can be immobilized after the PCR. Moreover...

  19. Structure and reactivity of oxalate surface complexes on lepidocrocite derived from infrared spectroscopy, DFT-calculations, adsorption, dissolution and photochemical experiments

    Science.gov (United States)

    Borowski, Susan C.; Biswakarma, Jagannath; Kang, Kyounglim; Schenkeveld, Walter D. C.; Hering, Janet G.; Kubicki, James D.; Kraemer, Stephan M.; Hug, Stephan J.

    2018-04-01

    Oxalate, together with other ligands, plays an important role in the dissolution of iron(hdyr)oxides and the bio-availability of iron. The formation and properties of oxalate surface complexes on lepidocrocite were studied with a combination of infrared spectroscopy (IR), density functional theory (DFT) calculations, dissolution, and photochemical experiments. IR spectra measured as a function of time, concentration, and pH (50-200 μM oxalate, pH 3-7) showed that several surface complexes are formed at different rates and in different proportions. Measured spectra could be separated into three contributions described by Gaussian line shapes, with frequencies that agreed well with the theoretical frequencies of three different surface complexes: an outer-sphere complex (OS), an inner-sphere monodentate mononuclear complex (MM), and a bidentate mononuclear complex (BM) involving one O atom from each carboxylate group. At pH 6, OS was formed at the highest rate. The contribution of BM increased with decreasing pH. In dissolution experiments, lepidocrocite was dissolved at rates proportional to the surface concentration of BM, rather than to the total adsorbed concentration. Under UV-light (365 nm), BM was photolyzed at a higher rate than MM and OS. Although the comparison of measured spectra with calculated frequencies cannot exclude additional possible structures, the combined results allowed the assignment of three main structures with different reactivities consistent with experiments. The results illustrate the importance of the surface speciation of adsorbed ligands in dissolution and photochemical reactions.

  20. Efficacy of photochemical internalisation using disulfonated chlorin and porphyrin photosensitisers: An in vitro study in 2D and 3D prostate cancer models.

    Science.gov (United States)

    Martinez de Pinillos Bayona, Alejandra; Woodhams, Josephine H; Pye, Hayley; Hamoudi, Rifat A; Moore, Caroline M; MacRobert, Alexander J

    2017-05-01

    This study shows the therapeutic outcome of Photochemical Internalisation (PCI) in prostate cancer in vitro surpasses that of Photodynamic Therapy (PDT) and could improve prostate PDT in the clinic, whilst avoiding chemotherapeutics side effects. In addition, the study assesses the potential of PCI with two different photosensitisers (TPCS 2a and TPPS 2a ) in prostate cancer cells (human PC3 and rat MatLyLu) using standard 2D monolayer culture and 3D biomimetic model. Photosensitisers were used alone for photodynamic therapy (PDT) or with the cytotoxin saporin (PCI). TPPS 2a and TPCS 2a were shown to be located in discrete cytoplasmic vesicles before light treatment and redistribute into the cytosol upon light excitation. PC3 cells exhibit a higher uptake than MatLyLu cells for both photosensitisers. In the 2D model, PCI resulted in greater cell death than PDT alone in both cell lines. In 3D model, morphological changes were also observed. Saporin-based toxicity was negligible in PC3 cells, but pronounced in MatLyLu cells (IC50 = 18 nM). In conclusion, the study showed that tumour features such as tumour cell growth rate or interaction with drugs determine therapeutic conditions for optimal photochemical treatment in metastatic prostate cancer. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  1. Photochemical studies on aromatic γ,δ-epoxy ketones: efficient synthesis of benzocyclobutanones and indanones.

    Science.gov (United States)

    Shao, Yutian; Yang, Chao; Gui, Weijun; Liu, Yang; Xia, Wujiong

    2012-04-11

    Irradiation of terminal aromatic γ,δ-epoxy ketones with a 450 W UV lamp led to Norrish type II cyclization/semi-pinacol rearrangement cascade reaction which formed the benzocyclobutanones containing a full-carbon quaternary center, whereas irradiation of substituted aromatic γ,δ-epoxy ketones led to the indanones through a photochemical epoxy rearrangement and 1,5-biradicals cyclization tandem reaction. This journal is © The Royal Society of Chemistry 2012

  2. Photochemical degradation of the carbapenem antibiotics imipenem and meropenem in aqueous solutions under solar radiation.

    Science.gov (United States)

    Reina, Alejandro Cabrera; Martínez-Piernas, Ana B; Bertakis, Yannis; Brebou, Christina; Xekoukoulotakis, Nikolaos P; Agüera, Ana; Sánchez Pérez, José Antonio

    2018-01-01

    This paper deals with the photochemical fate of two representative carbapenem antibiotics, namely imipenem and meropenem, in aqueous solutions under solar radiation. The analytical method employed for the determination of the target compounds in various aqueous matrices, such as ultrapure water, municipal wastewater treatment plant effluents, and river water, at environmentally relevant concentrations, was liquid chromatography coupled with hybrid triple quadrupole-linear ion trap-mass spectrometry. The absorption spectra of both compounds were measured in aqueous solutions at pH values from 6 to 8, and both compounds showed a rather strong absorption band centered at about 300 nm, while their molar absorption coefficient was in the order from 9 × 10 3 -10 4  L mol -1  cm -1 . The kinetics of the photochemical degradation of the target compounds was studied in aqueous solutions under natural solar radiation in a solar reactor with compound parabolic collectors. It was found that the photochemical degradation of both compounds at environmentally relevant concentrations follows first order kinetics and the quantum yield was in the order of 10 -3  mol einsten -1 . Several parameters were studied, such as solution pH, the presence of nitrate ions and humic acids, and the effect of water matrix. In all cases, it was found that the presence of various organic and inorganic constituents in the aqueous matrices do not contribute significantly, either positively or negatively, to the photochemical degradation of both compounds under natural solar radiation. In a final set of photolysis experiments, the effect of the level of irradiance was studied under simulated solar radiation and it was found that the quantum yield for the direct photodegradation of both compounds remained practically constant by changing the incident solar irradiance from 28 to 50 W m -2 . Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Photochemical internalisation of chemotherapy potentiates killing of multidrug-resistant breast and bladder cancer cells

    OpenAIRE

    Adigbli, D. K.; Wilson, D. G. G.; Farooqui, N.; Sousi, E.; Risley, P.; Taylor, I.; MacRobert, A. J.; Loizidou, M.

    2007-01-01

    Multidrug resistance (MDR) is the major confounding factor in adjuvant solid tumour chemotherapy. Increasing intracellular amounts of chemotherapeutics to circumvent MDR may be achieved by a novel delivery method, photochemical internalisation (PCI). PCI consists of the co-administration of drug and photosensitiser; upon light activation the latter induces intracellular release of organelle-bound drug. We investigated whether co-administration of hypericin ( photosensitiser) with mitoxantrone...

  4. Photochemical internalisation of chemotherapy potentiates killing of multidrug-resistant breast and bladder cancer cells

    OpenAIRE

    Adigbli, D K; Wilson, D G G; Farooqui, N; Sousi, E; Risley, P; Taylor, I; MacRobert, A J; Loizidou, M

    2007-01-01

    Multidrug resistance (MDR) is the major confounding factor in adjuvant solid tumour chemotherapy. Increasing intracellular amounts of chemotherapeutics to circumvent MDR may be achieved by a novel delivery method, photochemical internalisation (PCI). PCI consists of the co-administration of drug and photosensitiser; upon light activation the latter induces intracellular release of organelle-bound drug. We investigated whether co-administration of hypericin (photosensitiser) with mitoxantrone ...

  5. Molecular orbital study of iron pentacarbonyl and its photochemical fragments Fe(CO) sub(n)

    International Nuclear Information System (INIS)

    Guenzburger, D.J.R.; Saitovitch, E.M.B.; De Paoli, M.-A.; Manella, H.

    1982-01-01

    Self-consistent Molecular Orbital calculations were performed for Fe(CO) 5 and its photofragments Fe(CO) sub(n), 1 5 , photoelectron and optical spectra are analysed, and photochemical behaviour is discussed. The Moessbauer isomer shifts and quadrupole splittings are investigated. In the case of Fe(CO) 5 and Fe(CO) 4 , the values derived for these hyperfine interactions are compared to experimental measurements reported in a polyethylene matrix. (Author) [pt

  6. Effects of Photo-chemically Activated Alkylating Agents of the FR900482 Family on Chromatin

    OpenAIRE

    Subramanian, Vidya; Ducept, Pascal; Williams, Robert M.; Luger, Karolin

    2007-01-01

    Bioreductive alkylating agents are an important class of clinical antitumor antibiotics that cross-link and mono-alkylate DNA. Here we use a synthetic photochemically activated derivative of FR400482 to investigate the molecular mechanism of this class of drugs in a biologically relevant context. We find that the organization of DNA into nucleosomes effectively protects it against drug-mediated cross-linking, while permitting mono-alkylation. This modification has the potential to form covale...

  7. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies: Evaluation Number 18

    Science.gov (United States)

    Burkholder, J. B.; Sander, S. P.; Abbatt, J. P. D.; Barker, J. R.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Orkin, V. L.; Wilmouth, D. M.; Wine, P. H.

    2015-01-01

    This is the eighteenth in a series of evaluated sets of rate constants, photochemical cross sections, heterogeneous parameters, and thermochemical parameters compiled by the NASA Panel for Data Evaluation. The data are used primarily to model stratospheric and upper tropospheric processes, with particular emphasis on the ozone layer and its possible perturbation by anthropogenic and natural phenomena. The evaluation is available in electronic form from the following Internet URL: http://jpldataeval.jpl.nasa.gov/

  8. Plasmon mediated non-photochemical nucleation of nanoparticles by circularly polarized light

    OpenAIRE

    Karpov, Victor G.; Grigorchuk, Nicholas I.

    2014-01-01

    We predict nucleation of pancake shaped metallic nanoparticles having plasmonic frequencies in resonance with a non-absorbed circularly polarized electromagnetic field. We show that the same field can induce nucleation of randomly oriented needle shaped particles. The probabilities of these shapes are estimated vs. field frequency and strength, material parameters, and temperature. This constitutes a quantitative model of non-photochemical laser induced nucleation (NPLIN) consistent with the ...

  9. Using of Photochemical H2O2/UVC Decontamination Cell for Heavily Polluted Waters

    Czech Academy of Sciences Publication Activity Database

    Žebrák, R.; Mašín, P.; Klusoň, Petr; Krystyník, Pavel

    2014-01-01

    Roč. 2014, č. 2 (2014), s. 55-62 ISSN 1804-0195. [Symposium ODPADOVÉ FÓRUM 2014. Hustopeče u Brna, 23.042014-23.04.2013] R&D Projects: GA MPO(CZ) FR-TI1/065 Institutional support: RVO:67985858 Keywords : photochemical oxidation * remediation * pilot scale Subject RIV: CI - Industrial Chemistry, Chemical Engineering http://www.wasteforum.cz/

  10. Photochemical reaction of Si-substituted ethynylsilanes with 1,2-ethanedithiol

    Energy Technology Data Exchange (ETDEWEB)

    Voronkov, M.G.; Brodskaya, E.I.; Kalabin, G.A.; Vlasova, N.N.; Yarosh, O.G.; Zhila, G.Y.

    1985-12-01

    The authors investigate the chief products of the photochemical reactions of Si-substituted ethynylsilanes with 1,2,-ethanedithiol at 60-70 C. It is found that the chief products are 2-triorganylsilyl-substituted 1,4-dithiacyclopentanes and 1,4-dithiacyclohexanes. On lowering the temperature to -30 C, formation of bis (triorganylsilyl)-substituted 1,4,7,10-tetrathiacyclododecanes occurs along with the abo ve-mentioned five- and six-membered heterocycles.

  11. Spectrofluorometric study on photochemical interaction between chlorpromazine and nucleic acids

    International Nuclear Information System (INIS)

    Fujita, H.; Hayashi, H.; Suzuki, K.

    1981-01-01

    Near-UV irradiation of a mixture of chlorpromazine and single-stranded nucleic acids produced a non-dialyzable photoproduct which emitted characteristic fluorescence at around 520 nm. The same fluorescent species was also formed by the photoreaction with purine nucleotides but not with pyrimidine nucleotide. The highest photoreactivity was observed with GMP. Smaller amounts of the species were formed in a solution with a high salt concentration than in that with a low salt concentration. A higher rate was observed under anaerobic conditions than under aerobic conditions. (author)

  12. Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.

    Science.gov (United States)

    Perederina, Anna; Esakova, Olga; Quan, Chao; Khanova, Elena; Krasilnikov, Andrey S

    2010-02-17

    Ribonuclease (RNase) P is a site-specific endoribonuclease found in all kingdoms of life. Typical RNase P consists of a catalytic RNA component and a protein moiety. In the eukaryotes, the RNase P lineage has split into two, giving rise to a closely related enzyme, RNase MRP, which has similar components but has evolved to have different specificities. The eukaryotic RNases P/MRP have acquired an essential helix-loop-helix protein-binding RNA domain P3 that has an important function in eukaryotic enzymes and distinguishes them from bacterial and archaeal RNases P. Here, we present a crystal structure of the P3 RNA domain from Saccharomyces cerevisiae RNase MRP in a complex with RNase P/MRP proteins Pop6 and Pop7 solved to 2.7 A. The structure suggests similar structural organization of the P3 RNA domains in RNases P/MRP and possible functions of the P3 domains and proteins bound to them in the stabilization of the holoenzymes' structures as well as in interactions with substrates. It provides the first insight into the structural organization of the eukaryotic enzymes of the RNase P/MRP family.

  13. Mathematical model of reproductive death of irradiated eukaryotic cells, which considers saturation of DNA reparation system

    International Nuclear Information System (INIS)

    Knyigavko, V.G.; Ponomarenko, N.S.; Meshcheryakova, O.P.; Protasenya, S.Yu.

    2009-01-01

    A mathematical model of the processes determining reproductive death of the exposed cells was built. The model takes into account the phenomenon of saturation of the system of DNA radiation lesion reparation and structural functional peculiarities of chromatin structure in eukaryotes. The problem of assessment of the model parameters using experimental data was discussed.

  14. Avian leukosis virus is a versatile eukaryotic platform for polypeptide display

    International Nuclear Information System (INIS)

    Khare, Pranay D.; Russell, Stephen J.; Federspiel, Mark J.

    2003-01-01

    Display technology refers to methods of generating libraries of modularly coded biomolecules and screening them for particular properties. Retroviruses are good candidates to be a eukaryotic viral platform for the display of polypeptides synthesized in eukaryotic cells. Here we demonstrate that avian leukosis virus (ALV) provides an ideal platform for display of nonviral polyaeptides expressed in a eukaryotic cell substrate. Different sizes of polypeptides were genetically fused to the extreme N-terminus of the ALV envelope glycoprotein in an ALV infectious clone containing an alkaline phosphatase reporter gene. The chimeric envelope glycoproteins were efficiently incorporated into virions and were stably displayed on the surface of the virions through multiple virus replication cycles. The foreign polypeptides did not interfere with the attachment and entry functions of the underlying ALV envelope glycoproteins. The displayed polypeptides were fully functional and could efficiently mediate attachment of the recombinant viruses to their respective cognate receptors. This study demonstrates that ALV is an ideal display platform for the generation and selection of libraries of polypeptides where there is a need for expression, folding, and posttranslational modification in the endoplasmic reticulum of eukaryotic cells

  15. Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea.

    Science.gov (United States)

    Xu, Dapeng; Jiao, Nianzhi; Ren, Rui; Warren, Alan

    2017-05-01

    Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75-m depth. The communities of microbial eukaryotes were clustered into shallow-, middle-, and deep-water groups according to the depth from which they were collected, indicating a depth-related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50-m deep, being most abundant near the sea floor where they contributed ca. 64-97% and 40-74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  16. EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

    Directory of Open Access Journals (Sweden)

    Grover Atul

    2007-07-01

    Full Text Available Abstract Background Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database http://ipu.ac.in/usbt/EuMicroSatdb.htm is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes. Description A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP. The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect, repeat unit length (mono- to hexa-nucleotide, repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided. Conclusion The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.

  17. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

    Science.gov (United States)

    Monier, Adam; Pagarete, António; de Vargas, Colomban; Allen, Michael J.; Read, Betsy; Claverie, Jean-Michel; Ogata, Hiroyuki

    2009-01-01

    Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton–virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival. PMID:19451591

  18. Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins.

    Science.gov (United States)

    Li, Sanshu; Smith, Kathryn D; Davis, Jared H; Gordon, Patricia B; Breaker, Ronald R; Strobel, Scott A

    2013-11-19

    Fluorine is an abundant element and is toxic to organisms from bacteria to humans, but the mechanisms by which eukaryotes resist fluoride toxicity are unknown. The Escherichia coli gene crcB was recently shown to be regulated by a fluoride-responsive riboswitch, implicating it in fluoride response. There are >8,000 crcB homologs across all domains of life, indicating that it has an important role in biology. Here we demonstrate that eukaryotic homologs [renamed FEX (fluoride exporter)] function in fluoride export. FEX KOs in three eukaryotic model organisms, Neurospora crassa, Saccharomyces cerevisiae, and Candida albicans, are highly sensitized to fluoride (>200-fold) but not to other halides. Some of these KO strains are unable to grow in fluoride concentrations found in tap water. Using the radioactive isotope of fluoride, (18)F, we developed an assay to measure the intracellular fluoride concentration and show that the FEX deletion strains accumulate fluoride in excess of the external concentration, providing direct evidence of FEX function in fluoride efflux. In addition, they are more sensitive to lower pH in the presence of fluoride. These results demonstrate that eukaryotic FEX genes encode a previously unrecognized class of fluoride exporter necessary for survival in standard environmental conditions.

  19. Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.

    Science.gov (United States)

    Marques, Catarina A; Dickens, Nicholas J; Paape, Daniel; Campbell, Samantha J; McCulloch, Richard

    2015-10-19

    DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.

  20. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes.

    Science.gov (United States)

    Lawrence, J

    1999-12-01

    The Selfish Operon Model postulates that the organization of bacterial genes into operons is beneficial to the constituent genes in that proximity allows horizontal cotransfer of all genes required for a selectable phenotype; eukaryotic operons formed for very different reasons. Horizontal transfer of selfish operons most probably promotes bacterial diversification.