Aqueous two-phase system purification for superoxide dismutase induced by menadione from Phanerochaete chrysosporium.

Science.gov (United States)

Kavakcıoğlu, Berna; Tongul, Burcu; Tarhan, Leman

2017-03-01

In the present work, the partitioning behavior of menadione-induced superoxide dismutase (SOD; EC 1.15.1.1), an antioxidant enzyme that has various applications in the medical and cosmetic industries, from the white rot fungus Phanerochaete chrysosporium has been characterized on different types of aqueous two-phase systems (ATPSs) (poly(ethylene glycol)/polypropylene glycol (PEG/PPG)-dextran, PEG-salt and PPG-salt). PEG-salt combinations were found most optimal systems for the purification of SOD. The best partition conditions were found using the PEG-3350 24% and K 2 HPO 4 5% (w/w) with pH 7.0 at 25 °C. The partition coefficient of total SOD activity and total protein concentration observed in this system were 0.17 and 6.65, respectively, with the recovery percentage as 78.90% in the bottom phase and 13.17% in the top phase. The highest purification fold for SOD from P. chrysosporium was found as 6.04 in the bottom phase of PEG 3350%24 - K 2 HPO 4 %5 (w/w) system with pH 7.0. SOD purified from P. chrysosporium was determined to be a homodimer in its native state with a molecular weight of 60  ± 4 kDa. Consequently, simple and only one step PEG-salt ATPS system was developed for SOD purification from P. chrysosporium.

Influence of gamma rays radiation on lignin degradation potency of phanerochaete chrysosporium and ganoderma lucidum

International Nuclear Information System (INIS)

Tri Retno DL; Nana Mulyana; Nurhasni; Uswatun Hasanah

2016-01-01

This research aims to increase the activity of extracellular enzymes lignolitik fungi phanerochaete chrysosporium and ganoderma lucidum to degrade lignocellulosic waste. Lignocellulosic difficult to degrade because it is composed of lignin, cellulose and hemicellulose. Phanerochaete chrysosporium and ganoderma lucidum group white rot fungi can degrade lignin because it is able to synthesize enzymes lignin peroxidase (LiP). Irradiation low dose gamma rays capable menstimulsi increase extracellular enzyme activity. Fungi phanerochaete chrysosporium and ganoderma lucidum in medium slent exposed to gamma irradiation at doses of 0 (control), 200, 400, 600, 800 and 1000 Gy. In a liquid medium containing Potatoes Dextrose Broth (PDB), mineral salts with the substrate lignin alkali 0 and 5 % w/v, fungi phanerochaete chrysosporium were exposed to a dose of 600 Gy of gamma rays have LiP activity (30 U/mL) by 2.5 times higher compared with controls (12 U/mL). While ganoderma lucidum that are exposed to gamma radiation at a dose of 800 Gy has LiP activity (34 U/mL) was 1.7 times higher than the control (20 U/mL). On a solid substrate fermentation of white teak powder (Gmelina arborea Roxb.) For 12 days at pH 6.4 and water content of 79 % by fungi phanerochaete chrysosporium were exposed to gamma ray dose of 600 Gy has an efficiency of lignin degradation by 42 %, whereas on fungi ganoderma lucidum that are exposed gamma ray dose of 800 Gy has an efficiency of lignin degradation by 21 % with optimal conditions of pH 7. And; water content of 71.3 %. (author)

Potensi kapang pelapuk putih Phanerochaeta chrysosporium dalam pengolahan limbah industri tekstil

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Yulinah Trihadiningrum

2012-02-01

Full Text Available Phanerochaete chrysosporium was known as white rot mold which could biodegrade persistent organic pollutants. In this researchthe ability of the mold in biodegrading textile dye direct orange S and rhemazol yellow, which contained naphtol functional group, wasstudied. This research included characterization of the waste water and determination of optimum concentration of the waste water forbiodegradation. The optimum concentration for biodegradation was determined by measuring the radial growth of the mold in agarmedium containing various concentrations of textile dye. The final stage was the application of the mold for biodegrading the textiledye in aerobic batch reactor using the selected concentration.This research showed that P. chrysosporium could grow satisfactorily in minimum medium containing synthetic textile wastewaterin various concentrations. The highest colour removal efficiency of 93% was achieved in 3 days in the waste water with highest colorintensity (absorbance value l520 = 4.00, and 48% in the waste water with absorbance value l520 = 1.22. COD removal efficiency of87% was achieved within 12 days in the wastewater of 30% concentration, and 83% in the waste water of 100% concentration. The pHvalues decreased to 3.23 in the waste water with lower dye concentration and to 3.42 in the higher color intensity, from the initialvalues of 5.0-6.0. This research concluded that P. chrysosporium was capable to biodegrade naphtol textile dye with reasonably highefficiency.

Laboratory studies of the degradation of chloropyrifos pesticide in soils supplemented by the fungus Phanerochaete chrysosporium

International Nuclear Information System (INIS)

Lopera Mesa, Margarita Maria; Penuela Mesa, Gustavo Antonio; Dominguez Gual, Maria Carolina; Mejia Zapata, Gloria Maria

2005-01-01

Degradation of the insecticide chloropyrifos was investigated in sterilized soil samples supplemented by the white rot basidiomycetes Phanerochaete chrysosporium. Degradation rates were measured during 21-day incubation at pesticide concentrations of 0,95, 5,3, and 9,41 μ/g. Phanerochaete chrysosporium showed ability to biodegrade the insecticide in values of 96,3%, 82,4% and 62,2%, respectively, followed by rapid degradation at low initial concentration of chloropyrifos

Chrysosporium guarroi sp. nov. a new emerging pathogen of pet green iguanas (Iguana iguana).

Science.gov (United States)

Abarca, M L; Castellá, G; Martorell, J; Cabañes, F J

2010-03-01

Chrysosporium guarroi sp. nov. represented by five strains isolated from cases of dermatomycosis in pet green iguanas (Iguana iguana) in Spain, is described and illustrated. This taxon is characterized by its ability to grow at temperatures from 15 to 37 degrees C and by the presence of arthroconidia and aleurioconidia. The latter are unicellular, smooth, pyriform or clavate, sessile or borne at the ends of narrow stalks. The analysis of the sequences of the D1/D2 and ITS regions confirm the separation of this new species from others of the genus Chrysosporium.

Genetic recombination in auxotrophic strains of Phanerochaete chrysosporium

International Nuclear Information System (INIS)

Krejci, R.

1987-01-01

Four auxotrophic strains of ligninolytic basidiomycete Phanerochaete chrysosporium were obtained by UV mutagenesis. The heterokaryotic mycelium formed by complementation of different auxotrophic isolates was able to fruit and produce basidiospores. Prototrophic strains and strains with a recombined set of parental nutritional requirements were isolated from the basidiospore progeny of the heterokaryons. Genetic recombination hence takes place in fruit bodies produced by the heterokaryotic mycelium. (author). 3 tabs., 13 refs

Structure, organization, and transcriptional regulation of a family of copper radical oxidase genes in the lignin-degrading basidiomycete Phanerochaete chrysosporium

Science.gov (United States)

Amber Vanden Wymelenberg; Grzegorz Sabat; Michael Mozuch; Philip J. Kersten; Dan Cullen; Robert A. Blanchette

2006-01-01

The white rot basidiomycete Phanerochaete chrysosporium produces an array of nonspecific extracellular enzymes thought to be involved in lignin degradation, including lignin peroxidases, manganese peroxidases, and the H2O2-generating copper radical oxidase, glyoxal oxidase (GLX). Preliminary analysis of the P. chrysosporium draft genome had identified six sequences...

Transport of Phanerochaete chrysosporium and Mucor hiemalis f. irnsingii spores through water-saturated quartz sands; Transport von Phanerochaete chrysosporium- und Mucor hiemalis f. irnsingii-Sporen durch wassergesaettigten Quarzsand

Energy Technology Data Exchange (ETDEWEB)

Hoque, E.; Klotz, D.; Teichmann, G.; Lang, H.; Wolf, M. [GSF - Forschungszentrum fuer Umwelt und Gesundheit GmbH, Neuherberg (Germany). Inst. fuer Hydrologie; Beisker, W. [GSF, Inst. fuer Pathologie (Germany)

2001-11-01

Just as bacteria so can aquatic fungi contribute effectively to pollutant elimination, at least in superficial groundwaters. However, very little is known about this. Nor is it known whether fungal spores are capable of being transported through sedimentary cavities. At least fungal spores are for some part of similar size as bacteria. We here report for the first time on a demonstration of the migration through quartz sand of spores of the two fungal species Phanerochaete chrysosporium and Mucor hiemalis f. irnsingii. [German] Neben Bakterien koennen auch aquatische Pilze, zumindest im oberflaechennahen Grundwasser, effiziente Beitraege zur Schadstoffentgiftung leisten. Darueber ist aber sehr wenig bekannt. Es ist auch nicht bekannt, ob ueberhaupt Pilzsporen durch Sedimenthohlraeume transportiert werden koennen, obwohl die Pilzsporen z.T. aehnliche Abmessungen wie Bakterien haben. Hier berichten wir erstmalig ueber den Nachweis der Migration von Sporen der beiden Pilzarten Phanerochaete chrysosporium und Mucor hiemalis f. irnsingii durch Quarzsand. (orig.)

Simultaneous cadmium removal and 2,4-dichlorophenol degradation from aqueous solutions by Phanerochaete chrysosporium

Energy Technology Data Exchange (ETDEWEB)

Chen, Anwei; Zeng, Guangming; Chen, Guiqiu; Fan, Jiaqi; Zou, Zhengjun; Li, Hui; Hu, Xinjiang; Long, Fei [Hunan Univ., Changsha (China). College of Environmental Science and Engineering; Ministry of Education, Changsha (CN). Key Lab. of Environmental Biology and Pollution Control (Hunan Univ.)

2011-08-15

Phanerochaete chrysosporium has been recognised as an effective bioremediation agent due to its unique degradation to xenobiotic and biosorption ability to heavy metals. However, few studies have focused on the simultaneous removal of heavy metals and organic pollutants. The aim of this work was to study the feasibility of simultaneous cadmium removal and 2,4-dichlorophenol (2,4-DCP) degradation in P. chrysosporium liquid cultures. The removal efficiencies were pH dependent and the maximum removal efficiencies were observed at pH 6.5 under an initial cadmium concentration of 5 mg/L and an initial 2,4-DCP concentration of 20 mg/L. The removal efficiencies for cadmium and 2,4-DCP reached 63.62% and 83.90%, respectively, under the optimum conditions. The high production levels of lignin peroxidase (7.35 U/mL) and manganese peroxidase (8.30 U/mL) resulted in an increase in 2,4-DCP degradation. The protein content decreased with increasing cadmium concentration. The surface characteristics and functional groups of the biomass were studied by scanning electron microscopy and a Fourier-transformed infrared spectrometer. The results showed that the use of P. chrysosporium is promising for the simultaneous removal of cadmium and 2,4-DCP from liquid media. (orig.)

Pyranose 2-oxidase from Phanerochaete chrysosporium--Expression in E.coli and Biochemical Characterization

Czech Academy of Sciences Publication Activity Database

Pisanelli, I.; Kujawa, M.; Spadiut, O.; Kittl, R.; Halada, Petr; Volc, Jindřich; Mozuch, M. D.; Kersten, P.; Haltrich, D.; Peterbauer, C.

2009-01-01

Roč. 142, č. 2 (2009), s. 97-106 ISSN 0168-1656 Institutional research plan: CEZ:AV0Z50200510 Keywords : Pyranose 2-oxidase * Phanerochaete chrysosporium * Lignocellulose degradation Subject RIV: CE - Biochemistry Impact factor: 2.881, year: 2009

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

Science.gov (United States)

Elena Fernandez-Fueyo; Francisco J. Ruiz-Dueñas; Patricia Ferreira; Dimitrios Floudas; David S. Hibbett; Paulo Canessa; Luis F. Larrondo; Tim Y. James; Daniela Seelenfreund; Sergio Lobos; Rubén Polanco; Mario Tello; Yoichi Honda; Takahito Watanabe; Takashi Watanabe; Jae San Ryu; Christian P. Kubicek; Monika Schmoll; Jill Gaskell; Kenneth E. Hammel; Franz J. St. John; Amber Vanden Wymelenberg; Grzegorz Sabat; Sandra Splinter BonDurant; Khajamohiddin Syed; Jagjit S. Yadav; Harshavardhan Dodapaneni; Venkataramanan Subramanian; José L. Lavin; José A. Oguiza; Gumer Perez; Antonio G. Pisabarro; Lucia Ramirez; Francisco Santoyo; Emma Master; Pedro M. Coutinho; Bernard Henrissat; Vincent Lombard; Jon Karl Magnuson; Ursula Kües; Chiaki Hori; Kiyohiko Igarashi; Masahiro Samejima; Benjamin W. Held; Kerrie W. Barry; Kurt M. LaButti; Alla Lapidus; Erika A. Lindquist; Susan M. Lucas; Robert Riley; Asaf A. Salamov; Dirk Hoffmeister; Daniel Schwenk; Yitzhak Hadar; Oded Yarden; Ronald P. de Vries; Ad Wiebenga; Jan Stenlid; Daniel Eastwood; Igor V. Grigoriev; Randy M. Berka; Robert A. Blanchette; Phil Kersten; Angel T. Martinez; Rafael Vicuna; Daniel Cullen

2012-01-01

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little...

Comparative biodegradation of alkyl halide insecticides by the white rot fungus, Phanerochaete chrysosporium (BKM-F-1767)

International Nuclear Information System (INIS)

Kennedy, D.W.; Aust, S.D.; Bumpus, J.A.

1990-01-01

The ability of Phanerochaete chrysosporium to degrade six alkyl halide insecticides (aldrin, dieldrin, heptachlor, chlordane, lindane, and mirex) in liquid and soil-corncob matrices was compared by using 14 C-labeled compounds. Of these, only [ 14 C]lindane and [ 14 C]chlordane underwent extensive biodegradation, as evidenced by the fact that 9.4 to 23.4% of these compounds were degraded to 14 CO 2 in 30 days in liquid cultures and 60 days in soil-corncob cultures inoculated with P. chrysosporium. Although [ 14 C]aldrin, [ 14 C]dieldrin, [ 14 C]heptachlor, and [14D]mirex were poorly mineralized, substantial bioconversion occurred, as determined by substrate disappearance and metabolite formation. Nonbiological disappearance was observed only with chlordane and heptachlor

Nitrate reductase gene involvement in hexachlorobiphenyl dechlorination by Phanerochaete chrysosporium

International Nuclear Information System (INIS)

De, Supriyo; Perkins, Michael; Dutta, Sisir K.

2006-01-01

Polychlorobiphenyl (PCB) degradation usually occurs through reductive dechlorination under anaerobic conditions and phenolic ring cleavage under aerobic conditions. In this paper, we provide evidence of nitrate reductase (NaR) mediated dechlorination of hexachlorobiphenyl (PCB-153) in Phanerochaete chrysosporium under non-ligninolytic condition and the gene involved. The NaR enzyme and its cofactor, molybdenum (Mo), were found to mediate reductive dechlorination of PCBs even in aerobic condition. Tungsten (W), a competitive inhibitor of this enzyme, was found to suppress this dechlorination. Chlorine release assay provided further evidence of this nitrate reductase mediated dechlorination. Commercially available pure NaR enzyme from Aspergillus was used to confirm these results. Through homology search using TBLASTN program, NaR gene was identified, primers were designed and the RT-PCR product was sequenced. The NaR gene was then annotated in the P. chrysosporium genome (GenBank accession no. AY700576). This is the first report regarding the presence of nitrate reductase gene in this fungus with the explanation why this fungus can dechlorinate PCBs even in aerobic condition. These fungal inoculums are used commercially as pellets in sawdust for enhanced bioremediation of PCBs at the risk of depleting soil nitrates. Hence, the addition of nitrates to the pellets will reduce this risk as well as enhance its activity

Transcript patterns of Phanerochaete chrysosporium genes in organopollutant contaminated soils and in wood

Science.gov (United States)

Amber. Vanden Wymelenberg; Bernard. Janse; Jill. Gaskell; Diane. Dietrich; Marcelo. Vallim; Dan. Cullen

1998-01-01

We describe here recent methods for quantitative assessment of specific P. chrysosporium mRNAs in organopollutant contaminated soils and in Aspen wood chips. Magnetic capture techniques were used to rapidly purify poly(A)-RNA, and quantitative RT-PCR protocols were developed for all known lignin peroxidase (lip) and cellobiohydrolase (cbh1) genes. The methodology is...

Bioreduction of hexavalent chromium by live and active phanerochaete chrysosporium: kinetics and modeling

International Nuclear Information System (INIS)

Murugavelh, Somasundaram; Mohanty, Kaustubha

2012-01-01

In this work the potential of live and active Phanerochaete chrysosporium, a white rot fungi, to remove lower Cr(VI) concentration from aqueous solutions was reported for the first time. A medium pH had significant effect on the growth of the fungus and bioremoval of Cr(VI). Substrate inhibition on the growth of Phanerochaete chrysosporium was evident beyond 20 g L -1 of dextrose concentration. A maximum biomass concentration of 15.64 g L -1 was obtained for an initial dextrose concentration of 20 g L -1 in metal free medium at pH 6.0. An increase in Cr(VI) concentration beyond 10 mg L -1 inhibited the growth of the fungi, thereby, reducing the chromium bioremoval efficiency. A maximum reduction efficiency of 98.92% was reported for an initial metal concentration of 10 mg L -1 . A mathematical expression for the bioreduction of Cr(VI) considering the organic compounds in the cells was proposed. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Bioreduction of hexavalent chromium by live and active phanerochaete chrysosporium: kinetics and modeling

Energy Technology Data Exchange (ETDEWEB)

Murugavelh, Somasundaram; Mohanty, Kaustubha [Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam (India)

2012-07-15

In this work the potential of live and active Phanerochaete chrysosporium, a white rot fungi, to remove lower Cr(VI) concentration from aqueous solutions was reported for the first time. A medium pH had significant effect on the growth of the fungus and bioremoval of Cr(VI). Substrate inhibition on the growth of Phanerochaete chrysosporium was evident beyond 20 g L{sup -1} of dextrose concentration. A maximum biomass concentration of 15.64 g L{sup -1} was obtained for an initial dextrose concentration of 20 g L{sup -1} in metal free medium at pH 6.0. An increase in Cr(VI) concentration beyond 10 mg L{sup -1} inhibited the growth of the fungi, thereby, reducing the chromium bioremoval efficiency. A maximum reduction efficiency of 98.92% was reported for an initial metal concentration of 10 mg L{sup -1}. A mathematical expression for the bioreduction of Cr(VI) considering the organic compounds in the cells was proposed. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium

Science.gov (United States)

Jill Gaskell; Amber Marty; Michael Mozuch; Philip J. Kersten; Sandra Splinter Bondurant; Grzegorz Sabat; Ali Azarpira; John Ralph; Oleksandr Skyba; Shawn D. Mansfield; Robert A. Blanchette; Dan Cullen

2014-01-01

We examined gene expression patterns in the lignin-degrading fungus Phanerochaete chrysosporium when it colonizes hybrid poplar (Populus alba tremula) and syringyl (S)-rich transgenic derivatives. Acombination ofmicroarrays and liquid chromatography- tandem mass spectrometry (LC-MS/MS) allowed detection of a total of 9,959 transcripts and 793...

Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium

Science.gov (United States)

Amber J. Vanden Wymelenberg; Jill Gaskell; Michael Mozuch; Grzegorz Sabat; John Ralph; Oleksandr Skyba; Shawn D Mansfield; Robert A. Blanchette; Diego Martinez; Igor Grigoriev; Philip J Kersten; Daniel Cullen

2010-01-01

Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi...

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Energy Technology Data Exchange (ETDEWEB)

Suzuki, Hitoshi; MacDonald, Jacqueline; Syed, Khajamohiddin; Salamov, Asaf; Hori, Chiaki; Aerts, Andrea; Henrissat, Bernard; Wiebenga, Ad; vanKuyk, Patricia A.; Barry, Kerrie; Lindquist, Erika; LaButti, Kurt; Lapidus, Alla; Lucas, Susan; Coutinho, Pedro; Gong, Yunchen; Samejima, Masahiro; Mahadevan, Radhakrishnan; Abou-Zaid, Mamdouh; de Vries, Ronald P.; Igarashi, Kiyohiko; Yadav, Jagit S.; Grigoriev, Igor V.; Master, Emma R.

2012-02-17

Background Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome. Results P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood. Conclusions The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.

Pyranose 2-oxidase from Phanerochaete chrysosporium : expression in E. coli and biochemical characterization

Science.gov (United States)

Ines Pisanelli; Magdalena Kujawa; Oliver Spadiut; Roman Kittl; Petr Halada; Jindrich Volc; Michael D. Mozuch; Philip Kersten; Dietmar Haltrich; Clemens Peterbauer

2009-01-01

The presented work reports the isolation and heterologous expression of the p2ox gene encoding the flavoprotein pyranose 2-oxidase (P2Ox) from the basidiomycete Phanerochaete chrysosporium. The p2ox cDNA was inserted into the bacterial expression vector pET21a(+) and successfully expressed in Escherichia coli. We obtained active, fully flavinylated recombinant P2Ox in...

Delignification of Sawdust White Teak (Gmelina arborea Roxb. by Fungi Phanerochaete chrysosporium Irradiated Gamma Ray

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Nurhasni Nurhasni

2016-12-01

Full Text Available Abstrak Biomassa lignoselulosa yang merupakan limbah pemanenan kayu harus dilakukan proses untuk memisahkan selulosa, hemiselulosa dan lignin sehingga dapat termanfaatkan. Penelitian ini bertujuan untuk mengetahui efektivitas inokulan fungi Phanerochaete chrysosporium iradiasi gamma dan pretreatment kimia terhadap percepatan delignifikasi serbuk kayu jati putih (Gmelina arborea Roxb. sehingga dapat dimanfaatkan dalam proses pulping. Pada penelitian ini dilakukan pretreatment substrat kayu jati putih (Gmelina arborea Roxb. menggunakan larutan NaOH 1% dan H2SO4 1% serta iradiasi gamma Co-60, yang mempunyai daya ionisasi kecil, daya tembus yang tinggi serta Co-60 dapat memancarkan sinar gamma dengan waktu paruh pendek. Penelitian ini dilakukan dalam dua tahap, tahap pertama penentuan dosis optimum iradiasi gamma terhadap fungi Phanerochaete chrysosporium (0 Gy, 200 Gy, 400 Gy, 600 Gy, 800 Gy, dan 1000 Gy dan tahap kedua analisis karakteristik substrat kayu jati putih yang telah di pretreatment dengan metode Solid State Fermentation (SSF selama 21 hari. Hasil penelitian menunjukkan bahwa dosis optimum pemberian iradiasi gamma pada fungi Phanerochaete chrysosporium yaitu pada dosis 600 Gy yang dapat meningkatkan aktivitas enzim lignin peroksidase (LiP sebesar 22.18 U/mL. Proses pretreatment kimia dengan menggunakan H2SO4 1% dapat mempercepat proses biodelignifikasi yang menghasilkan efisiensi degradasi lignin tertinggi yaitu sebesar 25.65%.   Kata kunci: Lignoselulosa, delignifikasi, Solid State Fermentation (SSF, Phanerochaete chrysosporium,iradiasi gamma.   Abstract   Lignocellulose biomass is waste wood harvesting should be a process for separating cellulose, hemicellulose and lignin that can be utilized. This study aims to determine the effectiveness of the inoculant fungi Phanerochaete chrysosphorium gamma irradiation and chemical pretreatment to accelerate delignification powder white teak (Gmelina arborea Roxb.. In this research

ABILITY OF Phanerochaete chrysosporium AND Trametes versicolor TO REMOVE Zn2+, Cr3+, Pb2+ METAL IONS

Directory of Open Access Journals (Sweden)

Josué Solís Pacheco

2015-07-01

Full Text Available The use of fungal biomass as an alternative for removing heavy metals has become increasingly important in recent years, replacing conventional methods based on chemical physical processes. In this study, we evaluated the biosorption of Zn2+, Cr3+ and Pb2+, which were analyzed to determine their effect on growth kinetic parameters of Phanerochaete chrysosporium strain ATCC 32629 and Trametes versicolor ATCC 1267. Growth kinetics were performed in four liquid culture media: 1 Yeast Nitrogen Base (YNB used as control, 2 YNB medium plus Pb2+ (0.25, 1 and 2 mg L-1, 3 YNB medium plus Zn2+ (5, 10 and 20 mg L-1 and 4 YNB medium plus Cr3+ (0.5, 1 and 2 mg L-1. The flasks were incubated at 25 °C with shaking at 150 rpm. Metal concentrations were determined by inductively coupled plasma atomic emission spectroscopy (ICP-AES with prior acid digestion of the sample. The results demonstrated that Phanerochaete chrysosporium ATCC 32629 and Trametes versicolor ATCC 12679 are able to grow in the culture medium with Pb2+, Zn2+ and Cr3+ ions at different concentrations. However, P. chrysosporium ATCC 32629 showed greater adaptability and ability to adsorb Cr3+ in the culture medium at concentrations of 0.5 and 1 mg L-1, whereas T. versicolor ATCC 12679 was capable of Pb2+ biosorption at concentrations of 0.25, 1 and 2 mg L-1.

Detoxification of corn stover and corn starch pyrolysis liquors by ligninolytic enzymes of Phanerochaete chrysosporium.

Science.gov (United States)

Khiyami, Mohammad A; Pometto, Anthony L; Brown, Robert C

2005-04-20

Phanerochaete chrysosporium (ATCC 24725) shake flask culture with 3 mM veratryl alcohol addition on day 3 was able to grow and detoxify different concentrations of diluted corn stover (Dcs) and diluted corn starch (Dst) pyrolysis liquors [10, 25, and 50% (v/v)] in defined media. GC-MS analysis of reaction products showed a decrease and change in some compounds. In addition, the total phenolic assay with Dcs samples demonstrated a decrease in the phenolic compounds. A bioassay employing Lactobacillus casei growth and lactic acid production was developed to confirm the removal of toxic compounds from 10 and 25% (v/v) Dcs and Dst by the lignolytic enzymes, but not from 50% (v/v) Dcs and Dst. The removal did not occur when sodium azide or cycloheximide was added to Ph. chrysosporium culture media, confirming the participation of lignolytic enzymes in the detoxification process. A concentrated enzyme preparation decreased the phenolic compounds in 10% (v/v) corn stover and corn starch pyrolysis liquors to the same extent as the fungal cultures.

Dermatitis and cellulitis in leopard geckos (Eublepharis macularius) caused by the Chrysosporium anamorph of Nannizziopsis vriesii.

Science.gov (United States)

Toplon, D E; Terrell, S P; Sigler, L; Jacobson, E R

2013-07-01

An epizootic of ulcerative to nodular ventral dermatitis was observed in a large breeding colony of 8-month to 5-year-old leopard geckos (Eublepharis macularius) of both sexes. Two representative mature male geckos were euthanized for diagnostic necropsy. The Chrysosporium anamorph of Nannizziopsis vriesii (CANV) was isolated from the skin lesions, and identification was confirmed by sequencing of the internal transcribed spacer region of the rRNA gene. Histopathology revealed multifocal to coalescing dermal and subcutaneous heterophilic granulomas that contained septate fungal hyphae. There was also multifocal epidermal hyperplasia with hyperkeratosis, and similar hyphae were present within the stratum corneum, occasionally with terminal chains of arthroconidia consistent with the CANV. In one case, there was focal extension of granulomatous inflammation into the underlying masseter muscle. This is the first report of dermatitis and cellulitis due to the CANV in leopard geckos.

Degradation of Diuron by Phanerochaete chrysosporium: Role of Ligninolytic Enzymes and Cytochrome P450

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Jaqueline da Silva Coelho-Moreira

2013-01-01

Full Text Available The white-rot fungus Phanerochaete chrysosporium was investigated for its capacity to degrade the herbicide diuron in liquid stationary cultures. The presence of diuron increased the production of lignin peroxidase in relation to control cultures but only barely affected the production of manganese peroxidase. The herbicide at the concentration of 7 μg/mL did not cause any reduction in the biomass production and it was almost completely removed after 10 days. Concomitantly with the removal of diuron, two metabolites, DCPMU [1-(3,4-dichlorophenyl-3-methylurea] and DCPU [(3,4-dichlorophenylurea], were detected in the culture medium at the concentrations of 0.74 μg/mL and 0.06 μg/mL, respectively. Crude extracellular ligninolytic enzymes were not efficient in the in vitro degradation of diuron. In addition, 1-aminobenzotriazole (ABT, a cytochrome P450 inhibitor, significantly inhibited both diuron degradation and metabolites production. Significant reduction in the toxicity evaluated by the Lactuca sativa L. bioassay was observed in the cultures after 10 days of cultivation. In conclusion, P. chrysosporium can efficiently metabolize diuron without the accumulation of toxic products.

Degradation of diuron by Phanerochaete chrysosporium: role of ligninolytic enzymes and cytochrome P450.

Science.gov (United States)

Coelho-Moreira, Jaqueline da Silva; Bracht, Adelar; de Souza, Aline Cristine da Silva; Oliveira, Roselene Ferreira; de Sá-Nakanishi, Anacharis Babeto; de Souza, Cristina Giatti Marques; Peralta, Rosane Marina

2013-01-01

The white-rot fungus Phanerochaete chrysosporium was investigated for its capacity to degrade the herbicide diuron in liquid stationary cultures. The presence of diuron increased the production of lignin peroxidase in relation to control cultures but only barely affected the production of manganese peroxidase. The herbicide at the concentration of 7 μ g/mL did not cause any reduction in the biomass production and it was almost completely removed after 10 days. Concomitantly with the removal of diuron, two metabolites, DCPMU [1-(3,4-dichlorophenyl)-3-methylurea] and DCPU [(3,4-dichlorophenyl)urea], were detected in the culture medium at the concentrations of 0.74 μ g/mL and 0.06 μ g/mL, respectively. Crude extracellular ligninolytic enzymes were not efficient in the in vitro degradation of diuron. In addition, 1-aminobenzotriazole (ABT), a cytochrome P450 inhibitor, significantly inhibited both diuron degradation and metabolites production. Significant reduction in the toxicity evaluated by the Lactuca sativa L. bioassay was observed in the cultures after 10 days of cultivation. In conclusion, P. chrysosporium can efficiently metabolize diuron without the accumulation of toxic products.

In vitro and in vivo inhibitory effects of some fungicides on catalase produced and purified from white-rot fungus Phanerochaete chrysosporium.

Science.gov (United States)

Kavakçıoğlu, Berna; Tarhan, Leman

2014-10-01

In this study, in vitro and in vivo effects of some commonly used fungicides, antibiotics, and various chemicals on isolated and purified catalase from Phanerochaete chrysosporium were investigated. The catalase was purified 129.10-fold by using 60% ammonium sulfate and 60% ethanol precipitations, DEAE-cellulose anion exchange and Sephacryl-S-200 gel filtration chromatographies from P. chrysosporium growth in carbon- and nitrogen-limited medium for 12 days. The molecular weight of native purified catalase from P. chrysosporium was found to be 290 ± 10 kDa, and sodium dodecyl sulfate (SDS)-PAGE results indicated that enzyme consisted of four apparently identical subunits, with a molecular weight of 72.5 ± 2.5 kDa. Kinetic characterization studies showed that optimum pH and temperature, Km and Vmax values of the purified catalase which were stable in basic region and at comparatively high temperatures were 7.5, 30°C, 289.86 mM, and 250,000 U/mg, respectively. The activity of purified catalase from P. chrysosporium was significantly inhibited by dithiothreitol (DTT), 2-mercaptoethanol, iodoacetamide, EDTA, and sodium dodecyl sulfate (SDS). It was found that while antibiotics had no inhibitory effects, 45 ppm benomyl, 144 ppm captan, and 47.5 ppm chlorothalonil caused 14.52, 10.82, and 38.86% inhibition of purified catalase, respectively. The inhibition types of these three fungicides were found to be non-competitive inhibition with the Ki values of 1.158, 0.638, and 0.145 mM and IC50 values of 0.573, 0.158, 0.010 mM, respectively. The results of in vivo experiments also showed that benomyl, captan and chlorothalonil caused 15.25, 1.96, and 36.70% activity decreases after 24-h treatments compared to that of the control.

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Science.gov (United States)

Premsagar Korripally; Christopher G. Hunt; Carl J. Houtman; Don C. Jones; Peter J. Kitin; Dan Cullen; Kenneth E. Hammel; A. A. Brakhage

2015-01-01

Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew Phanerochaete chrysosporium on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in...

Isolation and purification of pyranose 2-oxidase from Phanerochaete chrysosporium and characterization of gene structure and regulation

Science.gov (United States)

Theodorus H. de Koker; Michael D. Mozuch; Daniel Cullen; Jill Gaskell; Philip J. Kersten

2004-01-01

Pyranose 2-oxidase (POX) was recovered from Phanerochaete chrysosporium BKM-F-1767 solid substrate culture using mild extraction conditions and was purified. 13C-nuclear magnetic resonance confirmed production of D- arabino -hexos-2-ulose (glucosone) from D-glucose with the oxidase. Peptide fingerprints generated by liquid chromatography-tandem mass spectrometry of...

Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species

Science.gov (United States)

Amber Vanden Wymelenberg; Jill Gaskell; Michael Mozuch; Sandra Splinter BonDurant; Grzegorz Sabat; John Ralph; Oleksandr Skyba; Shawn D. Mansfield; Robert A. Blanchette; Igor Grigoriev; Philip J. Kersten; Daniel Cullen

2011-01-01

Identification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungi Phanerochaete chrysosporium and Postia placenta are promising in this regard because they are able to utilize a wide range of simple and...

Characterization and mode of action of two acetyl xylan esterases from Chrysosporium lucknowense C1 active towards acetylated xylans

NARCIS (Netherlands)

Pouvreau, L.A.M.; Jonathan, M.C.; Kabel, M.A.; Hinz, S.W.A.; Gruppen, H.; Schols, H.A.

2011-01-01

Two novel acetyl xylan esterases, Axe2 and Axe3, from Chrysosporium lucknowense (C1), belonging to the carbohydrate esterase families 5 and 1, respectively, were purified and biochemically characterized. Axe2 and Axe3 are able to hydrolyze acetyl groups both from simple acetylated

Recent advances in the molecular genetics of the lignin degrading fungus, phanerochaete chrysosporium

International Nuclear Information System (INIS)

Covert, S.F.

1991-01-01

During the past several years, molecular genetics research on phanerochaete chrysosporium, a white-rot basidiomycete, has increased dramatically. It is known that families of highly homologous, clustered genes encode the lignin peroxidases. The same appears to be true with the exocellobiohydrolase genes. Functional domains and active sites have been tentatively identified from the deduced amino acid sequences of these genes. Current investigations focus on elucidating the genomic organization of gene families, the mechanism(s) of gene regulation, and the role and interaction of specific gene products in lignocellulose degradation. (author)

BIODEGRADATION OF DDT [1,1,1-TRICHLORO-2,2-BIS(4- CHLOROPHENYL) ETHANE] BY THE WHITE ROT FUNGUS PHANEROCHAETE CHRYSOSPORIUM

Science.gov (United States)

Extensive biodegradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by the white rot fungus Phanerochaete chrysosporium was demonstrated by disappearance and mineralization of [14C]DDT in nutrient nitrogen-deficient cultures. Mass balance studies demonstrated the form...

Biodegradation of TNT (2,4,6-Trinitrotoluene) by Phanerochaete chrysosporium

International Nuclear Information System (INIS)

Fernando, T.; Bumpus, J.A.; Aust, S.D.

1990-01-01

Extensive biodegradation of TNT (2,4,6-trinitrotoluene) by the white rot fungus Phanerochaete chrysosporium was observed. At an initial concentration of 1.3 mg/liter, 35.4 ± 3.6% of the [ 14 C]TNT was degraded to 14 CO 2 in 18 days. The addition of glucose 12 days after the addition of TNT did not stimulate mineralization, and, after 18 days of incubation with TNT only, about 3.3% of the initial TNT could be recovered. Mineralization of [ 14 C]TNT absorbed on soil was also examined. Ground corncobs served as the nutrient for slow but sustained degradation of [ 14 C]TNT to 14 CO 2 such that 6.3 ± 0.6% of the [ 14 C]TNT initially present was converted to 14 CO 2 during the 30-day incubation period. Mass balance analysis of liquid cultures and of soil-corncob cultures revealed that polar [ 14 C]TNT metabolites are formed in both systems, and high-performance liquid chromatography analyses revealed that less then 5% of the radioactivity remained as undegraded [ 14 C]TNT following incubation with the fungus in soil and liquid cultures. When the concentration of TNT in cultures (both liquid and soil) was adjusted to contamination levels that might be found in the environment, i.e., 10,000 mg/kg in soil and 100 mg/liter in water, mineralization studies showed that 18.4 ± 2.9% and 19.6 ± 3.5% of the initial TNT was converted to 14 CO 2 in 90 days in soil and liquid cultures, respectively. In both cases (90 days in water at 100 mg/liter and in soil at 10,000 mg/kg) approximately 85% of the TNT was degraded. These results suggest that this fungus may be useful for the decontamination of sites in the environment contaminated with TNT

Effect of peat extract on the hydrolytic enzymes of Phanerochaete chrysosporium

Energy Technology Data Exchange (ETDEWEB)

Nawaz, M; Gunasekaran, M

1988-08-01

Peat, a partially decomposed plant material rich in minerals and lignocellulose was tested as a substrate for the growth and production of hydrolytic enzymes viz. cellulase, cellobiase and xylanase in Phanerochaete chrysosporium. Three types of peat extracts such as cold, hot water and autoclaved were prepared and tested. Among them, autoclaved extract supported the maximal growth. The intracellular enzyme activities peaked on the fifth day after inoculation irrespective of the media and enzyme tested. Addition of cellobiose and lactose in the medium induced the production of cellulase, xylanase and to a lesser extent cellobiase. Addition of glucose and sucrose to the media resulted in the suppression of all the extracellular enzymes tested. 18 refs., 5 figs.

Cellulase enzyme production during continuous culture growth of Sporotrichum (Chrysosporium) thermophile

Energy Technology Data Exchange (ETDEWEB)

Cossar, D; Canevascini, G

1986-07-01

The cellulolytic fungus Sporotrichum (Chrysosporium) thermophile produces an extracellular cellobiose dehydrogenase during batch culture on cellulose or cellobiose. In chemostat culture at pH 5.6 on cellobiose this enzyme was produced in parallel with endo-cellulase. At pH 5.0 in continuous or fed-batch culture such a pattern was not evident. At constant growth rate in a chemostat with varying pH, activity of these enzymes was found to be poorly correlated. Thus the induction of cellobiose dehydrogenase shows a dependence on pH and cellobiose concentration which is different to that for endo-cellulase. The natural inducer of these enzymes and the role of cellubiose dehydrogenase remain to be elucidated.

Effect of inducers and culturing processes on laccase synthesis in Phanerochaete chrysosporium NCIM 1197 and the constitutive expression of laccase isozymes

DEFF Research Database (Denmark)

Manavalan, Arulmani

2006-01-01

Phanerochaete chrysosporium NCIM 1197 constitutively secretes considerable level of extracellular enzyme laccase in defined growth medium. Effect of several inducers on laccase production was attempted and found that copper sulphate alone at 30 mM concentration accelerate the laccase production...

EFFECTS OF CULTURE PARAMETERS ON DDT [1,1,1-TRICHLO- RO-2,2-BIS(4-CHLOROPHENYL) ETHANE] BIODEGRADATION BY PHANEROCHAETE CHRYSOSPORIUM

Science.gov (United States)

The lignin degrading system of the white rot fungus Phanerochaete chrysosporium is able to degrade a wide variety of structurally diverse organopollutants to carbon dioxide. Current research is focused on ways to increase or optimize rates of biodegradation in order to a...

Degradation of pentachlorophenol by the white rot fungus Phanerochaete chrysosporium grown in ammonium lignosulphonate media.

Science.gov (United States)

Aiken, B S; Logan, B E

1996-06-01

Removal and degradation of pentachlorophenol (PCP) by Phanerochaete chrysosporium in static flask cultures was studied using ammonium lignosulphonates (LS), a waste product of the papermill industry, as a carbon and nitrogen source. After 3 days, cultures of P. chrysosporium grown in either a 2% LS (nitrogen-sufficient) medium or a 0.23% LS and 2% glucose (nitrogen-deficient) medium removed 72 to 75% of PCP, slightly less than the 95% removal seen using nitrogen-deficient glucose and ammonia medium. PCP dehalogenation occurred despite the fact that extracellular enzyme (LiP) activity, measured by a veratryl alcohol oxidation assay and by PCP disappearance in cell-free extracts, was inhibited by LS. This inactivation of LiP likely contributed to the lower percent of PCP dehalogenation observed using the LS media. In order to better understand the relationship between PCP disappearance and dehalogenation, we measured the fate of the chlorine in PCP. After 13 days, only 1.8% of the initial PCP added was recoverable as PCP. The remainder of the PCP was either mineralized or transformed to breakdown intermediates collectively identified as organic halides. The largest fraction of the original chlorine (58%) was recovered as organic (non-PCP) halide, most of which (73%) was associated with the cell mass. Of the remaining chlorine, 40% was released as chloride ion, indicating a level of dehalogenation in agreement with previously reported values.

Caractérisation biochimique et fonctionnelle de glutathion-S-transferases (GSTs) chez Phanerochaete chrysosporium

OpenAIRE

Anak-Ngadin, Andrew

2011-01-01

Phanerochaete chrysosporium est un champignon ligninolytique largement étudié pour ses capacités à dégrader la lignine et certains xénobiotiques grâce à un important système d'enzymes extracellulaires. Son génome est entièrement séquencé et constitue un inventaire de séquences protéiques prédites qui a permis la description de nombreuses superfamilles de protéines. Parmi elles, les Glutathion S-transférases sont essentiellement impliquées dans le métabolisme secondaire du champignon. Cependan...

Ligninolytic system of Phanerochaete chrysosporium: inhibition by o-phthalate

Energy Technology Data Exchange (ETDEWEB)

Fenn, P.; Kirk, T.K.

1979-01-01

The degradation rate of (synthetic/sup 14/C)-lignin to /sup 14/CO/sub 2/ by Phanerochaete chrysosporium in cultures buffered with 0.01 M 2,2-dimethylsuccinate (DMS) was twice that in 0.01 M o-phthalate-buffered cultures. This difference could be totally accounted for by o-phthalate inhibition of the activity of the ligninolytic system. /sup 14/CO/sub 2/ production from ring-, sidechain-, and methoyxl-labled lignins was inhibited, the degree of inhibition being dependent on o-phthalate concentration. Oxidations of /sup 14/C-glucose, /sup 14/C-acetovanillone, and /sup 14/C-apocynol were not inhibited; thus o-phthalate is not a general inhibitor, and might inhibit activities involved in attach of the lignin polymer. DMS is a suitable buffer for the ligninolytic system. Degradation rates of ring-labeled lignin to /sup 14/CO/sub 2/ of 10 to 15% in 24 h were obtained consistently over the pH range 3.6 to 4.5, with an optimum near pH 4.0.

Characterization of a multicopper oxidase gene cluster in Phanerochaete chrysosporium and evidence of altered splicing of the mco transcripts

Science.gov (United States)

Luis F. Larrondo; Bernardo Gonzalez; Dan Cullen; Rafael Vicuna

2004-01-01

A cluster of multicopper oxidase genes (mco1, mco2, mco3, mco4) from the lignin-degrading basidiomycete Phanerochaete chrysosporium is described. The four genes share the same transcriptional orientation within a 25 kb region. mco1, mco2 and mco3 are tightly grouped, with intergenic regions of 2.3 and 0.8 kb, respectively, whereas mco4 is located 11 kb upstream of mco1...

Bio-remediation of colored industrial wastewaters by the white-rot fungi Phanerochaete chrysosporium and Pleurotus ostreatus and their enzymes.

Science.gov (United States)

Faraco, V; Pezzella, C; Miele, A; Giardina, P; Sannia, G

2009-04-01

The effect of Phanerochaete chrysosporium and Pleurotus ostreatus whole cells and their ligninolytic enzymes on models of colored industrial wastewaters was evaluated. Models of acid, direct and reactive dye wastewaters from textile industry have been defined on the basis of discharged amounts, economic relevance and representativeness of chemical structures of the contained dyes. Phanerochaete chrysosporium provided an effective decolourization of direct dye wastewater model, reaching about 45% decolourization in only 1 day of treatment, and about 90% decolourization within 7 days, whilst P. ostreatus was able to decolorize and detoxify acid dye wastewater model providing 40% decolourization in only 1 day, and 60% in 7 days. P. ostreatus growth conditions that induce laccase production (up to 130,000 U/l) were identified, and extra-cellular enzyme mixtures, with known laccase isoenzyme composition, were produced and used in wastewater models decolourization. The mixtures decolorized and detoxified the acid dye wastewater model, suggesting laccases as the main agents of wastewater decolourization by P. ostreatus. A laccase mixture was immobilized by entrapment in Cu-alginate beads, and the immobilized enzymes were shown to be effective in batch decolourization, even after 15 stepwise additions of dye for a total exposure of about 1 month.

Purification, cloning and characterisation of two forms of thermostable and highly active cellobiohydrolase I (Cel7A) produced by the industrial strain of Chrysosporium lucknowense

NARCIS (Netherlands)

Gusakov, A.V.; Sinitsyn, A.P.; Salanovich, T.N.; Bukhtojarov, F.E.; Markov, A.V.; Ustinov, B.B.; Zeijl, C.V.; Punt, P.; Burlingame, R.

2005-01-01

Two forms of cellobiohydrolase I (CBH I, Cel7A) were purified from the culture ultrafiltrate of a mutant strain of the fungus Chrysosporium lucknowense, an industrial producer of cellulases and hemicellulases. The enzymes had different molecular masses (52 and 65 kDa, SDS-PAGE data) but the same pI

Metabolic regulation at the tricarboxylic acid and glyoxylate cycles of the lignin-degrading basidiomycete Phanerochaete chrysosporium against exogenous addition of vanillin.

Science.gov (United States)

Shimizu, Motoyuki; Yuda, Naoki; Nakamura, Tomofumi; Tanaka, Hiroo; Wariishi, Hiroyuki

2005-10-01

A proteomic differential display technique was utilized to study cellular responses of Phanerochaete chrysosporium exposed to vanillin, one of the key intermediates found during lignin biodegradation. Intracellular proteins were resolved by 2-DE and target protein spots were identified using MALDI-MS after in-gel tryptic digestions. Upon addition of vanillin to P. chrysosporium, up-regulation of homogentisate 1,2-dioxygenase, 1,4-benzoquinone reductases, aldehyde dehydrogenase, and aryl-alcohol dehydrogenase, which seem to play roles in vanillin metabolism, was observed. Furthermore, enzymes involved in glycolysis, the tricarboxylic acid cycle, the pentose-phosphate cycle, and heme biosynthesis were also activated. Up-regulation of extracellular peroxidase was also observed. One of the most unique phenomena against exogenous vanillin was a switch from the glyoxylate cycle to the tricarboxylic acid cycle, where a drastic increase in isocitrate dehydrogenase activity was observed. The exogenous addition of other aromatic compounds also caused an increase in its activity, which in turn triggered NAD(P)H production via the action of dehydrogenases in the tricarboxylic acid cycle, heme biosynthesis via the action of aminolevulinic acid synthase on succinyl-CoA, and energy production via activation of the mitochondrial electron transfer system. These metabolic shifts seem to be required for activating a metabolic system for aromatic compounds.

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

Directory of Open Access Journals (Sweden)

Karin Voordeckers

2015-11-01

Full Text Available Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts.

Activity of the ligninolytic enzymes of the Phanerochaete chrysosporium and its variation with the Mn+2 addition

International Nuclear Information System (INIS)

Jimenez T, Gloria Alicia; Mejia G, Amanda I; Lopez O, Betty Lucy

1999-01-01

The activity of the ligninolytic enzymes, lignin peroxidase (LiP), manganese peroxidase (MnP) and Laccase, in submerged cultures of Phanerochaete chrysosporium, with limited amounts of carbon and nitrogen, were affected by the addition of Mn+2. In cultures with o and 1,25 ppm of Mn+2, only the lip was detected and its higher activity level was observed in the cultures with 1.25 ppm of Mn+2. The cultures with 40 ppm of Mn+2 showed activities of lip, MnP and Laccase. The presence of the three enzymes in the same culture had not been reported and it is of great importance because is shows that the fungus and its lignolitic machinery can act sequentially

Catabolic fate of Streptomyces viridosporus T7A-Produced, acid precipitable polymeric lignin upon incubation with ligninolytic Streptomyces species and Phanerochaete chrysosporium

International Nuclear Information System (INIS)

Pometto, A.L. III; Crawford, D.L.

1986-01-01

Degradation of ground and hot-water-extracted corn stover (Zea mays) lignocellulose by Streptomyces viridosporus T7A generates a water-soluble lignin degradation intermediate termed acid-precipitable polymeric lignin (APPL). The further catabolism of T7A-APPL by S. viridosporus T7A, S. badius 252, and S. setonii75Vi2 was followed for 3 weeks. APPL catabolism by Phanerochaete chrysosporium was followed in stationary cultures in a low-nitrogen medium containing 1% (wt/vol) glucose and 0.05% (wt/vol) T7A-APPL. Metabolism of the APPL was followed by turbidometric assay (600 nm) and by direct measurement of APPL recoverable from the medium. Accumulation and disappearance of soluble low-molecular-weight products of APPL catabolism were followed by gas-liquid chromatography and by high-pressure liquid chromatography, utilizing a diode array detector. Mineralization of a [ 14 C-lignin]APPL was also followed. The percent 14 C recovered as 14 CO 2 , 14 C-APPL, 14 C-labeled water-soluble products, and cell mass-associated radioactivity, were determined for each microorganism after 1 and 3 weeks of incubation in bubbler tube cultures at 37 0 C. P. chrysosporium evolved the most 14 CO 2 , and S. viridosporus gave the greatest decrease in recoverable 14 C-APPL. The results show that S. badius was not able to significantly degrade the APPL, while the other microorganisms demonstrated various APPL-degrading abilities

Transport, fate, and stimulating impact of silver nanoparticles on the removal of Cd(II) by Phanerochaete chrysosporium in aqueous solutions

International Nuclear Information System (INIS)

Zuo, Yanan; Chen, Guiqiu; Zeng, Guangming; Li, Zhongwu; Yan, Ming; Chen, Anwei; Guo, Zhi; Huang, Zhenzhen; Tan, Qiong

2015-01-01

Highlights: • Appropriate concentration of AgNPs can stimulate the biological removal of Cd(II). • Added AgNPs were oxidatively dissolved and transported to the surface of fungus. • AgNPs have undergone coarsening in the process of transport. • Amino, carboxyl, hydroxyl, and other reducing groups were involved in transportion. - Abstract: Despite the knowledge about increasing discharge of silver nanoparticles (AgNPs) into wastewater and its potential toxicity to microorganisms, the interaction of AgNPs with heavy metals in the biological removal process remains poorly understood. This study focused on the effect of AgNPs (hydrodynamic diameter about 24.3 ± 0.37 nm) on the removal of cadmium (Cd(II)) by using a model white rot fungus species, Phanerochaete chrysosporium. Results showed that the biological removal capacity of Cd(II) increased with the concentration of AgNPs increasing from 0.1 mg/L to 1 mg/L. The maximum removal capacity (4.67 mg/g) was located at 1 mg/L AgNPs, and then decreased with further increasing AgNPs concentration, suggesting that an appropriate concentration of AgNPs has a stimulating effect on the removal of Cd(II) by P. chrysosporium instead of an inhibitory effect. Results of Ag + and total Ag concentrations in the solutions together with those of SEM and XRD demonstrated that added AgNPs had undergone oxidative dissolution and transported from the solution to the surface of fungal mycelia (up to 94%). FTIR spectra confirmed that amino, carboxyl, hydroxyl, and other reducing functional groups were involved in Cd(II) removal, AgNPs transportation, and the reduction of Ag + to AgNPs

Transport, fate, and stimulating impact of silver nanoparticles on the removal of Cd(II) by Phanerochaete chrysosporium in aqueous solutions

Energy Technology Data Exchange (ETDEWEB)

Zuo, Yanan [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); Chen, Guiqiu, E-mail: gqchen@hnu.edu.cn [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); Zeng, Guangming, E-mail: zgming@hnu.edu.cn [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); Li, Zhongwu; Yan, Ming [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China); Chen, Anwei [College of Resources and Environment, Hunan Agricultural University, Changsha 410128 (China); Guo, Zhi; Huang, Zhenzhen; Tan, Qiong [College of Environmental Science and Engineering, Hunan University, Changsha 410082 (China); Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082 (China)

2015-03-21

Highlights: • Appropriate concentration of AgNPs can stimulate the biological removal of Cd(II). • Added AgNPs were oxidatively dissolved and transported to the surface of fungus. • AgNPs have undergone coarsening in the process of transport. • Amino, carboxyl, hydroxyl, and other reducing groups were involved in transportion. - Abstract: Despite the knowledge about increasing discharge of silver nanoparticles (AgNPs) into wastewater and its potential toxicity to microorganisms, the interaction of AgNPs with heavy metals in the biological removal process remains poorly understood. This study focused on the effect of AgNPs (hydrodynamic diameter about 24.3 ± 0.37 nm) on the removal of cadmium (Cd(II)) by using a model white rot fungus species, Phanerochaete chrysosporium. Results showed that the biological removal capacity of Cd(II) increased with the concentration of AgNPs increasing from 0.1 mg/L to 1 mg/L. The maximum removal capacity (4.67 mg/g) was located at 1 mg/L AgNPs, and then decreased with further increasing AgNPs concentration, suggesting that an appropriate concentration of AgNPs has a stimulating effect on the removal of Cd(II) by P. chrysosporium instead of an inhibitory effect. Results of Ag{sup +} and total Ag concentrations in the solutions together with those of SEM and XRD demonstrated that added AgNPs had undergone oxidative dissolution and transported from the solution to the surface of fungal mycelia (up to 94%). FTIR spectra confirmed that amino, carboxyl, hydroxyl, and other reducing functional groups were involved in Cd(II) removal, AgNPs transportation, and the reduction of Ag{sup +} to AgNPs.

Evaluación de la degradación del plaguicida clorpirifos en muestras de suelo utilizando el hongo Phanerochaete chrysosporium

Directory of Open Access Journals (Sweden)

Margarita María Lopera Mesa

2005-01-01

Full Text Available Se evaluó la degradación del insecticida clorpirifos en muestras de suelo durante 21 días, utilizando el hongo Phanerochaete chrysosporium. En los ensayos se obtuvieron porcentajes de degradación, en promedio, para las muestras con hongo, de 96,3, 82,4 y 62,2% cuando se trabajaron, respectivamente, con concentraciones iniciales de clorpirifos de 0,95, 5,3 y 9,4 µg/g. Igualmente, los porcentajes de degradación estuvieron acompañados del aumento en la velocidad de degradación, cuando se partió de la concentración inicial de 0,95 µg/g.

Deep fungal dermatitis caused by the Chrysosporium anamorph of Nannizziopsis vriesii in captive coastal bearded dragons (Pogona barbata).

Science.gov (United States)

Johnson, R S P; Sangster, C R; Sigler, L; Hambleton, S; Paré, J A

2011-12-01

Deep fungal dermatitis caused by the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) was diagnosed in a group of coastal bearded dragons (Pogona barbata). The outbreak extended over a 6-month period, with four of six lizards from the same zoological outdoor enclosure succumbing to infection. A fifth case of dermatomycosis was identified in a pet lizard originally sourced from the wild. Diagnosis of infection with the CANV was based on similar clinical signs and histopathology in all animals and confirmed by culture and sequencing of the fungus from one animal. This is the first report of the CANV causing disease in a terrestrial reptile species in Australia and the first in the coastal bearded dragon. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

Microbial pretreatment of corn stovers by solid-state cultivation of Phanerochaete chrysosporium for biogas production.

Science.gov (United States)

Liu, Shan; Wu, Shubiao; Pang, Changle; Li, Wei; Dong, Renjie

2014-02-01

The microbial pretreatment of corn stover and corn stover silage was achieved via the solid-state cultivation of Phanerochaete chrysosporium; pretreatment effects on the biodegradability and subsequent anaerobic production of biogas were investigated. The peak levels of daily biogas production and CH₄ yield from corn stover silage were approximately twice that of corn stover. Results suggested that ensiling was a potential pretreatment method to stimulate biogas production from corn stover. Surface morphology and Fourier-transform infrared spectroscopy analyses demonstrated that the microbial pretreatment of corn stover silage improved biogas production by 10.5 to 19.7% and CH4 yield by 11.7 to 21.2% because pretreatment could decrease dry mass loss (14.2%) and increase substrate biodegradability (19.9% cellulose, 32.4% hemicellulose, and 22.6% lignin). By contrast, the higher dry mass loss in corn stover (55.3%) after microbial pretreatment was accompanied by 54.7% cellulose, 64.0% hemicellulose, and 61.1% lignin degradation but did not significantly influence biogas production.

and Pb(ii) by Phanerochaete chrysosporium from a binary metal ...

African Journals Online (AJOL)

drinie

2001-01-01

Jan 1, 2001 ... Kinetic studies revealed that biosorption takes place in two stages: a rapid surface adsorption, within the ... With the help of multi-metal biosorption studies, these complex ..... bioreactor for color removal from bleach effluents.

Conjunctival lymphangioma in a 4-year-old girl revealed tuberous sclerosis complex

Directory of Open Access Journals (Sweden)

Freiberg, Florentina Joyce

2016-09-01

Full Text Available Background: To present a case of conjunctival lymphangioma in a girl with tuberous sclerosis complex.Methods/results: A 4-year-old girl presented with a relapsing cystic lesion of the bulbar conjunctiva in the right eye with string-of-pearl-like dilation of lymphatic vessels and right-sided facial swelling with mild pain. Best-corrected vision was not impaired. Examination of the skin revealed three hypomelanotic macules and a lumbal Shagreen patch. Magnetic resonance imaging (MRI findings displayed minimal enhancement of buccal fat on the right side. Cranial and orbital MRI showed signal enhancement in the right cortical and subcortical areas. Genetic analysis revealed a heterozygous deletion encompassing exon 1 and 2 of the gene (tuberous sclerosis complex 1 gene, confirming the diagnosis of tuberous sclerosis complex.Conclusion: In conjunctival lymphangioma, tuberous sclerosis complex should be considered as the primary disease.

Cloning and heterologous expression of two aryl-aldehyde dehydrogenases from the white-rot basidiomycete Phanerochaete chrysosporium

Energy Technology Data Exchange (ETDEWEB)

Nakamura, Tomofumi [Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan); Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu-shi, Fukuoka 818-0135 (Japan); Ichinose, Hirofumi [Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan); Wariishi, Hiroyuki, E-mail: hirowari@agr.kyushu-u.ac.jp [Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan); Bio-Architecture Center, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan); Innovation Center for Medical Redox Navigation, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581 (Japan)

2010-04-09

We identified two aryl-aldehyde dehydrogenase proteins (PcALDH1 and PcALDH2) from the white-rot basidiomycete Phanerochaete chrysosporium. Both PcALDHs were translationally up-regulated in response to exogenous addition of vanillin, one of the key aromatic compounds in the pathway of lignin degradation by basidiomycetes. To clarify the catalytic functions of PcALDHs, we isolated full-length cDNAs encoding these proteins and heterologously expressed the recombinant enzymes using a pET/Escherichia coli system. The open reading frames of both PcALDH1 and PcALDH2 consisted of 1503 nucleotides. The deduced amino acid sequences of both proteins showed high homologies with aryl-aldehyde dehydrogenases from other organisms and contained ten conserved domains of ALDHs. Moreover, a novel glycine-rich motif 'GxGxxxG' was located at the NAD{sup +}-binding site. The recombinant PcALDHs catalyzed dehydrogenation reactions of several aryl-aldehyde compounds, including vanillin, to their corresponding aromatic acids. These results strongly suggested that PcALDHs metabolize aryl-aldehyde compounds generated during fungal degradation of lignin and various aromatic xenobiotics.

Cloning and heterologous expression of two aryl-aldehyde dehydrogenases from the white-rot basidiomycete Phanerochaete chrysosporium

International Nuclear Information System (INIS)

Nakamura, Tomofumi; Ichinose, Hirofumi; Wariishi, Hiroyuki

2010-01-01

We identified two aryl-aldehyde dehydrogenase proteins (PcALDH1 and PcALDH2) from the white-rot basidiomycete Phanerochaete chrysosporium. Both PcALDHs were translationally up-regulated in response to exogenous addition of vanillin, one of the key aromatic compounds in the pathway of lignin degradation by basidiomycetes. To clarify the catalytic functions of PcALDHs, we isolated full-length cDNAs encoding these proteins and heterologously expressed the recombinant enzymes using a pET/Escherichia coli system. The open reading frames of both PcALDH1 and PcALDH2 consisted of 1503 nucleotides. The deduced amino acid sequences of both proteins showed high homologies with aryl-aldehyde dehydrogenases from other organisms and contained ten conserved domains of ALDHs. Moreover, a novel glycine-rich motif 'GxGxxxG' was located at the NAD + -binding site. The recombinant PcALDHs catalyzed dehydrogenation reactions of several aryl-aldehyde compounds, including vanillin, to their corresponding aromatic acids. These results strongly suggested that PcALDHs metabolize aryl-aldehyde compounds generated during fungal degradation of lignin and various aromatic xenobiotics.

Combining complexity measures of EEG data: multiplying measures reveal previously hidden information.

Science.gov (United States)

Burns, Thomas; Rajan, Ramesh

2015-01-01

Many studies have noted significant differences among human electroencephalograph (EEG) results when participants or patients are exposed to different stimuli, undertaking different tasks, or being affected by conditions such as epilepsy or Alzheimer's disease. Such studies often use only one or two measures of complexity and do not regularly justify their choice of measure beyond the fact that it has been used in previous studies. If more measures were added to such studies, however, more complete information might be found about these reported differences. Such information might be useful in confirming the existence or extent of such differences, or in understanding their physiological bases. In this study we analysed publically-available EEG data using a range of complexity measures to determine how well the measures correlated with one another. The complexity measures did not all significantly correlate, suggesting that different measures were measuring unique features of the EEG signals and thus revealing information which other measures were unable to detect. Therefore, the results from this analysis suggests that combinations of complexity measures reveal unique information which is in addition to the information captured by other measures of complexity in EEG data. For this reason, researchers using individual complexity measures for EEG data should consider using combinations of measures to more completely account for any differences they observe and to ensure the robustness of any relationships identified.

Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2).

Science.gov (United States)

Harel, Elad; Engel, Gregory S

2012-01-17

Light-harvesting antenna complexes transfer energy from sunlight to photosynthetic reaction centers where charge separation drives cellular metabolism. The process through which pigments transfer excitation energy involves a complex choreography of coherent and incoherent processes mediated by the surrounding protein and solvent environment. The recent discovery of coherent dynamics in photosynthetic light-harvesting antennae has motivated many theoretical models exploring effects of interference in energy transfer phenomena. In this work, we provide experimental evidence of long-lived quantum coherence between the spectrally separated B800 and B850 rings of the light-harvesting complex 2 (LH2) of purple bacteria. Spectrally resolved maps of the detuning, dephasing, and the amplitude of electronic coupling between excitons reveal that different relaxation pathways act in concert for optimal transfer efficiency. Furthermore, maps of the phase of the signal suggest that quantum mechanical interference between different energy transfer pathways may be important even at ambient temperature. Such interference at a product state has already been shown to enhance the quantum efficiency of transfer in theoretical models of closed loop systems such as LH2.

Microbial pretreatment of cotton stalks by Phanerochaete chrysosporium for bioethanol production

Science.gov (United States)

Shi, Jian

Lignocellulosic biomass has been recognized as a widespread, potentially low cost renewable source of mixed sugars for fermentation to fuel ethanol. Pretreatment, as the first step towards conversion of lignocellulose to ethanol, remains one of the main barriers to technical and commercial success of the processing technology. Existing pretreatment methods have largely been developed on the basis of physiochemical technologies which are considered relatively expensive and usually involve adverse environmental impacts. In this study, an environmentally benign alternative, microbial pretreatment using Phanerochaete chrysosporium, was explored to degrade lignin in cotton stalks and facilitate their conversion into ethanol. Two submerged liquid pretreatment techniques (SmC), shallow stationary and agitated cultivation, at three inorganic salt concentrations (no salts, modified salts without Mn2+, modified salts with Mn2+) were compared by evaluating their pretreatment efficiencies. Shallow stationary cultivation with no salt was superior to other pretreatment conditions and gave 20.7% lignin degradation along with 76.3% solids recovery and 29.0% carbohydrate availability over a 14 day period. The influence of substrate moisture content (65%, 75% and 80% M.C. wet-basis), inorganic salt concentration (no salts, modified salts without Mn2+ , modified salts with Mn2+) and culture time (0-14 days) on pretreatment effectiveness in solid state (SSC) systems was also examined. It was shown that solid state cultivation at 75% M.C. without salts was the most preferable pretreatment resulting in 27.6% lignin degradation, 71.1% solids recovery and 41.6% carbohydrate availability over a period of 14 days. A study on hydrolysis and fermentation of cotton stalks treated microbially using the most promising SmC (shallow stationary, no salts) and SSC (75% moisture content, no salts) methods resulted in no increase in cellulose conversion with direct enzyme application (10.98% and 3

Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

KAUST Repository

Simone, Giuseppina

2013-02-11

Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction\\'s strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

KAUST Repository

Simone, Giuseppina; Malara, Natalia Maria; Trunzo, Valentina; Perozziello, Gerardo; Neužil, Pavel; Francardi, Marco; Roveda, Laura; Renne, Maria; Prati, Ubaldo; Mollace, Vincenzo; Manz, Andreas; Di Fabrizio, Enzo M.

2013-01-01

Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction's strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lignin peroxidase isoenzyme: a novel approach to biodegrade the toxic synthetic polymer waste.

Science.gov (United States)

Khatoon, Nazia; Jamal, Asif; Ali, Muhammad Ishtiaq

2018-01-05

Fungal metabolites are playing an immense role in developing various sustainable waste treatment processes. The present study aimed at production and characterization of fungal lignin peroxidase (EC 1.11.1.14) with a potential to degrade Polyvinyl Chloride. Optimization studies revealed that the maximum enzyme production occurred at a temperature 25°C, pH 5 in the 4th week of the incubation period with fungal strain. Enzyme assay was performed to find out the dominating enzyme in the culture broth. The molecular weight of the enzyme was found to be 46 kDa. Partially purified lignin peroxidase from Phanerocheate chrysosporium was used for the degradation of PVC films. A significant reduction in the weight of PVC film was observed (31%) in shake flask experiment. FTIR spectra of the enzyme-treated plastic film revealed structural changes in the chemical composition, indicating a specific peak at 2943 cm -1 that corresponded to alkenyl C-H stretch. Moreover, deterioration on the surface of PVC films was confirmed by Scanning Electron Microscopy tracked through activity assay for the lignin peroxidase. Extracellular lignin peroxidases from P. chrysosporium play a significant role in the degradation of complex polymeric compounds like PVC.

The putative endoglucanase PcGH61D from Phanerochaete chrysosporium is a metal-dependent oxidative enzyme that cleaves cellulose.

Directory of Open Access Journals (Sweden)

Bjørge Westereng

Full Text Available Many fungi growing on plant biomass produce proteins currently classified as glycoside hydrolase family 61 (GH61, some of which are known to act synergistically with cellulases. In this study we show that PcGH61D, the gene product of an open reading frame in the genome of Phanerochaete chrysosporium, is an enzyme that cleaves cellulose using a metal-dependent oxidative mechanism that leads to generation of aldonic acids. The activity of this enzyme and its beneficial effect on the efficiency of classical cellulases are stimulated by the presence of electron donors. Experiments with reduced cellulose confirmed the oxidative nature of the reaction catalyzed by PcGH61D and indicated that the enzyme may be capable of penetrating into the substrate. Considering the abundance of GH61-encoding genes in fungi and genes encoding their functional bacterial homologues currently classified as carbohydrate binding modules family 33 (CBM33, this enzyme activity is likely to turn out as a major determinant of microbial biomass-degrading efficiency.

The effectiveness of arbuscular-mycorrhizal fungi and Aspergillus niger or Phanerochaete chrysosporium treated organic amendments from olive residues upon plant growth in a semi-arid degraded soil.

Science.gov (United States)

Medina, A; Roldán, A; Azcón, R

2010-12-01

Arbuscular mycorrhizal (AM) fungi and a residue from dry olive cake (DOC) supplemented with rock phosphate (RP) and treated with either Aspergillus niger (DOC-A) or Phanerochaete chrysosporium (DOC-P), were assayed in a natural, semi-arid soil using Trifolium repens or Dorycnium pentaphyllum plants. The effects of the AM fungi and/or DOC-A were compared with P-fertilisation (P) over eleven successive harvests to evaluate the persistence of the effectiveness of the treatments. The biomass of dually-treated plants after four successive harvests was greater than that obtained for non-treated plants or those receiving the AM inoculum or DOC-A treatments after eleven yields. The AM inoculation was critical for obtaining plant growth benefit from the application of fermented DOC-A residue. The abilities of the treatments to prevent plant drought stress were also assayed. Drought-alleviating effects were evaluated in terms of plant growth, proline and total sugars concentration under alternative drought and re-watering conditions (8th and 9th harvests). The concentrations of both compounds in plant biomass increased under drought when DOC-A amendment and AM inoculation were employed together: they reinforced the plant drought-avoidance capabilities and anti-oxidative defence. Water stress was less compensated in P-fertilised than in DOC-A-treated plants. DOC-P increased D. pentaphyllum biomass, shoot P content, nodule number and AM colonisation, indicating the greater DOC-transforming ability of P. chrysosporium compared to A. niger. The lack of AM colonisation and nodulation in this soil was compensated by the application of DOC-P, particularly with AM inoculum. The management of natural resources (organic amendments and soil microorganisms) represents an important strategy that assured the growth, nutrition and plant establishment in arid, degraded soils, preventing the damage that arises from limited water and nutrient supply. Copyright © 2010 Elsevier Ltd. All rights

Components of the ligninolytic system of Fusarium oxysporum and Trichoderma atroviride

Energy Technology Data Exchange (ETDEWEB)

Moenkemann, H.; Hoelker, U.; Hoefer, M. [Universitaet Bonn, Bonn (Germany). Botanisches Institut

1997-11-01

The ligninolytic system in the two deuteromycetous fungi Fusarium oxysporum and Trichoderma atroviride, which are able to solubilize low-rank coal, has been proved to have several components. Analysis of the chromosomal DNA of these fungi revealed distinct bands with probes coding for three ligninase isoenzymes, glyoxal oxidase and arylalcohol dehydrogenase of the basidiomycete Phanerochaete chrysosporium. These data constitute a strong indication for the existence in F. oxysporum and T. atroviride of a ligninolytic system comparable to that in P. chrysosporium that may be involved in the process of coal solubilization. 11 refs., 3 figs.

Biological composting of petroleum waste organics using the white rot fungus Phanerochaete chrysosporium

International Nuclear Information System (INIS)

McFarland, M.J.; Xiu J, Qiu; Aprill, W.A.; Sims, R.C.

1990-01-01

Environmental enrichment of the white rot fungus Phanerochaete chrysosporium in biological compost soil reactors was effective in enhancing the rates of Benzo(a)pyrene removal over that observed under natural soil conditions. In contaminated soil compost systems amended with fungal inoculum and primary substrate, maximum Benzo(a)pyrene removal rates of 0.31 mg B(a)p/kg compost material-day (0.25 mgB(a)p/kg soil-day) were observed while in unamended soil conditions, maximum removal rates of 0.13 mg B(a)p/kg soil-day were recorded. Additions of primary substrate without any fungal inoculum gave compound removal rates similar to soil only conditions (i.e., 14 mg B(a)p/kg soil-day). Differences in contaminant and radioactivity ( 14 C) removal rates indicated that Benzo(a)pyrene derived carbon was being incorporated into nonvolatile materials within the compost environment. Contaminated soil pH had a significant effect on Benzo(a)pyrene removal rates during composting treatment. With acid soils (pH-4.8), a maximum Benzo(a)pyrene removal rate of 0.11 mg B(a)p/kg compost material-day was determined compared to 0.31 mg B(a)p/kg compost material-day in alkaline (pH-8.0) soil. Oxygen availability appeared to be one of the most important process variables influencing both fungal growth and Benzo(a)pyrene removal. Periodic pulses of oxygen equivalent to a three volume turnover of reactor headspace every three days resulted in increasing the Benzo(a)pyrene removal rate from 0.31 mg B(a)p/kg compost material-day to 0.85 mg B(a)p/kg compost material day

Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex

DEFF Research Database (Denmark)

Laursen, Nick Stub; Andersen, Kasper Røjkjær; Braren, Ingke

2011-01-01

with a protease subunit (Bb or C2a). We determined the crystal structures of the C3b homologue cobra venom factor (CVF) in complex with C5, and in complex with C5 and the inhibitor SSL7 at 4.3 Å resolution. The structures reveal a parallel two-point attachment between C5 and CVF, where the presence of SSL7 only...

Mineralization of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and Mixtures of 2,4-D and 2,4,5-Trichlorophenoxyacetic Acid by Phanerochaete chrysosporium

Science.gov (United States)

Yadav, J. S.; Reddy, C. A.

1993-01-01

Evidence is presented for mineralization of 2,4-dichlorophenoxyacetic acid (2,4-D) in nutrient-rich media (high-nitrogen and malt extract media) by wild-type Phanerochaete chrysosporium and by a peroxidase-negative mutant of this organism. Mass balance analysis of [U-ring-14C]2,4-D mineralization in malt extract cultures showed 82.7% recovery of radioactivity. Of this, 38.6% was released as 14CO2 and 27.0, 11.2, and 5.9% were present in the aqueous, methylene chloride, and mycelial fractions, respectively. 2,4-D and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) were simultaneously mineralized when presented as a mixture, and mutual inhibition of degradation was not observed. In contrast, a relatively higher rate of mineralization of 2,4-D and 2,4,5-T was observed when these compounds were tested as mixtures than when they were tested alone. PMID:16349039

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

OpenAIRE

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

2012-01-01

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed...

Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly

Science.gov (United States)

Cottee, Matthew A; Muschalik, Nadine; Wong, Yao Liang; Johnson, Christopher M; Johnson, Steven; Andreeva, Antonina; Oegema, Karen; Lea, Susan M; Raff, Jordan W; van Breugel, Mark

2013-01-01

Centrioles organise centrosomes and template cilia and flagella. Several centriole and centrosome proteins have been linked to microcephaly (MCPH), a neuro-developmental disease associated with small brain size. CPAP (MCPH6) and STIL (MCPH7) are required for centriole assembly, but it is unclear how mutations in them lead to microcephaly. We show that the TCP domain of CPAP constitutes a novel proline recognition domain that forms a 1:1 complex with a short, highly conserved target motif in STIL. Crystal structures of this complex reveal an unusual, all-β structure adopted by the TCP domain and explain how a microcephaly mutation in CPAP compromises complex formation. Through point mutations, we demonstrate that complex formation is essential for centriole duplication in vivo. Our studies provide the first structural insight into how the malfunction of centriole proteins results in human disease and also reveal that the CPAP–STIL interaction constitutes a conserved key step in centriole biogenesis. DOI: http://dx.doi.org/10.7554/eLife.01071.001 PMID:24052813

Multilayer Stochastic Block Models Reveal the Multilayer Structure of Complex Networks

Directory of Open Access Journals (Sweden)

Toni Vallès-Català

2016-03-01

Full Text Available In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these studies assume that the interactions between systems components in each one of the layers are known, while typically for real-world systems we do not have that information. Here, we address the issue of uncovering the different interaction layers from aggregate data by introducing multilayer stochastic block models (SBMs, a generalization of single-layer SBMs that considers different mechanisms of layer aggregation. First, we find the complete probabilistic solution to the problem of finding the optimal multilayer SBM for a given aggregate-observed network. Because this solution is computationally intractable, we propose an approximation that enables us to verify that multilayer SBMs are more predictive of network structure in real-world complex systems.

454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

Directory of Open Access Journals (Sweden)

Gustafsson Lars

2010-12-01

Full Text Available Abstract Background Because of their functional significance, the Major Histocompatibility Complex (MHC class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family. Conclusions 454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective

Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

Directory of Open Access Journals (Sweden)

Aamena Alshamsi

Full Text Available Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

Science.gov (United States)

Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

2015-01-01

Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans.

Science.gov (United States)

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C G; Benavente, Ricardo

2012-10-09

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans.

Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

Science.gov (United States)

Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex

DEFF Research Database (Denmark)

Laursen, Nick Stub; Andersen, Kasper Røjkjær; Braren, Ingke

2011-01-01

with a protease subunit (Bb or C2a). We determined the crystal structures of the C3b homologue cobra venom factor (CVF) in complex with C5, and in complex with C5 and the inhibitor SSL7 at 4.3 Å resolution. The structures reveal a parallel two-point attachment between C5 and CVF, where the presence of SSL7 only...... slightly affects the C5-CVF interface, explaining the IgA dependence for SSL7-mediated inhibition of C5 cleavage. CVF functions as a relatively rigid binding scaffold inducing a conformational change in C5, which positions its cleavage site in proximity to the serine protease Bb. A general model...

Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states.

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Schlau-Cohen, Gabriela S; Wang, Quan; Southall, June; Cogdell, Richard J; Moerner, W E

2013-07-02

Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities.

Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids.

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Pitter F Huesgen

Full Text Available In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

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Takahiro Tsujikawa

2017-04-01

Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

Transmitter receptors reveal segregation of the arcopallium/amygdala complex in pigeons (Columba livia).

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Herold, Christina; Paulitschek, Christina; Palomero-Gallagher, Nicola; Güntürkün, Onur; Zilles, Karl

2018-02-15

At the beginning of the 20th century it was suggested that a complex group of nuclei in the avian posterior ventral telencephalon is comparable to the mammalian amygdala. Subsequent findings, however, revealed that most of these structures share premotor characteristics, while some indeed constitute the avian amygdala. These developments resulted in 2004 in a change of nomenclature of these nuclei, which from then on were named arcopallial or amygdala nuclei and referred to as the arcopallium/amygdala complex. The structural basis for the similarities between avian and mammalian arcopallial and amygdala subregions is poorly understood. Therefore, we analyzed binding site densities for glutamatergic AMPA, NMDA and kainate, GABAergic GABA A , muscarinic M 1 , M 2 and nicotinic acetylcholine (nACh; α 4 β 2 subtype), noradrenergic α 1 and α 2 , serotonergic 5-HT 1A and dopaminergic D 1/5 receptors using quantitative in vitro receptor autoradiography combined with a detailed analysis of the cyto- and myelo-architecture. Our approach supports a segregation of the pigeon's arcopallium/amygdala complex into the following subregions: the arcopallium anterius (AA), the arcopallium ventrale (AV), the arcopallium dorsale (AD), the arcopallium intermedium (AI), the arcopallium mediale (AM), the arcopallium posterius (AP), the nucleus posterioris amygdalopallii pars basalis (PoAb) and pars compacta (PoAc), the nucleus taeniae amgygdalae (TnA) and the area subpallialis amygdalae (SpA). Some of these subregions showed further subnuclei and each region of the arcopallium/amygdala complex are characterized by a distinct multi-receptor density expression. Here we provide a new detailed map of the pigeon's arcopallium/amygdala complex and compare the receptor architecture of the subregions to their possible mammalian counterparts. © 2017 Wiley Periodicals, Inc.

Voriconazole, a safe alternative for treating infections caused by the Chrysosporium anamorph of Nannizziopsis vriesii in bearded dragons (Pogona vitticeps).

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Van Waeyenberghe, L; Baert, K; Pasmans, F; van Rooij, P; Hellebuyck, T; Beernaert, L; de Backer, P; Haesebrouck, F; Martel, A

2010-09-01

Dermal and systemic infections caused by the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) are highly prevalent in reptiles and may result in severe disease and high mortality. Due to the high incidence of therapeutic failures, optimizing treatment is required. We first determined in this study the minimal inhibitory concentrations (MIC) of itraconazole, voriconazole, amphotericin B and terbinafine against 32 CANV isolates. For voriconazole, amphotericin B and terbinafine a monomodal MIC distribution was seen, whereas a bimodal MIC distribution was present for itraconazole, indicating acquired resistance in one isolate. Fourteen naturally-infected bearded dragons (Pogona vitticeps), from the same owner, were treated orally with either itraconazole (5 mg/kg q24h) or voriconazole (10 mg/kg q24h). The clinical condition, drug plasma concentrations and the presence of CANV in skin samples were followed. The animals were treated until complete clearance of the fungus. The plasma concentrations of voriconazole and itraconazole exceeded the minimal inhibitory concentrations of the CANV isolates. Elimination of CANV was achieved on average after 27 and 47 days of treatment with itraconazole and voriconazole, respectively. Whereas only 2 out of 7 survived after itraconazole treatment, only a single animal died in the voriconazole treated group. In conclusion, based on a limited number of animals, voriconazole applied at a regimen of 10 mg/kg bodyweight (BW) q24h seems to be a safe and effective antimycotic drug to eliminate CANV infections in bearded dragons.

A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

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Masakazu Kohda

2016-01-01

Full Text Available Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4 as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3 and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21 as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder.

Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors.

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Scott B Vafai

Full Text Available Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS. Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as "complex I bypass." In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology.

DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

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Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

2015-10-01

The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (pentropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Survey on the role of brown hares (Lepus europaeus, Pallas 1778 as carriers of zoonotic dermatophytes

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Francesca Mancianti

2010-02-01

Full Text Available The occurrence of dermatophytes and keratinophilic fungi was investigated by hair-brush technique on the coat of 986 apparently healthy brown hares (Lepus europaeus, Pallas 1778 caught in 9 restocking and capture zones in Central Italy. Overall, 7.5% hair samples gave positive results. Trichophyton terrestre (2.1%, Chrysosporium sp, Chrysosporium keratinophilum, Microsporum gypseum, Trichophyton gloriae and Trichophyton mentagrophytes (0.6% each, Trichophyton erinacei and Scopulariopsis brevicaulis (0.4% each, Chrysosporium asperatum (0.3%, Arthroderma sp and Microsporum canis (0.1% each were identified in cultures with single isolates, whereas Chrysosporium sp/T. mentagrophytes (0.3%, Chrysosporium sp/T. terrestre and M. gypseum/T. terrestre (0.2% each, Chrysosporium tropicum/T. terrestre, M. canis/T. terrestre and T. ajelloi/T. terrestre (0.1% each were identified in cultures with mixed isolates. T. erinacei and M. canis have not previously been isolated from hares. M. canis, T. erinacei and T. mentagrophytes were the most clinically important dermatophytes found. Altogether, they were isolated only from 1.5% hair samples. Thus, it is concluded that brown hares may play a limited epidemiological role as carriers of zoonotic dermatophytes. Nevertheless, this should be taken into consideration as many people may be exposed to zoonotic agents from brown hares during hunting and trapping activities.

Predictive ethoinformatics reveals the complex migratory behaviour of a pelagic seabird, the Manx Shearwater

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Freeman, Robin; Dean, Ben; Kirk, Holly; Leonard, Kerry; Phillips, Richard A.; Perrins, Chris M.; Guilford, Tim

2013-01-01

Understanding the behaviour of animals in the wild is fundamental to conservation efforts. Advances in bio-logging technologies have offered insights into the behaviour of animals during foraging, migration and social interaction. However, broader application of these systems has been limited by device mass, cost and longevity. Here, we use information from multiple logger types to predict individual behaviour in a highly pelagic, migratory seabird, the Manx Shearwater (Puffinus puffinus). Using behavioural states resolved from GPS tracking of foraging during the breeding season, we demonstrate that individual behaviours can be accurately predicted during multi-year migrations from low cost, lightweight, salt-water immersion devices. This reveals a complex pattern of migratory stopovers: some involving high proportions of foraging, and others of rest behaviour. We use this technique to examine three consecutive years of global migrations, revealing the prominence of foraging behaviour during migration and the importance of highly productive waters during migratory stopover. PMID:23635496

Deep Neural Networks Reveal a Gradient in the Complexity of Neural Representations across the Ventral Stream.

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Güçlü, Umut; van Gerven, Marcel A J

2015-07-08

Converging evidence suggests that the primate ventral visual pathway encodes increasingly complex stimulus features in downstream areas. We quantitatively show that there indeed exists an explicit gradient for feature complexity in the ventral pathway of the human brain. This was achieved by mapping thousands of stimulus features of increasing complexity across the cortical sheet using a deep neural network. Our approach also revealed a fine-grained functional specialization of downstream areas of the ventral stream. Furthermore, it allowed decoding of representations from human brain activity at an unsurpassed degree of accuracy, confirming the quality of the developed approach. Stimulus features that successfully explained neural responses indicate that population receptive fields were explicitly tuned for object categorization. This provides strong support for the hypothesis that object categorization is a guiding principle in the functional organization of the primate ventral stream. Copyright © 2015 the authors 0270-6474/15/3510005-10$15.00/0.

Nannizziopsis guarroi infection in 2 Inland Bearded Dragons (Pogona vitticeps): clinical, cytologic, histologic, and ultrastructural aspects.

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Le Donne, Viviana; Crossland, Nicholas; Brandão, João; Sokolova, Yuliya; Fowlkes, Natalie; Nevarez, Javier G; Langohr, Ingeborg M; Gaunt, Stephen D

2016-06-01

Chrysosporium-related infections have been increasingly reported in reptiles over the last 2 decades. In this report, we describe clinical, cytologic, histopathologic, and ultrastructural aspects of Chrysosporium-related infection in 2 Inland Bearded Dragons (Pogona vitticeps). Case 1 was presented for an enlarging raised lesion over the left eye and multiple additional masses over the dorsum. Case 2 was submitted to necropsy by the referring veterinarian for suspected yellow fungus disease. Impression smears of the nodules in case 1 revealed granulomatous to pyogranulomatous inflammation and many septate, variably long, 4-10 μm wide, often undulated hyphae, and very rare conidia. Postmortem impression smears of the superficial lesions of case 2 contained large numbers of solitary conidia and arthroconidia and low numbers of hyphae with similar morphology to case 1. Histopathology of the 2 cases revealed severe, multifocal, chronic, ulcerative, nodular pyogranulomatous dermatitis, with myriad intralesional septate hyphae, and arthroconidia. Fungal culture and molecular sequencing in both cases indicated infection with Nannizziopsis guarroi. © 2016 American Society for Veterinary Clinical Pathology.

Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

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Heidi Koldsø

2014-10-01

Full Text Available Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2, in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

Complex (Nonstandard) Six-Layer Polytypes of Lizardite Revealed from Oblique-Texture Electron Diffraction Patterns

International Nuclear Information System (INIS)

Zhukhlistov, A.P.; Zinchuk, N.N.; Kotel'nikov, D.D.

2004-01-01

Association of simple (1T and 3R) and two complex (nonstandard) orthogonal polytypes of the serpentine mineral lizardite from the Catoca kimberlite pipe (West Africa) association is revealed from oblique-texture electron diffraction patterns. A six-layer polytype with an ordered superposition of equally oriented layers (notation 3 2 3 2 3 4 3 4 3 6 3 6 or ++ - -00) belonging to the structural group A and a three-layer (336 or I,I,II) or a six-layer (336366 or I,I,II,I,II,II) polytype with alternating oppositely oriented layers and semi-disordered structure are identified using polytype analysis

Extracellular oxidases and the transformation of solubilised low-rank coal by wood-rot fungi

Energy Technology Data Exchange (ETDEWEB)

Ralph, J.P. [Flinders Univ. of South Australia, Bedford Park (Australia). School of Biological Sciences; Graham, L.A. [Flinders Univ. of South Australia, Bedford Park (Australia). School of Biological Sciences; Catcheside, D.E.A. [Flinders Univ. of South Australia, Bedford Park (Australia). School of Biological Sciences

1996-12-31

The involvement of extracellular oxidases in biotransformation of low-rank coal was assessed by correlating the ability of nine white-rot and brown-rot fungi to alter macromolecular material in alkali-solubilised brown coal with the spectrum of oxidases they produce when grown on low-nitrogen medium. The coal fraction used was that soluble at 3.0{<=}pH{<=}6.0 (SWC6 coal). In 15-ml cultures, Gloeophyllum trabeum, Lentinus lepideus and Trametes versicolor produced little or no lignin peroxidase, manganese (Mn) peroxidase or laccase activity and caused no change to SWC6 coal. Ganoderma applanatum and Pycnoporus cinnabarinus also produced no detectable lignin or Mn peroxidases or laccase yet increased the absorbance at 400 nm of SWC6 coal. G. applanatum, which produced veratryl alcohol oxidase, also increased the modal apparent molecular mass. SWC6 coal exposed to Merulius tremellosus and Perenniporia tephropora, which secreted Mn peroxidases and laccase and Phanerochaete chrysosporium, which produced Mn and lignin peroxidases was polymerised but had unchanged or decreased absorbance. In the case of both P. chrysosporium and M. tremellosus, polymerisation of SWC6 coal was most extensive, leading to the formation of a complex insoluble in 100 mM NaOH. Rigidoporus ulmarius, which produced only laccase, both polymerised and reduced the A{sub 400} of SWC6 coal. P. chrysosporium, M. tremellosus and P. tephropora grown in 10-ml cultures produced a spectrum of oxidases similar to that in 15-ml cultures but, in each case, caused more extensive loss of A{sub 400}, and P. chrysosporium depolymerised SWC6 coal. It is concluded that the extracellular oxidases of white-rot fungi can transform low-rank coal macromolecules and that increased oxygen availability in the shallower 10-ml cultures favours catabolism over polymerisation. (orig.)

COMBINED DELAY AND GRAPH EMBEDDING OF EPILEPTIC DISCHARGES IN EEG REVEALS COMPLEX AND RECURRENT NONLINEAR DYNAMICS.

Science.gov (United States)

Erem, B; Hyde, D E; Peters, J M; Duffy, F H; Brooks, D H; Warfield, S K

2015-04-01

The dynamical structure of the brain's electrical signals contains valuable information about its physiology. Here we combine techniques for nonlinear dynamical analysis and manifold identification to reveal complex and recurrent dynamics in interictal epileptiform discharges (IEDs). Our results suggest that recurrent IEDs exhibit some consistent dynamics, which may only last briefly, and so individual IED dynamics may need to be considered in order to understand their genesis. This could potentially serve to constrain the dynamics of the inverse source localization problem.

Comparative interactomics: analysis of arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants.

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Paul, Anna-Lisa; Liu, Li; McClung, Scott; Laughner, Beth; Chen, Sixue; Ferl, Robert J

2009-04-01

As a first step in the broad characterization of plant 14-3-3 multiprotein complexes in vivo, stringent and specific antibody affinity purification was used to capture 14-3-3s together with their interacting proteins from extracts of Arabidopsis cell suspension cultures. Approximately 120 proteins were identified as potential in vivo 14-3-3 interacting proteins by mass spectrometry of the recovered complexes. Comparison of the proteins in this data set with the 14-3-3 interacting proteins from a similar study in human embryonic kidney cell cultures revealed eight interacting proteins that likely represent reasonably abundant, fundamental 14-3-3 interaction complexes that are highly conserved across all eukaryotes. The Arabidopsis 14-3-3 interaction data set was also compared to a yeast in vivo 14-3-3 interaction data set. Four 14-3-3 interacting proteins are conserved in yeast, humans, and Arabidopsis. Comparisons of the data sets based on biochemical function revealed many additional similarities in the human and Arabidopsis data sets that represent conserved functional interactions, while also leaving many proteins uniquely identified in either Arabidopsis or human cells. In particular, the Arabidopsis interaction data set is enriched for proteins involved in metabolism.

Global terrestrial water storage connectivity revealed using complex climate network analyses

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Sun, A. Y.; Chen, J.; Donges, J.

2015-07-01

Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

Principles of assembly reveal a periodic table of protein complexes.

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Ahnert, Sebastian E; Marsh, Joseph A; Hernández, Helena; Robinson, Carol V; Teichmann, Sarah A

2015-12-11

Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering. Copyright © 2015, American Association for the Advancement of Science.

Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

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Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

2014-01-01

The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

Isolation of keratinophilic fungi from selected soils of Sanjay Gandhi National Park, Mumbai (India).

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Deshmukh, S K; Verekar, S A

2014-12-01

One hundred and twenty-five samples were collected from eight different sites in the vicinity of Sanjay Gandhi National Park (SGNP) and screened for the presence of keratinophilic fungi using hair baiting technique for isolation. Seventy-three isolates were recovered and identified. The cultures were identified using macro- and micro-morphological features. Their identification was also confirmed by the BLAST search of sequences of the ITS1-5.8S-ITS2 rDNA region against the NCBI/Genbank data and compared with deposited sequences for identification purpose. Thirteen species of nine genera were isolated viz. Aphanoascus durus (2.4%), Arthroderma corniculatum (1.6%), Auxarthron umbrinum (0.8%), Chrysosporium evolceanui (1.6%), Chrysosporium indicum (16.0%), Chrysosporium tropicum (2.4%), Chrysosporium zonatum (4.0%), Chrysosporium states of Arthroderma tuberculatum (0.8%), Chrysosporium state of Ctenomyces serratus (11.2%), Gymnascella dankaliensis (3.2%), Microsporum gypseum (12.0%), Myriodontium keratinophilum (0.8%) and Trichophyton mentagrophytes (1.6%). Representative of all thirteen species can release the protein in the range of 152.2-322.4 μg/mL in liquid media when grown on human hair in shake flask culture and also decompose 18.4-40.2% of human hair after four weeks of incubation. This study indicates that the soils of SGNP, Mumbai may be significant reservoirs of certain keratinophilic fungi. The keratinolytic activity of these fungi may be playing significant role in superficial infections to man and animals and recycling of keratinic material of this environment. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

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Mohan Babu

2014-02-01

Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

High-resolution crystal structure of Streptococcus pyogenes β-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

International Nuclear Information System (INIS)

Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

2013-01-01

The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD + glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD + glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN ct –IFS complex, which consists of the SPN C-terminal domain (SPN ct ; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN ct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope

Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.

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Paul De Barro

Full Text Available BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS: Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010. Only two species proposed in Dinsdale et al. (2010 departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED and Middle East - Asia Minor 1 (MEAM1, showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of

Biotechnological modification of lignin

Energy Technology Data Exchange (ETDEWEB)

1989-01-01

A literature search of organisms capable of degrading lignin was conducted. Four fungi were selected for study and these were Phanerochaete chrysosporium, Chrysosporium pruinosum, Phlebia tremellosus and Trametes versicolor. Other organisms, Pleurotus ostreatus, Pleurotus florida and Lentinus edodes were also tested in preliminary experiments. All cultures were screened for their ability to degrade the lignin component of aspen sawdust and also lignin extracted from steam-exploded wood. This type of screen was followed by analysis of culture filtrates for the presence of ligninase, the marker enzyme for lignin degradation. Phanerochaete chrysosporium and consequently chosen for further studies in fermentors. Considerable efforts were directed to production of ligninase in fermentors. Only when Chrysosporium pruinosum was pre-cultured in a shake flask for 4 days and then transferred to a fermentor could ligninase activity be detected. The enzyme from shake flasks has been concentrated ready for use in bench-scale studies on cell-free depolymerization of lignin. 13 refs., 8 tabs.

A theoretical lens for revealing the complexity of chronic care

NARCIS (Netherlands)

Borgermans, L.; de Maeseneer, J.; Wollersheim, H.; Vrijhoef, H.J.M.; Devroey, D.

2013-01-01

The increasing prevalence of co-occurring multiple chronic conditions in an aging population has influenced the debate on complexity in chronic care and nowadays provides an impetus to the reform of numerous health systems. This article presents a theoretical lens for understanding the complexity of

Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

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Toan, Ngo Minh; Thirumalai, D.

2018-03-01

Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments using atomic force spectroscopy on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells, bound to intercellular adhesion molecules (ICAM), we performed constant loading rate (rf) and constant force (F) simulations using the self-organized polymer model to describe the mechanism of ligand rupture from CACs. The simulations reproduce the major experimental finding on the kinetics of the rupture process, namely, the dependence of the most probable rupture forces (f*s) on ln rf (rf is the loading rate) exhibits two distinct linear regimes. The first, at low rf, has a shallow slope, whereas the slope at high rf is much larger, especially for a LFA-1/ICAM-1 complex with the transition between the two occurring over a narrow rf range. Locations of the two transition states (TSs) extracted from the simulations show an abrupt change from a high value at low rf or constant force, F, to a low value at high rf or F. This unusual behavior in which the CACs switch from one brittle (TS position is a constant over a range of forces) state to another brittle state is not found in forced-rupture in other protein complexes. We explain this novel behavior by constructing the free energy profiles, F(Λ)s, as a function of a collective reaction coordinate (Λ), involving many key charged residues and a critical metal ion (Mg2+). The TS positions in F(Λ), which quantitatively agree with the parameters extracted using the Bell-Evans model, change abruptly at a critical force, demonstrating that it, rather than the molecular extension, is a good reaction coordinate. Our combined analyses using simulations performed in both the pulling modes (constant rf and F) reveal a new mechanism for the two loading regimes observed in the

Selective ligand activity at Nur/retinoid X receptor complexes revealed by dimer-specific bioluminescence resonance energy transfer-based sensors

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Giner, Xavier C; Cotnoir-White, David; Mader, Sylvie; Lévesque, Daniel

2017-01-01

Retinoid X receptors (RXR) play a role as master regulators due to their capacity to form heterodimers with other nuclear receptors. Accordingly, retinoid signaling is involved in multiple biological processes, including development, cell differentiation, metabolism and cell death. However, the role and functions of RXR in different heterodimer complexes remain unsolved, mainly because most RXR drugs (called rexinoids) are not selective to specific heterodimer complexes. This also strongly limits the use of rexinoids for specific therapeutic approaches. In order to better characterize rexinoids at specific nuclear receptor complexes, we have developed and optimized luciferase protein complementation-based Bioluminescence Resonance Energy Transfer (BRET) assays, which can directly measure recruitment of a co-activator motif fused to yellow fluorescent protein (YFP) by specific nuclear receptor dimers. To validate the assays, we compared rexinoid modulation of co-activator recruitment by RXR homodimer, and heterodimers Nur77/RXR and Nurr1/RXR. Results reveal that some rexinoids display selective co-activator recruitment activities with homo- or hetero-dimer complexes. In particular, SR11237 (BMS649) has increased potency for recruitment of co-activator motif and transcriptional activity with the Nur77/RXR heterodimer compared to other complexes. This technology should prove useful to identify new compounds with specificity for individual dimeric species formed by nuclear receptors. PMID:26148973

Connected magma plumbing system between Cerro Negro and El Hoyo Complex, Nicaragua revealed by gravity survey

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MacQueen, Patricia; Zurek, Jeffrey; Williams-Jones, Glyn

2016-11-01

Cerro Negro, near León, Nicaragua is a young, relatively small basaltic cinder cone volcano that has been unusually active during its short lifespan. Multiple explosive eruptions have deposited significant amounts of ash on León and the surrounding rural communities. While a number of studies investigate the geochemistry and stress regime of the volcano, subsurface structures have only been studied by diffuse soil gas surveys. These studies have raised several questions as to the proper classification of Cerro Negro and its relation to neighboring volcanic features. To address these questions, we collected 119 gravity measurements around Cerro Negro volcano in an attempt to delineate deep structures at the volcano. The resulting complete Bouguer anomaly map revealed local positive gravity anomalies (wavelength 0.5 to 2 km, magnitude +4 mGal) and regional positive (10 km wavelength, magnitudes +10 and +8 mGal) and negative (12 and 6 km wavelength, magnitudes -18 and -13 mGal) Bouguer anomalies. Further analysis of these gravity data through inversion has revealed both local and regional density anomalies that we interpret as intrusive complexes at Cerro Negro and in the Nicaraguan Volcanic Arc. The local density anomalies at Cerro Negro have a density of 2700 kg m-3 (basalt) and are located between -250 and -2000 m above sea level. The distribution of recovered density anomalies suggests that eruptions at Cerro Negro may be tapping an interconnected magma plumbing system beneath El Hoyo, Cerro La Mula, and Cerro Negro, and more than seven other proximal volcanic features, implying that Cerro Negro should be considered the newest cone of a Cerro Negro-El Hoyo volcanic complex.

Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties

International Nuclear Information System (INIS)

Mikeska, Ruth; Wacker, Roland; Arni, Raghuvir; Singh, Tej P.; Mikhailov, Albert; Gabdoulkhakov, Azat; Voelter, Wolfgang; Betzel, Christian

2004-01-01

The structures of mistletoe lectin I in complex with lactose and galactose reveal differences in binding by the two known sites in subdomains α1 and γ2 and suggest the presence of a third low-affinity site in subdomain β1. The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (R free = 23.6%) and 20.9 (R free = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML-I B-chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose-binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit β1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound

A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.

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Rito, Teresa; Matos, Carlos; Carvalho, Carlos; Machado, Henrique; Rodrigues, Gabriela; Oliveira, Olena; Ferreira, Eduarda; Gonçalves, Jorge; Maio, Lurdes; Morais, Clara; Ramos, Helena; Guimarães, João Tiago; Santos, Catarina L; Duarte, Raquel; Correia-Neves, Margarida

2018-01-25

Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

Physical Damages of Wood Fiber in Acacia Mangium due to Biopulping Treatment

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Ridwan Yahya

2016-05-01

chrysosporium to Acacia mangium Willd can reduce lignin and improve holocellulose and cellulose content of the material. Fiber dimension recognized as other important factor for paper properties. The question is how the integrity and dimensions of the wood fiber that has been pretreated with the fungus. The objectives of present study were to know effect of pretreatment of P. chrysosporium to the integrity and dimensions of the fiber. The P. chrysosporium was cultured for 14 days in growth medium, and inoculated to wood chips 5% (w/v and incubated for 0, 15 and 30 days. The inoculated wood chips were chipped into 1 mm x 1 mm x 20 mm and macerated using franklin solution at 60 oC for 48 hours. Forty fibers from each incubated time were analized their physical damages using a light microscope at a 400 magnification. The inoculated fibers were measured theirs dimensions. The physical damage percentage of fibers pretreated using P. chrysosporium was 0%. Length and wall thickness of the pretreated fibers were can be categorized as middle class and thin fibers, respectively.

High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

Energy Technology Data Exchange (ETDEWEB)

Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

2013-11-01

The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

Survey of large protein complexes D. vulgaris reveals great structural diversity

Energy Technology Data Exchange (ETDEWEB)

Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

2009-08-15

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

Two conformational states of the membrane-associated Bacillus thuringiensis Cry4Ba δ-endotoxin complex revealed by electron crystallography: Implications for toxin-pore formation

International Nuclear Information System (INIS)

Ounjai, Puey; Unger, Vinzenz M.; Sigworth, Fred J.; Angsuthanasombat, Chanan

2007-01-01

The insecticidal nature of Cry δ-endotoxins produced by Bacillus thuringiensis is generally believed to be caused by their ability to form lytic pores in the midgut cell membrane of susceptible insect larvae. Here we have analyzed membrane-associated structures of the 65-kDa dipteran-active Cry4Ba toxin by electron crystallography. The membrane-associated toxin complex was crystallized in the presence of DMPC via detergent dialysis. Depending upon the charge of the adsorbed surface, 2D crystals of the oligomeric toxin complex have been captured in two distinct conformations. The projection maps of those crystals have been generated at 17 A resolution. Both complexes appeared to be trimeric; as in one crystal form, its projection structure revealed a symmetrical pinwheel-like shape with virtually no depression in the middle of the complex. The other form revealed a propeller-like conformation displaying an obvious hole in the center region, presumably representing the toxin-induced pore. These crystallographic data thus demonstrate for the first time that the 65-kDa activated Cry4Ba toxin in association with lipid membranes could exist in at least two different trimeric conformations, conceivably implying the closed and open states of the pore

Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex.

Science.gov (United States)

Brankovics, Balázs; van Dam, Peter; Rep, Martijn; de Hoog, G Sybren; J van der Lee, Theo A; Waalwijk, Cees; van Diepeningen, Anne D

2017-09-18

The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

The Complexome of Dehalococcoides mccartyi Reveals Its Organohalide Respiration-Complex Is Modular

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Katja Seidel

2018-06-01

Full Text Available Dehalococcoides mccartyi strain CBDB1 is a slow growing strictly anaerobic microorganism dependent on halogenated compounds as terminal electron acceptor for anaerobic respiration. Indications have been described that the membrane-bound proteinaceous organohalide respiration complex of strain CBDB1 is functional without quinone-mediated electron transfer. We here study this multi-subunit protein complex in depth in regard to participating protein subunits and interactions between the subunits using blue native gel electrophoresis coupled to mass spectrometric label-free protein quantification. Applying three different solubilization modes to detach the respiration complex from the membrane we describe different solubilization snapshots of the organohalide respiration complex. The results demonstrate the existence of a two-subunit hydrogenase module loosely binding to the rest of the complex, tight binding of the subunit HupX to OmeA and OmeB, predicted to be the two subunits of a molybdopterin-binding redox subcomplex, to form a second module, and the presence of two distinct reductive dehalogenase module variants with different sizes. In our data we obtained biochemical evidence for the specificity between a reductive dehalogenase RdhA (CbdbA80 and its membrane anchor protein RdhB (CbdbB3. We also observed weak interactions between the reductive dehalogenase and the hydrogenase module suggesting a not yet recognized contact surface between these two modules. Especially an interaction between the two integral membrane subunits OmeB and RdhB seems to promote the integrity of the complex. With the different solubilization strengths we observe successive disintegration of the complex into its subunits. The observed architecture would allow the association of different reductive dehalogenase modules RdhA/RdhB with the other two protein complex modules when the strain is growing on different electron acceptors. In the search for other respiratory

Structure of UreG/UreF/UreH Complex Reveals How Urease Accessory Proteins Facilitate Maturation of Helicobacter pylori Urease

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Fong, Yu Hang; Wong, Ho Chun; Yuen, Man Hon; Lau, Pak Ho; Chen, Yu Wai; Wong, Kam-Bo

2013-01-01

Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease. PMID:24115911

Differential network analysis reveals evolutionary complexity in secondary metabolism of Rauvolfia serpentina over Catharanthus roseus

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Shivalika Pathania

2016-08-01

Full Text Available Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Towards these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These mechanisms may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of Rauvolfia serpentina, and key genes that contribute towards diversification of specific metabolites.

Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus.

Science.gov (United States)

Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S

2016-01-01

Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion.

Science.gov (United States)

Rosenthal, Sara Brin; Twomey, Colin R; Hartnett, Andrew T; Wu, Hai Shan; Couzin, Iain D

2015-04-14

Coordination among social animals requires rapid and efficient transfer of information among individuals, which may depend crucially on the underlying structure of the communication network. Establishing the decision-making circuits and networks that give rise to individual behavior has been a central goal of neuroscience. However, the analogous problem of determining the structure of the communication network among organisms that gives rise to coordinated collective behavior, such as is exhibited by schooling fish and flocking birds, has remained almost entirely neglected. Here, we study collective evasion maneuvers, manifested through rapid waves, or cascades, of behavioral change (a ubiquitous behavior among taxa) in schooling fish (Notemigonus crysoleucas). We automatically track the positions and body postures, calculate visual fields of all individuals in schools of ∼150 fish, and determine the functional mapping between socially generated sensory input and motor response during collective evasion. We find that individuals use simple, robust measures to assess behavioral changes in neighbors, and that the resulting networks by which behavior propagates throughout groups are complex, being weighted, directed, and heterogeneous. By studying these interaction networks, we reveal the (complex, fractional) nature of social contagion and establish that individuals with relatively few, but strongly connected, neighbors are both most socially influential and most susceptible to social influence. Furthermore, we demonstrate that we can predict complex cascades of behavioral change at their moment of initiation, before they actually occur. Consequently, despite the intrinsic stochasticity of individual behavior, establishing the hidden communication networks in large self-organized groups facilitates a quantitative understanding of behavioral contagion.

Intersubject information mapping: revealing canonical representations of complex natural stimuli

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Nikolaus Kriegeskorte

2015-03-01

Full Text Available Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space. Here we introduce the more general approach of intersubject information mapping (IIM. For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These

Genomics reveals traces of fungal phenylpropanoid-flavonoid metabolic pathway in the f ilamentous fungus Aspergillus oryzae.

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Juvvadi, Praveen Rao; Seshime, Yasuyo; Kitamoto, Katsuhiko

2005-12-01

Fungal secondary metabolites constitute a wide variety of compounds which either play a vital role in agricultural, pharmaceutical and industrial contexts, or have devastating effects on agriculture, animal and human affairs by virtue of their toxigenicity. Owing to their beneficial and deleterious characteristics, these complex compounds and the genes responsible for their synthesis have been the subjects of extensive investigation by microbiologists and pharmacologists. A majority of the fungal secondary metabolic genes are classified as type I polyketide synthases (PKS) which are often clustered with other secondary metabolism related genes. In this review we discuss on the significance of our recent discovery of chalcone synthase (CHS) genes belonging to the type III PKS superfamily in an industrially important fungus, Aspergillus oryzae. CHS genes are known to play a vital role in the biosynthesis of flavonoids in plants. A comparative genome analyses revealed the unique character of A. oryzae with four CHS-like genes (csyA, csyB, csyC and csyD) amongst other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus) which contained none of the CHS-like genes. Some other fungi such as Neurospora crassa, Fusarium graminearum, Magnaporthe grisea, Podospora anserina and Phanerochaete chrysosporium also contained putative type III PKSs, with a phylogenic distinction from bacteria and plants. The enzymatically active nature of these newly discovered homologues is expected owing to the conservation in the catalytic residues across the different species of plants and fungi, and also by the fact that a majority of these genes (csyA, csyB and csyD) were expressed in A. oryzae. While this finding brings filamentous fungi closer to plants and bacteria which until recently were the only ones considered to possess the type III PKSs, the presence of putative genes encoding other principal enzymes involved in the phenylpropanoid and flavonoid biosynthesis (viz

Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

Science.gov (United States)

Mavhunga, Elizabeth

2018-04-01

Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.

Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

Science.gov (United States)

Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

2013-12-06

Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

Occurrence of keratinophilic fungi on Indian birds.

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Dixit, A K; Kushwaha, R K

1991-01-01

Keratinophilic fungi were isolated from feathers of most common Indian birds, viz. domestic chicken (Gallus domesticus), domestic pigeon (Columba livia), house sparrow (Passer domesticus), house crow (Corvus splendens), duck (Anas sp.), rose-ringed parakeet (Psittacula krameri). Out of 87 birds, 58 yielded 4 keratinophilic fungal genera representing 13 fungal species and one sterile mycelium. The isolated fungi were cultured on Sabouraud's dextrose agar at 28 +/- 2 degrees C. Chrysosporium species were isolated on most of the birds. Chrysosporium lucknowense and Chrysosporium tropicum were the most common fungal species associated with these Indian birds. Maximum occurrence of fungi (47%) was recorded on domestic chickens and the least number of keratinophilic fungi was isolated from the domestic pigeon and duck. The average number of fungi per bird was found to be the 0.44.

GlcNAc-1-P-transferase–tunicamycin complex structure reveals basis for inhibition of N-glycosylation

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Yoo, Jiho; Mashalidis, Ellene H.; Kuk, Alvin C. Y.; Yamamoto, Kazuki; Kaeser, Benjamin; Ichikawa, Satoshi; Lee, Seok-Yong

2018-02-19

N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. In conclusion, structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. We demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.

Biodegradation of the High Explosive Hexanitrohexaazaiso-wurtzitane (CL-20)

OpenAIRE

Karakaya, Pelin; Christodoulatos, Christos; Koutsospyros, Agamemnon; Balas, Wendy; Nicolich, Steve; Sidhoum, Mohammed

2009-01-01

The aerobic biodegradability of the high explosive CL-20 by activated sludge and the white rot fungus Phanerochaete chrysosporium has been investigated. Although activated sludge is not effective in degrading CL-20 directly, it can mineralize the alkaline hydrolysis products. Phanerochaete chrysosporium degrades CL-20 in the presence of supplementary carbon and nitrogen sources. Biodegradation studies were conducted using various nutrient media under diverse conditions. Variables included the...

FIBER QUALITIES OF PRETREATED BETUNG BAMBOO (Dendrocalamusasper BY MIXED CULTURE OF WHITE-ROT FUNGI WITH RESPECT TO ITS USE FOR PULP/PAPER

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Widya Fatriasari

2013-10-01

Full Text Available Previous research on anatomical structures of pretreated large (betung bamboo (Dendrocalamusasper using single culture of white-rot fungi has been investigated, which revealed that the pretreatment caused the decrease in the Runkel ratioas well as the coefficient rigidity and the increase in the flexibility ratio of their corresponding bamboo fibers. However, there is no study reported on the anatomical structure changes of them caused by pretreatment using mixed culture of white-rot fungi. This paper reports the results of the research on paper/pulp quality after different treatments. Pretreatment that used Trametes versicolor fungi and lasted for 45 days inflicted intensive fiber damages compared with those of untreated bamboo (control. Fresh and barkless large (betung bamboo chips of 2 year's old, and 1.6 cm in length, were inoculated by 10% of mixed culture of white-rot fungi inoculums stock for 30 and 45 days in room temperature. There were four treatment groups of mixed culture, i.e T. versi color and P. ostreatus (TVPO; P. ostreatus and P. chrysosporium (POPC; P. chrysosporium and T.versi color (PCTV; and P.chrysosporium,  T.versicolorand  P.ostreatus  (TVPCPO.After  the  inoculation  period,  the  chips  weremacerated into separate fibers using Scultze method to analyze the fiber dimension and its derived values. The fibers were then observed regarding their macro and microscopic structures by optical microscope. Mixed culture pretreatment of white-rot fungi accelerated improvement of fiber morphology and fiber derived value characteristics, except for Muhlsteph ratio. The fiber derived values oftreated bamboo tended to improve compared to those of untreated bamboo, there by requiring milder pulping conditions. Accordingly, the treated bamboo would indicatively produce a good quality pulp (grade I based on FAO and LPHH (Forest Product Research Report requirements. Co-culture treatment using P. chrysosporium and P. ostreatus for

Removal of Cr(VI) from aqueous solution by fungal biomass

Energy Technology Data Exchange (ETDEWEB)

Ahluwalia, Sarabjeet Singh [Department of Biotechnology, General Shivdev Singh Diwan Gurbachan Singh Khalsa College, Patiala, Punjab (India); Goyal, Dinesh [Department of Biotechnology and Environmental Sciences, Thapar University, Patiala, Punjab (India)

2010-10-15

Chromium compounds are released by industrial processes including leather production, mining, petroleum refining, in textile industry and dyeing. They are a significant threat to the environment and public health because of their toxicity. Removal of hexavalent chromium by living biomass of different fungi was effective in the order of Aspergillus terricola>Aspergillus niger>Acremonium strictum>Aureobasidium pullulans>Paecilomyces variotii>Aspergillus foetidus>Cladosporium resinae>Phanerochaete chrysosporium. Non-living dried fungal biomass showed higher potential for metal removal than living cells. Among all fungi dead biomass of P. chrysosporium, C. resinae and P. variotii had the maximum specific chromium uptake capacity, which was 11.02, 10.69 and 10.35 mg/g of dry biomass respectively at pH 4.0-5.0 in batch sorption. Removal of Cr(VI) by P. chrysosporium from multi-metallic synthetic solution as well as chrome effluent was significant by bringing down the residual concentration to 0.1 mg/L in the effluent, which falls within the permissible range and its removal was not affected by the presence of other metal ions such as Fe, Zn and Ni. Fourier transform infrared spectral analysis revealed the presence of carboxylate (C=O) and amine (-NH{sup +}{sub 3}-NH{sup +}{sub 2}) functional groups commonly present on the cell surface of all fungi, with possible involvement in chromium binding. The result indicates that non-living fungal biomass either obtained as a by-product of fermentation industry or mass produced using inexpensive culture media can be used for bioremediation of Cr(VI) from chrome effluent on large scale. (Copyright copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Conformational Complexity in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum Revealed by Hole-Burning Spectroscopy.

Science.gov (United States)

Kell, Adam; Jassas, Mahboobe; Acharya, Khem; Hacking, Kirsty; Cogdell, Richard J; Jankowiak, Ryszard

2017-06-15

This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800 R and B800 B . The energy differences between average site energies of conformations 1 and 2, and B800 R and B800 B are similar (∼200 cm -1 ), suggesting weak and strong hydrogen bonds linking two major subpopulations of BChls and the protein scaffolding. Although conformations 1 and 2 of the B850 chromophores, and B800 R and B800 B , exist in the ground state, selective excitation leads to 1 → 2 and B800 R → B800 B phototransformations. Different static inhomogeneous broadening is revealed for the lowest energy exciton states of B850 (fwhm ∼195 cm -1 ) and B800 R (fwhm ∼140 cm -1 ). To describe the 5 K absorption spectrum and the above-mentioned conformations, we employ an exciton model with dichotomous protein conformation disorder. We show that both experimental data and the modeling study support a two-site model with strongly and weakly hydrogen-bonded B850 and B800 BChls, which under illumination undergo conformational changes, most likely caused by proton dynamics.

Tracking Glideosome-associated protein 50 reveals the development and organization of the inner membrane complex of Plasmodium falciparum.

Science.gov (United States)

Yeoman, Jeffrey A; Hanssen, Eric; Maier, Alexander G; Klonis, Nectarios; Maco, Bohumil; Baum, Jake; Turnbull, Lynne; Whitchurch, Cynthia B; Dixon, Matthew W A; Tilley, Leann

2011-04-01

The most deadly of the human malaria parasites, Plasmodium falciparum, has different stages specialized for invasion of hepatocytes, erythrocytes, and the mosquito gut wall. In each case, host cell invasion is powered by an actin-myosin motor complex that is linked to an inner membrane complex (IMC) via a membrane anchor called the glideosome-associated protein 50 (PfGAP50). We generated P. falciparum transfectants expressing green fluorescent protein (GFP) chimeras of PfGAP50 (PfGAP50-GFP). Using immunoprecipitation and fluorescence photobleaching, we show that C-terminally tagged PfGAP50-GFP can form a complex with endogenous copies of the linker protein PfGAP45 and the myosin A tail domain-interacting protein (MTIP). Full-length PfGAP50-GFP is located in the endoplasmic reticulum in early-stage parasites and then redistributes to apical caps during the formation of daughter merozoites. In the final stage of schizogony, the PfGAP50-GFP profile extends further around the merozoite surface. Three-dimensional (3D) structured illumination microscopy reveals the early-stage IMC as a doubly punctured flat ellipsoid that separates to form claw-shaped apposed structures. A GFP fusion of PfGAP50 lacking the C-terminal membrane anchor is misdirected to the parasitophorous vacuole. Replacement of the acid phosphatase homology domain of PfGAP50 with GFP appears to allow correct trafficking of the chimera but confers a growth disadvantage.

[Tissue-specific nucleoprotein complexes].

Science.gov (United States)

Riadnova, I Iu; Shataeva, L K; Khavinson, V Kh

2000-01-01

A method of isolation of native nucleorprotein complexes from cattle cerebral cortex, thymus, and liver was developed. Compositions of these complexes were studied by means of gel-chromatography and ion-exchange chromatography. These preparations were shown to consist of several fractions of proteins and their complexes differ by molecular mass and electro-chemical properties. Native nucleoprotein complexes revealed high tissue specific activity, which was not species-specific.

Proteomic analysis of HIV-1 Nef cellular binding partners reveals a role for exocyst complex proteins in mediating enhancement of intercellular nanotube formation

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Mukerji Joya

2012-06-01

Full Text Available Abstract Background HIV-1 Nef protein contributes to pathogenesis via multiple functions that include enhancement of viral replication and infectivity, alteration of intracellular trafficking, and modulation of cellular signaling pathways. Nef stimulates formation of tunneling nanotubes and virological synapses, and is transferred to bystander cells via these intercellular contacts and secreted microvesicles. Nef associates with and activates Pak2, a kinase that regulates T-cell signaling and actin cytoskeleton dynamics, but how Nef promotes nanotube formation is unknown. Results To identify Nef binding partners involved in Pak2-association dependent Nef functions, we employed tandem mass spectrometry analysis of Nef immunocomplexes from Jurkat cells expressing wild-type Nef or Nef mutants defective for the ability to associate with Pak2 (F85L, F89H, H191F and A72P, A75P in NL4-3. We report that wild-type, but not mutant Nef, was associated with 5 components of the exocyst complex (EXOC1, EXOC2, EXOC3, EXOC4, and EXOC6, an octameric complex that tethers vesicles at the plasma membrane, regulates polarized exocytosis, and recruits membranes and proteins required for nanotube formation. Additionally, Pak2 kinase was associated exclusively with wild-type Nef. Association of EXOC1, EXOC2, EXOC3, and EXOC4 with wild-type, but not mutant Nef, was verified by co-immunoprecipitation assays in Jurkat cells. Furthermore, shRNA-mediated depletion of EXOC2 in Jurkat cells abrogated Nef-mediated enhancement of nanotube formation. Using bioinformatic tools, we visualized protein interaction networks that reveal functional linkages between Nef, the exocyst complex, and the cellular endocytic and exocytic trafficking machinery. Conclusions Exocyst complex proteins are likely a key effector of Nef-mediated enhancement of nanotube formation, and possibly microvesicle secretion. Linkages revealed between Nef and the exocyst complex suggest a new paradigm of

Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveals complex aggregation kinetics.

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Aaron M Streets

Full Text Available An apparatus that combines dynamic light scattering and Thioflavin T fluorescence detection is used to simultaneously probe fibril formation in polyglutamine peptides, the aggregating subunit associated with Huntington's disease, in vitro. Huntington's disease is a neurodegenerative disorder in a class of human pathologies that includes Alzheimer's and Parkinson's disease. These pathologies are all related by the propensity of their associated protein or polypeptide to form insoluble, β-sheet rich, amyloid fibrils. Despite the wide range of amino acid sequence in the aggregation prone polypeptides associated with these diseases, the resulting amyloids display strikingly similar physical structure, an observation which suggests a physical basis for amyloid fibril formation. Thioflavin T fluorescence reports β-sheet fibril content while dynamic light scattering measures particle size distributions. The combined techniques allow elucidation of complex aggregation kinetics and are used to reveal multiple stages of amyloid fibril formation.

Ligninolytic Activity of Ganoderma strains on Different Carbon Sources

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TYPUK ARTININGSIH

2006-10-01

Full Text Available Lignin is a phenylpropanoid polymers with only few carbon bonds might be hydrolized. Due to its complexity, lignin is particularly difficult to decompose. Ganoderma is one of white rot fungi capable of lignin degradation. The ligninolytic of several species Ganoderma growing under different carbon sources was studied under controlled conditions which P. chrysosporium was used as standard comparison.Three types of ligninolytic, namely LiP, MnP, and laccase were assessed quantitatively and qualitatively. Ratio between clear zone and diameter of fungal colony was used for measuring specific activity qualitatively.Four sspecies of Ganoderma showed positive ligninolytic qualitatively that G. lucidum KT2-32 gave the highest ligninolytic. Activity of LiP and MnP in different carbon sources was consistently resulted by G. lucidum KT2-32, while the highest activity of laccase was shown by G. ochrolaccatum SA2-14. Medium of Indulin AT affected production of protein extracellular and induced ligninolytic. Glucose, BMC, and pine sawdust did not affect the activity of ligninolytic. The specific activity of Ganoderma species was found to be higher than the one of P. chrysosporium.

Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting α-glycosidase.

Science.gov (United States)

Miyazaki, Takatsugu; Nishikawa, Atsushi; Tonozuka, Takashi

2016-12-01

Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1.8- and 2.1-Å resolutions, respectively. Because glucose and lactose molecules are found at the active sites in both structures, it is possible that these structures mimic the enzyme-product complex of YgjK. A glucose molecule found at subsite -1 in both structures adopts an unusual 1 S 3 skew-boat conformation. Comparison between these structures and the previously determined enzyme-substrate complex structure reveals that the glucose pyranose ring might be distorted immediately after nucleophilic attack by a water molecule. These structures represent the first enzyme-product complex for the GH63 family, as well as the structurally-related glycosidases, and it may provide insight into the catalytic mechanism of these enzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

Science.gov (United States)

Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J.; Loader, Simon P.; Simon, Chris; Nagel, Peter

2016-01-01

Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

Energy Technology Data Exchange (ETDEWEB)

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

2014-10-02

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

Perched Lava Pond Complex on South Rift of Axial Volcano Revealed in AUV Mapping

Science.gov (United States)

Paduan, J. B.; Clague, D. A.; Caress, D. W.; Thomas, H. J.

2013-12-01

An extraordinary lava pond complex is located on Axial Volcano's distal south rift. It was discovered in EM300 multibeam bathymetry collected in 1998, and explored and sampled with ROVs Tiburon in 2005 and Doc Ricketts in 2013. It was surveyed with the MBARI Mapping AUV D. Allan B. in 2011, in a complicated mission first flying above the levees at constant depth, then skimming ~5 m over the levees at a different constant depth to survey the floors, then twice switching to constant altitude mode to map outside the ponds. The AUV navigation was adjusted using the MB-System tool mbnavadjust so that bathymetric features match in overlapping and crossing swaths. The ~1-m resolution AUV bathymetry reveals extremely rough terrain, where low-resolution EM300 data had averaged acoustic returns and obscured details of walls, floors, a breach and surrounding flows, and gives context to the ROV observations and samples. The 6 x 1.5 km pond complex has 4 large and several smaller drained ponds with rims 67 to 106 m above the floors. The combined volume before draining was 0.56 km3. The ponds overflowed to build lobate-flow levees with elongate pillows draping outer flanks, then drained, leaving lava veneer on vertical inner walls. Levee rim depths vary by only 10 m and are deeper around the southern ponds. Deep collapse-pits in the levees suggest porosity of pond walls. The eastern levee of the northeastern pond breached, draining the interconnected ponds, and fed thick, rapidly-emplaced, sheet-flows along the complex's east side. These flows travelled at least 5.5 km down-rift and have 19-33 m deep drained ponds. They extended up-rift as well, forming a 10 x 2.5 km ponded flow with level 'bathtub rings' as high as 35 m above the floor marking that flow's high-stand. Despite the breach, at least 0.066 km3 of the molten interior of the large ponds also drained back down the eruptive fissures, as the pond floors are deeper than the sill and sea floor outside the complex. Tumulus

Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

Energy Technology Data Exchange (ETDEWEB)

Rockel, Beate [Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany); Schmaler, Tilo; Huang, Xiaohua [Division of Molecular Biology, Department of General, Visceral, Vascular and Thoracic Surgery, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin (Germany); Dubiel, Wolfgang, E-mail: Wolfgang.dubiel@charite.de [Division of Molecular Biology, Department of General, Visceral, Vascular and Thoracic Surgery, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin (Germany)

2014-07-25

Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts

Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

International Nuclear Information System (INIS)

Rockel, Beate; Schmaler, Tilo; Huang, Xiaohua; Dubiel, Wolfgang

2014-01-01

Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts

X-ray structure of a transition state analog complex reveals the molecular origins of the catalytic power and substrate specificity of acetylcholinesterase

Energy Technology Data Exchange (ETDEWEB)

Harel, M.; Silman, I. [Weizmann Inst. of Science, Rehovot (Israel); Quinn, D.M.; Nair, H.K. [Univ. of Iowa, Iowa City, IA (United States); Sussman, J.L. [Weizmann Inst. of Science, Rehovot (Israel)]|[Brookhaven National Lab., Upton, NY (United States)

1996-03-13

The structure of a complex of Torpedo californica acetylcholinesterase with the transition state analog inhibitor m-(N, N,N-trimethylammonio)-2,2,2-trifluoroacetophenone has been solved by X-ray crystallographic methods to 2.8 A resolution. Since the inhibitor binds to the enzyme about 10{sup 10}-fold more tightly than the substrate acetylcholine, this complex provides a visual accounting of the enzyme-ligand interactions that provide the molecular basis for the catalytic power of acetylcholinesterase. The acetyl ester hydrolytic specificity of the enzyme is revealed by the interaction of the CF{sub 3} function of the transition state analog with a concave binding site comprised of the residues G119, W233, F288, F290, and F331. The highly geometrically convergent array of enzyme-ligand interactions visualized in the complex described herein envelopes the acylation transition state and sequesters it from solvent, this being consistent with the location of the active site at the bottom of a deep and narrow gorge. 82 refs., 5 figs.

Solid State production of manganese peroxidases using arecanut husk as substrate

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Akhila Rajan

2010-06-01

Full Text Available The lignocellulosic biomass from arecanut husk (Areca catechu Linnaeus was evaluated as a new substrate for cultivation of Phanerochaete chrysosporium and Phanerochaete sp for solid state fermentation of manganese peroxidase (MnP. Arecanut had a moisture content of 79.84 % for ripe nut husk whereas green nut husk had 68.39 % moisture and a pH of 5.0, 3.0 and 7.0 for raw, ripe and dry husk. Reducing sugar content was 14.31, 19.21 and 1.77(mg/g of husk for raw, ripe and dry nut husk, respectively. Non reducing sugar was 1.04(mg/g of husk for raw and 0.68 (mg/g of husk for dry husk. Solid state fermentation carried out at different pH showed optimum enzyme production at pH 6.0 (52.60 IU/g for P.chrysosporium and pH 5.0 (44.08 IU/g for Phanerochaete sp. Optimum temperature was 30 ± 2º C for both the organisms. Lower concentration of MnSO4 (0.1 mM MnSO4 induced maximum enzyme production in P.chrysosporium whereas Phanerochaete sp. required 1 mM MnSO4 for induction. Absence of carbon and nitrogen stimulated enzyme production in P.chrysosporium while Phanerochaete sp. needed nitrogen. Enzyme was partially purified by ammonium sulphate precipitation followed by ion exchange chromatography.

Biodegradation of the High Explosive Hexanitrohexaazaiso-wurtzitane (CL-20

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Steve Nicolich

2009-04-01

Full Text Available The aerobic biodegradability of the high explosive CL-20 by activated sludge and the white rot fungus Phanerochaete chrysosporium has been investigated. Although activated sludge is not effective in degrading CL-20 directly, it can mineralize the alkaline hydrolysis products. Phanerochaete chrysosporium degrades CL-20 in the presence of supplementary carbon and nitrogen sources. Biodegradation studies were conducted using various nutrient media under diverse conditions. Variables included the CL-20 concentration; levels of carbon (as glycerol and ammonium sulfate and yeast extract as sources of nitrogen. Cultures that received CL-20 at the time of inoculation transformed CL-20 completely under all nutrient conditions studied. When CL-20 was added to pre-grown cultures, degradation was limited. The extent of mineralization was monitored by the 14CO2 time evolution; up to 51% mineralization was achieved when the fungus was incubated with [14C]-CL-20. The kinetics of CL-20 biodegradation by Phanerochaete chrysosporium follows the logistic kinetic growth model.

Complexity science and leadership in healthcare.

Science.gov (United States)

Burns, J P

2001-10-01

The emerging field of complexity science offers an alternative leadership strategy for the chaotic, complex healthcare environment. A survey revealed that healthcare leaders intuitively support principles of complexity science. Leadership that uses complexity principles offers opportunities in the chaotic healthcare environment to focus less on prediction and control and more on fostering relationships and creating conditions in which complex adaptive systems can evolve to produce creative outcomes.

Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

International Nuclear Information System (INIS)

Gunn, Shelly; Gorre, Mercedes; Mohammed, Mansoor; Yeh, I-Tien; Lytvak, Irina; Tirtorahardjo, Budi; Dzidic, Natasha; Zadeh, Soheila; Kim, Jaeweon; McCaskill, Chris; Lim, Lony

2010-01-01

HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin), remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods. In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE) tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms. Array-based comparative genomic hybridization (array CGH) analysis of chromosome 17 resolved HER2 gene status in [20/20] (100%) of cases and revealed additional chromosome 17 copy number changes in [18/20] (90%) of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to 'ratio skewing' caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability. These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17 abnormalities in these cases suggests that the two

Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories.

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S Elfekih

Full Text Available Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1 have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO. Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.

A Single-Cell Biochemistry Approach Reveals PAR Complex Dynamics during Cell Polarization.

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Dickinson, Daniel J; Schwager, Francoise; Pintard, Lionel; Gotta, Monica; Goldstein, Bob

2017-08-21

Regulated protein-protein interactions are critical for cell signaling, differentiation, and development. For the study of dynamic regulation of protein interactions in vivo, there is a need for techniques that can yield time-resolved information and probe multiple protein binding partners simultaneously, using small amounts of starting material. Here we describe a single-cell protein interaction assay. Single-cell lysates are generated at defined time points and analyzed using single-molecule pull-down, yielding information about dynamic protein complex regulation in vivo. We established the utility of this approach by studying PAR polarity proteins, which mediate polarization of many animal cell types. We uncovered striking regulation of PAR complex composition and stoichiometry during Caenorhabditis elegans zygote polarization, which takes place in less than 20 min. PAR complex dynamics are linked to the cell cycle by Polo-like kinase 1 and govern the movement of PAR proteins to establish polarity. Our results demonstrate an approach to study dynamic biochemical events in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

Cooperativity of complex salt bridges

OpenAIRE

Gvritishvili, Anzor G.; Gribenko, Alexey V.; Makhatadze, George I.

2008-01-01

The energetic contribution of complex salt bridges, in which one charged residue (anchor residue) forms salt bridges with two or more residues simultaneously, has been suggested to have importance for protein stability. Detailed analysis of the net energetics of complex salt bridge formation using double- and triple-mutant cycle analysis revealed conflicting results. In two cases, it was shown that complex salt bridge formation is cooperative, i.e., the net strength of the complex salt bridge...

Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

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Eileen eLuders

2013-07-01

Full Text Available Scientific studies addressing anatomical variations in meditators’ brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM. To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls, where meditators have been practicing close to twenty years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentate, entorhinal cortex, subiculum as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri- hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators – perhaps due to an attenuated release of stress hormones and decreased neurotoxicity.

Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

Science.gov (United States)

Luders, Eileen; Kurth, Florian; Toga, Arthur W.; Narr, Katherine L.; Gaser, Christian

2013-01-01

Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators—perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation.

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Peter Rellos

2010-07-01

Full Text Available Long-term potentiation (LTP, a long-lasting enhancement in communication between neurons, is considered to be the major cellular mechanism underlying learning and memory. LTP triggers high-frequency calcium pulses that result in the activation of Calcium/Calmodulin (CaM-dependent kinase II (CaMKII. CaMKII acts as a molecular switch because it remains active for a long time after the return to basal calcium levels, which is a unique property required for CaMKII function. Here we describe the crystal structure of the human CaMKIIdelta/Ca2+/CaM complex, structures of all four human CaMKII catalytic domains in their autoinhibited states, as well as structures of human CaMKII oligomerization domains in their tetradecameric and physiological dodecameric states. All four autoinhibited human CaMKIIs were monomeric in the determined crystal structures but associated weakly in solution. In the CaMKIIdelta/Ca2+/CaM complex, the inhibitory region adopted an extended conformation and interacted with an adjacent catalytic domain positioning T287 into the active site of the interacting protomer. Comparisons with autoinhibited CaMKII structures showed that binding of calmodulin leads to the rearrangement of residues in the active site to a conformation suitable for ATP binding and to the closure of the binding groove for the autoinhibitory helix by helix alphaD. The structural data, together with biophysical interaction studies, reveals the mechanism of CaMKII activation by calmodulin and explains many of the unique regulatory properties of these two essential signaling molecules.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3-D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the Web plugin are available in Text S1.

Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

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Jie Qiu

Full Text Available Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou and a wild line (Lanxi 1 collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1 no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2 besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3 high heterozygous rates (0.19-0.49 were observed in several semi-wild lines; and (4 over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

Structures of human Golgi-resident glutaminyl cyclase and its complexes with inhibitors reveal a large loop movement upon inhibitor binding.

Science.gov (United States)

Huang, Kai-Fa; Liaw, Su-Sen; Huang, Wei-Lin; Chia, Cho-Yun; Lo, Yan-Chung; Chen, Yi-Ling; Wang, Andrew H-J

2011-04-08

Aberrant pyroglutamate formation at the N terminus of certain peptides and proteins, catalyzed by glutaminyl cyclases (QCs), is linked to some pathological conditions, such as Alzheimer disease. Recently, a glutaminyl cyclase (QC) inhibitor, PBD150, was shown to be able to reduce the deposition of pyroglutamate-modified amyloid-β peptides in brain of transgenic mouse models of Alzheimer disease, leading to a significant improvement of learning and memory in those transgenic animals. Here, we report the 1.05-1.40 Å resolution structures, solved by the sulfur single-wavelength anomalous dispersion phasing method, of the Golgi-luminal catalytic domain of the recently identified Golgi-resident QC (gQC) and its complex with PBD150. We also describe the high-resolution structures of secretory QC (sQC)-PBD150 complex and two other gQC-inhibitor complexes. gQC structure has a scaffold similar to that of sQC but with a relatively wider and negatively charged active site, suggesting a distinct substrate specificity from sQC. Upon binding to PBD150, a large loop movement in gQC allows the inhibitor to be tightly held in its active site primarily by hydrophobic interactions. Further comparisons of the inhibitor-bound structures revealed distinct interactions of the inhibitors with gQC and sQC, which are consistent with the results from our inhibitor assays reported here. Because gQC and sQC may play different biological roles in vivo, the different inhibitor binding modes allow the design of specific inhibitors toward gQC and sQC.

Two-center three-electron bonding in ClNH{sub 3} revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl + NH{sub 3} → ClNH{sub 2} + H reaction

Energy Technology Data Exchange (ETDEWEB)

Moradi, Christopher P.; Douberly, Gary E., E-mail: douberly@uga.edu [Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556 (United States); Xie, Changjian; Guo, Hua [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Kaufmann, Matin [Department of Physical Chemistry II, Ruhr-University Bochum, D-44801 Bochum (Germany)

2016-04-28

Pyrolytic dissociation of Cl{sub 2} is employed to dope helium droplets with single Cl atoms. Sequential addition of NH{sub 3} to Cl-doped droplets leads to the formation of a complex residing in the entry valley to the substitution reaction Cl + NH{sub 3} → ClNH{sub 2} + H. Infrared Stark spectroscopy in the NH stretching region reveals symmetric and antisymmetric vibrations of a C{sub 3v} symmetric top. Frequency shifts from NH{sub 3} and dipole moment measurements are consistent with a ClNH{sub 3} complex containing a relatively strong two-center three-electron (2c–3e) bond. The nature of the 2c–3e bonding in ClNH{sub 3} is explored computationally and found to be consistent with the complexation-induced blue shifts observed experimentally. Computations of interconversion pathways reveal nearly barrierless routes to the formation of this complex, consistent with the absence in experimental spectra of two other complexes, NH{sub 3}Cl and Cl–HNH{sub 2}, which are predicted in the entry valley to the hydrogen abstraction reaction Cl + NH{sub 3} → HCl + NH{sub 2}.

Utilization of fruit peels as carbon source for white rot fungi biomass production under submerged state bioconversion

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Olorunnisola Kola Saheed

2016-04-01

Full Text Available The present generation of nutrient rich waste streams within the food and hospitality industry is inevitable and remained a matter of concern to stakeholders. Three white rot fungal strains were cultivated under submerged state bioconversion (SmB. Fermentable sugar conversion efficiency, biomass production and substrate utilization constant were indicators used to measure the success of the process. The substrates – banana peel (Bp, pineapple peel (PAp and papaya peel (Pp were prepared in wet and dried forms as substrates. Phanerochaete chrysosporium (P. chrysosporium, Panus tigrinus M609RQY, and RO209RQY were cultivated on sole fruit wastes and their composites. All fungal strains produced profound biomass on dry sole wet substrates, but wet composite substrates gave improved results. P. tigrinus RO209RQY was the most efficient in sugar conversion (99.6% on sole substrates while P. tigrinus M609RQY was efficient on composite substrates. Elevated substrate utilization constant (Ku and biomass production heralded wet composite substrates. P. chrysosporium was the most performing fungal strain for biomass production, while PApBp was the best composite substrate.

Communication complexity and information complexity

Science.gov (United States)

Pankratov, Denis

Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information

Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

Science.gov (United States)

Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

2016-01-01

Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

A holistic approach to dissecting SPARC family protein complexity reveals FSTL-1 as an inhibitor of pancreatic cancer cell growth.

Science.gov (United States)

Viloria, Katrina; Munasinghe, Amanda; Asher, Sharan; Bogyere, Roberto; Jones, Lucy; Hill, Natasha J

2016-11-25

SPARC is a matricellular protein that is involved in both pancreatic cancer and diabetes. It belongs to a wider family of proteins that share structural and functional similarities. Relatively little is known about this extended family, but evidence of regulatory interactions suggests the importance of a holistic approach to their study. We show that Hevin, SPOCKs, and SMOCs are strongly expressed within islets, ducts, and blood vessels, suggesting important roles for these proteins in the normal pancreas, while FSTL-1 expression is localised to the stromal compartment reminiscent of SPARC. In direct contrast to SPARC, however, FSTL-1 expression is reduced in pancreatic cancer. Consistent with this, FSTL-1 inhibited pancreatic cancer cell proliferation. The complexity of SPARC family proteins is further revealed by the detection of multiple cell-type specific isoforms that arise due to a combination of post-translational modification and alternative splicing. Identification of splice variants lacking a signal peptide suggests the existence of novel intracellular isoforms. This study underlines the importance of addressing the complexity of the SPARC family and provides a new framework to explain their controversial and contradictory effects. We also demonstrate for the first time that FSTL-1 suppresses pancreatic cancer cell growth.

Complexes of alkylphenols with aluminium halides

International Nuclear Information System (INIS)

Golounin, A.V.

1997-01-01

Interaction of aluminium halides with alkylphenols is studied through the NMR method. The peculiarity of complex formation of pentamethylphenol with AlI 3 is revealed. By AlI 3 action on the pentamethylphenol the complexes are formed both of keto- and oxy form [ru

Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes

Czech Academy of Sciences Publication Activity Database

Dean, S.; Moreira-Leite, F.; Varga, Vladimír; Gull, K.

2016-01-01

Roč. 113, č. 35 (2016), E5135-E5143 ISSN 0027-8424 Institutional support: RVO:68378050 Keywords : transition zone * cilium/flagellum * BBSome * MKS/B9 complex * trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.661, year: 2016

Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

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Alexander H. Li

2017-10-01

Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

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Matthias Merker

Full Text Available Multidrug-resistant (MDR Mycobacterium tuberculosis complex (MTBC strains represent a major threat for tuberculosis (TB control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A and nine (Patient B polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and

MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding.

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Kaori Asamitsu

Full Text Available In this study, we applied molecular dynamics (MD simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs, lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.

Improving Nutritional Quality of Cocoa Pod ( through Chemical and Biological Treatments for Ruminant Feeding: and Evaluation

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Erika B. Laconi

2015-03-01

Full Text Available Cocoa pod is among the by-products of cocoa (Theobroma cacao plantations. The aim of this study was to apply a number of treatments in order to improve nutritional quality of cocoa pod for feeding of ruminants. Cocoa pod was subjected to different treatments, i.e. C (cocoa pod without any treatment or control, CAm (cocoa pod+1.5% urea, CMo (cocoa pod+3% molasses, CRu (cocoa pod+3% rumen content and CPh (cocoa pod+3% molasses+Phanerochaete chrysosporium inoculum. Analysis of proximate and Van Soest’s fiber fraction were performed on the respective treatments. The pods were then subjected to an in vitro digestibility evaluation by incubation in rumen fluid-buffer medium, employing a randomized complete block design (n = 3 replicates. Further, an in vivo evaluation of the pods (35% inclusion level in total mixed ration was conducted by feeding to young Holstein steers (average body weight of 145±3.6 kg with a 5×5 latin square design arrangement (n = 5 replicates. Each experimental period lasted for 30 d; the first 20 d was for feed adaptation, the next 3 d was for sampling of rumen liquid, and the last 7 d was for measurements of digestibility and N balance. Results revealed that lignin content was reduced significantly when cocoa pod was treated with urea, molasses, rumen content or P. chrysosporium (pCAm>CRu>CMo. Among all treatments, CAm and CPh treatments significantly improved the in vitro dry matter and organic matter digestibility (p<0.05 of cocoa pod. Average daily gain of steers receiving CAm or CPh treatment was significantly higher than that of control (p<0.01 with an increase of 105% and 92%, respectively. Such higher daily gain was concomitant with higher N retention and proportion of N retention to N intake in CAm and CPh treatments than those of control (p<0.05. It can be concluded from this study that treatment with either urea or P. chrysosporium is effective in improving the nutritive value of cocoa pod.

Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit.

Science.gov (United States)

Cevher, Murat A; Shi, Yi; Li, Dan; Chait, Brian T; Malik, Sohail; Roeder, Robert G

2014-12-01

The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to MS (CX-MS). Whereas the reconstituted head and middle modules can stably associate, basal and coactivator functions are acquired only after incorporation of MED14 into the bimodular complex. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematic dissection of the multiple layers of functionality associated with the Mediator complex.

γ-Irradiation and characterization of synthesized methoxybenzylpyrimidine formimidate Schiff-base and some metal-complex derivatives

Directory of Open Access Journals (Sweden)

R.O. Aly

2016-09-01

The magnetic properties together with the UV–Vis reposted data revealed the octahedral coordination of the Zn- and La-complex and the tetragonal distortion geometry of the Cu-complex. The La-complexes revealed only moderate inhibition against the Gram-negative Escherichia coli, whereas the Zn-complex revealed significant inhibition. The latter showed also similar effect against the Gram-positive Bacillus subtilis and Streptococcus pyogens (ATCC-19615.

Reconstitution of active human core Mediator complex reveals a pivotal role of the MED14 subunit

Science.gov (United States)

Cevher, Murat A.; Shi, Yi; Li, Dan; Chait, Brian T.; Malik, Sohail; Roeder, Robert G.

2014-01-01

The evolutionarily conserved Mediator complex is a critical coactivator for RNA polymerase II (Pol II)-mediated transcription. Here, we report the reconstitution of a functional 15-subunit human core Mediator complex and its characterization by functional assays and chemical cross-linking coupled to mass spectrometry (CX-MS). Whereas the reconstituted head and middle modules can stably associate, only with incorporation of MED14 into the bi-modular complex does it acquire basal and coactivator functions. This results from a dramatically enhanced ability of MED14-containing complexes to associate with Pol II. Altogether, our analyses identify MED14 as both an architectural and a functional backbone of the Mediator complex. We further establish a conditional requirement for metazoan-specific MED26 that becomes evident in the presence of heterologous nuclear factors. This general approach paves the way for systematically dissecting the multiple layers of functionalities associated with the Mediator complex. PMID:25383669

Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

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Sepil Irem

2012-05-01

Full Text Available Abstract Background The critical role of Major Histocompatibility Complex (Mhc genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. Results In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. Conclusions We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help

Cryo-EM Structure of a KCNQ1/CaM Complex Reveals Insights into Congenital Long QT Syndrome.

Science.gov (United States)

Sun, Ji; MacKinnon, Roderick

2017-06-01

KCNQ1 is the pore-forming subunit of cardiac slow-delayed rectifier potassium (I Ks ) channels. Mutations in the kcnq1 gene are the leading cause of congenital long QT syndrome (LQTS). Here, we present the cryoelectron microscopy (cryo-EM) structure of a KCNQ1/calmodulin (CaM) complex. The conformation corresponds to an "uncoupled," PIP 2 -free state of KCNQ1, with activated voltage sensors and a closed pore. Unique structural features within the S4-S5 linker permit uncoupling of the voltage sensor from the pore in the absence of PIP 2 . CaM contacts the KCNQ1 voltage sensor through a specific interface involving a residue on CaM that is mutated in a form of inherited LQTS. Using an electrophysiological assay, we find that this mutation on CaM shifts the KCNQ1 voltage-activation curve. This study describes one physiological form of KCNQ1, depolarized voltage sensors with a closed pore in the absence of PIP 2 , and reveals a regulatory interaction between CaM and KCNQ1 that may explain CaM-mediated LQTS. Copyright © 2017 Elsevier Inc. All rights reserved.

High-Resolution Imaging Reveals New Features of Nuclear Export of mRNA through the Nuclear Pore Complexes

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Joseph M. Kelich

2014-08-01

Full Text Available The nuclear envelope (NE of eukaryotic cells provides a physical barrier for messenger RNA (mRNA and the associated proteins (mRNPs traveling from sites of transcription in the nucleus to locations of translation processing in the cytoplasm. Nuclear pore complexes (NPCs embedded in the NE serve as a dominant gateway for nuclear export of mRNA. However, the fundamental characterization of export dynamics of mRNPs through the NPC has been hindered by several technical limits. First, the size of NPC that is barely below the diffraction limit of conventional light microscopy requires a super-resolution microscopy imaging approach. Next, the fast transit of mRNPs through the NPC further demands a high temporal resolution by the imaging approach. Finally, the inherent three-dimensional (3D movements of mRNPs through the NPC demand the method to provide a 3D mapping of both transport kinetics and transport pathways of mRNPs. This review will highlight the recently developed super-resolution imaging techniques advanced from 1D to 3D for nuclear export of mRNPs and summarize the new features in the dynamic nuclear export process of mRNPs revealed from these technical advances.

Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

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Jaiswal Dinesh Kumar

2012-10-01

Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

Synchronizability on complex networks via pinning control

Indian Academy of Sciences (India)

Keywords. Complex network; the pinning synchronization; synchronizability. ... The findings reveal the relationship between the decreasing speed of maximum eigenvalue sequence of the principal submatrices for coupling matrix and the synchronizability on complex networks via pinning control. We discuss the ...

Critical Fluctuations in Spatial Complex Networks

Science.gov (United States)

Bradde, Serena; Caccioli, Fabio; Dall'Asta, Luca; Bianconi, Ginestra

2010-05-01

An anomalous mean-field solution is known to capture the nontrivial phase diagram of the Ising model in annealed complex networks. Nevertheless, the critical fluctuations in random complex networks remain mean field. Here we show that a breakdown of this scenario can be obtained when complex networks are embedded in geometrical spaces. Through the analysis of the Ising model on annealed spatial networks, we reveal, in particular, the spectral properties of networks responsible for critical fluctuations and we generalize the Ginsburg criterion to complex topologies.

Small-angle X-ray Solution Scattering Study of the Multi-aminoacyl-tRNA Synthetase Complex Reveals an Elongated and Multi-armed particle*

Science.gov (United States)

Dias, José; Renault, Louis; Pérez, Javier; Mirande, Marc

2013-01-01

In animal cells, nine aminoacyl-tRNA synthetases are associated with the three auxiliary proteins p18, p38, and p43 to form a stable and conserved large multi-aminoacyl-tRNA synthetase complex (MARS), whose molecular mass has been proposed to be between 1.0 and 1.5 MDa. The complex acts as a molecular hub for coordinating protein synthesis and diverse regulatory signal pathways. Electron microscopy studies defined its low resolution molecular envelope as an overall rather compact, asymmetric triangular shape. Here, we have analyzed the composition and homogeneity of the native mammalian MARS isolated from rabbit liver and characterized its overall internal structure, size, and shape at low resolution by hydrodynamic methods and small-angle x-ray scattering in solution. Our data reveal that the MARS exhibits a much more elongated and multi-armed shape than expected from previous reports. The hydrodynamic and structural features of the MARS are large compared with other supramolecular assemblies involved in translation, including ribosome. The large dimensions and non-compact structural organization of MARS favor a large protein surface accessibility for all its components. This may be essential to allow structural rearrangements between the catalytic and cis-acting tRNA binding domains of the synthetases required for binding the bulky tRNA substrates. This non-compact architecture may also contribute to the spatiotemporal controlled release of some of its components, which participate in non-canonical functions after dissociation from the complex. PMID:23836901

Structure of the Human FANCL RING-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection

Science.gov (United States)

Hodson, Charlotte; Purkiss, Andrew; Miles, Jennifer Anne; Walden, Helen

2014-01-01

Summary The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established. Nevertheless, the determinants of selective, specific E3-E2 recognition are not understood. There are ∼40 E2s and ∼600 E3s giving rise to a possible ∼24,000 E3-E2 pairs. Using the Fanconi Anemia pathway exclusive E3-E2 pair, FANCL-Ube2T, we report the atomic structure of the FANCL RING-Ube2T complex, revealing a specific and extensive network of additional electrostatic and hydrophobic interactions. Furthermore, we show that these specific interactions are required for selection of Ube2T over other E2s by FANCL. PMID:24389026

Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket And Transcription Activation Through Tyrosine Expulsion

Energy Technology Data Exchange (ETDEWEB)

Newberry, K.J.; Huffman, J.L.; Miller, M.C.; Vazquez-Laslop, N.; Neyfakh, A.A.; Brennan, R.G.

2009-05-22

BmrR is a member of the MerR family and a multidrug binding transcription factor that up-regulates the expression of the bmr multidrug efflux transporter gene in response to myriad lipophilic cationic compounds. The structural mechanism by which BmrR binds these chemically and structurally different drugs and subsequently activates transcription is poorly understood. Here, we describe the crystal structures of BmrR bound to rhodamine 6G (R6G) or berberine (Ber) and cognate DNA. These structures reveal each drug stacks against multiple aromatic residues with their positive charges most proximal to the carboxylate group of Glu-253 and that, unlike other multidrug binding pockets, that of BmrR is rigid. Substitution of Glu-253 with either alanine (E253A) or glutamine (E253Q) results in unpredictable binding affinities for R6G, Ber, and tetraphenylphosphonium. Moreover, these drug binding studies reveal that the negative charge of Glu-253 is not important for high affinity binding to Ber and tetraphenylphosphonium but plays a more significant, but unpredictable, role in R6G binding. In vitro transcription data show that E253A and E253Q are constitutively active, and structures of the drug-free E253A-DNA and E253Q-DNA complexes support a transcription activation mechanism requiring the expulsion of Tyr-152 from the multidrug binding pocket. In sum, these data delineate the mechanism by which BmrR binds lipophilic, monovalent cationic compounds and suggest the importance of the redundant negative electrostatic nature of this rigid drug binding pocket that can be used to discriminate against molecules that are not substrates of the Bmr multidrug efflux pump.

Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry

DEFF Research Database (Denmark)

Chen, Zhuo Angel; Jawhari, Anass; Fischer, Lutz

2010-01-01

Higher-order multi-protein complexes such as RNA polymerase II (Pol II) complexes with transcription initiation factors are often not amenable to X-ray structure determination. Here, we show that protein cross-linking coupled to mass spectrometry (MS) has now sufficiently advanced as a tool to ex...

A structurally characterized organometallic plutonium(IV) complex

Energy Technology Data Exchange (ETDEWEB)

Apostolidis, Christos; Walter, Olaf [European Commission, Joint Research Centre, Directorate G - Nuclear Safety and Security, Karlsruhe (Germany); Vogt, Jochen; Liebing, Phil; Edelmann, Frank T. [Chemisches Institut, Otto-von-Guericke-Universitaet Magdeburg (Germany); Maron, Laurent [Laboratoire de Physique et Chimie des Nanoobjets (LPCNO), Universite de Toulouse/INSA/CNRS (UMR5215), Toulouse (France)

2017-04-24

The blood-red plutonocene complex Pu(1,3-COT'')(1,4-COT'') (4; COT''=η{sup 8}-bis(trimethylsilyl)cyclooctatetraenyl) has been synthesized by oxidation of the anionic sandwich complex Li[Pu(1,4-COT''){sub 2}] (3) with anhydrous cobalt(II) chloride. The first crystal structure determination of an organoplutonium(IV) complex revealed an asymmetric sandwich structure for 4 where one COT'' ring is 1,3-substituted while the other retains the original 1,4-substitution pattern. The electronic structure of 4 has been elucidated by a computational study, revealing a probable cause for the unexpected silyl group migration. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

Science.gov (United States)

Bestembayeva, Aizhan; Kramer, Armin; Labokha, Aksana A.; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V.; Ford, Ian J.; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W.

2015-01-01

The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.

Gene Coexpression Analysis Reveals Complex Metabolism of the Monoterpene Alcohol Linalool in Arabidopsis Flowers[W][OPEN

Science.gov (United States)

Ginglinger, Jean-François; Boachon, Benoit; Höfer, René; Paetz, Christian; Köllner, Tobias G.; Miesch, Laurence; Lugan, Raphael; Baltenweck, Raymonde; Mutterer, Jérôme; Ullmann, Pascaline; Beran, Franziska; Claudel, Patricia; Verstappen, Francel; Fischer, Marc J.C.; Karst, Francis; Bouwmeester, Harro; Miesch, Michel; Schneider, Bernd; Gershenzon, Jonathan; Ehlting, Jürgen; Werck-Reichhart, Danièle

2013-01-01

The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. Gene coexpression analysis pointed to two P450s that were coexpressed with two monoterpene synthases in flowers and were thus predicted to be involved in monoterpenoid metabolism. We show that all four selected genes, the two terpene synthases (TPS10 and TPS14) and the two cytochrome P450s (CYP71B31 and CYP76C3), are simultaneously expressed at anthesis, mainly in upper anther filaments and in petals. Upon transient expression in Nicotiana benthamiana, the TPS enzymes colocalize in vesicular structures associated with the plastid surface, whereas the P450 proteins were detected in the endoplasmic reticulum. Whether they were expressed in Saccharomyces cerevisiae or in N. benthamiana, the TPS enzymes formed two different enantiomers of linalool: (−)-(R)-linalool for TPS10 and (+)-(S)-linalool for TPS14. Both P450 enzymes metabolize the two linalool enantiomers to form different but overlapping sets of hydroxylated or epoxidized products. These oxygenated products are not emitted into the floral headspace, but accumulate in floral tissues as further converted or conjugated metabolites. This work reveals complex linalool metabolism in Arabidopsis flowers, the ecological role of which remains to be determined. PMID:24285789

How Can We Explain Poverty? Case Study of Dee Reveals the Complexities

Science.gov (United States)

Seccombe, Karen

2011-01-01

Many theories have been offered to explain why people are impoverished. This article by Karen Seccombe uses the case study of "Dee," a newly single mother, to explore four of the most common: individualism, social structuralism, the culture of poverty, and fatalism. She concludes that poverty is a highly complex phenomenon, and it is likely that…

In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes.

Science.gov (United States)

Husbands, Aman Y; Aggarwal, Vasudha; Ha, Taekjip; Timmermans, Marja C P

2016-08-01

Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies. © 2016 American Society of Plant Biologists. All rights reserved.

3D complex: a structural classification of protein complexes.

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Emmanuel D Levy

2006-11-01

Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

SCAR/WAVE: A complex issue.

Science.gov (United States)

Davidson, Andrew J; Insall, Robert H

2013-11-01

The SCAR/WAVE complex drives the actin polymerisation that underlies protrusion of the front of the cell and thus drives migration. However, it is not understood how the activity of SCAR/WAVE is regulated to generate the infinite range of cellular shape changes observed during cell motility. What are the relative roles of the subunits of the SCAR/WAVE complex? What signaling molecules do they interact with? And how does the complex integrate all this information in order to control the temporal and spatial polymerisation of actin during protrusion formation? Unfortunately, the interdependence of SCAR complex members has made genetic dissection hard. In our recent paper,(1) we describe stabilization of the Dictyostelium SCAR complex by a small fragment of Abi. Here we summarize the main findings and discuss how this approach can help reveal the inner workings of this impenetrable complex.

Spectral simplicity of apparent complexity. II. Exact complexities and complexity spectra

Science.gov (United States)

Riechers, Paul M.; Crutchfield, James P.

2018-03-01

The meromorphic functional calculus developed in Part I overcomes the nondiagonalizability of linear operators that arises often in the temporal evolution of complex systems and is generic to the metadynamics of predicting their behavior. Using the resulting spectral decomposition, we derive closed-form expressions for correlation functions, finite-length Shannon entropy-rate approximates, asymptotic entropy rate, excess entropy, transient information, transient and asymptotic state uncertainties, and synchronization information of stochastic processes generated by finite-state hidden Markov models. This introduces analytical tractability to investigating information processing in discrete-event stochastic processes, symbolic dynamics, and chaotic dynamical systems. Comparisons reveal mathematical similarities between complexity measures originally thought to capture distinct informational and computational properties. We also introduce a new kind of spectral analysis via coronal spectrograms and the frequency-dependent spectra of past-future mutual information. We analyze a number of examples to illustrate the methods, emphasizing processes with multivariate dependencies beyond pairwise correlation. This includes spectral decomposition calculations for one representative example in full detail.

Managing uncertainty for sustainability of complex projects

DEFF Research Database (Denmark)

Brink, Tove

2017-01-01

Purpose – The purpose of this paper is to reveal how management of uncertainty can enable sustainability of complex projects. Design/methodology/approach – The research was conducted from June 2014 to May 2015 using a qualitative deductive approach among operation and maintenance actors in offshore...... wind farms. The research contains a focus group interview with 11 companies, 20 individual interviews and a seminar presenting preliminary findings with 60 participants. Findings – The findings reveal the need for management of uncertainty through two different paths. First, project management needs...... to join efforts. Research limitations/implications – Further research is needed to reveal the generalisability of the findings in other complex project contexts containing “unknown unknowns”. Practical implications – The research leads to the development of a tool for uncertainty management...

CW EPR parameters reveal cytochrome P450 ligand binding modes.

Science.gov (United States)

Lockart, Molly M; Rodriguez, Carlo A; Atkins, William M; Bowman, Michael K

2018-06-01

Cytochrome P450 (CYP) monoxygenses utilize heme cofactors to catalyze oxidation reactions. They play a critical role in metabolism of many classes of drugs, are an attractive target for drug development, and mediate several prominent drug interactions. Many substrates and inhibitors alter the spin state of the ferric heme by displacing the heme's axial water ligand in the resting enzyme to yield a five-coordinate iron complex, or they replace the axial water to yield a nitrogen-ligated six-coordinate iron complex, which are traditionally assigned by UV-vis spectroscopy. However, crystal structures and recent pulsed electron paramagnetic resonance (EPR) studies find a few cases where molecules hydrogen bond to the axial water. The water-bridged drug-H 2 O-heme has UV-vis spectra similar to nitrogen-ligated, six-coordinate complexes, but are closer to "reverse type I" complexes described in older liteature. Here, pulsed and continuous wave (CW) EPR demonstrate that water-bridged complexes are remarkably common among a range of nitrogenous drugs or drug fragments that bind to CYP3A4 or CYP2C9. Principal component analysis reveals a distinct clustering of CW EPR spectral parameters for water-bridged complexes. CW EPR reveals heterogeneous mixtures of ligated states, including multiple directly-coordinated complexes and water-bridged complexes. These results suggest that water-bridged complexes are under-represented in CYP structural databases and can have energies similar to other ligation modes. The data indicates that water-bridged binding modes can be identified and distinguished from directly-coordinated binding by CW EPR. Copyright © 2018 Elsevier Inc. All rights reserved.

Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

Science.gov (United States)

Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

2016-11-01

Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

Phylogenetic diversity and genotypical complexity of H9N2 influenza A viruses revealed by genomic sequence analysis.

Directory of Open Access Journals (Sweden)

Guoying Dong

Full Text Available H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A-G. Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses.

Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

DEFF Research Database (Denmark)

Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

2015-01-01

species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...... enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some...

Molecular Epidemiology Reveals Genetic Diversity amongst Isolates of the Cryptococcus neoformans/C. gattii Species Complex in Thailand

Science.gov (United States)

Kaocharoen, Sirada; Ngamskulrungroj, Popchai; Firacative, Carolina; Trilles, Luciana; Piyabongkarn, Dumrongdej; Banlunara, Wijit; Poonwan, Natteewan; Chaiprasert, Angkana; Meyer, Wieland; Chindamporn, Ariya

2013-01-01

To gain a more detailed picture of cryptococcosis in Thailand, a retrospective study of 498 C. neoformans and C. gattii isolates has been conducted. Among these, 386, 83 and 29 strains were from clinical, environmental and veterinary sources, respectively. A total of 485 C. neoformans and 13 C. gattii strains were studied. The majority of the strains (68.9%) were isolated from males (mean age of 37.97 years), 88.5% of C. neoformans and only 37.5% of C. gattii strains were from HIV patients. URA5-RFLP and/or M13 PCR-fingerprinting analysis revealed that the majority of the isolates were C. neoformans molecular type VNI regardless of their sources (94.8%; 94.6% of the clinical, 98.8% of the environmental and 86.2% of the veterinary isolates). In addition, the molecular types VNII (2.4%; 66.7% of the clinical and 33.3% of the veterinary isolates), VNIV (0.2%; 100% environmental isolate), VGI (0.2%; 100% clinical isolate) and VGII (2.4%; 100% clinical isolates) were found less frequently. Multilocus Sequence Type (MLST) analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex identified a total of 20 sequence types (ST) in Thailand combining current and previous data. The Thai isolates are an integrated part of the global cryptococcal population genetic structure, with ST30 for C. gattii and ST82, ST83, ST137, ST141, ST172 and ST173 for C. neoformans being unique to Thailand. Most of the C. gattii isolates were ST7 = VGIIb, which is identical to the less virulent minor Vancouver island outbreak genotype, indicating Thailand as a stepping stone in the global spread of this outbreak strain. The current study revealed a greater genetic diversity and a wider range of major molecular types being present amongst Thai cryptococcal isolates than previously reported. PMID:23861989

Musical rhythm and pitch: A differential effect on auditory dynamics as revealed by the N1/MMN/P3a complex.

Science.gov (United States)

Lelo-de-Larrea-Mancera, E Sebastian; Rodríguez-Agudelo, Yaneth; Solís-Vivanco, Rodolfo

2017-06-01

Music represents a complex form of human cognition. To what extent our auditory system is attuned to music is yet to be clearly understood. Our principal aim was to determine whether the neurophysiological operations underlying pre-attentive auditory change detection (N1 enhancement (N1e)/Mismatch Negativity (MMN)) and the subsequent involuntary attentional reallocation (P3a) towards infrequent sound omissions, are influenced by differences in musical content. Specifically, we intended to explore any interaction effects that rhythmic and pitch dimensions of musical organization may have over these processes. Results showed that both the N1e and MMN amplitudes were differentially influenced by rhythm and pitch dimensions. MMN latencies were shorter for musical structures containing both features. This suggests some neurocognitive independence between pitch and rhythm domains, but also calls for further address on possible interactions between both of them at the level of early, automatic auditory detection. Furthermore, results demonstrate that the N1e reflects basic sensory memory processes. Lastly, we show that the involuntary switch of attention associated with the P3a reflects a general-purpose mechanism not modulated by musical features. Altogether, the N1e/MMN/P3a complex elicited by infrequent sound omissions revealed evidence of musical influence over early stages of auditory perception. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

Science.gov (United States)

Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

2016-07-14

The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Science.gov (United States)

Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki

2013-01-01

To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

Biomass pyrolysis liquid to citric acid via 2-step bioconversion.

Science.gov (United States)

Yang, Zhiguang; Bai, Zhihui; Sun, Hongyan; Yu, Zhisheng; Li, Xingxing; Guo, Yifei; Zhang, Hongxun

2014-12-31

The use of fossil carbon sources for fuels and petrochemicals has serious impacts on our environment and is unable to meet the demand in the future. A promising and sustainable alternative is to substitute fossil carbon sources with microbial cell factories converting lignocellulosic biomass into desirable value added products. However, such bioprocesses require tolerance to inhibitory compounds generated during pretreatment of biomass. In this study, the process of sequential two-step bio-conversion of biomass pyrolysis liquid containing levoglucosan (LG) to citric acid without chemical detoxification has been explored, which can greatly improve the utilization efficiency of lignocellulosic biomass. The sequential two-step bio-conversion of corn stover pyrolysis liquid to citric acid has been established. The first step conversion by Phanerochaete chrysosporium (P. chrysosporium) is desirable to decrease the content of other compounds except levoglucosan as a pretreatment for the second conversion. The remaining levoglucosan in solution was further converted into citric acid by Aspergillus niger (A. niger) CBX-209. Thus the conversion of cellulose to citric acid is completed by both pyrolysis and bio-conversion technology. Under experimental conditions, levoglucosan yield is 12% based on the feedstock and the citric acid yield can reach 82.1% based on the levoglucosan content in the pyrolysis liquid (namely 82.1 g of citric acid per 100 g of levoglucosan). The study shows that P. chrysosporium and A. niger have the potential to be used as production platforms for value-added products from pyrolyzed lignocellulosic biomass. Selected P. chrysosporium is able to decrease the content of other compounds except levoglucosan and levoglucosan can be further converted into citric acid in the residual liquids by A. niger. Thus the conversion of cellulose to citric acid is completed by both pyrolysis and bio-conversion technology.

Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes.

Science.gov (United States)

Ball, Robyn L; Fujiwara, Yasuhiro; Sun, Fengyun; Hu, Jianjun; Hibbs, Matthew A; Handel, Mary Ann; Carter, Gregory W

2016-08-12

The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes.

Molecular systematics reveals increased diversity within the South African Laurencia complex (Rhodomelaceae, Rhodophyta).

Science.gov (United States)

Francis, Caitlynne; Bolton, John J; Mattio, Lydiane; Mandiwana-Neudani, Tshifhiwa G; Anderson, Robert J

2017-08-01

Previous publications list ten species in the Laurencia complex from South Africa with all ascribed to the genus Laurencia sensu stricto. However, the diversity of the complex in South Africa has not yet been re-assessed following the numerous recent taxonomic changes. This study investigated the phylogenetic relationships and taxonomy of this group in South Africa using recent collections. Methods included molecular phylogenetic analyses of plastid rbcL gene sequences (a total of 146; including eleven outgroup taxa) using Maximum Likelihood and Bayesian Inference, and the examination of morphological and anatomical characters, including the number of corps en cerise when present. The seven genera of the Laurencia complex formed monophyletic clades with high posterior probabilities. Seventeen morphotypes were identified: 14 in the genus Laurencia sensu stricto, among which eight corresponded to Laurencia species currently recognized from South Africa and one each to species of Palisada, Chondrophycus, and Laurenciella. The six remaining morphotypes in Laurencia sensu stricto did not match any descriptions and are described here as five new species: Laurencia alfredensis sp. nov., Laurencia dichotoma sp. nov., Laurencia digitata sp. nov., Laurencia multiclavata sp. nov. and Laurencia sodwaniensis sp. nov. and a new variety: Laurencia pumila var. dehoopiensis var. nov. Laurencia stegengae nom. nov. is established to replace Laurencia peninsularis Stegenga, Bolton and Anderson nom. illeg. The diversity is likely greater, with six additional unidentified specimens found in this molecular investigation. These findings place South Africa alongside Australia in having one of the most diverse floras of this group in the world. © 2017 Phycological Society of America.

Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

DEFF Research Database (Denmark)

Börnigen, Daniela; Pers, Tune Hannes; Thorrez, Lieven

2013-01-01

Disease-causing variants in human genes usually lead to phenotypes specific to only a few tissues. Here, we present a method for predicting tissue specificity based on quantitative deregulation of protein complexes. The underlying assumption is that the degree of coordinated expression among prot...

Simple, complex and hyper-complex understanding - enhanced sensitivity in observation of information

DEFF Research Database (Denmark)

Bering Keiding, Tina

for construction and analysis of empirical information. A quick overview on empirical research drawing on Luhmann reveals a diverse complex of analytical strategies and empirical methods. Despite differences between strategies and methods they have in common that understanding of uttered information is crucial...... in their production of empirically founded knowledge. However research generally seems to pay more attention to production of uttered information than to selection of understanding. The aim of this contribution is to sketch out a suggestion to how selection of understanding can be systematized in order to produce...... enhanced transparency in selection of understanding as well as enhanced sensitivity and definition in dept. The contribution suggest that we distinguish between three types of understanding; simple, complex and hyper-complex understanding. Simple understanding is the simultaneous selection of understanding...

Comparative Examination of the Olive Mill Wastewater Biodegradation Process by Various Wood-Rot Macrofungi

Science.gov (United States)

Koutrotsios, Georgios; Zervakis, Georgios I.

2014-01-01

Olive mill wastewater (OMW) constitutes a major cause of environmental pollution in olive-oil producing regions. Sixty wood-rot macrofungi assigned in 43 species were evaluated for their efficacy to colonize solidified OMW media at initially established optimal growth temperatures. Subsequently eight strains of the following species were qualified: Abortiporus biennis, Ganoderma carnosum, Hapalopilus croceus, Hericium erinaceus, Irpex lacteus, Phanerochaete chrysosporium, Pleurotus djamor, and P. pulmonarius. Fungal growth in OMW (25%v/v in water) resulted in marked reduction of total phenolic content, which was significantly correlated with the effluent's decolorization. A. biennis was the best performing strain (it decreased phenolics by 92% and color by 64%) followed by P. djamor and I. lacteus. Increase of plant seeds germination was less pronounced evidencing that phenolics are only partly responsible for OMW's phytotoxicity. Laccase production was highly correlated with all three biodegradation parameters for H. croceus, Ph. chrysosporium, and Pleurotus spp., and so were manganese-independent and manganese dependent peroxidases for A. biennis and I. lacteus. Monitoring of enzymes with respect to biomass production indicated that Pleurotus spp., H. croceus, and Ph. chrysosporium shared common patterns for all three activities. Moreover, generation of enzymes at the early biodegradation stages enhanced the efficiency of OMW treatment. PMID:24987685

Enhancement of Cotton Stalks Composting with Certain Microbial Inoculations

Directory of Open Access Journals (Sweden)

Osama Abdel-Twab Seoudi

2013-01-01

Full Text Available Effect of inoculation with Phanerochaete chrysosporium and Azotobacter chrococcum microbes on cotton stalks composting was studied in an attempt to achieve rapid maturity and desirable characteristics of produced compost. Composting process was maintained for 16 weeks under aerobic conditions with proper moisture content and turning piles. The C/N ratio of the mixtures was adjusted to about 30:1 before composting using chicken manure. Temperature evolution and its profile were monitored throughout the composting period. Mineralization rates of organic matter and changes in nitrogen content during composting stages were evaluated. Total plate count of mesophilic and thermophilic bacteria, cellulose decomposers and Azotobacter were determined during composting periods. The treatment of cotton stalks inoculated with both P. chrysosporium and Azotobacter gave the most desirable characteristics of the final product with respect to the narrow C/N ratio, high nitrogen content and high numbers of Azotobacter. The phytotoxicity test of compost extracts was evaluated. The use of P. chrysosporium in composting accelerated markedly decomposition process, so that 16 weeks composting enough to produce a stable and mature compost suitable for use as fertilizer while the fertilizer obtained by composting cotton stalks mixed with chicken manure and inoculated with microorganisms is highest quality Compost.

Comparative Examination of the Olive Mill Wastewater Biodegradation Process by Various Wood-Rot Macrofungi

Directory of Open Access Journals (Sweden)

Georgios Koutrotsios

2014-01-01

Full Text Available Olive mill wastewater (OMW constitutes a major cause of environmental pollution in olive-oil producing regions. Sixty wood-rot macrofungi assigned in 43 species were evaluated for their efficacy to colonize solidified OMW media at initially established optimal growth temperatures. Subsequently eight strains of the following species were qualified: Abortiporus biennis, Ganoderma carnosum, Hapalopilus croceus, Hericium erinaceus, Irpex lacteus, Phanerochaete chrysosporium, Pleurotus djamor, and P. pulmonarius. Fungal growth in OMW (25%v/v in water resulted in marked reduction of total phenolic content, which was significantly correlated with the effluent’s decolorization. A. biennis was the best performing strain (it decreased phenolics by 92% and color by 64% followed by P. djamor and I. lacteus. Increase of plant seeds germination was less pronounced evidencing that phenolics are only partly responsible for OMW’s phytotoxicity. Laccase production was highly correlated with all three biodegradation parameters for H. croceus, Ph. chrysosporium, and Pleurotus spp., and so were manganese-independent and manganese dependent peroxidases for A. biennis and I. lacteus. Monitoring of enzymes with respect to biomass production indicated that Pleurotus spp., H. croceus, and Ph. chrysosporium shared common patterns for all three activities. Moreover, generation of enzymes at the early biodegradation stages enhanced the efficiency of OMW treatment.

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.

Science.gov (United States)

Lemmens, Karen; De Bie, Tijl; Dhollander, Thomas; De Keersmaecker, Sigrid C; Thijs, Inge M; Schoofs, Geert; De Weerdt, Ami; De Moor, Bart; Vanderleyden, Jos; Collado-Vides, Julio; Engelen, Kristof; Marchal, Kathleen

2009-01-01

We present DISTILLER, a data integration framework for the inference of transcriptional module networks. Experimental validation of predicted targets for the well-studied fumarate nitrate reductase regulator showed the effectiveness of our approach in Escherichia coli. In addition, the condition dependency and modularity of the inferred transcriptional network was studied. Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.

Intraparticulate Metal Speciation Analysis of Soft Complexing Nanoparticles. The Intrinsic Chemical Heterogeneity of Metal-Humic Acid Complexes

DEFF Research Database (Denmark)

Town, R. M.; van Leeuwen, Herman P.

2016-01-01

ion condensation potential for higher valency counterions within the intraparticulate double layer zone of the soft NP. The approach offers new insights into the intrinsic heterogeneity of the HA. complexes, as revealed by the intraparticulate speciation as a function of the true degree of inner......-sphere complexation, theta(M). The ensuing intrinsic heterogeneity parameters, Gamma, for CdHA and CuHA complexes are in very good agreement with those obtained from dynamic electrochemical stripping chronopotentiometric measurements. The overall intraparticulate metal ion speciation is found to depend on theta...

eQTL Networks Reveal Complex Genetic Architecture in the Immature Soybean Seed

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Yung-Tsi Bolon

2014-03-01

Full Text Available The complex network of regulatory factors and interactions involved in transcriptional regulation within the seed is not well understood. To evaluate gene expression regulation in the immature seed, we utilized a genetical genomics approach on a soybean [ (L. Merr.] recombinant inbred line (RIL population and produced a genome-wide expression quantitative trait loci (eQTL dataset. The validity of the dataset was confirmed by mapping the eQTL hotspot for flavonoid biosynthesis-related genes to a region containing repeats of chalcone synthase (CHS genes known to correspond to the soybean inhibitor locus that regulates seed color. We then identified eQTL for genes with seed-specific expression and discovered striking eQTL hotspots at distinct genomic intervals on chromosomes (Chr 20, 7, and 13. The main eQTL hotspot for transcriptional regulation of fatty acid biosynthesis genes also coincided with regulation of oleosin genes. Transcriptional upregulation of genesets from eQTL with opposite allelic effects were also found. Gene–eQTL networks were constructed and candidate regulatory genes were identified from these three key loci specific to seed expression and enriched in genes involved in seed oil accumulation. Our data provides new insight into the complex nature of gene networks in the immature soybean seed and the genetic architecture that contributes to seed development.

Differential proteomic analysis of the secretome of Irpex lacteus and other white-rot fungi during wheat straw pretreatment.

Science.gov (United States)

Salvachúa, Davinia; Martínez, Angel T; Tien, Ming; López-Lucendo, María F; García, Francisco; de Los Ríos, Vivian; Martínez, María Jesús; Prieto, Alicia

2013-08-10

Identifying new high-performance enzymes or enzyme complexes to enhance biomass degradation is the key for the development of cost-effective processes for ethanol production. Irpex lacteus is an efficient microorganism for wheat straw pretreatment, yielding easily hydrolysable products with high sugar content. Thus, this fungus was selected to investigate the enzymatic system involved in lignocellulose decay, and its secretome was compared to those from Phanerochaete chrysosporium and Pleurotus ostreatus which produced different degradation patterns when growing on wheat straw. Extracellular enzymes were analyzed through 2D-PAGE, nanoLC/MS-MS, and homology searches against public databases. In wheat straw, I. lacteus secreted proteases, dye-decolorizing and manganese-oxidizing peroxidases, and H2O2 producing-enzymes but also a battery of cellulases and xylanases, excluding those implicated in cellulose and hemicellulose degradation to their monosaccharides, making these sugars poorly available for fungal consumption. In contrast, a significant increase of β-glucosidase production was observed when I. lacteus grew in liquid cultures. P. chrysosporium secreted more enzymes implicated in the total hydrolysis of the polysaccharides and P. ostreatus produced, in proportion, more oxidoreductases. The protein pattern secreted during I. lacteus growth in wheat straw plus the differences observed among the different secretomes, justify the fitness of I. lacteus for biopretreatment processes in 2G-ethanol production. Furthermore, all these data give insight into the biological degradation of lignocellulose and suggest new enzyme mixtures interesting for its efficient hydrolysis.

Complex deformation in western Tibet revealed by anisotropic tomography

Science.gov (United States)

Zhang, Heng; Zhao, Junmeng; Zhao, Dapeng; Yu, Chunquan; Liu, Hongbing; Hu, Zhaoguo

2016-10-01

The mechanism and pattern of deformation beneath western Tibet are still an issue of debate. In this work we present 3-D P- and S-wave velocity tomography as well as P-wave radial and azimuthal anisotropy along the ANTILOPE-I profile and surrounding areas in western Tibet, which are determined by using a large number of P and S arrival-time data of local earthquakes and teleseismic events. Our results show that low-velocity (low-V) zones exist widely in the middle crust, whereas low-V zones are only visible in the lower crust beneath northwestern Tibet, indicating the existence of significant heterogeneities and complex flow there. In the upper mantle, a distinct low-V gap exists between the Indian and Asian plates. Considering the P- and S-wave tomography and P-wave azimuthal and radial anisotropy results, we interpret the gap to be caused mainly by shear heating. Depth-independent azimuthal anisotropy and high-velocity zones exist beneath the northern part of the study region, suggesting a vertically coherent deformation beneath the Tarim Basin. In contrast, tomographic and anisotropic features change with depth beneath the central and southern parts of the study region, which reflects depth-dependent (or decoupled) deformations there. At the northern edge of the Indian lithospheric mantle (ILM), P-wave azimuthal anisotropy shows a nearly east-west fast-velocity direction, suggesting that the ILM was re-built by mantle materials flowing to the north.

Structural characterization of inclusion complex of arbutin and ...

African Journals Online (AJOL)

Scanning electron micrographs of the inclusion complex showed that the original morphology of both components disappeared, and some tiny aggregates of amorphous areas of irregular size were present, revealing that the arbutin was dispersed in HP-β-CD. The powder XRD pattern of the inclusion complex was more ...

Molecular Epidemiology and Phylogeny Reveal Complex Spatial Dynamics in Areas Where Canine Parvovirus Is Endemic ▿†

Science.gov (United States)

Clegg, S. R.; Coyne, K. P.; Parker, J.; Dawson, S.; Godsall, S. A.; Pinchbeck, G.; Cripps, P. J.; Gaskell, R. M.; Radford, A. D.

2011-01-01

-sectional study of national and global CPV phylogeographic segregation reveals a substantially more complex epidemic structure than previously described. PMID:21593180

Complex nuclear-structure phenomena revealed from the nuclide production in fragmentation reactions

International Nuclear Information System (INIS)

Ricciardi, M.V.; Kelic, A.; Napolitani, P.; Schmidt, K.H.; Yordanov, O.; Ignatyuk, A.V.; Rejmund, F.

2003-12-01

Complex structural effects in the nuclide production from the projectile fragmentation of 1 A GeV 238 U nuclei in a titanium target are reported. The structure seems to be insensitive to the excitation energy induced in the reaction. This is in contrast to the prominent structural features found in nuclear fission and in transfer reactions, which gradually disappear with increasing excitation energy. Using the statistical model of nuclear reactions, relations to structural effects in nuclear binding and in the nuclear level density are demonstrated. (orig.)

ALMA Reveals Sequential High-mass Star Formation in the G9.62+0.19 Complex

Energy Technology Data Exchange (ETDEWEB)

Liu, Tie; Kim, Kee-Tae [Korea Astronomy and Space Science Institute 776, Daedeokdae-ro, Yuseong-gu, Daejeon, Korea 34055 (Korea, Republic of); Lacy, John [Department of Astronomy, University of Texas at Austin, Austin, TX 78712 (United States); Li, Pak Shing [Astronomy Department, University of California, Berkeley, CA 94720 (United States); Wang, Ke [European Southern Observatory, Karl-Schwarzschild-Str.2, D-85748 Garching bei München (Germany); Qin, Sheng-Li [Department of Astronomy, Yunnan University, and Key Laboratory of Astroparticle Physics of Yunnan Province, Kunming, 650091 (China); Zhang, Qizhou [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Garay, Guido; Mardones, Diego [Departamento de Astronomía, Universidad de Chile, Casilla 36-D, Santiago (Chile); Wu, Yuefang [Department of Astronomy, Peking University, Beijing 100871 (China); Zhu, Qingfeng [Astronomy Department, University of Science and Technology, Chinese Academy of Sciences, Hefei 210008 (China); Tatematsu, Ken’ichi; Hirota, Tomoya [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Ren, Zhiyuan; Li, Di [National Astronomical Observatories, Chinese Academy of Science, A20 Datun Road, Chaoyang District, Beijing 100012 (China); Liu, Sheng-Yuan; Chen, Huei-Ru; Su, Yu-Nung, E-mail: liutiepku@gmail.com [Academia Sinica, Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 106, Taiwan (China)

2017-11-01

Stellar feedback from high-mass stars (e.g., H ii regions) can strongly influence the surrounding interstellar medium and regulate star formation. Our new ALMA observations reveal sequential high-mass star formation taking place within one subvirial filamentary clump (the G9.62 clump) in the G9.62+0.19 complex. The 12 dense cores (MM1–MM12) detected by ALMA are at very different evolutionary stages, from the starless core phase to the UC H ii region phase. Three dense cores (MM6, MM7/G, MM8/F) are associated with outflows. The mass–velocity diagrams of the outflows associated with MM7/G and MM8/F can be well-fit by broken power laws. The mass–velocity diagram of the SiO outflow associated with MM8/F breaks much earlier than other outflow tracers (e.g., CO, SO, CS, HCN), suggesting that SiO traces newly shocked gas, while the other molecular lines (e.g., CO, SO, CS, HCN) mainly trace the ambient gas continuously entrained by outflow jets. Five cores (MM1, MM3, MM5, MM9, MM10) are massive starless core candidates whose masses are estimated to be larger than 25 M {sub ☉}, assuming a dust temperature of ≤20 K. The shocks from the expanding H ii regions (“B” and “C”) to the west may have a great impact on the G9.62 clump by compressing it into a filament and inducing core collapse successively, leading to sequential star formation. Our findings suggest that stellar feedback from H ii regions may enhance the star formation efficiency and suppress low-mass star formation in adjacent pre-existing massive clumps.

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

Science.gov (United States)

Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

Species delimitation in the Stenocereus griseus (Cactaceae species complex reveals a new species, S. huastecorum.

Directory of Open Access Journals (Sweden)

Hernán Alvarado-Sizzo

Full Text Available The Stenocereus griseus species complex (SGSC has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

Complexes of pentavalent plutonium in lithium nitrate solutions

International Nuclear Information System (INIS)

Mekhail, F.M.; Zaki, M.R.

1977-01-01

Pu 0 2 ion can form nitrate complexes in concentrated solution of lithium nitrate of PH 3.5. Spectrophotometric and ion exchange studies revealed the existence of two complexes, presumably the mono-and the dinitro. The rate of adsorption of the dinitrato complex, formed in 4 to 6 M-lithium nitrate solutions, on De-Acidite FF has been investigated and suggested to be diffusion controlled. The adsorption isotherm found to obey satisfactorily Freundlich equation

(VI) ML6 Complexes

African Journals Online (AJOL)

A geometric analysis revealed that beta-(C-H) and alpha-(C-C) can occupy the seventh and eighth coordination sites in the title Fischer carbene complexes as agostic interactions, which allows classifying the carbene as a η3 ligand in these cases. This theory was supported by the relative energies of the conformers and an ...

Complex Adaptive Schools: Educational Leadership and School Change

Science.gov (United States)

Kershner, Brad; McQuillan, Patrick

2016-01-01

This paper utilizes the theoretical framework of complexity theory to compare and contrast leadership and educational change in two urban schools. Drawing on the notion of a complex adaptive system--an interdependent network of interacting elements that learns and evolves in adapting to an ever-shifting context--our case studies seek to reveal the…

Liquid-crystalline dendrimer Cu(II) complexes and Cu(0) nanoclusters based on the Cu(II) complexes: An electron paramagnetic resonance investigation

Science.gov (United States)

Domracheva, N. E.; Mirea, A.; Schwoerer, M.; Torre-Lorente, L.; Lattermann, G.

2007-07-01

New nanostructured materials, namely, the liquid-crystalline copper(II) complexes that contain poly(propylene imine) dendrimer ligands of the first (ligand 1) and second (ligand 2) generations and which have a columnar mesophase and different copper contents (x = Cu/L), are investigated by EPR spectroscopy. The influence of water molecules and nitrate counterions on the magnetic properties of complex 2 (x = 7.3) is studied. It is demonstrated that water molecules can extract some of the copper ions from dendrimer complexes and form hexaaqua copper complexes with free ions. The dimer spectra of fully hydrated complex 2 (x = 7.3) are observed at temperatures T dendrimer copper(II) complex. The temperature-induced valence tautomerism attended by electron transport is revealed for the first time in blue dendrimer complexes 1 (x = 1.9) with a dimer structure. The activation energy for electron transport is estimated to be 0.35 meV. The coordination of the copper ion site (NO4) and the structural arrangement of green complexes 1 (x = 1.9) in the columnar mesophase are determined. Complexes of this type form linear chains in which nitrate counterions serve as bridges between copper centers. It is revealed that green complexes 1 (x = 1.9) dissolved in isotropic inert solvents can be oriented in the magnetic field (B 0 = 8000 G). The degree of orientation of these complexes is rather high (S z = 0.76) and close to that of systems with a complete ordering (S z = 1) in the magnetic field. Copper(0) nanoclusters prepared by reduction of complex 2 (x = 7.3) in two reducing agents (NaBH4, N2H4 · H2O) are examined. A model is proposed for a possible location of Cu(0) nanoclusters in a dendrimer matrix.

Generalised power graph compression reveals dominant relationship patterns in complex networks.

Science.gov (United States)

Ahnert, Sebastian E

2014-03-25

We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified.

Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

NARCIS (Netherlands)

Taylor, D.W.; Zhu, Y.; Staals, R.H.J.; Kornfeld, J.E.; Shinkai, A.; Oost, van der J.; Nogales, E.; Doudna, J.A.

2015-01-01

Adaptive immunity in bacteria involves RNA-guided surveillance complexes that use CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target invasive nucleic acids for degradation. Whereas type I and type II CRISPR-Cas

Disentangling the Trichoderma viridescens complex

NARCIS (Netherlands)

Jaklitsch, W.M.; Samuels, G.J.; Ismaiel, A.; Voglmayr, H.

2013-01-01

Trichoderma viridescens is recognised as a species complex. Multigene analyses based on the translation elongation factor 1-alpha encoding gene (tef1), a part of the rpb2 gene, encoding the second largest RNA polymerase subunit and the larger subunit of ATP citrate lyase (acl1) reveals 13

Structure defects in malachite revealed by positron annihilation

International Nuclear Information System (INIS)

Geffroy, B.; Diallo, I.; Paulin, R.

1984-01-01

Positron lifetime is measured between 77 and 400 K in two malachite samples with different mineralogical structures. The complex spectrum found in zoned malachite reveals a microporosity which remains stable in this range of temperature. Besides, above 200 K, equilibrium defects appear. Their formation energy is estimated to be Esub(f) = 0.27 +- 0.02 eV [fr

Structure defects in malachite revealed by positron annihilation

Energy Technology Data Exchange (ETDEWEB)

Geffroy, B; Diallo, I; Paulin, R [Institut National des Sciences et Techniques Nucleaires, CEN/Saclay, 91 - Gif-sur-Yvette (France)

1984-01-01

Positron lifetime is measured between 77 and 400 K in two malachite samples with different mineralogical structures. The complex spectrum found in zoned malachite reveals a microporosity which remains stable in this range of temperature. Besides, above 200 K, equilibrium defects appear. Their formation energy is estimated to be Esub(f) = 0.27 +- 0.02 eV.

Terbutaline causes immobilization of single β2-adrenergic receptor-ligand complexes in the plasma membrane of living A549 cells as revealed by single-molecule microscopy

Science.gov (United States)

Sieben, Anne; Kaminski, Tim; Kubitscheck, Ulrich; Häberlein, Hanns

2011-02-01

G-protein-coupled receptors are important targets for various drugs. After signal transduction, regulatory processes, such as receptor desensitization and internalization, change the lateral receptor mobility. In order to study the lateral diffusion of β2-adrenergic receptors (β2AR) complexed with fluorescently labeled noradrenaline (Alexa-NA) in plasma membranes of A549 cells, trajectories of single receptor-ligand complexes were monitored using single-particle tracking. We found that a fraction of 18% of all β2ARs are constitutively immobile. About 2/3 of the β2ARs moved with a diffusion constant of D2 = 0.03+/-0.001 μm2/s and about 17% were diffusing five-fold faster (D3 = 0.15+/-0.02 μm2/s). The mobile receptors moved within restricted domains and also showed a discontinuous diffusion behavior. Analysis of the trajectory lengths revealed two different binding durations with τ1 = 77+/-1 ms and τ2 = 388+/-11 ms. Agonistic stimulation of the β2AR-Alexa-NA complexes with 1 μM terbutaline caused immobilization of almost 50% of the receptors within 35 min. Simultaneously, the mean area covered by the mobile receptors decreased significantly. Thus, we demonstrated that agonistic stimulation followed by cell regulatory processes results in a change in β2AR mobility suggesting that different receptor dynamics characterize different receptor states.

Characterization of the mycobacterial acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism.

Directory of Open Access Journals (Sweden)

Matthias T Ehebauer

2015-02-01

Full Text Available Biotin-mediated carboxylation of short-chain fatty acid coenzyme A esters is a key step in lipid biosynthesis that is carried out by multienzyme complexes to extend fatty acids by one methylene group. Pathogenic mycobacteria have an unusually high redundancy of carboxyltransferase genes and biotin carboxylase genes, creating multiple combinations of protein/protein complexes of unknown overall composition and functional readout. By combining pull-down assays with mass spectrometry, we identified nine binary protein/protein interactions and four validated holo acyl-coenzyme A carboxylase complexes. We investigated one of these--the AccD1-AccA1 complex from Mycobacterium tuberculosis with hitherto unknown physiological function. Using genetics, metabolomics and biochemistry we found that this complex is involved in branched amino-acid catabolism with methylcrotonyl coenzyme A as the substrate. We then determined its overall architecture by electron microscopy and found it to be a four-layered dodecameric arrangement that matches the overall dimensions of a distantly related methylcrotonyl coenzyme A holo complex. Our data argue in favor of distinct structural requirements for biotin-mediated γ-carboxylation of α-β unsaturated acid esters and will advance the categorization of acyl-coenzyme A carboxylase complexes. Knowledge about the underlying structural/functional relationships will be crucial to make the target category amenable for future biomedical applications.

Ultrafast laser spectroscopy in complex solid state materials

Energy Technology Data Exchange (ETDEWEB)

Li, Tianqi [Iowa State Univ., Ames, IA (United States)

2014-12-01

This thesis summarizes my work on applying the ultrafast laser spectroscopy to the complex solid state materials. It shows that the ultrafast laser pulse can coherently control the material properties in the femtosecond time scale. And the ultrafast laser spectroscopy can be employed as a dynamical method for revealing the fundamental physical problems in the complex material systems.

SUMO modification through rapamycin-mediated heterodimerization reveals a dual role for Ubc9 in targeting RanGAP1 to nuclear pore complexes

International Nuclear Information System (INIS)

Zhu Shanshan; Zhang Hong; Matunis, Michael J.

2006-01-01

SUMOs (small ubiquitin-related modifiers) are eukaryotic proteins that are covalently conjugated to other proteins and thereby regulate a wide range of important cellular processes. The molecular mechanisms by which SUMO modification influences the functions of most target proteins and cellular processes, however, remain poorly defined. A major obstacle to investigating the effects of SUMO modification is the availability of a system for selectively inducing the modification or demodification of an individual protein. To address this problem, we have developed a procedure using the rapamycin heterodimerizer system. This procedure involves co-expression of rapamycin-binding domain fusion proteins of SUMO and candidate SUMO substrates in living cells. Treating cells with rapamycin induces a tight association between SUMO and a single SUMO substrate, thereby allowing specific downstream effects to be analyzed. Using RanGAP1 as a model SUMO substrate, the heterodimerizer system was used to investigate the molecular mechanism by which SUMO modification targets RanGAP1 from the cytoplasm to nuclear pore complexes (NPCs). Our results revealed a dual role for Ubc9 in targeting RanGAP1 to NPCs: In addition to conjugating SUMO-1 to RanGAP1, Ubc9 is also required to form a stable ternary complex with SUMO-1 modified RanGAP1 and Nup358. As illustrated by our studies, the rapamycin heterodimerizer system represents a novel tool for studying the molecular effects of SUMO modification

Mitochondrial and nuclear DNA reveals a complete lineage sorti ng ...

African Journals Online (AJOL)

Glossogobius callidus exhibits broad salinity tolerance and is distributed in both estuarine and freshwater environments in southern Africa. Previous studies revealed substantial morphological and molecular variation among populations, suggesting they constitute a species complex. The present study utilised phylogenetic ...

Mixed Metal Complexes of Isoniazid and Ascorbic Acid: Chelation ...

African Journals Online (AJOL)

HP

these ligands and their metal complexes have revealed the bi-dentate coordination of isoniazid ligand to ... of the drugs on coordination with a metal is enhanced ..... James, O.O., Nwinyi, C.O. and. Allensela, M.A. (2008). Cobalt(II) complexes of mixed antibiotics: Synthesis,. Characterization, antimicrobial potential and their.

Novel binding motif and new flexibility revealed by structural analyses of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase subcomplex from the Escherichia coli pyruvate dehydrogenase multienzyme complex.

Science.gov (United States)

Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

2014-10-24

The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Novel Binding Motif and New Flexibility Revealed by Structural Analyses of a Pyruvate Dehydrogenase-Dihydrolipoyl Acetyltransferase Subcomplex from the Escherichia coli Pyruvate Dehydrogenase Multienzyme Complex*

Science.gov (United States)

Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S.; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

2014-01-01

The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. PMID:25210042

Generation of a haptoglobin-hemoglobin complex-specific Fab antibody blocking the binding of the complex to CD163

DEFF Research Database (Denmark)

Horn, Ivo R; Nielsen, Marianne Jensby; Madsen, Mette

2003-01-01

During intravascular hemolysis hemoglobin (Hb) binds to haptoglobin (Hp) leading to endocytosis of the complex by the macrophage receptor, CD163. In the present study, we used a phage-display Fab antibody strategy to explore if the complex formation between Hp and Hb leads to exposure of antigenic...... epitopes specific for the complex. By Hp-Hb-affinity screening of a phage-Fab library, we isolated a phage clone against the ligand complex. Surface plasmon resonance analyses of the Fab part expressed as a recombinant protein revealed a high affinity binding (KD = 3.9 nm) to Hp-Hb, whereas no binding...... was measured for non-complexed Hp or Hb. The Fab antibody completely inhibited the binding of 125I-labeled Hp-Hb complexes to CD163 and blocked their uptake in CD163-transfected cells. In conclusion, we have raised a receptor-blocking antibody specifically recognizing the Hp-Hb complex. In addition to provide...

DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes.

Science.gov (United States)

Iftikhar, Romana; Ashfaq, Muhammad; Rasool, Akhtar; Hebert, Paul D N

2016-01-01

Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

Structure, magnetic behavior, and anisotropy of homoleptic trinuclear lanthanoid 8-quinolinolate complexes.

Science.gov (United States)

Chilton, Nicholas F; Deacon, Glen B; Gazukin, Olga; Junk, Peter C; Kersting, Berthold; Langley, Stuart K; Moubaraki, Boujemaa; Murray, Keith S; Schleife, Frederik; Shome, Mahasish; Turner, David R; Walker, Julia A

2014-03-03

Three complexes of the form [Ln(III)3(OQ)9] (Ln = Gd, Tb, Dy; OQ = 8-quinolinolate) have been synthesized and their magnetic properties studied. The trinuclear complexes adopt V-shaped geometries with three bridging 8-quinolinolate oxygen atoms between the central and peripheral eight-coordinate metal atoms. The magnetic properties of these three complexes differ greatly. Variable-temperature direct-current (dc) magnetic susceptibility measurements reveal that the gadolinium and terbium complexes display weak antiferromagnetic nearest-neighbor magnetic exchange interactions. This was quantified in the isotropic gadolinium case with an exchangecoupling parameter of J = -0.068(2) cm(-1). The dysprosium compound displays weak ferromagnetic exchange. Variable-frequency and -temperature alternating-current magnetic susceptibility measurements on the anisotropic cases reveal that the dysprosium complex displays single-molecule-magnet behavior, in zero dc field, with two distinct relaxation modes of differing time scales within the same molecule. Analysis of the data revealed anisotropy barriers of Ueff = 92 and 48 K for the two processes. The terbium complex, on the other hand, displays no such behavior in zero dc field, but upon application of a static dc field, slow magnetic relaxation can be observed. Ab initio and electrostatic calculations were used in an attempt to explain the origin of the experimentally observed slow relaxation of the magnetization for the dysprosium complex.

A new information dimension of complex networks

Energy Technology Data Exchange (ETDEWEB)

Wei, Daijun [School of Computer and Information Science, Southwest University, Chongqing 400715 (China); School of Science, Hubei University for Nationalities, Enshi 445000 (China); Wei, Bo [School of Computer and Information Science, Southwest University, Chongqing 400715 (China); Hu, Yong [Institute of Business Intelligence and Knowledge Discovery, Guangdong University of Foreign Studies, Guangzhou 510006 (China); Zhang, Haixin [School of Computer and Information Science, Southwest University, Chongqing 400715 (China); Deng, Yong, E-mail: ydeng@swu.edu.cn [School of Computer and Information Science, Southwest University, Chongqing 400715 (China); School of Engineering, Vanderbilt University, TN 37235 (United States)

2014-03-01

Highlights: •The proposed measure is more practical than the classical information dimension. •The difference of information for box in the box-covering algorithm is considered. •Results indicate the measure can capture the fractal property of complex networks. -- Abstract: The fractal and self-similarity properties are revealed in many complex networks. The classical information dimension is an important method to study fractal and self-similarity properties of planar networks. However, it is not practical for real complex networks. In this Letter, a new information dimension of complex networks is proposed. The nodes number in each box is considered by using the box-covering algorithm of complex networks. The proposed method is applied to calculate the fractal dimensions of some real networks. Our results show that the proposed method is efficient when dealing with the fractal dimension problem of complex networks.

A new information dimension of complex networks

International Nuclear Information System (INIS)

Wei, Daijun; Wei, Bo; Hu, Yong; Zhang, Haixin; Deng, Yong

2014-01-01

Highlights: •The proposed measure is more practical than the classical information dimension. •The difference of information for box in the box-covering algorithm is considered. •Results indicate the measure can capture the fractal property of complex networks. -- Abstract: The fractal and self-similarity properties are revealed in many complex networks. The classical information dimension is an important method to study fractal and self-similarity properties of planar networks. However, it is not practical for real complex networks. In this Letter, a new information dimension of complex networks is proposed. The nodes number in each box is considered by using the box-covering algorithm of complex networks. The proposed method is applied to calculate the fractal dimensions of some real networks. Our results show that the proposed method is efficient when dealing with the fractal dimension problem of complex networks.

Transcriptome, carbohydrate, and phytohormone analysis of Petunia hybrida reveals a complex disturbance of plant functional integrity under mild chilling stress

Science.gov (United States)

Bauerfeind, Martin Andreas; Winkelmann, Traud; Franken, Philipp; Druege, Uwe

2015-01-01

Cultivation of chilling-tolerant ornamental crops at lower temperature could reduce the energy demands of heated greenhouses. To provide a better understanding of how sub-optimal temperatures (12°C vs. 16°C) affect growth of the sensitive Petunia hybrida cultivar ‘SweetSunshine Williams’, the transcriptome, carbohydrate metabolism, and phytohormone homeostasis were monitored in aerial plant parts over 4 weeks by use of a microarray, enzymatic assays and GC-MS/MS. The data revealed three consecutive phases of chilling response. The first days were marked by a strong accumulation of sugars, particularly in source leaves, preferential up-regulation of genes in the same tissue and down-regulation of several genes in the shoot apex, especially those involved in the abiotic stress response. The midterm phase featured a partial normalization of carbohydrate levels and gene expression. After 3 weeks of chilling exposure, a new stabilized balance was established. Reduced hexose levels in the shoot apex, reduced ratios of sugar levels between the apex and source leaves and a higher apical sucrose/hexose ratio, associated with decreased activity and expression of cell wall invertase, indicate that prolonged chilling induced sugar accumulation in source leaves at the expense of reduced sugar transport to and reduced sucrose utilization in the shoot. This was associated with reduced levels of indole-3-acetic acid and abscisic acid in the apex and high numbers of differentially, particularly up-regulated genes, especially in the source leaves, including those regulating histones, ethylene action, transcription factors, and a jasmonate-ZIM-domain protein. Transcripts of one Jumonji C domain containing protein and one expansin accumulated in source leaves throughout the chilling period. The results reveal a dynamic and complex disturbance of plant function in response to mild chilling, opening new perspectives for the comparative analysis of differently tolerant cultivars

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

Science.gov (United States)

Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P; Rai, Vandna; Singh, Ashok K; Singh, Nagendra K

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon , and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho - taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

Science.gov (United States)

Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P.; Rai, Vandna; Singh, Ashok K.; Singh, Nagendra K.

2018-01-01

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones

Effect of metal ions on autofluorescence of the dry rot fungus Serpula lacrymans grown on spruce wood

Czech Academy of Sciences Publication Activity Database

Gabriel, Jiří; Žižka, Zdeněk; Švec, Karel; Nasswettrová, A.; Šmíra, P.; Kofroňová, Olga; Benada, Oldřich

2016-01-01

Roč. 61, č. 2 (2016), s. 119-128 ISSN 0015-5632 Institutional support: RVO:61388971 Keywords : HEAVY-METALS * CELL-WALL * PHANEROCHAETE-CHRYSOSPORIUM Subject RIV: EE - Microbiology, Virology Impact factor: 1.521, year: 2016

Time irreversibility and intrinsics revealing of series with complex network approach

Science.gov (United States)

Xiong, Hui; Shang, Pengjian; Xia, Jianan; Wang, Jing

2018-06-01

In this work, we analyze time series on the basis of the visibility graph algorithm that maps the original series into a graph. By taking into account the all-round information carried by the signals, the time irreversibility and fractal behavior of series are evaluated from a complex network perspective, and considered signals are further classified from different aspects. The reliability of the proposed analysis is supported by numerical simulations on synthesized uncorrelated random noise, short-term correlated chaotic systems and long-term correlated fractal processes, and by the empirical analysis on daily closing prices of eleven worldwide stock indices. Obtained results suggest that finite size has a significant effect on the evaluation, and that there might be no direct relation between the time irreversibility and long-range correlation of series. Similarity and dissimilarity between stock indices are also indicated from respective regional and global perspectives, showing the existence of multiple features of underlying systems.

Complexation of carboxylate on smectite surfaces.

Science.gov (United States)

Liu, Xiandong; Lu, Xiancai; Zhang, Yingchun; Zhang, Chi; Wang, Rucheng

2017-07-19

We report a first principles molecular dynamics (FPMD) study of carboxylate complexation on clay surfaces. By taking acetate as a model carboxylate, we investigate its inner-sphere complexes adsorbed on clay edges (including (010) and (110) surfaces) and in interlayer space. Simulations show that acetate forms stable monodentate complexes on edge surfaces and a bidentate complex with Ca 2+ in the interlayer region. The free energy calculations indicate that the complexation on edge surfaces is slightly more stable than in interlayer space. By integrating pK a s and desorption free energies of Al coordinated water calculated previously (X. Liu, X. Lu, E. J. Meijer, R. Wang and H. Zhou, Geochim. Cosmochim. Acta, 2012, 81, 56-68; X. Liu, J. Cheng, M. Sprik, X. Lu and R. Wang, Geochim. Cosmochim. Acta, 2014, 140, 410-417), the pH dependence of acetate complexation has been revealed. It shows that acetate forms inner-sphere complexes on (110) in a very limited mildly acidic pH range while it can complex on (010) in the whole common pH range. The results presented in this study form a physical basis for understanding the geochemical processes involving clay-organics interactions.

Diminazene aceturate-sodium oleate complex for the treatment of ...

African Journals Online (AJOL)

The aim of this study is to improve the efficacy of diminazene aceturate via complex formation with sodium oleate. The complex was subjected to various in vitro and in vivo tests to assess its properties, toxicity and efficacy against Trypanosoma brucei brucei infections in comparison to pure drug. Results revealed that the ...

Single molecule magnet behaviour in robust dysprosium-biradical complexes.

Science.gov (United States)

Bernot, Kevin; Pointillart, Fabrice; Rosa, Patrick; Etienne, Mael; Sessoli, Roberta; Gatteschi, Dante

2010-09-21

A Dy-biradical complex was synthesized and characterized down to very low temperature. ac magnetic measurements reveal single molecule magnet behaviour visible without any application of dc field. The transition to the quantum tunneling regime is evidenced. Photophysical and EPR measurements provide evidence of the excellent stability of these complexes in solution.

MANAGEMENT OF SPORT COMPLEXES

Directory of Open Access Journals (Sweden)

Marian STAN

2015-07-01

Full Text Available The actuality of the investigated theme. Nowadays, human evolution, including his intellectual development, proves the fact that especially the creation manpower and the employment was the solution of all life’s ambitions in society. So, the fact is that in reality, man is the most important capital of the society. Also, in an individual’s life, the practice of sport plays a significant role and that’s why the initiation, the launch and the management of sports complexes activity reveal the existence of specific management features that we will identify and explain in the current study. The aim of the research refers to the elaboration of a theoretical base of the management of the sport complexes, to the pointing of the factors that influence the efficient existence and function of a sport complex in our country and to the determination of the responsibilities that have a manager who directs successfully the activity of the sport complexes. The investigation is based on theoretical methods, such as: scientific documentation, analysis, synthesis, comparison and on empirical research methods, like: study of researched literature and observation. The results of the research indicate the fact that the profitability of a sport complex must assure a particular structure to avoid the bankruptcy risk and also, that the administration of the sport complexes activity must keep in view the reliable functions of the contemporaneous management.

Fitness effects of a selfish gene (the Mus t complex) are revealed in an ecological context.

Science.gov (United States)

Carroll, Lara S; Meagher, Shawn; Morrison, Linda; Penn, Dustin J; Potts, Wayne K

2004-06-01

In wild house mice, genes linked to the t transmission distortion complex cause meiotic drive by sabotaging wild-type gametes. The t complex is consequently inherited at frequencies higher than 90%. Yet, for unclear reasons, in wild mouse populations this selfish DNA is found at frequencies much lower than expected. Here, we examine selection on the t complex in 10 seminatural populations of wild mice based on data from 234 founders and nearly 2000 progeny. Eight of the 10 populations decreased in t frequency over one generation, and the overall frequency of t haplotypes across all 10 populations was 48.5% below expectations based on transmission distortion and 34.3% below Mendelian (or Hardy-Weinberg) expectations. Behavioral and reproductive data were collected for 10 months for each population, and microsatellite genotyping was performed on seven of the populations to determine parentage. These combined data show t-associated fitness declines in both males and females. This is the first study to show evidence for a reduction in the ability of +/t males to maintain territories. Because females tend to mate with dominant males, impairment of territorial success can explain much of the selection against t observed in our populations. In nature, selection against heterozygote carriers of the t complex helps solve the puzzlingly low t frequencies found in wild populations. This ecological approach for determining fitness consequences of genetic variants has broad application for the discovery of gene function in general.

Proteomic analysis of human norepinephrine transporter complexes reveals associations with protein phosphatase 2A anchoring subunit and 14-3-3 proteins

International Nuclear Information System (INIS)

Sung, Uhna; Jennings, Jennifer L.; Link, Andrew J.; Blakely, Randy D.

2005-01-01

The norepinephrine transporter (NET) terminates noradrenergic signals by clearing released NE at synapses. NET regulation by receptors and intracellular signaling pathways is supported by a growing list of associated proteins including syntaxin1A, protein phosphatase 2A (PP2A) catalytic subunit (PP2A-C), PICK1, and Hic-5. In the present study, we sought evidence for additional partnerships by mass spectrometry-based analysis of proteins co-immunoprecipitated with human NET (hNET) stably expressed in a mouse noradrenergic neuroblastoma cell line. Our initial proteomic analyses reveal multiple peptides derived from hNET, peptides arising from the mouse PP2A anchoring subunit (PP2A-Ar) and peptides derived from 14-3-3 proteins. We verified physical association of NET with PP2A-Ar via co-immunoprecipitation studies using mouse vas deferens extracts and with 14-3-3 via a fusion pull-down approach, implicating specifically the hNET NH 2 -terminus for interactions. The transporter complexes described likely support mechanisms regulating transporter activity, localization, and trafficking

Complex cytogeographical patterns reveal a dynamic tetraploid–octoploid contact zone

Science.gov (United States)

Castro, Mariana; Castro, Sílvia; Figueiredo, Albano; Husband, Brian; Loureiro, João

2018-01-01

Abstract The distribution of cytotypes in mixed-ploidy species is crucial for evaluating ecological processes involved in the establishment and evolution of polyploid taxa. Here, we use flow cytometry and chromosome counts to explore cytotype diversity and distributions within a tetraploid–octoploid contact zone. We then use niche modelling and ploidy seed screening to assess the roles of niche differentiation among cytotypes and reproductive interactions, respectively, in promoting cytotype coexistence. Two cytotypes, tetraploids and octoploids, were dominant within the contact zone. They were most often distributed parapatrically or allopatrically, resulting in high geographic isolation. Still, 16.7 % of localities comprised two or more cytotypes, including the intermediate hexaploid cytotype. Tetraploids and octoploids had high environmental niche overlap and associated with similar climatic environments, suggesting they have similar ecological requirements. Given the geographical separation and habitat similarity among cytotypes, mixed-ploidy populations may be transitional and subject to the forces of minority cytotype exclusion which lead to pure-ploidy populations. However, seed ploidy analysis suggests that strong reproductive barriers may enforce assortative mating which favours stable cytotype coexistence. High cytogenetic diversity detected in the field suggests that unreduced gamete formation and hybridization events seem frequent in the studied polyploid complex and might be involved with the recurrent polyploid formation, governing, as well, the gene flow between cytogenetic entities. PMID:29593853

Korean Conference on Several Complex Variables

CERN Document Server

Byun, Jisoo; Gaussier, Hervé; Hirachi, Kengo; Kim, Kang-Tae; Shcherbina, Nikolay

2015-01-01

This volume includes 28 chapters by authors who are leading researchers of the world describing many of the up-to-date aspects in the field of several complex variables (SCV). These contributions are based upon their presentations at the 10th Korean Conference on Several Complex Variables (KSCV10), held as a satellite conference to the International Congress of Mathematicians (ICM) 2014 in Seoul, Korea. SCV has been the term for multidimensional complex analysis, one of the central research areas in mathematics. Studies over time have revealed a variety of rich, intriguing, new knowledge in complex analysis and geometry of analytic spaces and holomorphic functions which were "hidden" in the case of complex dimension one. These new theories have significant intersections with algebraic geometry, differential geometry, partial differential equations, dynamics, functional analysis and operator theory, and sheaves and cohomology, as well as the traditional analysis of holomorphic functions in all dimensions. This...

Pentacoordinated organoaluminum complexes: A computational insight

KAUST Repository

Milione, Stefano

2012-12-24

The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

Pentacoordinated organoaluminum complexes: A computational insight

KAUST Repository

Milione, Stefano; Milano, Giuseppe; Cavallo, Luigi

2012-01-01

The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

Science.gov (United States)

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

2017-07-06

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Master stability functions reveal diffusion-driven pattern formation in networks

Science.gov (United States)

Brechtel, Andreas; Gramlich, Philipp; Ritterskamp, Daniel; Drossel, Barbara; Gross, Thilo

2018-03-01

We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space. For illustration, we consider a generalized model of ecological meta-food webs. This fairly complex model describes the dispersal of many different species across a region consisting of a network of individual habitats while subject to realistic, nonlinear predator-prey interactions. In this example, the method reveals the intricate dependence of the dynamics on the spatial structure. The ability of the proposed approach to deal with this fairly complex system highlights it as a promising tool for ecology and other applications.

Chemical Information revealed by Mössbauer spectroscopy and DFT calculations

Energy Technology Data Exchange (ETDEWEB)

Nakashima, Satoru, E-mail: snaka@hiroshima-u.ac.jp [Hiroshima University, Natural Science Center for Basic Research and Development (Japan)

2017-11-15

Mixed-valence state of binuclear metallocene derivatives and spin-crossover (SCO) phenomena of the assembled Fe(II) complexes have been studied by using Mössbauer spectroscopy. The understanding of the results obtained by Mössbauer spectra is well supported by means of X-ray structural analysis and density functional theory (DFT) calculation. Benchmark study of relativisitic DFT calculation by using Mössbauer isomer shifts of Eu, Np complexes reveals the validity of the calculation. Such study sheds light on the bonding character of 4f and 5f electron. These results are reviewed.

SOLID-PHASE TREATMENT OF A PENTACHLOROPHENOL- CONTAMINATED SOIL USING LIGNIN-DEGRADING FUNGI

Science.gov (United States)

The abilities of three lignin-degrading fungi, Phanerochaete chrysosporium, Phanerochaete sordida, and Trametes hirsuta, to deplete pentachlorophenol (PCP) from soil contaminated with PCP and creosote were evaluated. A total of seven fungal and three control treatments ...

Three perspectives on complexity: entropy, compression, subsymmetry

Science.gov (United States)

Nagaraj, Nithin; Balasubramanian, Karthi

2017-12-01

There is no single universally accepted definition of `Complexity'. There are several perspectives on complexity and what constitutes complex behaviour or complex systems, as opposed to regular, predictable behaviour and simple systems. In this paper, we explore the following perspectives on complexity: effort-to-describe (Shannon entropy H, Lempel-Ziv complexity LZ), effort-to-compress (ETC complexity) and degree-of-order (Subsymmetry or SubSym). While Shannon entropy and LZ are very popular and widely used, ETC is relatively a new complexity measure. In this paper, we also propose a novel normalized complexity measure SubSym based on the existing idea of counting the number of subsymmetries or palindromes within a sequence. We compare the performance of these complexity measures on the following tasks: (A) characterizing complexity of short binary sequences of lengths 4 to 16, (B) distinguishing periodic and chaotic time series from 1D logistic map and 2D Hénon map, (C) analyzing the complexity of stochastic time series generated from 2-state Markov chains, and (D) distinguishing between tonic and irregular spiking patterns generated from the `Adaptive exponential integrate-and-fire' neuron model. Our study reveals that each perspective has its own advantages and uniqueness while also having an overlap with each other.

Transcription regulation by the Mediator complex.

Science.gov (United States)

Soutourina, Julie

2018-04-01

Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.

SACCHARIFICATION WITH Phanerochaete chrysosporium and ...

African Journals Online (AJOL)

cantocanche

2011-05-09

May 9, 2011 ... and Pleurotus ostreatus enzymatic extracts of pretreated banana ... reduction in the cost of production (Hahn-Hägerdal et al., ... economy, the saccharification of these materials is necessary ... To efficiently process lignocellulosic wastes, the lignin ..... industries depend on the success in saccharification.

Complex brain networks: From topological communities to clustered

Indian Academy of Sciences (India)

Complex brain networks: From topological communities to clustered dynamics ... Recent research has revealed a rich and complicated network topology in the cortical connectivity of mammalian brains. ... Pramana – Journal of Physics | News.

Studies of mn (ii) and ni (ii) complexes with schiff base derived from ...

African Journals Online (AJOL)

However, manganese(II) complex is insoluble in most organic solvents but soluble in dimethylsulphoxide (DMSO). The molar conductance of the complexes measured are, indicating their non-electrolytic nature. The potentiometric and spectrophotometric studies of the complex compounds revealed 1:1 metal to ligand ratio.

Studies of Mn (II) and Ni (II) complexes with Schiff base derived from ...

African Journals Online (AJOL)

However, manganese(II) complex is insoluble in most organic solvents but soluble in dimethylsulphoxide (DMSO). The molar conductance of the complexes measured are low, indicating their non-electrolytic nature. The potentiometric and spectrophotometric studies of the complex compounds revealed 1:1 metal to ligand ...

Structure-based characterization of multiprotein complexes.

Science.gov (United States)

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Transition metal M(II complexes with isonicotinoylhydrazone-9-anthraldehyde

Directory of Open Access Journals (Sweden)

Dianu M.L.

2010-01-01

Full Text Available New complexes of isonicotinoylhydrazone-9-anthraldehyde with Cu(II, Co(II and Ni(II have been prepared and characterized by analytical and physico-chemical techniques, such as elemental and thermal analyses, magnetic susceptibility and conductivity measurements, and electronic, EPR and IR spectral studies. The infrared spectral studies revealed the bidentate or monodentate nature of the Schiff base in the complexes; the pyridine nitrogen does not participate in the coordination. A tetrahedral geometry is suggested for the nitrate-complexes and an octahedral geometry for the others. Thermal studies support the chemical formulation of these complexes.

Conformational changes in DNA gyrase revealed by limited proteolysis

DEFF Research Database (Denmark)

Kampranis, S C; Maxwell, A

1998-01-01

We have used limited proteolysis to identify conformational changes in DNA gyrase. Gyrase exhibits a proteolytic fingerprint dominated by two fragments, one of approximately 62 kDa, deriving from the A protein, and another of approximately 25 kDa from the B protein. Quinolone binding to the enzyme......-DNA intermediate by calcium ions does not reveal any protection, suggesting that the quinolone-induced conformational change is different from an "open-gate" state of the enzyme. A quinolone-resistant mutant of gyrase fails to give the characteristic quinolone-associated proteolytic signature. The ATP...... does not prevent dimerization since incubation of the enzyme-DNA complex with both ADPNP and quinolones gives rise to a complex whose proteolytic pattern retains the characteristic signature of dimerization but has lost the quinolone-induced protection. As a result, the quinolone-gyrase complex can...

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B.

Science.gov (United States)

Krause-Kyora, Ben; Susat, Julian; Key, Felix M; Kühnert, Denise; Bosse, Esther; Immel, Alexander; Rinne, Christoph; Kornell, Sabin-Christin; Yepes, Diego; Franzenburg, Sören; Heyne, Henrike O; Meier, Thomas; Lösch, Sandra; Meller, Harald; Friederich, Susanne; Nicklisch, Nicole; Alt, Kurt W; Schreiber, Stefan; Tholey, Andreas; Herbig, Alexander; Nebel, Almut; Krause, Johannes

2018-05-10

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses. © 2018, Krause-Kyora et al.

Comparison of MukB homodimer versus MukBEF complex molecular architectures by electron microscopy reveals a higher-order multimerization

International Nuclear Information System (INIS)

Matoba, Kyoko; Yamazoe, Mitsuyoshi; Mayanagi, Kouta; Morikawa, Kosuke; Hiraga, Sota

2005-01-01

The complex of MukF, MukE, and MukB proteins participates in organization of sister chromosomes and partitioning into both daughter cells in Escherichia coli. We purified the MukB homodimer and the MukBEF complex and analyzed them by electron microscopy to compare both structures. A MukB homodimer shows a long rod-hinge-rod v-shape with small globular domains at both ends. The MukBEF complex shows a similar structure having larger globular domains than those of the MukB homodimer. These results suggest that MukF and MukE bind to the globular domains of a MukB homodimer. The globular domains of the MukBEF complex frequently associate with each other in an intramolecular fashion, forming a ring. In addition, MukBEF complex molecules tend to form multimers by the end-to-end joining with other MukBEF molecules in an intermolecular fashion, resulting in fibers and rosette-form structures in the absence of ATP and DNA in vitro

Characterization and biological activity of Solidago canadensis complex.

Science.gov (United States)

Šutovská, M; Capek, P; Kocmálová, M; Fraňová, S; Pawlaczyk, I; Gancarz, R

2013-01-01

Polyphenolic-polysaccharide-protein complex has been isolated from flowers of Solidago canadensis L. by hot alkaline extraction procedure. Compositional analyses of S canadensis complex revealed the presence of carbohydrates (43 wt%), protein (27 wt%), phenolics (12 wt%), uronic acids (10 wt%) and inorganic material (8 wt%). The carbohydrate part was rich in neutral sugars (81 wt%) while uronids were determined in lower amount (19 wt%). Monosaccharide analysis of carbohydrate part revealed the presence of five main sugar components, i.e. rhamnose (~23 wt%), arabinose (~20 wt%), uronic acids (~19 wt%), galactose (~17 wt%) and glucose (~14 wt%), and indicated thus the presence of rhamnogalacturonan and arabinogalactan in S. canadensis complex. HPLC analysis of complex showed one single peak of molecule mass at 11.2 kDa. Antitussive activity tests, performed in three doses of Solidago complex, showed the reduction of the number of cough efforts in the dose-dependent manner. Higher doses (50 and 75 mg/kg b.w.) were shown to be by 15 and 20% more effective than that of lower one (25mg/kg b.w.). However, the antitussive effect of the highest dose (75 mg/kg b.w.) was by 10% lower in comparison with that of codeine, the strongest antitussive agent. Besides, the highest dose of the complex (75 mg/kg b.w.) significantly decreased values of specific airways resistance and their effect remained longer as that of salbutamol, a representative of classic antiasthmatic drugs. Copyright © 2012 Elsevier B.V. All rights reserved.

Four not six: Revealing culturally common facial expressions of emotion.

Science.gov (United States)

Jack, Rachael E; Sun, Wei; Delis, Ioannis; Garrod, Oliver G B; Schyns, Philippe G

2016-06-01

As a highly social species, humans generate complex facial expressions to communicate a diverse range of emotions. Since Darwin's work, identifying among these complex patterns which are common across cultures and which are culture-specific has remained a central question in psychology, anthropology, philosophy, and more recently machine vision and social robotics. Classic approaches to addressing this question typically tested the cross-cultural recognition of theoretically motivated facial expressions representing 6 emotions, and reported universality. Yet, variable recognition accuracy across cultures suggests a narrower cross-cultural communication supported by sets of simpler expressive patterns embedded in more complex facial expressions. We explore this hypothesis by modeling the facial expressions of over 60 emotions across 2 cultures, and segregating out the latent expressive patterns. Using a multidisciplinary approach, we first map the conceptual organization of a broad spectrum of emotion words by building semantic networks in 2 cultures. For each emotion word in each culture, we then model and validate its corresponding dynamic facial expression, producing over 60 culturally valid facial expression models. We then apply to the pooled models a multivariate data reduction technique, revealing 4 latent and culturally common facial expression patterns that each communicates specific combinations of valence, arousal, and dominance. We then reveal the face movements that accentuate each latent expressive pattern to create complex facial expressions. Our data questions the widely held view that 6 facial expression patterns are universal, instead suggesting 4 latent expressive patterns with direct implications for emotion communication, social psychology, cognitive neuroscience, and social robotics. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.

Science.gov (United States)

Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; Del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

2017-01-04

We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

Investigation of the complex structure, comparative DNA-binding and DNA cleavage of two water-soluble mono-nuclear lanthanum(III) complexes and cytotoxic activity of chitosan-coated magnetic nanoparticles as drug delivery for the complexes

Science.gov (United States)

Asadi, Zahra; Nasrollahi, Neda; Karbalaei-Heidari, Hamidreza; Eigner, Vaclav; Dusek, Michal; Mobaraki, Nabiallah; Pournejati, Roya

2017-05-01

Two water-soluble mono-nuclear macrocyclic lanthanum(III) complexes of 2,6-diformyl-4-methylphenol with 1,3-diamino-2-propanol (C1) or 1,3-propylenediamine (C2) were synthesized and characterized by UV-Vis, FT-IR, 13C and 1H NMR spectroscopy and elemental analysis. C1 complex was structurally characterized by single-crystal X-ray diffraction, which revealed that the complex was mononuclear and ten-coordinated. The coordination sites around lanthanum(III) were occupied with a five-dentate ligand, two bidentate nitrates, and one water molecule. The interaction of complexes with DNA was studied in buffered aqueous solution at pH 7.4. UV-Vis absorption spectroscopy, emission spectroscopy, circular dichroism (CD) and viscometric measurements provided clear evidence of the intercalation mechanism of binding. The obtained intrinsic binding constants (Kb) 9.3 × 103 and 1.2 × 103 M- 1 for C1 and C2, respectively confirmed that C1 is better intercalator than C2. The DNA docking studies suggested that the complexes bind with DNA in a groove binding mode with the binding affinity of C1 > C2. Moreover, agarose gel electrophoresis study of the DNA-complex for both compounds revealed that the C1 intercalation cause ethidium bromide replacement in a competitive manner which confirms the suggested mechanism of binding. Finally, the anticancer experiments for the treated cancerous cell lines with both synthesized compounds show that these hydrophilic molecules need a suitable carrier to pass through the hydrophobic nature of cell membrane efficiently.

Immobilization of Irpex lacteus to liquid-core alginate beads and their application to degradation of pollutants

Czech Academy of Sciences Publication Activity Database

Šíma, J.; Milne, R.; Novotný, Čeněk; Hasal, P.

2017-01-01

Roč. 62, č. 4 (2017), s. 335-342 ISSN 0015-5632 Institutional support: RVO:61388971 Keywords : WHITE-ROT FUNGI * ROTATING BIOLOGICAL CONTACTOR * PHANEROCHAETE-CHRYSOSPORIUM Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 1.521, year: 2016

Protein dynamics during presynaptic complex assembly on individual ssDNA molecules

Science.gov (United States)

Gibb, Bryan; Ye, Ling F.; Kwon, YoungHo; Niu, Hengyao; Sung, Patrick; Greene, Eric C.

2014-01-01

Homologous recombination is a conserved pathway for repairing double–stranded breaks, which are processed to yield single–stranded DNA overhangs that serve as platforms for presynaptic complex assembly. Here we use single–molecule imaging to reveal the interplay between Saccharomyce cerevisiae RPA, Rad52, and Rad51 during presynaptic complex assembly. We show that Rad52 binds RPA–ssDNA and suppresses RPA turnover, highlighting an unanticipated regulatory influence on protein dynamics. Rad51 binding extends the ssDNA, and Rad52–RPA clusters remain interspersed along the presynaptic complex. These clusters promote additional binding of RPA and Rad52. Together, our work illustrates the spatial and temporal progression of RPA and Rad52 association with the presynaptic complex, and reveals a novel RPA–Rad52–Rad51–ssDNA intermediate, which has implications for understanding how the activities of Rad52 and RPA are coordinated with Rad51 during the later stages recombination. PMID:25195049

The complex patient: A concept clarification.

Science.gov (United States)

Manning, Eli; Gagnon, Marilou

2017-03-01

Over the last decade, the concept of the "complex patient" has not only been more widely used in multidisciplinary healthcare teams and across various healthcare disciplines, but it has also become more vacuous in meaning. The uptake of the concept of the "complex patient" spans across disciplines, such as medicine, nursing, and social work, with no consistent definition. We review the chronological evolution of this concept and its surrogate terms, namely "comorbidity," "multimorbidity," "polypathology," "dual diagnosis," and "multiple chronic conditions." Drawing on key principles of concept clarification, we highlight disciplinary usage in the literature published between 2005 and 2015 in health sciences, attending to overlaps and revealing nuances of the complex patient concept. Finally, we discuss the implications of this concept for practice, research, and theory. © 2017 John Wiley & Sons Australia, Ltd.

The Role of Drosophila Merlin in the Control of Mitosis Exit and Development

Science.gov (United States)

2008-07-01

chrysosporium --- http://genome.jgi-p Aspergillus flavus --- http://www.tigr.or Arabidopsis thaliana --- http://www.tigr.or Oryza sativa --- http...distinguish colon and ovarian adenocarcinomas: identi- fication, genomic, proteomic , and tissue array profiling. Cancer Res 2003;63:5243–50. 108

Using neutral theory to reveal the contribution of meta-community processes to assembly in complex landscapes

Directory of Open Access Journals (Sweden)

Dominique Gravel

2014-04-01

Full Text Available The metacommunity perspective appears as an appropriate conceptual framework to make ecology more predictive. It is particularly relevant to limnology, where exchanges of organisms and nutrients affect community and ecosystem properties from the local to the regional scales. The recent development of neutral theory appears as a step back in that direction because of the assumption of ecological equivalence and the absence of any effect of the environment on community organization. A remarkable strength of neutral theory is nonetheless to provide a general theory of diversity that accounts for a wide range of empirical observations. In this paper, we argue that neutral theory can be useful to understand the impact of dispersal on community assembly in landscapes of various complexities. Our analysis focus on spatially explicit landscapes conceptualized as networks of local communities (e.g., lakes connected to each other by dispersal channels (e.g., rivers. The main objective of the paper is to use neutral theory to stress the importance of landscape structure on the distribution of diversity. We refer to the landscape organization as a spatial contingency that could potentially affect the coexistence mechanisms at play. We briefly review the main approaches to describe spatial networks and describe three simple toy models of metacommunity dynamics. We take this opportunity to review their assumptions and main predictions. We then conduct simulations of these models to reveal with simple examples the impact of spatial network structure on diversity distribution. The simulation results show that competitive interactions buffer the potential impact of landscape structure. The strongest relationship between node position in the landscape and species richness was observed for the patch dynamics model without any interactions. On the other hand, strong and unequal competitive interactions minimized the effect of node position. We conclude that the

Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis

Science.gov (United States)

Elsholz, Alexander K. W.; Birk, Marlene S.; Charpentier, Emmanuelle; Turgay, Kürşad

2017-01-01

Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics. PMID:28748186

Functional Diversity of AAA+ Protease Complexes in Bacillus subtilis.

Science.gov (United States)

Elsholz, Alexander K W; Birk, Marlene S; Charpentier, Emmanuelle; Turgay, Kürşad

2017-01-01

Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis . We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics.

RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis

Directory of Open Access Journals (Sweden)

Garcia Tzintzuni I

2012-09-01

Full Text Available Abstract Background The release of oil resulting from the blowout of the Deepwater Horizon (DH drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants. This event impacted a wide range of ecological habitats with a complex mix of pollutants whose biological impact is still not yet fully understood. To better understand the effects on a vertebrate genome, we studied gene expression in the salt marsh minnow Fundulus grandis, which is local to the northern coast of the Gulf of Mexico and is a sister species of the ecotoxicological model Fundulus heteroclitus. To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq in F. grandis populations in the marshes and estuaries impacted by DH oil release. This application of RNA-Seq to a non-model, wild, and ecologically significant organism is an important evaluation of the technology to quickly assess similar events in the future. Results Our de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. In many cases several of these could be associated with a common reference sequence using blast to query a reference database. This reduced the set of significant genes to 1,070 down-regulated and 1,251 up-regulated genes. These genes indicate a broad and complex genomic response to DH oil exposure including the expected AHR-mediated response and CYP genes. In addition a response to hypoxic conditions and an immune response are also indicated. Several genes in the choriogenin family were down-regulated in the exposed group; a response that is consistent with AH exposure. These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set. Conclusion RNA-Seq may be successfully applied to feral and

Breast-axillary complex in HIV/AIDS patients.

Science.gov (United States)

Eni, U E; Naaya, H U; Yawe, K D T; Lawan, M A; Bakari, A A

2010-01-01

HIV/AIDS have not only increased the health care burden especially in developing countries, it equally complicates the presentation of many diseases. Some well known disease entities now occur in fulminant complexities not previously described or known as such. The objective of this article is to report an unusual presentation of HIV/AIDS patients to the surgeon with Axillary and ipsilateral breast swelling. This is a report of three cases seen and managed by the authors. Three adult female patients presented with progressively increasing axillary and ipsilateral breast swellings. They also had associated fevers and weight loss. Their main concern had been development of breast cancer. One of the patients was a known retroviral positive on Highly Active Anti-Retroviral Therapy (HAART). Examination revealed axillary abscess and ipsilateral breast oedema in two cases. The patient on HAART had a hard breast-axillary mass complex. Biopsy (FNAB) revealed inflammatory cells and no malignancy in all three cases. HIV screening was positive in all cases. One of the patients had excision of breast-axillary mass complex, and the histology showed features of chronic inflammation, with no malignant cells. The other two had incision and drainage of their axillary abscess. This shows the ubiquitous presentation of HIV/AIDS in our environment and surgeons should be aware of the breast axillary complex in HIV/AIDS. Medical practitioners should be careful to obtain accurate diagnosis before embarking on treatment especially mutilating surgical procedures.

Nicotine affects protein complex rearrangement in Caenorhabditis elegans cells.

Science.gov (United States)

Sobkowiak, Robert; Zielezinski, Andrzej; Karlowski, Wojciech M; Lesicki, Andrzej

2017-10-01

Nicotine may affect cell function by rearranging protein complexes. We aimed to determine nicotine-induced alterations of protein complexes in Caenorhabditis elegans (C. elegans) cells, thereby revealing links between nicotine exposure and protein complex modulation. We compared the proteomic alterations induced by low and high nicotine concentrations (0.01 mM and 1 mM) with the control (no nicotine) in vivo by using mass spectrometry (MS)-based techniques, specifically the cetyltrimethylammonium bromide (CTAB) discontinuous gel electrophoresis coupled with liquid chromatography (LC)-MS/MS and spectral counting. As a result, we identified dozens of C. elegans proteins that are present exclusively or in higher abundance in either nicotine-treated or untreated worms. Based on these results, we report a possible network that captures the key protein components of nicotine-induced protein complexes and speculate how the different protein modules relate to their distinct physiological roles. Using functional annotation of detected proteins, we hypothesize that the identified complexes can modulate the energy metabolism and level of oxidative stress. These proteins can also be involved in modulation of gene expression and may be crucial in Alzheimer's disease. The findings reported in our study reveal putative intracellular interactions of many proteins with the cytoskeleton and may contribute to the understanding of the mechanisms of nicotinic acetylcholine receptor (nAChR) signaling and trafficking in cells.

Nonexplicit change detection in complex dynamic settings: what eye movements reveal.

Science.gov (United States)

Vachon, François; Vallières, Benoît R; Jones, Dylan M; Tremblay, Sébastien

2012-12-01

We employed a computer-controlled command-and-control (C2) simulation and recorded eye movements to examine the extent and nature of the inability to detect critical changes in dynamic displays when change detection is implicit (i.e., requires no explicit report) to the operator's task. Change blindness-the failure to notice significant changes to a visual scene-may have dire consequences on performance in C2 and surveillance operations. Participants performed a radar-based risk-assessment task involving multiple subtasks. Although participants were not required to explicitly report critical changes to the operational display, change detection was critical in informing decision making. Participants' eye movements were used as an index of visual attention across the display. Nonfixated (i.e., unattended) changes were more likely to be missed than were fixated (i.e., attended) changes, supporting the idea that focused attention is necessary for conscious change detection. The finding of significant pupil dilation for changes undetected but fixated suggests that attended changes can nonetheless be missed because of a failure of attentional processes. Change blindness in complex dynamic displays takes the form of failures in establishing task-appropriate patterns of attentional allocation. These findings have implications in the design of change-detection support tools for dynamic displays and work procedure in C2 and surveillance.

THO/TREX complex

KAUST Repository

Dö ll, Stefanie; Kuhlmann, Markus; Rutten, Twan; Mette, Michael F.; Scharfenberg, Sarah; Petridis, Antonios; Berreth, Dorothee-Carina; Mock, Hans-Peter

2017-01-01

Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low-temperature stress in Arabidopsis thaliana. A genetic screen for altered scopolin levels in A. thaliana revealed a mutant compromised in scopolin accumulation in response to stress; the lesion was present in a homologue of THO1 coding for a subunit of the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants defective in THO, AGO1, SDS3 and RDR6 were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing such as the trans-acting small interfering RNA pathway, which requires THO/TREX function.

Microbial degradation of coconut coir dust for biomass production

Energy Technology Data Exchange (ETDEWEB)

Uyenco, F.R.; Ochoa, J.A.K.

Several species of white-rot fungi were studied for its ability to degrade the lignocellulose components of coir dust at optimum conditions. The most effective fungi was Phanerochaeta chrysosporium UPCC 4003. This organism degraded the lignocellulose complex of coir dust at a rate of about 25 percent in 4 weeks. The degradation process was carried on with minimal nitrogen concentration, coconut water supplementation and moisture levels between 85-90 percent. Shake flask cultures of the degraded coir dust using cellulolytic fungi were not effective. In fermentor cultures with Chaetomium cellulolyticum UPCC 3934, supplemented coir dust was converted into a microbial biomass product (MBP) with 15.58 percent lignin, 19.20 percent cellulose and 18.87 percent protein. More work is being done on the utilization of coir dust on a low technology.

Fractal analysis reveals reduced complexity of retinal vessels in CADASIL.

Directory of Open Access Journals (Sweden)

Michele Cavallari

2011-04-01

Full Text Available The Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL affects mainly small cerebral arteries and leads to disability and dementia. The relationship between clinical expression of the disease and progression of the microvessel pathology is, however, uncertain as we lack tools for imaging brain vessels in vivo. Ophthalmoscopy is regarded as a window into the cerebral microcirculation. In this study we carried out an ophthalmoscopic examination in subjects with CADASIL. Specifically, we performed fractal analysis of digital retinal photographs. Data are expressed as mean fractal dimension (mean-D, a parameter that reflects complexity of the retinal vessel branching. Ten subjects with genetically confirmed diagnosis of CADASIL and 10 sex and age-matched control subjects were enrolled. Fractal analysis of retinal digital images was performed by means of a computer-based program, and the data expressed as mean-D. Brain MRI lesion volume in FLAIR and T1-weighted images was assessed using MIPAV software. Paired t-test was used to disclose differences in mean-D between CADASIL and control groups. Spearman rank analysis was performed to evaluate potential associations between mean-D values and both disease duration and disease severity, the latter expressed as brain MRI lesion volumes, in the subjects with CADASIL. The results showed that mean-D value of patients (1.42±0.05; mean±SD was lower than control (1.50±0.04; p = 0.002. Mean-D did not correlate with disease duration nor with MRI lesion volumes of the subjects with CADASIL. The findings suggest that fractal analysis is a sensitive tool to assess changes of retinal vessel branching, likely reflecting early brain microvessel alterations, in CADASIL patients.

Metallacyclopentadienes: structural features and coordination in transition metal complexes

International Nuclear Information System (INIS)

Dolgushin, Fedor M; Yanovsky, Aleksandr I; Antipin, Mikhail Yu

2004-01-01

Results of structural studies of polynuclear transition metal complexes containing the metallacyclopentadiene fragment are overviewed. The structural features of the complexes in relation to the nature of the substituents in the organic moiety of the metallacycles, the nature of the transition metals and their ligand environment are analysed. The main structural characteristics corresponding to different modes of coordination of metallacyclopentadienes to one or two additional metal centres are revealed.

A systems level approach reveals new gene regulatory modules in the developing ear

OpenAIRE

Chen, Jingchen; Tambalo, Monica; Barembaum, Meyer; Ranganathan, Ramya; Simões-Costa, Marcos; Bronner, Marianne E.; Streit, Andrea

2017-01-01

The inner ear is a complex vertebrate sense organ, yet it arises from a simple epithelium, the otic placode. Specification towards otic fate requires diverse signals and transcriptional inputs that act sequentially and/or in parallel. Using the chick embryo, we uncover novel genes in the gene regulatory network underlying otic commitment and reveal dynamic changes in gene expression. Functional analysis of selected transcription factors reveals the genetic hierarchy underlying the transition ...

Biodegradation of Phenol Adsorbed on Soil in the Presence of Polycyclic Aromatic Hydrocarbons.

Czech Academy of Sciences Publication Activity Database

Maléterová, Ywetta; Matějková, Martina; Demnerová, K.; Stiborová, H.; Kaštánek, František; Šolcová, Olga

2016-01-01

Roč. 3, č. 1 (2016), s. 87-98 ISSN 2397-2076 R&D Projects: GA TA ČR TA04020700 Institutional support: RVO:67985858 Keywords : polycyclic artomatic hydrocarbons * phenol * bioremediation * candida tropicalis * phanerochaete chrysosporium Subject RIV: CI - Industrial Chemistry, Chemical Engineering

Testing the Tolerance and Growth of eleven Trichoderma Strains to crude oil, naphthalene and phenanthrene

Energy Technology Data Exchange (ETDEWEB)

Argumedo-Delira, R.; Alarcon, A.; Ferrera-Cerrato, R.; Pena-Cabriales, J. J.

2009-07-01

Petroleum hydrocarbons (PH) are major organic contaminants in soils, and are subjected to degradation process mediated by either rhizospheric or soil microorganisms. Filamentous fungi such as cunninghamella elegans and Phanerochaete chrysosporium have a significant role on degradation of organic contaminants in soils. (Author)

Testing the Tolerance and Growth of eleven Trichoderma Strains to crude oil, naphthalene and phenanthrene

International Nuclear Information System (INIS)

Argumedo-Delira, R.; Alarcon, A.; Ferrera-Cerrato, R.; Pena-Cabriales, J. J.

2009-01-01

Petroleum hydrocarbons (PH) are major organic contaminants in soils, and are subjected to degradation process mediated by either rhizospheric or soil microorganisms. Filamentous fungi such as cunninghamella elegans and Phanerochaete chrysosporium have a significant role on degradation of organic contaminants in soils. (Author)

Eigenspaces of networks reveal the overlapping and hierarchical community structure more precisely

International Nuclear Information System (INIS)

Ma, Xiaoke; Gao, Lin; Yong, Xuerong

2010-01-01

Identifying community structure is fundamental for revealing the structure–functionality relationship in complex networks, and spectral algorithms have been shown to be powerful for this purpose. In a traditional spectral algorithm, each vertex of a network is embedded into a spectral space by making use of the eigenvectors of the adjacency matrix or Laplacian matrix of the graph. In this paper, a novel spectral approach for revealing the overlapping and hierarchical community structure of complex networks is proposed by not only using the eigenvalues and eigenvectors but also the properties of eigenspaces of the networks involved. This gives us a better characterization of community. We first show that the communicability between a pair of vertices can be rewritten in term of eigenspaces of a network. An agglomerative clustering algorithm is then presented to discover the hierarchical communities using the communicability matrix. Finally, these overlapping vertices are discovered with the corresponding eigenspaces, based on the fact that the vertices more densely connected amongst one another are more likely to be linked through short cycles. Compared with the traditional spectral algorithms, our algorithm can identify both the overlapping and hierarchical community without increasing the time complexity O(n 3 ), where n is the size of the network. Furthermore, our algorithm can also distinguish the overlapping vertices from bridges. The method is tested by applying it to some computer-generated and real-world networks. The experimental results indicate that our algorithm can reveal community structure more precisely than the traditional spectral approaches

Camelid genomes reveal evolution and adaptation to desert environments.

Science.gov (United States)

Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

2014-10-21

Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed.

Science.gov (United States)

Boykin, Laura M; Bell, Charles D; Evans, Gregory; Small, Ian; De Barro, Paul J

2013-10-18

Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and has been driven in part by human-assisted dispersal supported through rapid global trade and low-cost air passenger transport. One of these pests, is the whitefly, Bemisia tabaci, a cryptic species complex that contains some of the world's most damaging pests of agriculture. The complex shows considerable genetic diversity and strong phylogeographic relationships. One consequence of the considerable impact that members of the B. tabaci complex have on agriculture, is the view that human activity, particularly in relation to agricultural practices, such as use of insecticides, has driven the diversification found within the species complex. This has been particularly so in the case of two members of the complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), which have become globally distributed invasive species. An alternative hypothesis is that diversification is due to paleogeographic and paleoclimatological changes. The idea that human activity is driving speciation within the B. tabaci complex has never been tested, but the increased interest in fossil whiteflies and the growth in molecular data have enabled us to apply a relaxed molecular clock and so estimate divergence dates for the major lineages within the B. tabaci species complex. The divergence estimates do not support the view that human activity has been a major driver of diversification. Our analysis suggests that the major lineages within the complex arose approximately 60-30 mya and the highly invasive MED and MEAM1 split from the rest of the species complex around 12 mya well before the evolution of Homo sapiens and agriculture. Furthermore, the divergence dates coincide with a period

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

Biodegradation of hazardous waste using white rot fungus: Project planning and concept development document

International Nuclear Information System (INIS)

Luey, J.; Brouns, T.M.; Elliott, M.L.

1990-11-01

The white rot fungus Phanerochaete chrysosporium has been shown to effectively degrade pollutants such as trichlorophenol, polychlorinated biphenyls (PCBs), dioxins and other halogenated aromatic compounds. These refractory organic compounds and many others have been identified in the tank waste, groundwater and soil of various US Department of Energy (DOE) sites. The treatment of these refractory organic compounds has been identified as a high priority for DOE's Research, Development, Demonstration, Testing, and Evaluation (RDDT ampersand E) waste treatment programs. Unlike many bacteria, the white rot fungus P. chrysosporium is capable of degrading these types of refractory organics and may be valuable for the treatment of wastes containing multiple pollutants. The objectives of this project are to identify DOE waste problems amenable to white rot fungus treatment and to develop and demonstrate white rot fungus treatment process for these hazardous organic compounds. 32 refs., 6 figs., 7 tabs

Effects of Rhamnolipid and Microbial Inoculants on the Vermicomposting of Green Waste with Eisenia fetida.

Science.gov (United States)

Gong, Xiaoqiang; Wei, Le; Yu, Xin; Li, Suyan; Sun, Xiangyang; Wang, Xinyu

2017-01-01

The effects of adding the biosurfactant rhamnolipid, the lignolytic and cellulolytic fungus Phanerochete chrysosporium, and the free-living nitrogen-fixing bacterium Azotobacter chrococcum on vermicomposting of green waste with Eisenia fetida was investigated. The addition of rhamnolipid and/or either microorganism alone or in all combinations significantly increased E. fetida growth rate, the number of E. fetida juveniles and cocoons, the population densities of cellulolytic fungi and Azotobacter bacteria, and cellulase and urease activities in the vermicomposts. The quality of the final vermicompost (in terms of electrical conductivity, nutrient content, C/N ratio, humic acid content, lignin and cellulose contents, and phytotoxicity to germinating seeds) was enhanced by addition of rhamnolipid and/or microorganisms. The physical characteristics of vermicomposts produced with rhamnolipid and/or microorganisms were acceptable for agricultural application. The best quality vermicompost was obtained with the combined addition of P. chrysosporium, A. chrococcum, and rhamnolipid.

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.

Ecomorph or endangered coral? DNA and microstructure reveal hawaiian species complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli.

Directory of Open Access Journals (Sweden)

Zac H Forsman

2010-12-01

Full Text Available M. dilatata, M. flabellata, and M. patula and 80 other scleractinian corals were petitioned to be listed under the US Endangered Species Act (ESA, which would have major conservation implications. One of the difficulties with this evaluation is that reproductive boundaries between morphologically defined coral species are often permeable, and morphology can be wildly variable. We examined genetic and morphological variation in Hawaiian Montipora with a suite of molecular markers (mitochondrial: COI, CR, Cyt-B, 16S, ATP6; nuclear: ATPsβ, ITS and microscopic skeletal measurements. Mitochondrial markers and the ITS region revealed four distinct clades: I M. patula/M. verrilli, II M. cf. incrassata, III M. capitata, IV M. dilatata/M. flabellata/M. cf. turgescens. These clades are likely to occur outside of Hawai'i according to mitochondrial control region haplotypes from previous studies. The ATPsβ intron data showed a pattern often interpreted as resulting from hybridization and introgression; however, incomplete lineage sorting may be more likely since the multicopy nuclear ITS region was consistent with the mitochondrial data. Furthermore, principal components analysis (PCA of skeletal microstructure was concordant with the mitochondrial clades, while nominal taxa overlapped. The size and shape of verrucae or papillae contributed most to identifying groups, while colony-level morphology was highly variable. It is not yet clear if these species complexes represent population-level variation or incipient speciation (CA<1MYA, two alternatives that have very different conservation implications. This study highlights the difficulty in understanding the scale of genetic and morphological variation that corresponds to species as opposed to population-level variation, information that is essential for conservation and for understanding coral biodiversity.

Differential patterns of cortical activation as a function of fluid reasoning complexity.

Science.gov (United States)

Perfetti, Bernardo; Saggino, Aristide; Ferretti, Antonio; Caulo, Massimo; Romani, Gian Luca; Onofrj, Marco

2009-02-01

Fluid intelligence (gf) refers to abstract reasoning and problem solving abilities. It is considered a human higher cognitive factor central to general intelligence (g). The regions of the cortex supporting gf have been revealed by recent bioimaging studies and valuable hypothesis on the neural correlates of individual differences have been proposed. However, little is known about the interaction between individual variability in gf and variation in cortical activity following task complexity increase. To further investigate this, two samples of participants (high-IQ, N = 8; low-IQ, N = 10) with significant differences in gf underwent two reasoning (moderate and complex) tasks and a control task adapted from the Raven progressive matrices. Functional magnetic resonance was used and the recorded signal analyzed between and within the groups. The present study revealed two opposite patterns of neural activity variation which were probably a reflection of the overall differences in cognitive resource modulation: when complexity increased, high-IQ subjects showed a signal enhancement in some frontal and parietal regions, whereas low-IQ subjects revealed a decreased activity in the same areas. Moreover, a direct comparison between the groups' activation patterns revealed a greater neural activity in the low-IQ sample when conducting moderate task, with a strong involvement of medial and lateral frontal regions thus suggesting that the recruitment of executive functioning might be different between the groups. This study provides evidence for neural differences in facing reasoning complexity among subjects with different gf level that are mediated by specific patterns of activation of the underlying fronto-parietal network.

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

LENUS (Irish Health Repository)

Casey, Fergal

2011-08-22

Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

Factors influencing efficient structure of fuel and energy complex

Science.gov (United States)

Sidorova, N. G.; Novikova, S. A.

2017-10-01

The development of the Russian fuel-energy complex is a priority for the national economic policy, and the Far East is a link between Russia and the Asia-Pacific region. Large-scale engineering of numerous resources of the Far East will force industrial development, increase living standard and strengthen Russia’s position in the global energy market. So, revealing the factors which influence rational structure of the fuel-energy complex is very urgent nowadays. With the use of depth analysis of development tendencies of the complex and its problems the authors show ways of its efficiency improvement.

Structural systematics of some metal complexes with 4,5 ...

Indian Academy of Sciences (India)

study reveals that each metal(II) centre in the four complexes adopts distorted octahedral geometry with MN6 ... potassium permanganate (E Merck, India), potassium. 717 ... The final reaction solu- ..... ble in water, methanol, acetonitrile, etc.

Improving Nutritional Quality of Cocoa Pod (Theobroma cacao) through Chemical and Biological Treatments for Ruminant Feeding: In vitro and In vivo Evaluation.

Science.gov (United States)

Laconi, Erika B; Jayanegara, Anuraga

2015-03-01

Cocoa pod is among the by-products of cocoa (Theobroma cacao) plantations. The aim of this study was to apply a number of treatments in order to improve nutritional quality of cocoa pod for feeding of ruminants. Cocoa pod was subjected to different treatments, i.e. C (cocoa pod without any treatment or control), CAm (cocoa pod+1.5% urea), CMo (cocoa pod+3% molasses), CRu (cocoa pod+3% rumen content) and CPh (cocoa pod+3% molasses+Phanerochaete chrysosporium inoculum). Analysis of proximate and Van Soest's fiber fraction were performed on the respective treatments. The pods were then subjected to an in vitro digestibility evaluation by incubation in rumen fluid-buffer medium, employing a randomized complete block design (n = 3 replicates). Further, an in vivo evaluation of the pods (35% inclusion level in total mixed ration) was conducted by feeding to young Holstein steers (average body weight of 145±3.6 kg) with a 5×5 latin square design arrangement (n = 5 replicates). Each experimental period lasted for 30 d; the first 20 d was for feed adaptation, the next 3 d was for sampling of rumen liquid, and the last 7 d was for measurements of digestibility and N balance. Results revealed that lignin content was reduced significantly when cocoa pod was treated with urea, molasses, rumen content or P. chrysosporium (pCAm>CRu>CMo. Among all treatments, CAm and CPh treatments significantly improved the in vitro dry matter and organic matter digestibility (pcocoa pod. Average daily gain of steers receiving CAm or CPh treatment was significantly higher than that of control (pcocoa pod.

Proteomic analysis of the crayfish gastrolith chitinous extracellular matrix reveals putative protein complexes and a central role for GAP 65.

Science.gov (United States)

Glazer, Lilah; Roth, Ziv; Weil, Simy; Aflalo, Eliahu D; Khalaila, Isam; Sagi, Amir

2015-10-14

Chitin is a major component of arthropod cuticles, where it forms a three-dimensional network that constitutes the scaffold upon which cuticles form. The chitin fibers that form this network are closely associated with specific structural proteins, while the cuticular matrix contains many additional structural, enzymatic and other proteins. We study the crayfish gastrolith as a simple model for the assembly of calcified cuticular structures, with particular focus on the proteins involved in this process. The present study integrates a gastrolith-forming epithelium transcriptomic library with data from mass spectrometry analysis of proteins extracted from the gastrolith matrix to obtain a near-complete picture of gastrolith protein content. Using native protein separation we identified 24 matrix proteins, of which 14 are novel. Further analysis led to discovery of three putative protein complexes, all containing GAP 65 the most abundant gastrolith structural protein. Using immunological methods we further studied the role of GAP 65 in the gastrolith matrix and forming epithelium, as well as in the newly identified protein complexes. We propose that gastrolith matrix construction is a sequential process in which protein complexes are dynamically assembled and disassembled around GAP 65, thus changing their functional properties to perform each step in the construction process. The scientific interest on which this study is based arises from three main features of gastroliths: (1) Gastroliths possess partial analogy to cuticles both in structural and molecular properties, and may be regarded, with the appropriate reservations (see Introduction), as simple models for cuticle assembly. At the same time, gastroliths are terminally assembled during a well-defined period, which can be controlled in the laboratory, making them significantly easier to study than cuticles. (2) Gastroliths, like the crayfish exoskeleton, contain stable amorphous calcium carbonate (ACC) rather

Evaluation of Potential Fungal Species for the in situ Simultaneous Saccharification and Fermentation (SSF of Cellulosic Material

Directory of Open Access Journals (Sweden)

Leeuwen, J.

2011-01-01

Full Text Available Three fungal species were evaluated for their abilities to saccharify pure cellulose. The three species chosen represented three major wood-rot molds; brown rot (Gloeophyllum trabeum, white rot (Phanerochaete chrysosporium and soft rot (Trichoderma reesei. After solid state fermentation of the fungi on the filter paper for four days, the saccharified cellulose was then fermented to ethanol by using Saccharomyces cerevisiae. The efficiency of the fungal species in saccharifying the filter paper was compared against a low dose (25 FPU/g cellulose of a commercial cellulase. Total sugar, cellobiose and glucose were monitored during the fermentation period, along with ethanol, acetic acid and lactic acid. Results indicated that the most efficient fungal species in saccharifying the filter paper was T. reesei with 5.13 g/100 g filter paper of ethanol being produced at days 5, followed by P. chrysosporium at 1.79 g/100 g filter paper. No ethanol was detected for the filter paper treated with G. trabeum throughout the five day fermentation stage. Acetic acid was only produced in the sample treated with T. reesei and the commercial enzyme, with concentration 0.95 and 2.57 g/100 g filter paper, respectively at day 5. Lactic acid production was not detected for all the fungal treated filter paper after day 5. Our study indicated that there is potential in utilizing in situ enzymatic saccharification of biomass by using T. reesei and P. chrysosporium that may lead to an economical simultaneous saccharification and fermentation process for the production of fuel ethanol.

Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage.

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Drissi, Romain; Dubois, Marie-Line; Douziech, Mélanie; Boisvert, François-Michel

2015-07-01

The minichromosome maintenance complex (MCM) proteins are required for processive DNA replication and are a target of S-phase checkpoints. The eukaryotic MCM complex consists of six proteins (MCM2-7) that form a heterohexameric ring with DNA helicase activity, which is loaded on chromatin to form the pre-replication complex. Upon entry in S phase, the helicase is activated and opens the DNA duplex to recruit DNA polymerases at the replication fork. The MCM complex thus plays a crucial role during DNA replication, but recent work suggests that MCM proteins could also be involved in DNA repair. Here, we employed a combination of stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics with immunoprecipitation of green fluorescent protein-tagged fusion proteins to identify proteins interacting with the MCM complex, and quantify changes in interactions in response to DNA damage. Interestingly, the MCM complex showed very dynamic changes in interaction with proteins such as Importin7, the histone chaperone ASF1, and the Chromodomain helicase DNA binding protein 3 (CHD3) following DNA damage. These changes in interactions were accompanied by an increase in phosphorylation and ubiquitination on specific sites on the MCM proteins and an increase in the co-localization of the MCM complex with γ-H2AX, confirming the recruitment of these proteins to sites of DNA damage. In summary, our data indicate that the MCM proteins is involved in chromatin remodeling in response to DNA damage. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Decoding Complex Cognitive States Online by Manifold Regularization in Real-Time fMRI

DEFF Research Database (Denmark)

Hansen, Toke Jansen; Hansen, Lars Kai; Madsen, Kristoffer Hougaard

2011-01-01

Human decision making is complex and influenced by many factors on multiple time scales, reflected in the numerous brain networks and connectivity patterns involved as revealed by fMRI. We address mislabeling issues in paradigms involving complex cognition, by considering a manifold regularizing...

New levels of language processing complexity and organization revealed by granger causation.

Science.gov (United States)

Gow, David W; Caplan, David N

2012-01-01

Granger causation analysis of high spatiotemporal resolution reconstructions of brain activation offers a new window on the dynamic interactions between brain areas that support language processing. Premised on the observation that causes both precede and uniquely predict their effects, this approach provides an intuitive, model-free means of identifying directed causal interactions in the brain. It requires the analysis of all non-redundant potentially interacting signals, and has shown that even "early" processes such as speech perception involve interactions of many areas in a strikingly large network that extends well beyond traditional left hemisphere perisylvian cortex that play out over hundreds of milliseconds. In this paper we describe this technique and review several general findings that reframe the way we think about language processing and brain function in general. These include the extent and complexity of language processing networks, the central role of interactive processing dynamics, the role of processing hubs where the input from many distinct brain regions are integrated, and the degree to which task requirements and stimulus properties influence processing dynamics and inform our understanding of "language-specific" localized processes.

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity.

Science.gov (United States)

Alström, Per; Barnes, Keith N; Olsson, Urban; Barker, F Keith; Bloomer, Paulette; Khan, Aleem Ahmed; Qureshi, Masood Ahmed; Guillaumet, Alban; Crochet, Pierre-André; Ryan, Peter G

2013-12-01

The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data. We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g. in Melanocorypha mongolica and Alauda leucoptera [both

Complex Dynamics in Nonequilibrium Economics and Chemistry

Science.gov (United States)

Wen, Kehong

Complex dynamics provides a new approach in dealing with economic complexity. We study interactively the empirical and theoretical aspects of business cycles. The way of exploring complexity is similar to that in the study of an oscillatory chemical system (BZ system)--a model for modeling complex behavior. We contribute in simulating qualitatively the complex periodic patterns observed from the controlled BZ experiments to narrow the gap between modeling and experiment. The gap between theory and reality is much wider in economics, which involves studies of human expectations and decisions, the essential difference from natural sciences. Our empirical and theoretical studies make substantial progress in closing this gap. With the help from the new development in nonequilibrium physics, i.e., the complex spectral theory, we advance our technique in detecting characteristic time scales from empirical economic data. We obtain correlation resonances, which give oscillating modes with decays for correlation decomposition, from different time series including S&P 500, M2, crude oil spot prices, and GNP. The time scales found are strikingly compatible with business experiences and other studies in business cycles. They reveal the non-Markovian nature of coherent markets. The resonances enhance the evidence of economic chaos obtained by using other tests. The evolving multi-humped distributions produced by the moving-time -window technique reveal the nonequilibrium nature of economic behavior. They reproduce the American economic history of booms and busts. The studies seem to provide a way out of the debate on chaos versus noise and unify the cyclical and stochastic approaches in explaining business fluctuations. Based on these findings and new expectation formulation, we construct a business cycle model which gives qualitatively compatible patterns to those found empirically. The soft-bouncing oscillator model provides a better alternative than the harmonic oscillator

Radiolysis of DNA-protein complexes

Energy Technology Data Exchange (ETDEWEB)

Begusova, Marie [Department of Radiation Dosimetry, Nuclear Physics Institute, Na Truhlarce 39/64, CZ-18086, Prague 8 (Czech Republic)]. E-mail: begusova@ujf.cas.cz; Gillard, Nathalie [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Sy, Denise [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Castaing, Bertrand [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Charlier, Michel [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France); Spotheim-Maurizot, Melanie [Centre de Biophysique Moleculaire, CNRS, rue Charles-Sadron, F-45071 Orleans Cedex 2 (France)

2005-02-01

We discuss here modifications of DNA and protein radiolysis due to the interaction of these two partners in specific complexes. Experimental patterns of frank strand breaks (FSB) and alkali revealed breaks (ARB) obtained for DNA lac operator bound to the lac repressor and for a DNA containing an abasic site analog bound to the formamidopyrimidine-DNA glycosylase are reported. Experimental data are compared to predicted damage distribution obtained using the theoretical model RADACK.

Radiolysis of DNA-protein complexes

International Nuclear Information System (INIS)

Begusova, Marie; Gillard, Nathalie; Sy, Denise; Castaing, Bertrand; Charlier, Michel; Spotheim-Maurizot, Melanie

2005-01-01

We discuss here modifications of DNA and protein radiolysis due to the interaction of these two partners in specific complexes. Experimental patterns of frank strand breaks (FSB) and alkali revealed breaks (ARB) obtained for DNA lac operator bound to the lac repressor and for a DNA containing an abasic site analog bound to the formamidopyrimidine-DNA glycosylase are reported. Experimental data are compared to predicted damage distribution obtained using the theoretical model RADACK

HAB1–SWI3B Interaction Reveals a Link between Abscisic Acid Signaling and Putative SWI/SNF Chromatin-Remodeling Complexes in Arabidopsis[C][W

Science.gov (United States)

Saez, Angela; Rodrigues, Americo; Santiago, Julia; Rubio, Silvia; Rodriguez, Pedro L.

2008-01-01

Abscisic acid (ABA) has an important role for plant growth, development, and stress adaptation. HYPERSENSITIVE TO ABA1 (HAB1) is a protein phosphatase type 2C that plays a key role as a negative regulator of ABA signaling; however, the molecular details of HAB1 action in this process are not known. A two-hybrid screen revealed that SWI3B, an Arabidopsis thaliana homolog of the yeast SWI3 subunit of SWI/SNF chromatin-remodeling complexes, is a prevalent interacting partner of HAB1. The interaction mapped to the N-terminal half of SWI3B and required an intact protein phosphatase catalytic domain. Bimolecular fluorescence complementation and coimmunoprecipitation assays confirmed the interaction of HAB1 and SWI3B in the nucleus of plant cells. swi3b mutants showed a reduced sensitivity to ABA-mediated inhibition of seed germination and growth and reduced expression of the ABA-responsive genes RAB18 and RD29B. Chromatin immunoprecipitation experiments showed that the presence of HAB1 in the vicinity of RD29B and RAB18 promoters was abolished by ABA, which suggests a direct involvement of HAB1 in the regulation of ABA-induced transcription. Additionally, our results uncover SWI3B as a novel positive regulator of ABA signaling and suggest that HAB1 modulates ABA response through the regulation of a putative SWI/SNF chromatin-remodeling complex. PMID:19033529

CYP63A2, a catalytically versatile fungal P450 monooxygenase capable of oxidizing higher-molecular-weight polycyclic aromatic hydrocarbons, alkylphenols, and alkanes

Science.gov (United States)

Cytochrome P450 monooxygenases (P450s) are known to oxidize hydrocarbons albeit with limited substrate specificity across classes of these compounds. Here we report a P450 monooxygenase (CYP63A2) from the model ligninolytic white rot fungus Phanerochaete chrysosporium that was fo...

Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

Science.gov (United States)

Kachhap, Sangita; Singh, Balvinder

2015-01-01

In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

Science.gov (United States)

Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

Science.gov (United States)

Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

2014-01-01

Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

Homology modeling and docking of AahII-Nanobody complexes reveal the epitope binding site on AahII scorpion toxin.

Science.gov (United States)

Ksouri, Ayoub; Ghedira, Kais; Ben Abderrazek, Rahma; Shankar, B A Gowri; Benkahla, Alia; Bishop, Ozlem Tastan; Bouhaouala-Zahar, Balkiss

2018-02-19

Scorpion envenoming and its treatment is a public health problem in many parts of the world due to highly toxic venom polypeptides diffusing rapidly within the body of severely envenomed victims. Recently, 38 AahII-specific Nanobody sequences (Nbs) were retrieved from which the performance of NbAahII10 nanobody candidate, to neutralize the most poisonous venom compound namely AahII acting on sodium channels, was established. Herein, structural computational approach is conducted to elucidate the Nb-AahII interactions that support the biological characteristics, using Nb multiple sequence alignment (MSA) followed by modeling and molecular docking investigations (RosettaAntibody, ZDOCK software tools). Sequence and structural analysis showed two dissimilar residues of NbAahII10 CDR1 (Tyr27 and Tyr29) and an inserted polar residue Ser30 that appear to play an important role. Indeed, CDR3 region of NbAahII10 is characterized by a specific Met104 and two negatively charged residues Asp115 and Asp117. Complex dockings reveal that NbAahII17 and NbAahII38 share one common binding site on the surface of the AahII toxin divergent from the NbAahII10 one's. At least, a couple of NbAahII10 - AahII residue interactions (Gln38 - Asn44 and Arg62, His64, respectively) are mainly involved in the toxic AahII binding site. Altogether, this study gives valuable insights in the design and development of next generation of antivenom. Copyright © 2018 Elsevier Inc. All rights reserved.

A complex regulatory network coordinating cell cycles during C. elegans development is revealed by a genome-wide RNAi screen.

Science.gov (United States)

Roy, Sarah H; Tobin, David V; Memar, Nadin; Beltz, Eleanor; Holmen, Jenna; Clayton, Joseph E; Chiu, Daniel J; Young, Laura D; Green, Travis H; Lubin, Isabella; Liu, Yuying; Conradt, Barbara; Saito, R Mako

2014-02-28

The development and homeostasis of multicellular animals requires precise coordination of cell division and differentiation. We performed a genome-wide RNA interference screen in Caenorhabditis elegans to reveal the components of a regulatory network that promotes developmentally programmed cell-cycle quiescence. The 107 identified genes are predicted to constitute regulatory networks that are conserved among higher animals because almost half of the genes are represented by clear human orthologs. Using a series of mutant backgrounds to assess their genetic activities, the RNA interference clones displaying similar properties were clustered to establish potential regulatory relationships within the network. This approach uncovered four distinct genetic pathways controlling cell-cycle entry during intestinal organogenesis. The enhanced phenotypes observed for animals carrying compound mutations attest to the collaboration between distinct mechanisms to ensure strict developmental regulation of cell cycles. Moreover, we characterized ubc-25, a gene encoding an E2 ubiquitin-conjugating enzyme whose human ortholog, UBE2Q2, is deregulated in several cancers. Our genetic analyses suggested that ubc-25 acts in a linear pathway with cul-1/Cul1, in parallel to pathways employing cki-1/p27 and lin-35/pRb to promote cell-cycle quiescence. Further investigation of the potential regulatory mechanism demonstrated that ubc-25 activity negatively regulates CYE-1/cyclin E protein abundance in vivo. Together, our results show that the ubc-25-mediated pathway acts within a complex network that integrates the actions of multiple molecular mechanisms to control cell cycles during development. Copyright © 2014 Roy et al.

Modularized Functions of the Fanconi Anemia Core Complex

Directory of Open Access Journals (Sweden)

Yaling Huang

2014-06-01

Full Text Available The Fanconi anemia (FA core complex provides the essential E3 ligase function for spatially defined FANCD2 ubiquitination and FA pathway activation. Of the seven FA gene products forming the core complex, FANCL possesses a RING domain with demonstrated E3 ligase activity. The other six components do not have clearly defined roles. Through epistasis analyses, we identify three functional modules in the FA core complex: a catalytic module consisting of FANCL, FANCB, and FAAP100 is absolutely required for the E3 ligase function, and the FANCA-FANCG-FAAP20 and the FANCC-FANCE-FANCF modules provide nonredundant and ancillary functions that help the catalytic module bind chromatin or sites of DNA damage. Disruption of the catalytic module causes complete loss of the core complex function, whereas loss of any ancillary module component does not. Our work reveals the roles of several FA gene products with previously undefined functions and a modularized assembly of the FA core complex.

Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species

NARCIS (Netherlands)

Thompson, S.M.; Tan, Y.P.; Young, A.J.; Neate, S.M.; Aitken, E.A.B.; Shivas, R.G.

2012-01-01

The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are

EXAFS Studies of Some Copper(II) Mixed-Ligand Complexes

International Nuclear Information System (INIS)

Joshi, S. K.; Katare, R. K.; Shrivastava, B. D.

2007-01-01

X-ray K-absorption spectroscopic studies have been carried out on copper (II) mixed-ligand complexes with glutamic acid and aspartic acid as the primary ligands, where as water, pyridine, imidazole and benz-imidazole have been used as secondary ligands. Chemical shifts obtained from the X-ray absorption data have indicated that the glutamic acid complexes are more ionic as compared to their corresponding aspartic acid complexes having similar secondary ligands. Further, we have estimated the average metal-ligand bond distances from the from structure data. For the different complexes studied under the present investigation, the studies reveal that the bonding parameter α1 decreases with the increase in the percentage covalency of the metal-ligand bond. Thus, the bonding parameter α1 may be used for the estimation of percentage covalency of the metal-ligand bond in other similar complexes

Ten-a affects the fusion of central complex primordia in Drosophila.

Directory of Open Access Journals (Sweden)

Xuebo Cheng

Full Text Available The central complex of Drosophila melanogaster plays important functions in various behaviors, such as visual and olfactory memory, visual orientation, sleep, and movement control. However little is known about the genes regulating the development of the central complex. Here we report that a mutant gene affecting central complex morphology, cbd (central brain defect, was mapped to ten-a, a type II trans-membrane protein coding gene. Down-regulation of ten-a in pan-neural cells contributed to abnormal morphology of central complex. Over-expression of ten-a by C767-Gal4 was able to partially restore the abnormal central complex morphology in the cbd mutant. Tracking the development of FB primordia revealed that C767-Gal4 labeled interhemispheric junction that separated fan-shaped body precursors at larval stage withdrew to allow the fusion of the precursors. While the C767-Gal4 labeled structure did not withdraw properly and detached from FB primordia, the two fan-shaped body precursors failed to fuse in the cbd mutant. We propose that the withdrawal of C767-Gal4 labeled structure is related to the formation of the fan-shaped body. Our result revealed the function of ten-a in central brain development, and possible cellular mechanism underlying Drosophila fan-shaped body formation.

Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

Science.gov (United States)

Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

2015-09-01

The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.

COMPLEX HOST-PARASITE SYSTEMS IN MARTES: IMPLICATIONS FOR CONSERVATION BIOLOGY OF ENDEMIC FAUNAS.

Science.gov (United States)

Complex assemblages of hosts and parasites reveal insights about biogeography and ecology and inform us about processes which serve to structure faunal diversity and the biosphere in space and time. Exploring aspects of parasite diversity among martens (species of Martes) and other mustelids reveal...

The lemur diversity of the Fiherenana - Manombo Complex ...

African Journals Online (AJOL)

We conducted the first comprehensive lemur survey of the. Fiherenana - Manombo Complex (Atsimo - Andrefana Region), site of PK32-Ranobe, a new protected area within the Madagascar Protected Area System. Our cross - seasonal surveys of three sites revealed the presence of eight lemur species representing seven ...

β-cyclodextrin inclusion complexes containing Citrus sinensis (L.) Osbeck essential oil: An alternative to control Aedes aegypti larvae

Energy Technology Data Exchange (ETDEWEB)

Galvão, J.G., E-mail: julianaggalvao@gmail.com [Pharmacy Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); Silva, V.F.; Ferreira, S.G. [Pharmacy Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); França, F.R.M. [Chemical Engineering Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); Santos, D.A.; Freitas, L.S.; Alves, P.B. [Chemistry Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); Araújo, A.A.S.; Cavalcanti, S.C.H.; Nunes, R.S. [Pharmacy Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil)

2015-05-20

Highlights: • Thermal analysis was useful to determine the formation of inclusion complexes by paste and co-precipitation methods. • HS/GC-FID quantitative analysis revealed that the best method of obtaining a CSEO/β-CD complex was the PWE, with the largest inclusion content [78.5%]. • The inclusion complex revealed LC{sub 50} of 23.01 ppm, close to CSEO LC{sub 50} 21.5 ppm. - Abstract: The development of β-cyclodextrin (β-CD) complexes is an interesting way for increasing the aqueous solubility of essential oils. The aim of this study was to prepare inclusion complexes of Citrus sinensis essential oil (CSEO) with β-CD using paste complexation (with and without co-solvent) and co-precipitation methods. Additionally, the physicochemical properties of the inclusion complexes using thermal analysis, X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy were evaluated. Furthermore, CSEO content (%) and solubility of complexes were measured. The biological activity against the Aedes aegypti Linn. larvae was further evaluated. For comparison purposes, a physical mixture between β-CD and CSEO was prepared and evaluated. Thermal analysis clearly indicated the formation of complexes by paste and co-precipitation methods. The headspace/gas chromatography quantitative analysis showed inclusions contents higher than 50%. On the other hand, the product revealed LC{sub 50} of 23.01 ppm, close to CSEO LC{sub 50} 21.5 ppm.

β-cyclodextrin inclusion complexes containing Citrus sinensis (L.) Osbeck essential oil: An alternative to control Aedes aegypti larvae

International Nuclear Information System (INIS)

Galvão, J.G.; Silva, V.F.; Ferreira, S.G.; França, F.R.M.; Santos, D.A.; Freitas, L.S.; Alves, P.B.; Araújo, A.A.S.; Cavalcanti, S.C.H.; Nunes, R.S.

2015-01-01

Highlights: • Thermal analysis was useful to determine the formation of inclusion complexes by paste and co-precipitation methods. • HS/GC-FID quantitative analysis revealed that the best method of obtaining a CSEO/β-CD complex was the PWE, with the largest inclusion content [78.5%]. • The inclusion complex revealed LC 50 of 23.01 ppm, close to CSEO LC 50 21.5 ppm. - Abstract: The development of β-cyclodextrin (β-CD) complexes is an interesting way for increasing the aqueous solubility of essential oils. The aim of this study was to prepare inclusion complexes of Citrus sinensis essential oil (CSEO) with β-CD using paste complexation (with and without co-solvent) and co-precipitation methods. Additionally, the physicochemical properties of the inclusion complexes using thermal analysis, X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy were evaluated. Furthermore, CSEO content (%) and solubility of complexes were measured. The biological activity against the Aedes aegypti Linn. larvae was further evaluated. For comparison purposes, a physical mixture between β-CD and CSEO was prepared and evaluated. Thermal analysis clearly indicated the formation of complexes by paste and co-precipitation methods. The headspace/gas chromatography quantitative analysis showed inclusions contents higher than 50%. On the other hand, the product revealed LC 50 of 23.01 ppm, close to CSEO LC 50 21.5 ppm

Lanthanide (III) complexes of 2-(N-salicylideneamino)-4-phenylthiazole

International Nuclear Information System (INIS)

Sasidharan, G.N.; Mohanan, K.; Lakshmi Prabha, A.N.

2002-01-01

Lanthanide(III) complexes of 2-(N-salicylideneamino)-4- phenylthiazole (HSAT) have been synthesised and characterised by elemental, analytical, thermogravimetric, molar conductance, UV- visible, IR and NMR spectral data. The ligand coordinates to the lanthanide(III) ion in a tridentate fashion without deprotonation, giving complexes of the type [Ln(HSAT) 2 (NO 3 ) 3 ] and [Ln(HSAT) 2 (H 2 0) 3 Cl 3 ]. The spectral data reveal that the ligand is bonded to the lanthanide ion through azomethine nitrogen, ring nitrogen and phenolic oxygen without deprotonation. The nitrate group acts in a bidentate fashion. The ligand and the metal complexes exhibit antibacterial and antifungal activities. (author)

Antidiabetic phospholipid-nuclear receptor complex reveals the mechanism for phospholipid-driven gene regulation

Energy Technology Data Exchange (ETDEWEB)

Musille, Paul M; Pathak, Manish C; Lauer, Janelle L; Hudson, William H; Griffin, Patrick R; Ortlund, Eric A [Emory-MED; (Scripps)

2013-01-31

The human nuclear receptor liver receptor homolog-1 (LRH-1) has an important role in controlling lipid and cholesterol homeostasis and is a potential target for the treatment of diabetes and hepatic diseases. LRH-1 is known to bind phospholipids, but the role of phospholipids in controlling LRH-1 activation remains highly debated. Here we describe the structure of both apo LRH-1 and LRH-1 in complex with the antidiabetic phospholipid dilauroylphosphatidylcholine (DLPC). Together with hydrogen-deuterium exchange MS and functional data, our studies show that DLPC binding is a dynamic process that alters co-regulator selectivity. We show that the lipid-free receptor undergoes previously unrecognized structural fluctuations, allowing it to interact with widely expressed co-repressors. These observations enhance our understanding of LRH-1 regulation and highlight its importance as a new therapeutic target for controlling diabetes.

New levels of language processing complexity and organization revealed by Granger causation

Directory of Open Access Journals (Sweden)

David W Gow

2012-11-01

Full Text Available Granger causation analysis of high spatiotemporal resolution reconstructions of brain activation offers a new window on the dynamic interactions between brain areas that support language processing. Premised on the observation that causes both precede and uniquely predict their effects, this approach provides an intuitive, model-free means of identifying directed causal interactions in the brain. It requires the analysis of all nonredundant potentially interacting signals, and has shown that even early processes such as speech perception involve interactions of many areas in a strikingly large network that extends well beyond traditional left hemisphere perisylvian cortex that play out over hundreds of milliseconds. In this paper we describe this technique and review several general findings that reframe the way we think about language processing and brain function in general. These include the extent and complexity of language processing networks, the central role of interactive processing dynamics, the role of processing hubs where the input from many distinct brain regions are integrated, and the degree to which task requirements and stimulus properties influence processing dynamics and inform our understanding of language-specific localized processes.

Protein dynamics revealed in the excitonic spectra of single LH2 complexes

International Nuclear Information System (INIS)

Valkunas, Leonas; Janusonis, Julius; Rutkauskas, Danielis; Grondelle, Rienk van

2007-01-01

The fluorescence emission spectrum of single peripheral light-harvesting (LH2) complexes of the photosynthetic purple bacterium Rhodopseudomonas acidophila exhibits remarkable dynamics on a time scale of several minutes. Often the spectral properties are quasi-stable; sometimes large spectral jumps to the blue or to the red are observed. To explain the dynamics, every pigment is proposed to be in two conformational substates with different excitation energies, which originate from the conformational state of the protein as a result of pigment-protein interaction. Due to the excitonic coupling in the ring of 18 pigments, the two-state assumption generates a substantial amount of distinct spectroscopic states, which reflect part of the inhomogeneous distributed spectral properties of LH2. To describe the observed dynamics, spontaneous and light-induced transitions are introduced between the two states. For each 'realization of the disorder', the spectral properties are calculated using a disordered exciton model combined with the modified Redfield theory to obtain realistic spectral line shapes. The single-molecule fluorescence peak (FLP) distribution, the distribution dependence on the excitation intensity, and the FLP time traces are well described within the framework of this model

Prospects for bioprocess development based on recent genome advances in lignocellulose degrading basidiomycetes

Science.gov (United States)

Chiaki Hori; Daniel Cullen

2016-01-01

Efficient and complete degradation of woody plant cell walls requires the concerted action of hydrolytic and oxidative systems possessed by a relatively small group of filamentous basidiomycetous fungi. Among these wood decay species, Phanerochaete chrysosporium was the first to be sequenced (Martinez et al. 2004). In...

Charge Transfer at the Qo-Site of the Cytochrome bc1 Complex Leads to Superoxide Production

DEFF Research Database (Denmark)

Bøgh Salo, Adrian; Husen, Peter; Solov'yov, Ilia A

2017-01-01

The cytochrome bc1 complex is the third protein complex in the electron transport chain of mitochondria or photosynthetic bacteria, and it serves to create an electrochemical gradient across a cellular membrane, which is used to drive ATP synthesis. The purpose of this study is to investigate...... interactions involving an occasionally trapped oxygen molecule (O2) at the so-called Qo site of the bc1 complex, which is one of the central active sites of the protein complex, where redox reactions are expected to occur. The investigation focuses on revealing the possibility of the oxygen molecule...... to influence the normal operation of the bc1 complex and acquire an extra electron, thus becoming superoxide, a biologically toxic free radical. The process is modeled by applying quantum chemical calculations to previously performed classical molecular dynamics simulations. Investigations reveal several...

Comparative efficacy and pathogenicity of keratinophilic soil fungi against Culex quinquefasciatus larvae.

Science.gov (United States)

Mohanty, Suman Sundar; Prakash, Soam

2010-09-01

Out of seven fungal species belonging to four genera isolated from pond and wallow soils using feathers of Pavo cristatus as bait, four species viz., Aspergillus flavus, Aspergillus niger, Chrysosporium pseudomerdarium and Trichophyton ajelloi were most frequent. Chrysosporium and Trichophyton spp. were more pathogenic on Culex quinquefasciatus larvae than Aspergillus and Penicillium. The bioefficacy tests conducted as per the protocol of World Health Organization and the LC(50) values calculated by the Probit analysis showed that 3(rd)-instar C. quinquefasciatus were more susceptible to the conidia of above fungi. Highest mortality was observed in the larvae of C. quinquefasciatus when exposed to T. ajelloi. The density of fungal conidia was greatest on the ventral brush, palmate hair and anal region of the mosquito larvae after exposing for 72 hours. The potentiality of these fungi for use in the control of C. quinquefasciatus is discussed which can be exploited as a suitable biocontrol agent in the tropics.

Biosoftening of coir fiber using selected microorganisms.

Science.gov (United States)

Rajan, Akhila; Senan, Resmi C; Pavithran, C; Abraham, T Emilia

2005-12-01

Coir fiber belongs to the group of hard structural fibers obtained from coconut husk. As lignin is the main constituent of coir responsible for its stiffness, microbes that selectively remove lignin without loss of appreciable amounts of cellulose are extremely attractive in biosoftening. Five isolated strains were compared with known strains of bacteria and fungi. The raw fiber treated with Pseudomonas putida and Phanerocheate chrysosporium produced better softened fiber at 30+/-2 degrees C and neutral pH. FeSO4 and humic acid were found to be the best inducers for P. chrysosporium and P. putida, respectively, while sucrose and dextrose were the best C-sources for both. Biosoftening of unretted coir fibers was more advantageous than the retted fibers. Unlike the weak chemically softened fiber, microbial treatment produced soft, whiter fibers having better tensile strength and elongation (44.6-44.8%) properties. Scanning electron microscopy photos showed the mycelia penetrating the pores of the fiber, removing the tylose plug and degrading lignin.

Effect of Saprotrophic Soil Fungi on Toxocara canis Eggs

Directory of Open Access Journals (Sweden)

Ciarmela, M. L.

2010-01-01

Full Text Available The purpose of this work was to assess the ovicidal activity of Chrysosporium merdarium, Trichoderma harzianum, Fusarium oxysporum, F. moniliforme and F. sulphureum isolated from public areas in the city of La Plata, Argentina, on Toxocara canis eggs in vitro. Each species were cultured on water agar 2% with a suspension of immature-stage T. canis eggs. At 4, 7, 14, 21 and 28 days post-culture, they were observed by light and scanning electron microscopy. One hundred eggs were evaluated and scored according to Lỳsek’s ovicidal effect classification. These procedures were repeated three times which each fungal species. Chrysosporium merdarium and F. oxysporum showed very high ovicidal activity, F. sulphureum high ovicidal activity, F. moniliforme intermediate ovicidal activity and T. harzianum did not affect the viability of T. canis eggs. Taking into account the effects on human and animal health and the environment, the species with better prospects for studying its potential use as biological control was F. sulphureum.

Sequential low and medium frequency ultrasound assists biodegradation of wheat chaff by white rot fungal enzymes.

Science.gov (United States)

Oliver, Christine M; Mawson, Raymond; Melton, Laurence D; Dumsday, Geoff; Welch, Jessica; Sanguansri, Peerasak; Singh, Tanoj K; Augustin, Mary Ann

2014-10-13

The consequences of ultrasonic pre-treatment using low (40 kHz) and medium (270 kHz) frequency (40 kHz followed by 270 kHz) on the degradation of wheat chaff (8 g 100ml(-1) acetate buffer, pH 5) were evaluated. In addition, the effects of the ultrasonic pre-treatment on the degradation of the wheat chaff when subsequently exposed to enzyme extracts from two white rot fungi (Phanerochaete chrysosporium and Trametes sp.) were investigated. Pre-treatment by sequential low and medium frequency ultrasound had a disruptive effect on the lignocellulosic matrix. Analysis of the phenolic-derived volatiles after enzymatic hydrolysis showed that biodegradation with the enzyme extract obtained from P. chrysosporium was more pronounced compared to that of the Trametes sp. The efficacy of the ultrasonic pre-treatment was attributed to increased enzyme accessibility of the cellulose fibrils due to sonication-induced disruption of the plant surface structure, as shown by changes in the microstructure. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synthesis, structural characterization and cytotoxic activity of two new organoruthenium(II complexes

Directory of Open Access Journals (Sweden)

SANJA GRGURIC-SIPKA

2008-06-01

Full Text Available Two new p-cymene ruthenium(II complexes containing as additional ligands N-methylpiperazine ([(η6-p-cymeneRuCl2(CH3NH(CH24NH]PF6, complex 1 or vitamin K3-thiosemicarbazone ([(η6-p-cymeneRuCl2(K3tsc], complex 2 were synthesized starting from [(η6-p-cymene2RuCl2]2 and the corresponding ligand. The complexes were characterized by elemental analysis, IR, electronic absorption and NMR spectroscopy. The X-ray crystal structure determination of complex 1 revealed “piano-stool” geometry. The differences in the cytotoxic activity of the two complexes are discussed in terms of the ligand present.

fMRI Reveals Distinct CNS Processing during Symptomatic and Recovered Complex Regional Pain Syndrome in Children

Science.gov (United States)

Lebel, A.; Becerra, L.; Wallin, D.; Moulton, E. A.; Morris, S.; Pendse, G.; Jasciewicz, J.; Stein, M.; Aiello-Lammens, M.; Grant, E.; Berde, C.; Borsook, D.

2008-01-01

Complex regional pain syndrome (CRPS) in paediatric patients is clinically distinct from the adult condition in which there is often complete resolution of its signs and symptoms within several months to a few years. The ability to compare the symptomatic and asymptomatic condition in the same individuals makes this population interesting for the…

Perturbation of whole-brain dynamics in silico reveals mechanistic differences between brain states

NARCIS (Netherlands)

Deco, Gustavo; Cabral, Joana; Saenger, Victor M; Boly, Melanie; Tagliazucchi, Enzo; Laufs, Helmut; Van Someren, Eus; Jobst, Beatrice; Stevner, Angus; Kringelbach, Morten L

2017-01-01

Human neuroimaging research has revealed that wakefulness and sleep involve very different activity patterns. Yet, it is not clear why brain states differ in their dynamical complexity, e.g. in the level of integration and segregation across brain networks over time. Here, we investigate the

Perturbation of whole-brain dynamics in silico reveals mechanistic differences between brain states

NARCIS (Netherlands)

Deco, Gustavo; Cabral, Joana; Saenger, Victor M; Boly, Melanie; Tagliazucchi, Enzo; Laufs, Helmut; Van Someren, Eus; Jobst, Beatrice M; Stevner, Angus B A; Kringelbach, Morten L

2018-01-01

Human neuroimaging research has revealed that wakefulness and sleep involve very different activity patterns. Yet, it is not clear why brain states differ in their dynamical complexity, e.g. in the level of integration and segregation across brain networks over time. Here, we investigate the

Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2

DEFF Research Database (Denmark)

Broutin, Isabelle; Jomain, Jean-Baptiste; Tallet, Estelle

2010-01-01

We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely relate...... and prostate cancer.......We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely related...... PRL receptor (PRLR) ligand. This structure allows one to draw up an exhaustive inventory of the residues involved at the PRL.PRLR site 2 interface, consistent with all previously reported site-directed mutagenesis data. We propose, with this description, an interaction model involving three structural...

Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history

Science.gov (United States)

da Silva Santos, Anelisie; Trigo, Tatiane Campos; de Oliveira, Tadeu Gomes; Silveira, Leandro

2018-01-01

Abstract The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species’ history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America. PMID:29668017

Plutonium(IV) complexation by diglycolamide ligands - coordination chemistry insight into TODGA-based actinide separations

NARCIS (Netherlands)

Reilly, S.D.; Gaunt, A.J.; Scott, B.L.; Modolo, G.; Iqbal, M.; Verboom, Willem; Sarsfield, M.J.

2012-01-01

Complexation of Pu(IV) with TMDGA, TEDGA, and TODGA diglycolamide ligands was followed by vis-NIR spectroscopy. A crystal structure determination reveals that TMDGA forms a 1:3 homoleptic Pu(IV) complex with the nitrate anions forced into the outer coordination sphere

Peeling Back the Layers of Policy and School Reform: Revealing the Structural and Social Complexities within

Science.gov (United States)

Woodside-Jiron, Haley; Gehsmann, Kristin M.

2009-01-01

This article explores the complex process of school change over a six-year period in one high-poverty, urban elementary school in a northeastern city of the United States. The school included in this instrumental case study was identified by its State Department of Education as "being in need of improvement" in March 2000. Findings…

Chemistry of plutonium revealed

International Nuclear Information System (INIS)

Connick, R.E.

1992-01-01

In 1941 one goal of the Manhattan Project was to unravel the chemistry of the synthetic element plutonium as rapidly as possible. In this paper the work carried out at Berkeley from the spring of 1942 to the summer of 1945 is described briefly. The aqueous chemistry of plutonium is quite remarkable. Important insights were obtained from tracer experiments, but the full complexity was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were based on aqueous solutions, such solution chemistry was emphasized, particularly precipitation and oxidation-reduction behavior. The latter turned out to be unusually intricate when it was discovered that two more oxidation states existed in aqueous solution than had previously been suspected. Further, an equilibrium was rapidly established among the four aqueous oxidation states, while at the same time any three were not in equilibrium. These and other observations made while doing a crash study of a previously unknown element are reported

Biogenesis of the yeast cytochrome bc1 complex.

Science.gov (United States)

Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L

2009-01-01

The mitochondrial respiratory chain is composed of four different protein complexes that cooperate in electron transfer and proton pumping across the inner mitochondrial membrane. The cytochrome bc1 complex, or complex III, is a component of the mitochondrial respiratory chain. This review will focus on the biogenesis of the bc1 complex in the mitochondria of the yeast Saccharomyces cerevisiae. In wild type yeast mitochondrial membranes the major part of the cytochrome bc1 complex was found in association with one or two copies of the cytochrome c oxidase complex. The analysis of several yeast mutant strains in which single genes or pairs of genes encoding bc1 subunits had been deleted revealed the presence of a common set of bc1 sub-complexes. These sub-complexes are represented by the central core of the bc1 complex, consisting of cytochrome b bound to subunit 7 and subunit 8, by the two core proteins associated with each other, by the Rieske protein associated with subunit 9, and by those deriving from the unexpected interaction of each of the two core proteins with cytochrome c1. Furthermore, a higher molecular mass sub-complex is that composed of cytochrome b, cytochrome c1, core protein 1 and 2, subunit 6, subunit 7 and subunit 8. The identification and characterization of all these sub-complexes may help in defining the steps and the molecular events leading to bc1 assembly in yeast mitochondria.

Molecular data reveal complex hybridization and a cryptic species of neotropical wild cat.

Science.gov (United States)

Trigo, Tatiane C; Schneider, Alexsandra; de Oliveira, Tadeu G; Lehugeur, Livia M; Silveira, Leandro; Freitas, Thales R O; Eizirik, Eduardo

2013-12-16

Hybridization among animal species has recently become more recognized as an important phenomenon, especially in the context of recent radiations. Here we show that complex hybridization has led to contrasting patterns of genomic composition among closely related species of the Neotropical cat genus Leopardus. We show strong evidence of ancient hybridization and introgression between the pampas cat (L. colocolo) and northeastern populations of tigrina (L. tigrinus), leading to remarkable cytonuclear discordance in the latter. In contrast, southern tigrina populations show recent and continuing hybridization with Geoffroy's cat (L. geoffroyi), leading to extreme levels of interspecific admixture at their contact zone. Finally, we demonstrate that two seemingly continuous Brazilian tigrina populations show no evidence of ongoing gene flow between them, leading us to support their formal recognition as distinct species, namely L. tigrinus in the northeast and L. guttulus in the south. Copyright © 2013 Elsevier Ltd. All rights reserved.

Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

Energy Technology Data Exchange (ETDEWEB)

Resch, Michael G.; Donohoe, Byron; Ciesielski, Peter; Nill, Jennifer; McKinney, Kellene; Mittal, Ashutosh; Katahira, Rui; Himmel, Michael; Biddy, Mary; Beckham, Gregg; Decker, Steve

2014-09-08

Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution.

Structures of the APC–ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners

Science.gov (United States)

Zhang, Zhenyi; Akyildiz, Senem; Xiao, Yafei; Gai, Zhongchao; An, Ying; Behrens, Jürgen; Wu, Geng

2015-01-01

The tumor suppressor APC employs its conserved armadillo repeat (ARM) domain to recognize many of its binding partners, including Amer1/WTX, which is mutated in Wilms' tumor and bone overgrowth syndrome. The APC–Amer1 complex has important roles in regulating Wnt signaling and cell adhesion. Three sites A1, A2, and A3 of Amer1 have been reported to mediate its interaction with APC-ARM. In this study, crystal structures of APC–ARM in complexes with Amer1-A1, -A2, and -A4, which is newly identified in this work, were determined. Combined with our GST pull-down, yeast two-hybrid, and isothermal titration calorimetry (ITC) assay results using mutants of APC and Amer1 interface residues, our structures demonstrate that Amer1-A1, -A2, and -A4, as well as other APC-binding proteins such as Asef and Sam68, all employ a common recognition pattern to associate with APC–ARM. In contrast, Amer1-A3 binds to the C-terminal side of APC–ARM through a bipartite interaction mode. Composite mutations on either APC or Amer1 disrupting all four interfaces abrogated their association in cultured cells and impaired the membrane recruitment of APC by Amer1. Our study thus comprehensively elucidated the recognition mechanism between APC and Amer1, and revealed a consensus recognition sequence employed by various APC–ARM binding partners. PMID:27462415

Structures of the APC-ARM domain in complexes with discrete Amer1/WTX fragments reveal that it uses a consensus mode to recognize its binding partners.

Science.gov (United States)

Zhang, Zhenyi; Akyildiz, Senem; Xiao, Yafei; Gai, Zhongchao; An, Ying; Behrens, Jürgen; Wu, Geng

2015-01-01

The tumor suppressor APC employs its conserved armadillo repeat (ARM) domain to recognize many of its binding partners, including Amer1/WTX, which is mutated in Wilms' tumor and bone overgrowth syndrome. The APC-Amer1 complex has important roles in regulating Wnt signaling and cell adhesion. Three sites A1, A2, and A3 of Amer1 have been reported to mediate its interaction with APC-ARM. In this study, crystal structures of APC-ARM in complexes with Amer1-A1, -A2, and -A4, which is newly identified in this work, were determined. Combined with our GST pull-down, yeast two-hybrid, and isothermal titration calorimetry (ITC) assay results using mutants of APC and Amer1 interface residues, our structures demonstrate that Amer1-A1, -A2, and -A4, as well as other APC-binding proteins such as Asef and Sam68, all employ a common recognition pattern to associate with APC-ARM. In contrast, Amer1-A3 binds to the C-terminal side of APC-ARM through a bipartite interaction mode. Composite mutations on either APC or Amer1 disrupting all four interfaces abrogated their association in cultured cells and impaired the membrane recruitment of APC by Amer1. Our study thus comprehensively elucidated the recognition mechanism between APC and Amer1, and revealed a consensus recognition sequence employed by various APC-ARM binding partners.

Oxovanadium(IV) complexes of non-steroidal anti-inflammatory drugs: synthesis, spectroscopy, and antimicrobial activity

International Nuclear Information System (INIS)

Muhammad, N.; Ali, S.; Shahzadi, S.; Khan, A.N.

2008-01-01

Oxovanadium(IV) complexes with four different non-steroidal anti-inflammatory drugs have been synthesized. These complexes were characterized by different analytical techniques such as CHN, IR, UV-Vis spectroscopy, and mass spectrometry. The IR data show the bidentate nature of the ligands and reveal hexacoordinate geometry in the solid state. The complexes were tested for their biological activity against six different bacterial strains and plant pathogens, and all complexes showed good biological activity with few exceptions [ru

Biosorption characteristics of Aspergillus fumigatus in removal of ...

African Journals Online (AJOL)

STORAGESEVER

2009-09-01

Sep 1, 2009 ... in growth medium, thus about 20% of the isolates can grow up to 50 mg Cd/100 ml medium and only ... have the highest Cd biosorption, compared to yeast malt extract (YM) and sabourad (Sb) media. ... chemical parameters of the solution, say, temperature, ...... inactivated Phanerochaete chrysosporium.

Architecture of the human mTORC2 core complex.

Science.gov (United States)

Stuttfeld, Edward; Aylett, Christopher Hs; Imseng, Stefan; Boehringer, Daniel; Scaiola, Alain; Sauer, Evelyn; Hall, Michael N; Maier, Timm; Ban, Nenad

2018-02-09

The mammalian target of rapamycin (mTOR) is a key protein kinase controlling cellular metabolism and growth. It is part of the two structurally and functionally distinct multiprotein complexes mTORC1 and mTORC2. Dysregulation of mTOR occurs in diabetes, cancer and neurological disease. We report the architecture of human mTORC2 at intermediate resolution, revealing a conserved binding site for accessory proteins on mTOR and explaining the structural basis for the rapamycin insensitivity of the complex. © 2018, Stuttfeld et al.

Single-particle fusion of influenza viruses reveals complex interactions with target membranes

Science.gov (United States)

van der Borg, Guus; Braddock, Scarlett; Blijleven, Jelle S.; van Oijen, Antoine M.; Roos, Wouter H.

2018-05-01

The first step in infection of influenza A virus is contact with the host cell membrane, with which it later fuses. The composition of the target bilayer exerts a complex influence on both fusion efficiency and time. Here, an in vitro, single-particle approach is used to study this effect. Using total internal reflection fluorescence (TIRF) microscopy and a microfluidic flow cell, the hemifusion of single virions is visualized. Hemifusion efficiency and kinetics are studied while altering target bilayer cholesterol content and sialic-acid donor. Cholesterol ratios tested were 0%, 10%, 20%, and 40%. Sialic-acid donors GD1a and GYPA were used. Both cholesterol ratio and sialic-acid donors proved to have a significant effect on hemifusion efficiency. Furthermore, comparison between GD1a and GYPA conditions shows that the cholesterol dependence of the hemifusion time is severely affected by the sialic-acid donor. Only GD1a shows a clear increasing trend in hemifusion efficiency and time with increasing cholesterol concentration of the target bilayer with maximum rates for GD1A and 40% cholesterol. Overall our results show that sialic acid donor and target bilayer composition should be carefully chosen, depending on the desired hemifusion time and efficiency in the experiment.

Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation

Energy Technology Data Exchange (ETDEWEB)

Jiang, Jiansheng; Natarajan, Kannan; Boyd, Lisa F.; Morozov, Giora I.; Mage, Michael G.; Margulies, David H. (NIH); (Hebrew)

2017-10-12

Central to CD8+ T cell–mediated immunity is the recognition of peptide–major histocompatibility complex class I (p–MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein–related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.

Characterisation of a chimeric Phanerochaete chrysosporium ...

African Journals Online (AJOL)

Fred

soaked tissue paper, the lid of the plastic box was closed and the reaction were incubated at 37oC for 3–4 days. The plastic box with soaked tissue paper provided a humid environment that prevented the media from drying-out. After incubation, the plates were ... cbhI.1 when it was cloned into a pET vector to generate.

Cloning and expression of Phanerochaete chrysosporium ...

African Journals Online (AJOL)

Owner

various industries such as chemicals, fuel, food, brewery and wine, animal-feed, .... and transformed into competent E. coli BL21 cells for vector amplification, repurified ..... Hydrolysis of lignocellulose material for ethanol production: A Review: ...

Saccharification with Phanerochaete chrysosporium and Pleurotus ...

African Journals Online (AJOL)

Lignocellulosic biomass has a great potential as raw material for second and third generation biofuels since it is the most abundant carbohydrate on earth and the main component of agricultural waste; however, saccharification of lignocellulosic biomass is crucial for the establishment of a carbohydratebased economy.

Zein/caseinate/pectin complex nanoparticles: Formation and characterization.

Science.gov (United States)

Chang, Chao; Wang, Taoran; Hu, Qiaobin; Luo, Yangchao

2017-11-01

In this study, pectin was used as coating material to form zein/caseinate/pectin complex nanoparticles through pH adjustment and heating treatment for potential oral delivery applications. The preparation conditions were studied by applying heating treatment at different pHs, either the isoelectric point of zein (pH 6.2) or caseinate (pH 4.6), or consecutively at both pHs. The particulate characteristics, including particle size, polydispersity index, and zeta potential were monitored for complex nanoparticles formed under different preparation conditions. The complex nanoparticles generally exhibited particle size smaller than 200nm with narrow distribution, spherical shape, and strong negative charge. Fourier transform infrared and fluorescence spectroscopy revealed that hydrophobic interactions and hydrogen bonds were involved in the formation of complex nanoparticles, in addition to electrostatic interactions. Fresh colloidal dispersion and freeze-dried powders varied in their morphology, depending on their preparation conditions. Our results suggested that heating pH and sequence significantly affected the morphology of complex nanoparticles, and pectin coating exerted stabilization effect under simulated gastrointestinal conditions. The present study provides insight into the formation of protein/polysaccharide complex nanoparticles under different preparation conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Revisiting the Delphinium viscosum Hook. f. & Thoms. (Ranunculaceae complex in the Himalaya

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Priyanka Agnihotri

2016-03-01

Full Text Available The paper highlights the complex nature of Delphinium viscosum Hook. f. & Thoms. in the Himalaya and enumerates two subspecies and two varieties. Critical appraisal of the morphological and distributional data revealed that subsp. viscosum and subsp. gigantobracteum having two varieties var. gigantobracteum and chrysotrichum are distinct. Delphinium viscosum complex is solved out and two subspecies and two varieties with clear cut distinct macro and micro-morphological characters have been identified. The taxonomic status of different taxa of this complex species has been established. Delphinium viscosum, a taxonomic complex species is described and illustrated.

Isolation and characterization of PSI-LHCI super-complex and their sub-complexes from a red alga Cyanidioschyzon merolae.

Science.gov (United States)

Tian, Lirong; Liu, Zheyi; Wang, Fangjun; Shen, Liangliang; Chen, Jinghua; Chang, Lijing; Zhao, Songhao; Han, Guangye; Wang, Wenda; Kuang, Tingyun; Qin, Xiaochun; Shen, Jian-Ren

2017-09-01

Photosystem I (PSI)-light-harvesting complex I (LHCI) super-complex and its sub-complexes PSI core and LHCI, were purified from a unicellular red alga Cyanidioschyzon merolae and characterized. PSI-LHCI of C. merolae existed as a monomer with a molecular mass of 580 kDa. Mass spectrometry analysis identified 11 subunits (PsaA, B, C, D, E, F, I, J, K, L, O) in the core complex and three LHCI subunits, CMQ142C, CMN234C, and CMN235C in LHCI, indicating that at least three Lhcr subunits associate with the red algal PSI core. PsaG was not found in the red algae PSI-LHCI, and we suggest that the position corresponding to Lhca1 in higher plant PSI-LHCI is empty in the red algal PSI-LHCI. The PSI-LHCI complex was separated into two bands on native PAGE, suggesting that two different complexes may be present with slightly different protein compositions probably with respective to the numbers of Lhcr subunits. Based on the results obtained, a structural model was proposed for the red algal PSI-LHCI. Furthermore, pigment analysis revealed that the C. merolae PSI-LHCI contained a large amount of zeaxanthin, which is mainly associated with the LHCI complex whereas little zeaxanthin was found in the PSI core. This indicates a unique feature of the carotenoid composition of the Lhcr proteins and may suggest an important role of Zea in the light-harvesting and photoprotection of the red algal PSI-LHCI complex.

Computational model of dose response for low-LET-induced complex chromosomal aberrations

International Nuclear Information System (INIS)

Eidelman, Y.A.; Andreev, S.G.

2015-01-01

Experiments with full-colour mFISH chromosome painting have revealed high yield of radiation-induced complex chromosomal aberrations (CAs). The ratio of complex to simple aberrations is dependent on cell type and linear energy transfer. Theoretical analysis has demonstrated that the mechanism of CA formation as a result of interaction between lesions at a surface of chromosome territories does not explain high complexes-to-simples ratio in human lymphocytes. The possible origin of high yields of γ-induced complex CAs was investigated in the present work by computer simulation. CAs were studied on the basis of chromosome structure and dynamics modelling and the hypothesis of CA formation on nuclear centres. The spatial organisation of all chromosomes in a human interphase nucleus was predicted by simulation of mitosis-to-interphase chromosome structure transition. Two scenarios of CA formation were analysed, 'static' (existing in a nucleus prior to irradiation) centres and 'dynamic' (formed in response to irradiation) centres. The modelling results reveal that under certain conditions, both scenarios explain quantitatively the dose-response relationships for both simple and complex γ-induced inter-chromosomal exchanges observed by mFISH chromosome painting in the first post-irradiation mitosis in human lymphocytes. (authors)

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy.

Science.gov (United States)

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G; Zhang, Xiaoyi; Liu, Cunming; Mulfort, Karen L; Chen, Lin X

2018-01-28

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)-Ru(ii) analogs of the homodinuclear Cu(i)-Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.

Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis

Science.gov (United States)

Li, Yuanyuan; Jin, Suoqin; Lei, Lei; Pan, Zishu; Zou, Xiufen

2015-03-01

The early diagnosis and investigation of the pathogenic mechanisms of complex diseases are the most challenging problems in the fields of biology and medicine. Network-based systems biology is an important technique for the study of complex diseases. The present study constructed dynamic protein-protein interaction (PPI) networks to identify dynamical network biomarkers (DNBs) and analyze the underlying mechanisms of complex diseases from a systems level. We developed a model-based framework for the construction of a series of time-sequenced networks by integrating high-throughput gene expression data into PPI data. By combining the dynamic networks and molecular modules, we identified significant DNBs for four complex diseases, including influenza caused by either H3N2 or H1N1, acute lung injury and type 2 diabetes mellitus, which can serve as warning signals for disease deterioration. Function and pathway analyses revealed that the identified DNBs were significantly enriched during key events in early disease development. Correlation and information flow analyses revealed that DNBs effectively discriminated between different disease processes and that dysfunctional regulation and disproportional information flow may contribute to the increased disease severity. This study provides a general paradigm for revealing the deterioration mechanisms of complex diseases and offers new insights into their early diagnoses.

The chemistry of plutonium revealed

International Nuclear Information System (INIS)

Connick, R.E.

1990-01-01

In 1941 one goal of the Manhattan Project was to unravel the chemistry of the synthetic element plutonium as rapidly as possible. Important insights were obtained from tracer experiments, but the full complexity of plutonium chemistry was not revealed until macroscopic amounts (milligrams) became available. Because processes for separation from fission products were aqueous solution based, such solution chemistry was emphasized, particularly precipitation and oxidation-reduction behavior. The latter turned out to be unusually intricate when it was discovered that two more oxidation states existed in aqueous solution than had previously been suspected. Further, it was found that an equilibrium was rapidly established among the four aqueous oxidation states while at the same time any three were not in equilibrium. These and other observations made while doing a crash study of a previously unknown element will be reported

VLA Zeeman Observations of the NGC 6334 Complex

Science.gov (United States)

Mayo, E. A.; Sarma, A. P.; Troland, T. H.

2004-05-01

We present OH 1665 and 1667 MHz observations of the NGC 6334 complex taken with the Very Large Array in the BnA configuration. We have combined our data with the lower resolution CnB data of Sarma et al (1999), in order to perform a detailed study of Source A, a compact continuum source in the SW region of the complex. Our observations reveal magnetic fields with peak values of the order of 700μ G toward Source A. Virial estimates presented indicate the significance of the magnetic field in the support of the molecular cloud against gravitational collapse.

Molecular architecture of the yeast Mediator complex

Science.gov (United States)

Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

2015-01-01

The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

Complexity of EEG-signal in Time Domain - Possible Biomedical Application

Science.gov (United States)

Klonowski, Wlodzimierz; Olejarczyk, Elzbieta; Stepien, Robert

2002-07-01

Human brain is a highly complex nonlinear system. So it is not surprising that in analysis of EEG-signal, which represents overall activity of the brain, the methods of Nonlinear Dynamics (or Chaos Theory as it is commonly called) can be used. Even if the signal is not chaotic these methods are a motivating tool to explore changes in brain activity due to different functional activation states, e.g. different sleep stages, or to applied therapy, e.g. exposure to chemical agents (drugs) and physical factors (light, magnetic field). The methods supplied by Nonlinear Dynamics reveal signal characteristics that are not revealed by linear methods like FFT. Better understanding of principles that govern dynamics and complexity of EEG-signal can help to find `the signatures' of different physiological and pathological states of human brain, quantitative characteristics that may find applications in medical diagnostics.

Behaviors of nitrato complexes of nitrosylruthenium in aqueous solutions

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, S [Radia Industry Co. Ltd., Takasaki (Japan)

1979-11-01

Nitrato nitrosylruthenium complexes (RuNO(NO/sub 3/)sub(x)(H/sub 2/O)sub(5-x))sup((3-x)+) readily dissociate in aqueous solutions with decrease in pH and increase in electrical conductivity of the solutions. This study aimed to elucidate the behaviours of dissociation of the complexes with time. The change in the amount of undissociated complexes was determined with time. The results indicated that the dissociation was a multi-order reaction involving both protolysis and hydrolysis. The protolysis completed in relatively short period within (several tens of minutes), but it depended on the concentration of the complexes in the solution. The completion of the protolysis and the formation of the resulting dissociation products were observed by absorption spectrometry. The dissociation products, which were assumed as aquohydroxy complexes, underwent the successive step-wise dissociation for a prolonged period as revealed by pH measurements. The rate constants involved in the step-wise dissociation, process were obtained. The degree of dissociation and dissociation constant of the complexes were measured by conductometry.

Behaviors of nitrato complexes of nitrosylruthenium in aqueous solutions

International Nuclear Information System (INIS)

Sugimoto, Senichi

1979-01-01

Nitrato nitrosylruthenium complexes [RuNO(NO 3 )sub(x)(H 2 O)sub(5-x)]sup((3-x)+) readily dissociate in aqueous solutions with decrease in pH and increase in electrical conductivity of the solutions. This study aimed to elucidate the behaviours of dissociation of the complexes with time. The change in the amount of undissociated complexes was determined with time. The results indicated that the dissociation was a multi-order reaction involving both protolysis and hydrolysis. The protolysis completed in relatively short period within (several tens of minutes), but it depended on the concentration of the complexes in the solution. The completion of the protolysis and the formation of the resulting dissociation products were observed by absorption spectrometry. The dissociation products, which were assumed as aquohydroxy complexes, underwent the successive step-wise dissociation for a prolonged period as revealed by pH measurements. The rate constants involved in the step-wise dissociation, process were obtained. The degree of dissociation and dissociation constant of the complexes were measured by conductometry. (author)

The primed SNARE–complexin–synaptotagmin complex for neuronal exocytosis

Energy Technology Data Exchange (ETDEWEB)

Zhou, Qiangjun; Zhou, Peng; Wang, Austin L.; Wu, Dick; Zhao, Minglei; Südhof, Thomas C.; Brunger, Axel T.

2017-08-16

Synaptotagmin, complexin, and neuronal SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) proteins mediate evoked synchronous neurotransmitter release, but the molecular mechanisms mediating the cooperation between these molecules remain unclear. Here we determine crystal structures of the primed pre-fusion SNARE–complexin–synaptotagmin-1 complex. These structures reveal an unexpected tripartite interface between synaptotagmin-1 and both the SNARE complex and complexin. Simultaneously, a second synaptotagmin-1 molecule interacts with the other side of the SNARE complex via the previously identified primary interface. Mutations that disrupt either interface in solution also severely impair evoked synchronous release in neurons, suggesting that both interfaces are essential for the primed pre-fusion state. Ca2+ binding to the synaptotagmin-1 molecules unlocks the complex, allows full zippering of the SNARE complex, and triggers membrane fusion. The tripartite SNARE–complexin–synaptotagmin-1 complex at a synaptic vesicle docking site has to be unlocked for triggered fusion to start, explaining the cooperation between complexin and synaptotagmin-1 in synchronizing evoked release on the sub-millisecond timescale.

Plasmonic bio-sensing for the Fenna-Matthews-Olson complex

Science.gov (United States)

Chen, Guang-Yin; Lambert, Neill; Shih, Yen-An; Liu, Meng-Han; Chen, Yueh-Nan; Nori, Franco

2017-01-01

We study theoretically the bio-sensing capabilities of metal nanowire surface plasmons. As a specific example, we couple the nanowire to specific sites (bacteriochlorophyll) of the Fenna-Matthews-Olson (FMO) photosynthetic pigment protein complex. In this hybrid system, we find that when certain sites of the FMO complex are subject to either the suppression of inter-site transitions or are entirely disconnected from the complex, the resulting variations in the excitation transfer rates through the complex can be monitored through the corresponding changes in the scattering spectra of the incident nanowire surface plasmons. We also find that these changes can be further enhanced by changing the ratio of plasmon-site couplings. The change of the Fano lineshape in the scattering spectra further reveals that “site 5” in the FMO complex plays a distinct role from other sites. Our results provide a feasible way, using single photons, to detect mutation-induced, or bleaching-induced, local defects or modifications of the FMO complex, and allows access to both the local and global properties of the excitation transfer in such systems.

Sustainability Assessment of a Biorefinery Complex in Thailand

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Pariyapat Nilsalab

2011-03-01

Full Text Available In this paper, a biorefinery complex in Thailand was assessed vis-à-vis sustainability. The complex studied includes plantations of sugarcane and a biorefinery system composed of several units including, a sugar mill, power plant, ethanol factory and fertilizer plant. The assessment aimed at evaluating the environmental and socio-economic implications relating to molasses-based ethanol production and use, and maximized utilization of the biomass materials produced as part of the biorefinery complex. Global warming potential, human development index and total value added are the three indicators that were selected to perform the assessment. The results obtained revealed that the maximization of biomass utilization at the level of the biorefinery complex provide greenhouse gases emissions reduction benefits, enhanced living conditions for sugarcane farmers and employees of the biorefinery, and economic benefits, particularly with regard to profit and income generation. These results could serve as a first step to further improve and design indicators for sustainability assessment of biomass utilization.

The Mycoflora of Hot Spring Soil in Northern Taiwan

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Kuei-Yu Chen

2003-09-01

Full Text Available An investigation of the mycoflora in northern Taiwan from August 1999 to June 2000, particularly of thermophilic and thermotolerant fungi inhabiting sulfurous hot spring soils, resulted in identification 12 taxa: Aspergillus fumigatus var. fumigatus (66.85 %, A. fumigatus var. 1 with green colony (7.86 %, A. fumigatus var. 2 with brown colony (4.81 %, A. niger (1.14 %, unidentified Asperigillus sp. (0.045 %, Chrysosporium sp. (0.18 %, Papulaspora thermophila (2.72 %, Scytalidium thermophilum (0.045 %, Sporotrichum sp. (0.045 %, Mycelia sterilia sp.1 with white colony (6.63 %, Mycelia sterilia sp.2 with yellow colony (5.27 % and Mycelia sterilia sp. 3 with gray colony (4.405 %. A total of 2202 colonies were isolated from three sampling sites: site 1 (hot springhead, site 2 (2 m from site 1 and site 3 (4 m from site 1. Fungal colonies isolated as well as species percentage at three sites were as follows: 32.92 % in 9 taxa from site 1, 37.87 % in 11 taxa from site 2, and 29.21 % in 8 taxa from site 3. The dominant species was Aspergillus fumigatus var. fumigatus, which was isolated year around from three sampling sites. A. fumigatus var. 1 appeared from February to June 2000. A. fumigatus var. 2 was isolated only in August and October 1999. Within the sampling range of hot spring niches, there was evidence of the presence of ecotypes in the A. fumigatus complex. Chrysosporium sp. and Sporotrichum sp. were isolated only from the soils without hot water treatment, but Aspergillus sp. and Scytalidium thermophilum were isolated only from the soils pre-treated with hot water for 30 min. at 60℃. The significance level (P value of fungal communities between hot water treatment and no treatment was 0.866, indicating that no significant difference between both treatments.

Extrinsic and intrinsic complexities of the Los Alamos plutonium processing facility

International Nuclear Information System (INIS)

Bearse, R.C.; Roberts, N.J.; Longmire, V.L.

1985-01-01

Analysis of the data obtained in one year of plutonium accounting at Los Alamos reveals significant complexity. Much of this complexity arises from the complexity of the processes themselves. Additional complexity is induced by errors in the data entry process. It is important to note that there is no evidence that this complexity is adversely affecting the accounting in the plant. The authors have been analyzing transaction data from fiscal year 1983 processing. This study involved 62,595 transactions. The data have been analyzed using the relational database program INGRES on a VAX 11/780 computer. This software allows easy manipulation of the original data and subsets drawn from it. The authors have been attempting for several years to understand the global features of the TA-55 accounting data. This project has underscored several of the system's complexities

Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

KAUST Repository

Matsuda, Shayle B.

2017-03-01

Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

KAUST Repository

Matsuda, Shayle B.; Gosliner, Terrence M.

2017-01-01

Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

Uranium nucleophilic carbene complexes

International Nuclear Information System (INIS)

Tourneux, Jean-Christophe

2012-01-01

The only stable f-metal carbene complexes (excluding NHC) metals f present R 2 C 2- groups having one or two phosphorus atoms in the central carbon in alpha position. The objective of this work was to develop the chemistry of carbenes for uranium (metal 5f) with the di-anion C{Ph 2 P(=S)} 2 2- (SCS 2- ) to extend the organometallic chemistry of this element in its various oxidation states (+3-+6), and to reveal the influence of the 5f orbitals on the nature and reactivity of the double bond C=U. We first isolated the reactants M(SCHS) (M = Li and K) and demonstrated the role of the cation M + on the evolution of the di-anion M 2 SCS (M = Li, K, Tl) which is transformed into LiSCHS in THF or into product of intramolecular cyclization K 2 [C(PhPS) 2 (C 6 H 4 )]. We have developed the necessary conditions mono-, bis- and tris-carbene directly from the di-anion SCS 2- and UCl 4 , as the precursor used in uranium chemistry. The protonolysis reactions of amides compounds (U-NEt 2 ) by the neutral ligand SCH 2 S were also studied. The compounds [Li(THF)] 2 [U(SCS)Cl 3 ] and [U(SCS)Cl 2 (THF) 2 ] were then used to prepare a variety of cyclopentadienyl and mono-cyclo-octa-tetra-enyliques uranium(IV) carbene compounds of the DFT analysis of compounds [M(SCS)Cl 2 (py) 2 ] and [M(Cp) 2 (SCS)] (M = U, Zr) reveals the strong polarization of the M=C double bond, provides information on the nature of the σ and π interactions in this binding, and shows the important role of f orbitals. The influence of ancillary ligands on the M=C bond is revealed by examining the effects of replacing Cl - ligands and pyridine by C 5 H 5 - groups. Mulliken and NBO analyzes show that U=C bond, unlike the Zr=C bond, is not affected by the change in environment of the metal center. While the oxidation tests of carbene complexes of U(IV) were disappointing, the first carbene complex of uranium (VI), [UO 2 (SCS)(THF) 2 ], was isolated with the uranyl ion UO 2 2+ . The reactions of compounds UO 2 X 2

A complex suicide by vehicle assisted ligature strangulation and wrist-cutting

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Ramazan Akçan

2016-12-01

Conclusion: A complete forensic investigation revealed the case was an unusual complex suicide by vehicle assisted ligature strangulation and wrist-cutting. The case was interesting in terms of involving car assisted ligature strangulation.

The complexity of nurses' attitudes toward euthanasia: a review of the literature.

Science.gov (United States)

Berghs, M; Dierckx de Casterlé, B; Gastmans, C

2005-08-01

In this literature review, a picture is given of the complexity of nursing attitudes toward euthanasia. The myriad of data found in empirical literature is mostly framed within a polarised debate and inconclusive about the complex reality behind attitudes toward euthanasia. Yet, a further examination of the content as well as the context of attitudes is more revealing. The arguments for euthanasia have to do with quality of life and respect for autonomy. Arguments against euthanasia have to do with non-maleficence, sanctity of life, and the notion of the slippery slope. When the context of attitudes is examined a number of positive correlates for euthanasia such as age, nursing specialty, and religion appear. In a further analysis of nurses' comments on euthanasia, it is revealed that part of the complexity of nursing attitudes toward euthanasia arises because of the needs of nurses at the levels of clinical practice, communication, emotions, decision making, and ethics.

Photonic crystals, light manipulation, and imaging in complex nematic structures

Science.gov (United States)

Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

2016-03-01

Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

Complexity and competition in appetitive and aversive neural circuits

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Crista L. Barberini

2012-11-01

Full Text Available Decision-making often involves using sensory cues to predict possible rewarding or punishing reinforcement outcomes before selecting a course of action. Recent work has revealed complexity in how the brain learns to predict rewards and punishments. Analysis of neural signaling during and after learning in the amygdala and orbitofrontal cortex, two brain areas that process appetitive and aversive stimuli, reveals a dynamic relationship between appetitive and aversive circuits. Specifically, the relationship between signaling in appetitive and aversive circuits in these areas shifts as a function of learning. Furthermore, although appetitive and aversive circuits may often drive opposite behaviors – approaching or avoiding reinforcement depending upon its valence – these circuits can also drive similar behaviors, such as enhanced arousal or attention; these processes also may influence choice behavior. These data highlight the formidable challenges ahead in dissecting how appetitive and aversive neural circuits interact to produce a complex and nuanced range of behaviors.

A new mechanism of biopulping : attachment of acid groups on fiber

Science.gov (United States)

William R. Kenealy; Chris Hunt; Eric Horn; Carl Houtman

2004-01-01

We analyzed the physical properties of wood chips incubated with Ceriporiopsis subvermispora and cultural parameters of biopulping incubations of Phanerochaete chrysosporium and C. subvermispora. Dynamic mechanical analyses indicated a reduction in the modulus of elasticity (MOE) and loss modulus of spruce during the time where the biopulping energy savings effect...

Mechanisms Underlying the Formation of Complexes between Maize Starch and Lipids.

Science.gov (United States)

Chao, Chen; Yu, Jinglin; Wang, Shuo; Copeland, Les; Wang, Shujun

2018-01-10

This study aimed to reveal the mechanism of formation of complexes between native maize starch (NMS) and different types of lipids, namely palmitic acid (PA), monopalmitate glycerol (MPG), dipalmitate glycerol (DPG), and tripalmitate glycerol (TPG). The complexing index followed the order of MPG (96.3%) > PA (41.8%) > TPG (8.3%) > DPG (1.1%), indicating that MPG formed more complexes with NMS than PA, and that few complexes were formed between NMS and DPG and TPG. The NMS-PA complex presented higher thermal transition temperatures and lower enthalpy change than the NMS-MPG complex, indicating that although MPG formed more starch complexes, they had less stable crystalline structures than the complex between NMS and PA. X-ray diffraction (XRD) and Raman spectroscopy showed that both MPG and PA formed V-type crystalline structures with NMS, and confirmed that no complexes were formed between NMS and DPG and TPG. We conclude that the monoglyceride formed more starch-lipid complex with maize starch than PA, but that the monoglyceride complex had a less stable structure than that formed with PA. The di- and triglycerides did not form complexes with maize starch.

Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex.

Science.gov (United States)

Ma, Jiong; Kelich, Joseph M; Junod, Samuel L; Yang, Weidong

2017-04-01

The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside of the sub-micrometer supramolecular complex. Here, we combined super-resolution single-point edge-excitation subdiffraction (SPEED) microscopy and nanobody-specific labeling to reveal the spatial distribution of scaffold Nups within three separate layers in the native NPC with a precision of ∼3 nm. Our data reveal both the radial and axial spatial distributions for Pom121, Nup37 and Nup35 and provide evidence for their copy numbers of 8, 32 and 16, respectively, per NPC. This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes. © 2017. Published by The Company of Biologists Ltd.

The geosystems of complex geographical atlases

Directory of Open Access Journals (Sweden)

Jovanović Jasmina

2012-01-01

Full Text Available Complex geographical atlases represent geosystems of different hierarchical rank, complexity and diversity, scale and connection. They represent a set of large number of different pieces of information about geospace. Also, they contain systematized, correlative and in the apparent form represented pieces of information about space. The degree of information revealed in the atlas is precisely explained by its content structure and the form of presentation. The quality of atlas depends on the method of visualization of data and the quality of geodata. Cartographic visualization represents cognitive process. The analysis converts geospatial data into knowledge. A complex geographical atlas represents information complex of spatial - temporal coordinated database on geosystems of different complexity and territorial scope. Each geographical atlas defines a concrete geosystem. Systemic organization (structural and contextual determines its complexity and concreteness. In complex atlases, the attributes of geosystems are modeled and pieces of information are given in systematized, graphically unique form. The atlas can be considered as a database. In composing a database, semantic analysis of data is important. The result of semantic modeling is expressed in structuring of data information, in emphasizing logic connections between phenomena and processes and in defining their classes according to the degree of similarity. Accordingly, the efficiency of research of needed pieces of information in the process of the database use is enabled. An atlas map has a special power to integrate sets of geodata and present information contents in user - friendly and understandable visual and tactile way using its visual ability. Composing an atlas by systemic cartography requires the pieces of information on concrete - defined geosystems of different hierarchical level, the application of scientific methods and making of adequate number of analytical, synthetic

Synthesis, Characterization, and Antibacterial Studies of Mixed Ligand Dioxouranium Complexes with 8-Hydroxyquinoline and Some Amino Acids

Science.gov (United States)

Patil, Sunil S.; Thakur, Ganesh A.; Shaikh, Manzoor M.

2011-01-01

Mixed ligand complexes of dioxouranium (VI) of the type [UO2(Q)(L)·2H2O] have been synthesized using 8-hydroxyquinoline (HQ) as a primary ligand and amino acids (HL) such as L-threonine, L-tryptophan, and L-isoleucine as secondary ligands. The metal complexes have been characterized by elemental analysis, electrical conductance, magnetic susceptibility measurements, and spectral and thermal studies. The electrical conductance studies of the complexes indicate their nonelectrolytic nature. Magnetic susceptibility measurements revealed diamagnetic nature of the complexes. Electronic absorption spectra of the complexes show intraligand and charge transfer transitions, respectively. Bonding of the metal ion through N- and O-donor atoms of the ligands is revealed by IR studies, and the chemical environment of the protons is confirmed by NMR studies. The thermal analysis data of the complexes indicate the presence of coordinated water molecules. The agar cup and tube dilution methods have been used to study the antibacterial activity of the complexes against the pathogenic bacteria S. aureus, C. diphtheriae, S. typhi, and E. coli. PMID:22389843

Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

Energy Technology Data Exchange (ETDEWEB)

Wubben, T.; Mesecar, A.D. (Purdue); (UIC)

2014-10-02

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observed in the MtPPAT-CoA complex.

Removal combined with reduction of hexavalent chromium from aqueous solution by Fe-ethylene glycol complex microspheres

Energy Technology Data Exchange (ETDEWEB)

Zhang, Yong-Xing [School of Physics and Electronic Information, Huaibei Normal University, Huaibei 235000 (China); Jia, Yong, E-mail: yjiaahedu@163.com [School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012 (China)

2016-12-15

Highlights: • Fe-EG complex microspheres were synthesized by a hydrothermal method. • The removal properties towards Cr(VI) ions were investigated. • The adsorption and reduction mechanism was revealed by FTIR and XPS. - Abstract: Three-dimensional Fe-ethylene glycol (Fe-EG) complex microspheres were synthesized by a facile hydrothermal method, and were characterized by field emission scanning electron microscopy and transmission electron microscopy. The adsorption as well as reduction properties of the obtained Fe-EG complex microspheres towards Cr(VI) ions were studied. The experiment data of adsorption kinetic and isotherm were fitted by nonlinear regression approach. In neutral condition, the maximum adsorption capacity was 49.78 mg g{sup −1} at room temperature, and was increased with the increasing of temperature. Thermodynamic parameters including the Gibbs free energy, standard enthalpy and standard entropy revealed that adsorption of Cr(VI) was a feasible, spontaneous and endothermic process. Spectroscopic analysis revealed the adsorption of Cr(VI) was a physical adsorption process. The adsorbed CrO{sub 4}{sup 2−} ions were partly reduced to Cr(OH){sub 3} by Fe(II) ions and the organic groups in the Fe-EG complex.

EPR Study of [Cu(Him)4]·2Br Complex

International Nuclear Information System (INIS)

Yıldırım, İ; Karabulut, B

2016-01-01

The single crystal of [Cu(Him) 4 ]·2Br (Him: C 3 H 4 N 2 , imidazole) complex has been investigated at ambient temperature in three mutually perpendicular planes by EPR technique. The magnetic environments of [Cu(Him) 4 ]·2Br complex have been identified by EPR technique. The study reveals the existence of two magnetically inequivalent Cu 2+ sites. The principal values of g tensors were obtained. The EPR parameters show that the paramagnetic centers have rhombic symmetry. (paper)

Molecular fingerprinting of complex grass allergoids: size assessments reveal new insights in epitope repertoires and functional capacities.

Science.gov (United States)

Starchenka, S; Bell, A J; Mwange, J; Skinner, M A; Heath, M D

2017-01-01

Subcutaneous allergen immunotherapy (SCIT) is a well-documented treatment for allergic disease which involves injections of native allergen or modified (allergoid) extracts. The use of allergoid vaccines is a growing sector of the allergy immunotherapy market, associated with shorter-course therapy. The aim of this study was the structural and immunological characterisation of group 1 (Lol p 1) IgG-binding epitopes within a complex mix grass allergoid formulation containing rye grass. HP-SEC was used to resolve a mix grass allergoid preparation of high molecular weight into several distinct fractions with defined molecular weight and elution profiles. Allergen verification of the HP-SEC allergoid fractions was confirmed by mass spectrometry analysis. IgE and IgG immunoreactivity of the allergoid preparations was explored and Lol p 1 specific IgG-binding epitopes mapped by SPOT synthesis technology (PepSpot™) with structural analysis based on a Lol p 1 homology model. Grass specific IgE reactivity of the mix grass modified extract (allergoid) was diminished in comparison with the mix grass native extract. A difference in IgG profiles was observed between an intact mix grass allergoid preparation and HP-SEC allergoid fractions, which indicated enhancement of accessible reactive IgG epitopes across size distribution profiles of the mix grass allergoid formulation. Detailed analysis of the epitope specificity showed retention of six Lol p 1 IgG-binding epitopes in the mix grass modified extract. The structural and immunological changes which take place following the grass allergen modification process was further unravelled revealing distinct IgG immunological profiles. All epitopes were mapped on the solvent exposed area of Lol p 1 homology model accessible for IgG binding. One of the epitopes was identified as an 'immunodominant' Lol p 1 IgG-binding epitope (62-IFKDGRGCGSCFEIK-76) and classified as a novel epitope. The results from this study support the concept

COMPLEX TREATMENT OF PATIENTS WITH POSTURAL PHOBIC DIZZINESS

Directory of Open Access Journals (Sweden)

M. V. Romanоva

2013-01-01

Full Text Available A total of 25 patients with postural phobic dizziness were examined. Somatic state and neurological status were assessed, neurovisualization and stabilometric investigation were carried out as well as a neuropsychological testing using estimation scales. The efficiency of complex rehabilitation was revealed including vestibular gymnastics, stabilometric training, psychotherapy, and pharmacotherapy in correction of psychoemotional disturbances. 

Alkali-crown ether complexes at metal surfaces

Energy Technology Data Exchange (ETDEWEB)

Thontasen, Nicha; Deng, Zhitao; Rauschenbach, Stephan [Max Planck Institute for Solid State Research, Stuttgart (Germany); Levita, Giacomo [University of Trieste, Trieste (Italy); Malinowski, Nikola [Max Planck Institute for Solid State Research, Stuttgart (Germany); Bulgarian Academy of Sciences, Sofia (Bulgaria); Kern, Klaus [Max Planck Institute for Solid State Research, Stuttgart (Germany); EPFL, Lausanne (Switzerland)

2010-07-01

Crown ethers are polycyclic ethers which, in solution, selectively bind cations depending on the size of the ring cavity. The study of a single host-guest complex is highly desirable in order to reveal the characteristics of these specific interactions at the atomic scale. Such detailed investigation is possible at the surface where high resolution imaging tools like scanning tunneling microscopy (STM) can be applied. Here, electrospray ion beam deposition (ES-IBD) is employed for the deposition of Dibenzo-24-crown-8 (DB24C8)-H{sup +}, -Na{sup +} and -Cs{sup +} complexes on a solid surface in ultrahigh vacuum (UHV). Where other deposition techniques have not been successful, this deposition technique combines the advantages of solution based preparation of the complex ions with a highly clean and controlled deposition in UHV. Single molecular structures and the cation-binding of DB24C8 at the surface are studied in situ by STM and MALDI-MS (matrix assisted laser desorption ionization mass spectrometry). The internal structure of the complex, i.e. ring and cavity, is observable only when alkali cations are incorporated. The BD24C8-H{sup +} complex in contrast appears as a compact feature. This result is in good agreement with theoretical models based on density functional theory calculations.

SSU rRNA reveals a sequential increase in shell complexity among the euglyphid testate amoebae (Rhizaria: Euglyphida)

DEFF Research Database (Denmark)

Lara, Enrique; Heger, Thierry J; Mitchell, Edward A D

2007-01-01

The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a stu...

Protein dynamics during presynaptic complex assembly on individual ssDNA molecules

OpenAIRE

Gibb, Bryan; Ye, Ling F.; Kwon, YoungHo; Niu, Hengyao; Sung, Patrick; Greene, Eric C.

2014-01-01

Homologous recombination is a conserved pathway for repairing double?stranded breaks, which are processed to yield single?stranded DNA overhangs that serve as platforms for presynaptic complex assembly. Here we use single?molecule imaging to reveal the interplay between Saccharomyce cerevisiae RPA, Rad52, and Rad51 during presynaptic complex assembly. We show that Rad52 binds RPA?ssDNA and suppresses RPA turnover, highlighting an unanticipated regulatory influence on protein dynamics. Rad51 b...

Single photon emission computed tomography in AIDS dementia complex

International Nuclear Information System (INIS)

Pohl, P.; Vogl, G.; Fill, H.; Roessler, H.Z.; Zangerle, R.; Gerstenbrand, F.

1988-01-01

Single photon emission computed tomography (SPECT) studies were performed in AIDS dementia complex using IMP in 12 patients (and HM-PAO in four of these same patients). In all patients, SPECT revealed either multiple or focal uptake defects, the latter corresponding with focal signs or symptoms in all but one case. Computerized tomography showed a diffuse cerebral atrophy in eight of 12 patients, magnetic resonance imaging exhibited changes like atrophy and/or leukoencephalopathy in two of five cases. Our data indicate that both disturbance of cerebral amine metabolism and alteration of local perfusion share in the pathogenesis of AIDS dementia complex. SPECT is an important aid in the diagnosis of AIDS dementia complex and contributes to the understanding of the pathophysiological mechanisms of this disorder

Tapping to a slow tempo in the presence of simple and complex meters reveals experience-specific biases for processing music.

Directory of Open Access Journals (Sweden)

Sangeeta Ullal-Gupta

Full Text Available Musical meters vary considerably across cultures, yet relatively little is known about how culture-specific experience influences metrical processing. In Experiment 1, we compared American and Indian listeners' synchronous tapping to slow sequences. Inter-tone intervals contained silence or to-be-ignored rhythms that were designed to induce a simple meter (familiar to Americans and Indians or a complex meter (familiar only to Indians. A subset of trials contained an abrupt switch from one rhythm to another to assess the disruptive effects of contradicting the initially implied meter. In the unfilled condition, both groups tapped earlier than the target and showed large tap-tone asynchronies (measured in relative phase. When inter-tone intervals were filled with simple-meter rhythms, American listeners tapped later than targets, but their asynchronies were smaller and declined more rapidly. Likewise, asynchronies rose sharply following a switch away from simple-meter but not from complex-meter rhythm. By contrast, Indian listeners performed similarly across all rhythm types, with asynchronies rapidly declining over the course of complex- and simple-meter trials. For these listeners, a switch from either simple or complex meter increased asynchronies. Experiment 2 tested American listeners but doubled the duration of the synchronization phase prior to (and after the switch. Here, compared with simple meters, complex-meter rhythms elicited larger asynchronies that declined at a slower rate, however, asynchronies increased after the switch for all conditions. Our results provide evidence that ease of meter processing depends to a great extent on the amount of experience with specific meters.

Tapping to a slow tempo in the presence of simple and complex meters reveals experience-specific biases for processing music.

Science.gov (United States)

Ullal-Gupta, Sangeeta; Hannon, Erin E; Snyder, Joel S

2014-01-01

Musical meters vary considerably across cultures, yet relatively little is known about how culture-specific experience influences metrical processing. In Experiment 1, we compared American and Indian listeners' synchronous tapping to slow sequences. Inter-tone intervals contained silence or to-be-ignored rhythms that were designed to induce a simple meter (familiar to Americans and Indians) or a complex meter (familiar only to Indians). A subset of trials contained an abrupt switch from one rhythm to another to assess the disruptive effects of contradicting the initially implied meter. In the unfilled condition, both groups tapped earlier than the target and showed large tap-tone asynchronies (measured in relative phase). When inter-tone intervals were filled with simple-meter rhythms, American listeners tapped later than targets, but their asynchronies were smaller and declined more rapidly. Likewise, asynchronies rose sharply following a switch away from simple-meter but not from complex-meter rhythm. By contrast, Indian listeners performed similarly across all rhythm types, with asynchronies rapidly declining over the course of complex- and simple-meter trials. For these listeners, a switch from either simple or complex meter increased asynchronies. Experiment 2 tested American listeners but doubled the duration of the synchronization phase prior to (and after) the switch. Here, compared with simple meters, complex-meter rhythms elicited larger asynchronies that declined at a slower rate, however, asynchronies increased after the switch for all conditions. Our results provide evidence that ease of meter processing depends to a great extent on the amount of experience with specific meters.

Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for beta-lactam acetylation.

Science.gov (United States)

He, Hongzhen; Ding, Yi; Bartlam, Mark; Sun, Fei; Le, Yi; Qin, Xincheng; Tang, Hong; Zhang, Rongguang; Joachimiak, Andrzej; Liu, Jinyuan; Zhao, Nanming; Rao, Zihe

2003-01-31

Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55A resolution. The binary complex forms a characteristic "V" shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

The occurrence of Photorhabdus-like toxin complexes in Bacillus thuringiensis

Science.gov (United States)

Recently, genomic sequencing of a Bacillus thuringiensis (Bt) isolate from our collection revealed the presence of an apparent operon encoding an insecticidal toxin complex (Tca) similar to that first described from the entomopathogen Photorhabdus luminescens. To determine whether these genes are w...

Preparation of Palladium-Impregnated Ceria by Metal Complex Decomposition for Methane Steam Reforming Catalysis

Directory of Open Access Journals (Sweden)

Worawat Wattanathana

2017-01-01

Full Text Available Palladium-impregnated ceria materials were successfully prepared via an integrated procedure between a metal complex decomposition method and a microwave-assisted wetness impregnation. Firstly, ceria (CeO2 powders were synthesized by thermal decomposition of cerium(III complexes prepared by using cerium(III nitrate or cerium(III chloride as a metal source to form a metal complex precursor with triethanolamine or benzoxazine dimer as an organic ligand. Palladium(II nitrate was consequently introduced to the preformed ceria materials using wetness impregnation while applying microwave irradiation to assist dispersion of the dopant. The palladium-impregnated ceria materials were obtained by calcination under reduced atmosphere of 10% H2 in He stream at 700°C for 2 h. Characterization of the palladium-impregnated ceria materials reveals the influences of the metal complex precursors on the properties of the obtained materials. Interestingly, the palladium-impregnated ceria prepared from the cerium(III-benzoxazine dimer complex revealed significantly higher BET specific surface area and higher content of the more active Pdδ+ (δ > 2 species than the materials prepared from cerium(III-triethanolamine complexes. Consequently, it exhibited the most efficient catalytic activity in the methane steam reforming reaction. By optimization of the metal complex precursors, characteristics of the obtained palladium-impregnated ceria catalysts can be modified and hence influence the catalytic activity.

Extrinsic and intrinsic complexities of the Los Alamos Plutonium Processing Facility

International Nuclear Information System (INIS)

Bearse, R.C.; Longmire, V.L.; Roberts, N.J.

1985-01-01

Analysis of the data obtained in one year of plutonium accounting at Los Alamos reveals significant complexity. Much of this complexity arises from the complexity of the processes themselves. Additional complexity is induced by errors in the data entry process. It is important to note that there is no evidence that this complexity is adversely affecting the accounting in the plant. We have been analyzing transaction data from fiscal year 1983 processing. This study involved 62,595 transactions. The data have been analyzed using the relational database program INGRES on a VAX 11/780 computer. This software allows easy manipulation of the original data and subsets drawn from it. We have been attempting for several years to understand the global features of the TA-55 accounting data. This project has underscored several of the system's complexities. Examples that will be reported here include audit trails, lot-name multiplicity, etc

Amputation effects on the underlying complexity within transtibial amputee ankle motion

Energy Technology Data Exchange (ETDEWEB)

Wurdeman, Shane R., E-mail: shanewurdeman@gmail.com [Nebraska Biomechanics Core Facility, University of Nebraska at Omaha, Omaha, Nebraska 68182 (United States); Advanced Prosthetics Center, Omaha, Nebraska 68134 (United States); Myers, Sara A. [Nebraska Biomechanics Core Facility, University of Nebraska at Omaha, Omaha, Nebraska 68182 (United States); Stergiou, Nicholas [Nebraska Biomechanics Core Facility, University of Nebraska at Omaha, Omaha, Nebraska 68182 (United States); College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198 (United States)

2014-03-15

The presence of chaos in walking is considered to provide a stable, yet adaptable means for locomotion. This study examined whether lower limb amputation and subsequent prosthetic rehabilitation resulted in a loss of complexity in amputee gait. Twenty-eight individuals with transtibial amputation participated in a 6 week, randomized cross-over design study in which they underwent a 3 week adaptation period to two separate prostheses. One prosthesis was deemed “more appropriate” and the other “less appropriate” based on matching/mismatching activity levels of the person and the prosthesis. Subjects performed a treadmill walking trial at self-selected walking speed at multiple points of the adaptation period, while kinematics of the ankle were recorded. Bilateral sagittal plane ankle motion was analyzed for underlying complexity through the pseudoperiodic surrogation analysis technique. Results revealed the presence of underlying deterministic structure in both prostheses and both the prosthetic and sound leg ankle (discriminant measure largest Lyapunov exponent). Results also revealed that the prosthetic ankle may be more likely to suffer loss of complexity than the sound ankle, and a “more appropriate” prosthesis may be better suited to help restore a healthy complexity of movement within the prosthetic ankle motion compared to a “less appropriate” prosthesis (discriminant measure sample entropy). Results from sample entropy results are less likely to be affected by the intracycle periodic dynamics as compared to the largest Lyapunov exponent. Adaptation does not seem to influence complexity in the system for experienced prosthesis users.

Amputation effects on the underlying complexity within transtibial amputee ankle motion

International Nuclear Information System (INIS)

Wurdeman, Shane R.; Myers, Sara A.; Stergiou, Nicholas

2014-01-01

The presence of chaos in walking is considered to provide a stable, yet adaptable means for locomotion. This study examined whether lower limb amputation and subsequent prosthetic rehabilitation resulted in a loss of complexity in amputee gait. Twenty-eight individuals with transtibial amputation participated in a 6 week, randomized cross-over design study in which they underwent a 3 week adaptation period to two separate prostheses. One prosthesis was deemed “more appropriate” and the other “less appropriate” based on matching/mismatching activity levels of the person and the prosthesis. Subjects performed a treadmill walking trial at self-selected walking speed at multiple points of the adaptation period, while kinematics of the ankle were recorded. Bilateral sagittal plane ankle motion was analyzed for underlying complexity through the pseudoperiodic surrogation analysis technique. Results revealed the presence of underlying deterministic structure in both prostheses and both the prosthetic and sound leg ankle (discriminant measure largest Lyapunov exponent). Results also revealed that the prosthetic ankle may be more likely to suffer loss of complexity than the sound ankle, and a “more appropriate” prosthesis may be better suited to help restore a healthy complexity of movement within the prosthetic ankle motion compared to a “less appropriate” prosthesis (discriminant measure sample entropy). Results from sample entropy results are less likely to be affected by the intracycle periodic dynamics as compared to the largest Lyapunov exponent. Adaptation does not seem to influence complexity in the system for experienced prosthesis users

Investigation of REE perchlorates complexing with benzimidazole in aqua-dioxane media

International Nuclear Information System (INIS)

Akhrimenko, Z.M.; Panyushkin, V.T.; Ishbulatova, S.K.

1992-01-01

Stability constant (K 1 ) of complexes of rare earth perchlorates with benzimidazole were determined by the method of pH-metric titration. Nonmonotonous change in lgK 1 with rare earth ordinal number increase was revealed

Vitamin D receptor (VDR) promoter targeting through a novel chromatin remodeling complex.

Science.gov (United States)

Kato, Shigeaki; Fujiki, Ryoji; Kitagawa, Hirochika

2004-05-01

We have purified nuclear complexes for Vitamin D receptor (VDR), and identified one of them as a novel ATP-dependent chromatine remodeling containing Williams syndrome transcription factor (WSTF), that is supposed to be responsible for Williams syndrome. This complex (WSTF including nucleosome assembly complex (WINAC)) exhibited an ATP-dependent chromatin remodeling activity in vitro. Transient expression assays revealed that WINAC potentiates ligand-induced function of VDR in gene activation and repression. Thus, this study describes a molecular basis of the VDR function on chromosomal DNA through chromatine remodeling.

Collaborative Management of Complex Major Construction Projects: AnyLogic-Based Simulation Modelling

Directory of Open Access Journals (Sweden)

Na Zhao

2016-01-01

Full Text Available Complex supply chain system collaborative management of major construction projects effectively integrates the different participants in the construction project. This paper establishes a simulation model based on AnyLogic to reveal the collaborative elements in the complex supply chain management system and the modes of action as well as the transmission problems of the intent information. Thus it is promoting the participants to become an organism with coordinated development and coevolution. This study can help improve the efficiency and management of the complex system of major construction projects.

Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability.

Directory of Open Access Journals (Sweden)

Riffat I Munir

Full Text Available Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active enzymes (CAZymes, sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199 and carbohydrate binding modules (95 were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly.

Cancer initiation and progression: an unsimplifiable complexity

Directory of Open Access Journals (Sweden)

Frezza Eldo E

2006-10-01

Full Text Available Abstract Background Cancer remains one of the most complex diseases affecting humans and, despite the impressive advances that have been made in molecular and cell biology, how cancer cells progress through carcinogenesis and acquire their metastatic ability is still widely debated. Conclusion There is no doubt that human carcinogenesis is a dynamic process that depends on a large number of variables and is regulated at multiple spatial and temporal scales. Viewing cancer as a system that is dynamically complex in time and space will, however, probably reveal more about its underlying behavioural characteristics. It is encouraging that mathematicians, biologists and clinicians continue to contribute together towards a common quantitative understanding of cancer complexity. This way of thinking may further help to clarify concepts, interpret new and old experimental data, indicate alternative experiments and categorize the acquired knowledge on the basis of the similarities and/or shared behaviours of very different tumours.

Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

Science.gov (United States)

Kashif, Muhammad; Andersson, Claes; Mansoori, Sharmineh; Larsson, Rolf; Nygren, Peter; Gustafsson, Mats G

2017-11-28

We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

Effects of Polyelectrolyte Complex Micelles and Their Components on the Enzymatic Activity of Lipase

NARCIS (Netherlands)

Lindhoud, Saskia; Norde, Willem; Stuart, Martien Cohen

2010-01-01

The enzymatic activity of Hi-lipase embedded in complexes of poly-2-methylvinylpyridinium-co-poly(ethylene oxide) (P2MVP(41)-PEG(205)) and poly(acrylic acid)(PAA(139)) is studied as a function of the PAA(139) + P2MVP(41) - PEO(205) complex composition. The measurements revealed that there are

Reconstitution of chlorophyll a/b light-harvesting complexes: xanthophyll-dependent assembly and energy transfer

Energy Technology Data Exchange (ETDEWEB)

Plumley, F.G.; Schmidt, G.W.

1987-01-01

A method for in vitro reconstitution of the chlorophyll a/b light-harvesting complex from LiDodSO/sub 4//heat-denatured or acetone-extracted photosynthetic membranes has been developed. Characterization of the minimum components necessary for the functional organization or pigments in these membrane complexes reveals that xanthophylls are essential structural components.

Enzyme-like catalysis via ternary complex mechanism: alkoxy-bridged dinuclear cobalt complex mediates chemoselective O-esterification over N-amidation.

Science.gov (United States)

Hayashi, Yukiko; Santoro, Stefano; Azuma, Yuki; Himo, Fahmi; Ohshima, Takashi; Mashima, Kazushi

2013-04-24

Hydroxy group-selective acylation in the presence of more nucleophilic amines was achieved using acetates of first-row late transition metals, such as Mn, Fe, Co, Cu, and Zn. Among them, cobalt(II) acetate was the best catalyst in terms of reactivity and selectivity. The combination of an octanuclear cobalt carboxylate cluster [Co4(OCOR)6O]2 (2a: R = CF3, 2b: R = CH3, 2c: R = (t)Bu) with nitrogen-containing ligands, such as 2,2'-bipyridine, provided an efficient catalytic system for transesterification, in which an alkoxide-bridged dinuclear complex, Co2(OCO(t)Bu)2(bpy)2(μ2-OCH2-C6H4-4-CH3)2 (10), was successfully isolated as a key intermediate. Kinetic studies and density functional theory calculations revealed Michaelis-Menten behavior of the complex 10 through an ordered ternary complex mechanism similar to dinuclear metallo-enzymes, suggesting the formation of alkoxides followed by coordination of the ester.

Optimization and Characterization of Magnetic Nano Particle - Vesicular Stomatitis Virus complexes for Therapy of Hepatocellular Carcinoma

OpenAIRE

Wille, Florian

2017-01-01

This thesis describes the complex formation of oncolytic viral particles (VSV) and magnetic nanoparticles (MNP). Surface decoration of the complexes with hyaluronic acid resulted in reduced antibody mediated inactivation in vitro and prolonged circulation time in vivo. First in vivo results of intra-tumoral complex application in HCC bearing rats revealed a higher viral titer compared to naked VSV particles and the ability to visualize these complexes by MRI. Diese Arbeit beschreibt die K...

Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for {beta}-lactam acetylation.

Energy Technology Data Exchange (ETDEWEB)

He, H.; Ding, Y.; Bartlam, M.; Sun, F.; Le, Y.; Qin, X.; Tang, H.; Zhang, R.; Joachimiak, A.; Liu, J.; Zhao, N.; Rao, Z.; Biosciences Division; Tsinghua Univ.; Chinese Academy of Science

2003-01-31

Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55 {angstrom} resolution. The binary complex forms a characteristic 'V' shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

Studies on a network of complex neurons

Science.gov (United States)

Chakravarthy, Srinivasa V.; Ghosh, Joydeep

1993-09-01

In the last decade, much effort has been directed towards understanding the role of chaos in the brain. Work with rabbits reveals that in the resting state the electrical activity on the surface of the olfactory bulb is chaotic. But, when the animal is involved in a recognition task, the activity shifts to a specific pattern corresponding to the odor that is being recognized. Unstable, quasiperiodic behavior can be found in a class of conservative, deterministic physical systems called the Hamiltonian systems. In this paper, we formulate a complex version of Hopfield's network of real parameters and show that a variation on this model is a conservative system. Conditions under which the complex network can be used as a Content Addressable memory are studied. We also examine the effect of singularities of the complex sigmoid function on the network dynamics. The network exhibits unpredictable behavior at the singularities due to the failure of a uniqueness condition for the solution of the dynamic equations. On incorporating a weight adaptation rule, the structure of the resulting complex network equations is shown to have an interesting similarity with Kosko's Adaptive Bidirectional Associative Memory.

Our Galactic Neighbor Hosts Complex Organic Molecules

Science.gov (United States)

Hensley, Kerry

2018-03-01

For the first time, data from the Atacama Large Millimeter/submillimeter Array (ALMA) reveal the presence of methyl formate and dimethyl ether in a star-forming region outside our galaxy. This discovery has important implications for the formation and survival of complex organic compounds importantfor the formation of life in low-metallicity galaxies bothyoung and old.No Simple Picture of Complex Molecule FormationALMA, pictured here with the Magellanic Clouds above, has observed organic molecules in our Milky Way Galaxy and beyond. [ESO/C. Malin]Complex organic molecules (those with at least six atoms, one or more of which must be carbon) are the precursors to the building blocks of life. Knowing how and where complex organic molecules can form is a key part of understanding how life came to be on Earth and how it might arise elsewhere in the universe. From exoplanet atmospheres to interstellar space, complex organic molecules are ubiquitous in the Milky Way.In our galaxy, complex organic molecules are often found in the intense environments of hot cores clumps of dense molecular gas surrounding the sites of star formation. However, its not yet fully understood how the complex organic molecules found in hot cores come to be. One possibility is that the compounds condense onto cold dust grains long before the young stars begin heating their natal shrouds. Alternatively, they might assemble themselves from the hot, dense gas surrounding the blazing protostars.Composite infrared and optical image of the N 113 star-forming region in the LMC. The ALMA coverage is indicated by the gray line. Click to enlarge. [Sewio et al. 2018]Detecting Complexity, a Galaxy AwayUsing ALMA, a team of researchers led by Marta Sewio (NASA Goddard Space Flight Center) recently detected two complex organic molecules methyl formate and dimethyl ether for the first time in our neighboring galaxy, the Large Magellanic Cloud (LMC). Previous searches for organic molecules in the LMC detected

Highly Luminescent Lanthanide Complexes of 1 Hydroxy-2-pyridinones

Energy Technology Data Exchange (ETDEWEB)

University of California, Berkeley; Lawrence National Laboratory; Raymond, Kenneth; Moore, Evan G.; Xu, Jide; Jocher, Christoph J.; Castro-Rodriguez, Ingrid; Raymond, Kenneth N.

2007-11-01

The synthesis, X-ray structure, stability, and photophysical properties of several trivalent lanthanide complexes formed from two differing bis-bidentate ligands incorporating either alkyl or alkyl ether linkages and featuring the 1-hydroxy-2-pyridinone (1,2-HOPO) chelate group in complex with Eu(III), Sm(III) and Gd(III) are reported. The Eu(III) complexes are among some of the best examples, pairing highly efficient emission ({Phi}{sub tot}{sup Eu} {approx} 21.5%) with high stability (pEu {approx} 18.6) in aqueous solution, and are excellent candidates for use in biological assays. A comparison of the observed behavior of the complexes with differing backbone linkages shows remarkable similarities, both in stability and photophysical properties. Low temperature photophysical measurements for a Gd(III) complex were also used to gain insight into the electronic structure, and were found to agree with corresponding TD-DFT calculations for a model complex. A comparison of the high resolution Eu(III) emission spectra in solution and from single crystals also revealed a more symmetric coordination geometry about the metal ion in solution due to dynamic rotation of the observed solid state structure.

Mechanism of management of competitiveness of production of agrarian and industrial complex

Directory of Open Access Journals (Sweden)

Buryak E. A.

2016-04-01

Full Text Available the concept of competitiveness and mechanisms of management of competitiveness of production is considered. Major factors of ensuring competitiveness of production of agrarian and industrial complex are allocated. The main problems of production of wheat in the Republic of Crimea making negative impact on the level of her competitiveness are revealed. The mechanism of management of competitiveness of production of agrarian and industrial complex is developed.

Complexes of uranyl nitrate with 2,6-pyridinedicarboxamides: synthesis, crystal structure, and DFT study

Energy Technology Data Exchange (ETDEWEB)

Alyapyshev, Mikhail; Babain, Vasiliy [ITMO University, 49, Kronverksky pr., 197101, St. Petersburg (Russian Federation); ThreeArc Mining Ltd., 5, Stary Tolmachevskiy per., 115184, Moscow (Russian Federation); Tkachenko, Lyudmila; Lumpov, Alexander [Khlopin Radium Institute, 28, 2nd Murinskiy pr., 194021, St. Petersburg (Russian Federation); Gurzhiy, Vladislav; Zolotarev, Andrey; Dar' in, Dmitriy [St. Petersburg State University, 7-9, Universitetskaya nab., 199034, St. Petersburg (Russian Federation); Ustynyuk, Yuriy; Gloriozov, Igor [M.V. Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Paulenova, Alena [Department of Nuclear Engineering, Oregon State University, Corvallis, OR (United States)

2017-05-04

Two complexes of uranyl nitrate with N,N,N',N'-tetrabutyl-2,6-pyridinedicarboxamide (TBuDPA) and N,N'-diethyl-N,N'-diphenyl-2,6-pyridinedicarboxamide (EtPhDPA) were synthesized and studied. The complex of tetraalkyl-2,6-pyridinedicarboxamide with metal nitrate was synthesized for the first time. XRD analysis revealed the different type of complexation: a 1:1 metal:ligand complex for EtPhDPA and complex with polymeric structure for TBuDPA. The quantum chemical calculations (DFT) confirm that both ligands form the most stable complexes that match the minimal values pre-organization energy of the ligands. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis

International Nuclear Information System (INIS)

Vetcher, Alexandre A; Srinivasan, Srimeenakshi; Vetcher, Ivan A; Abramov, Semen M; Kozlov, Mikhail; Baughman, Ray H; Levene, Stephen D

2006-01-01

We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique

Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis

Energy Technology Data Exchange (ETDEWEB)

Vetcher, Alexandre A [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States); Srinivasan, Srimeenakshi [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States); Vetcher, Ivan A [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States); Abramov, Semen M [NanoTech Institute, University of Texas at Dallas, Richardson, TX 75083 (United States); Kozlov, Mikhail [NanoTech Institute, University of Texas at Dallas, Richardson, TX 75083 (United States); Baughman, Ray H [NanoTech Institute, University of Texas at Dallas, Richardson, TX 75083 (United States); Levene, Stephen D [Institute of Biomedical Sciences and Technology and Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 (United States)

2006-08-28

We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.

Managing Programmatic Risk for Complex Space System Developments

Science.gov (United States)

Panetta, Peter V.; Hastings, Daniel; Brumfield, Mark (Technical Monitor)

2001-01-01

Risk management strategies have become a recent important research topic to many aerospace organizations as they prepare to develop the revolutionary complex space systems of the future. Future multi-disciplinary complex space systems will make it absolutely essential for organizations to practice a rigorous, comprehensive risk management process, emphasizing thorough systems engineering principles to succeed. Project managers must possess strong leadership skills to direct high quality, cross-disciplinary teams for successfully developing revolutionary space systems that are ever increasing in complexity. Proactive efforts to reduce or eliminate risk throughout a project's lifecycle ideally must be practiced by all technical members in the organization. This paper discusses some of the risk management perspectives that were collected from senior managers and project managers of aerospace and aeronautical organizations by the use of interviews and surveys. Some of the programmatic risks which drive the success or failure of projects are revealed. Key findings lead to a number of insights for organizations to consider for proactively approaching the risks which face current and future complex space systems projects.

Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine.

Science.gov (United States)

Volkan, Ender; Ford, Bradley A; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Thanassi, David G; Waksman, Gabriel; Hultgren, Scott J

2012-06-12

P pili are prototypical chaperone-usher pathway-assembled pili used by Gram-negative bacteria to adhere to host tissues. The PapC usher contains five functional domains: a transmembrane β-barrel, a β-sandwich Plug, an N-terminal (periplasmic) domain (NTD), and two C-terminal (periplasmic) domains, CTD1 and CTD2. Here, we delineated usher domain interactions between themselves and with chaperone-subunit complexes and showed that overexpression of individual usher domains inhibits pilus assembly. Prior work revealed that the Plug domain occludes the pore of the transmembrane domain of a solitary usher, but the chaperone-adhesin-bound usher has its Plug displaced from the pore, adjacent to the NTD. We demonstrate an interaction between the NTD and Plug domains that suggests a biophysical basis for usher gating. Furthermore, we found that the NTD exhibits high-affinity binding to the chaperone-adhesin (PapDG) complex and low-affinity binding to the major tip subunit PapE (PapDE). We also demonstrate that CTD2 binds with lower affinity to all tested chaperone-subunit complexes except for the chaperone-terminator subunit (PapDH) and has a catalytic role in dissociating the NTD-PapDG complex, suggesting an interplay between recruitment to the NTD and transfer to CTD2 during pilus initiation. The Plug domain and the NTD-Plug complex bound all of the chaperone-subunit complexes tested including PapDH, suggesting that the Plug actively recruits chaperone-subunit complexes to the usher and is the sole recruiter of PapDH. Overall, our studies reveal the cooperative, active roles played by periplasmic domains of the usher to initiate, grow, and terminate a prototypical chaperone-usher pathway pilus.

Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

Energy Technology Data Exchange (ETDEWEB)

Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

2006-01-01

Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

Synthesis and Spectral Evaluation of Some Unsymmetrical Mesoporphyrinic Complexes

Directory of Open Access Journals (Sweden)

Rica Boscencu

2012-06-01

Full Text Available Synthesis and spectral evaluation of new zinc and copper unsymmetrical mesoporphyrinic complexes are reported. Zn(II-5-(4-acetoxy-3-methoxyphenyl-10,15,20-tris-(4-carboxymethylphenylporphyrin, Zn(II-5-[(3,4-methylenedioxyphenyl]-10,15,20-tris-(4-carboxymethylphenylporphyrin, Cu(II-5-(4-acetoxy-3-methoxyphenyl-10,15,20-tris-(4-carboxymethylphenylporphyrin and Cu(II-5-[(3,4-methylenedioxyphenyl]-10,15,20-tris-(4-carboxymethylphenylporphyrin were synthesized using microwave-assisted synthesis. The complexes were characterized by elemental analysis, FT-IR, UV-Vis, EPR and NMR spectroscopy, which fully confirmed their structure. The spectral absorption properties of the porphyrinic complexes were studied in solvents with different polarities. Fluorescence emission and singlet oxygen formation quantum yields were evaluated for the compounds under study, revealing high yields for the zinc derivatives. The copper complexes are not emissive and only display residual capacity for singlet oxygen formation.

Chitosan-based Schiff base-metal complexes (Mn, Cu, Co) as ...

Indian Academy of Sciences (India)

and A C PISE. Chemistry Research ... Data obtained by thermal analysis revealed that these complexes showed good thermal ... vents along with its inherent chirality makes chitosan .... resulting Schiff base IC was cooled, filtered and washed with ethanol ..... experiments with homogeneous Mn-salen catalyst at different ...

Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

International Nuclear Information System (INIS)

Oyama, Takuji; Toyota, Kenji; Waku, Tsuyoshi; Hirakawa, Yuko; Nagasawa, Naoko; Kasuga, Jun-ichi; Hashimoto, Yuichi; Miyachi, Hiroyuki; Morikawa, Kosuke

2009-01-01

The structures of the ligand-binding domains (LBDs) of human peroxisome proliferator-activated receptors (PPARα, PPARγ and PPARδ) in complexes with a pan agonist, an α/δ dual agonist and a PPARδ-specific agonist were determined. The results explain how each ligand is recognized by the PPAR LBDs at an atomic level. Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPAR subtypes display different tissue distribution patterns and distinct pharmacological profiles, they all are essentially related to fatty-acid and glucose metabolism. Since the PPARs share similar three-dimensional structures within the LBDs, synthetic ligands which simultaneously activate two or all of the PPARs could be potent candidates in terms of drugs for the treatment of abnormal metabolic homeostasis. The structures of several PPAR LBDs were determined in complex with synthetic ligands, derivatives of 3-(4-alkoxyphenyl)propanoic acid, which exhibit unique agonistic activities. The PPARα and PPARγ LBDs were complexed with the same pan agonist, TIPP-703, which activates all three PPARs and their crystal structures were determined. The two LBD–ligand complex structures revealed how the pan agonist is adapted to the similar, but significantly different, ligand-binding pockets of the PPARs. The structures of the PPARδ LBD in complex with an α/δ-selective ligand, TIPP-401, and with a related δ-specific ligand, TIPP-204, were also determined. The comparison between the two PPARδ complexes revealed how each ligand exhibits either a ‘dual selective’ or ‘single specific’ binding mode

Antibacterial, antimalarial and leishmanicidal activities of Cu (II) and nickel (II) complexes of diclofenac sodium

International Nuclear Information System (INIS)

Rehman, F.U.; Khan, M.F.; Khan, G.M.; Khan, H.; Khan, I.U.

2010-01-01

Metal complexes are famous for a wide array of chemotherapeutic effects. The current study was designed to synthesize and evaluate unexplored chemotherapeutic effects of Cu (II) and Nickel (II) complexes of the non-steroidal anti-inflammatory drug diclofenac. Nickel complex exhibited significant leishmanicidal activity against Lieshmania major, while the copper complex was found to possess low activity against the same pathogen. Both of the complexes revealed low antibacterial activities and were interestingly failed to produce any considerable antimalarial activity against Plasmodium falciparum 3D7. Selective leishmanicidal activities of Nickel (II) complex of diclofenac needs further improvement to be developed as potential new metal-based leishmanicidal agent.(author)

Antibacterial, antimalarial and leishmanicidal activities of Cu (II) and nickel (II) complexes of diclofenac sodium

Energy Technology Data Exchange (ETDEWEB)

Rehman, F U; Khan, M F; Khan, G M; Khan, H [Gomal University, D.I. Khan (Pakistan). Dept. of Faculty of Pharmacy; Khan, I U [University of Peshawar (Pakistan). Dept. of Faculty of Pharmacy

2010-08-15

Metal complexes are famous for a wide array of chemotherapeutic effects. The current study was designed to synthesize and evaluate unexplored chemotherapeutic effects of Cu (II) and Nickel (II) complexes of the non-steroidal anti-inflammatory drug diclofenac. Nickel complex exhibited significant leishmanicidal activity against Lieshmania major, while the copper complex was found to possess low activity against the same pathogen. Both of the complexes revealed low antibacterial activities and were interestingly failed to produce any considerable antimalarial activity against Plasmodium falciparum 3D7. Selective leishmanicidal activities of Nickel (II) complex of diclofenac needs further improvement to be developed as potential new metal-based leishmanicidal agent.(author)

Influence of complexes of iron on genetic changes at gamma-irradiated wheat

International Nuclear Information System (INIS)

Shamilov, E. N.; Rzayev, A.A.; Huseynova, Z.H; Mamedli, S.A; Azizov, I.V.

2006-01-01

Full text: At the result of research action of salts of some metals on living organisms their preventive and therapeutic action is revealed. It was revealed, that metals in structure of organic complex connections are less toxic, than as inorganic salts. Presence of organic ligand gives metallic-complexes lipophilically, will neutralize electrostatistical charges of metals therefore their transport through cellular membranes is strongly facilitated. In this connection rather expedient study of radioprotector properties of trivalent metals and their complexes is represented. Use of iron as a radioprotector is caused with its ability to steady complexing biogenic character. As objects of researches are taken seeds drought-resistant firm of wheat Triticum L. Seeds subjected to the general uniform scale of irradiation-from a source 60 Co and gamma to installation R khund a t average capacity of a doze of radiation dose rate (D R=0,024 Gy/s). Before the irradiation seeds have been processed pyrocatechol, iron pyrocatechol, thiocarbamide, iron-thiocarbamide, rutin and iron rutin at concentration 10 2 M. For synthesis of complexes used chloride of iron (III), thiocarbamide, pyrocatechol marks a .p.a. . Routines (3- ramnoglycoside-3,5,7,3,4-penta-oksi-flavone, chartreuse fine-grained a powder) have received from (Sophora japonica L.): Synthesis complexes of iron carried out by the following technique: stoichiometric quantity of thiocarbamide, pyrocatechol and routine dissolved separately in 50 ml isopropyl alcohol. A solution of chloride of iron (III) deposits dropped out, separated, dried up to constant weight was added to the received solutions in the portions at hashing.

Effects of Polyelectrolyte Complex Micelles and Their Components on the Enzymatic Activity of Lipase

NARCIS (Netherlands)

Lindhoud, Saskia; Norde, Willem; Cohen Stuart, Martinus Abraham

2010-01-01

The enzymatic activity of Hl-lipase embedded in complexes of poly-2-methylvinylpyridinium-co-poly(ethylene oxide) (P2MVP41−PEO205) and poly(acrylic acid)(PAA139) is studied as a function of the PAA139 + P2MVP41−PEO205 complex composition. The measurements revealed that there are several factors that

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.

Directory of Open Access Journals (Sweden)

Katherine Belov

2006-03-01

Full Text Available The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum sequence to construct the first map of a marsupial major histocompatibility complex (MHC. The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.

Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.

Directory of Open Access Journals (Sweden)

Shane E Gordon

2016-03-01

Full Text Available Dihydrodipicolinate synthase (DHDPS catalyzes the first committed step in the diaminopimelate pathway of bacteria, yielding amino acids required for cell wall and protein biosyntheses. The essentiality of the enzyme to bacteria, coupled with its absence in humans, validates DHDPS as an antibacterial drug target. Conventional drug design efforts have thus far been unsuccessful in identifying potent DHDPS inhibitors. Here, we make use of contemporary molecular dynamics simulation and Markov state models to explore the interactions between DHDPS from the human pathogen Staphylococcus aureus and its cognate substrate, pyruvate. Our simulations recover the crystallographic DHDPS-pyruvate complex without a priori knowledge of the final bound structure. The highly conserved residue Arg140 was found to have a pivotal role in coordinating the entry of pyruvate into the active site from bulk solvent, consistent with previous kinetic reports, indicating an indirect role for the residue in DHDPS catalysis. A metastable binding intermediate characterized by multiple points of intermolecular interaction between pyruvate and key DHDPS residue Arg140 was found to be a highly conserved feature of the binding trajectory when comparing alternative binding pathways. By means of umbrella sampling we show that these binding intermediates are thermodynamically metastable, consistent with both the available experimental data and the substrate binding model presented in this study. Our results provide insight into an important enzyme-substrate interaction in atomistic detail that offers the potential to be exploited for the discovery of more effective DHDPS inhibitors and, in a broader sense, dynamic protein-drug interactions.

Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug-binding site

OpenAIRE

Handing, Katarzyna B.; Shabalin, Ivan G.; Szlachta, Karol; Majorek, Karolina A.; Minor, Wladek

2016-01-01

Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1 ?. Cetirizine is bound in two sites ? a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizi...

Formation of competitive potential of the machine-building complex of the region

Directory of Open Access Journals (Sweden)

Oleg Ivanovich Botkin

2014-03-01

Full Text Available The article describes the features of competitive potential of regional machine-building complex in a globalized world economy. The purpose of the research is the development of theoretically reasonable economic basis of the machine-building complex considering  the  features of business in the conditions of the WTO. In the work, the hypothesis of a special role of the external economic factors locates in development of the enterprises of regional industrial complexes. The study of the theoretical provisions defining the development of the region revealed the factors determining influence of the international trade agreements on spatial localization of the industry. The main attention is paid to an analytical assessment of the current state and the trends, which have developed in the period of post-crisis economic recovery. Analysis of the main indicators of attractiveness has revealed the weak position of local industrial enterprises in the WTO. The directions of strengthening of the competitive capacity of the local industrial enterprises are defined. The obtained results allow us to increase the sustainability of the industry by means of effective management mechanism improvements and to create favorable operating conditions of a machine-building complex of the region

Self-sustained oscillations of complex genomic regulatory networks

International Nuclear Information System (INIS)

Ye Weiming; Huang Xiaodong; Huang Xuhui; Li Pengfei; Xia Qinzhi; Hu Gang

2010-01-01

Recently, self-sustained oscillations in complex networks consisting of non-oscillatory nodes have attracted great interest in diverse natural and social fields. Oscillatory genomic regulatory networks are one of the most typical examples of this kind. Given an oscillatory genomic network, it is important to reveal the central structure generating the oscillation. However, if the network consists of large numbers of genes and interactions, the oscillation generator is deeply hidden in the complicated interactions. We apply the dominant phase-advanced driving path method proposed in Qian et al. (2010) to reduce complex genomic regulatory networks to one-dimensional and unidirectionally linked network graphs where negative regulatory loops are explored to play as the central generators of the oscillations, and oscillation propagation pathways in the complex networks are clearly shown by tree branches radiating from the loops. Based on the above understanding we can control oscillations of genomic networks with high efficiency.

Interpreting Popov criteria in Lure´ systems with complex scaling stability analysis

Science.gov (United States)

Zhou, J.

2018-06-01

The paper presents a novel frequency-domain interpretation of Popov criteria for absolute stability in Lure´ systems by means of what we call complex scaling stability analysis. The complex scaling technique is developed for exponential/asymptotic stability in LTI feedback systems, which dispenses open-loop poles distribution, contour/locus orientation and prior frequency sweeping. Exploiting the technique for alternatively revealing positive realness of transfer functions, re-interpreting Popov criteria is explicated. More specifically, the suggested frequency-domain stability conditions are conformable both in scalar and multivariable cases, and can be implemented either graphically with locus plotting or numerically without; in particular, the latter is suitable as a design tool with auxiliary parameter freedom. The interpretation also reveals further frequency-domain facts about Lure´ systems. Numerical examples are included to illustrate the main results.

Spin Propensities of Octahedral Complexes From Density Functional Theory

DEFF Research Database (Denmark)

Mortensen, Sara R.; Kepp, Kasper Planeta

2015-01-01

assessment of spin state propensities versus ligand and metal type and reveal, e.g., that CN- is consistently weaker than CO for M(II) but stronger than CO for M(III) and SCN- and NCS- change order in M(II) versus M(III) complexes. Contrary to expectation based on the spectrochemical series, Cl- and Br...

Half-Sandwich Ru(II and Os(II Bathophenanthroline Complexes Containing a Releasable Dichloroacetato Ligand

Directory of Open Access Journals (Sweden)

Pavel Štarha

2018-02-01

Full Text Available We report on the preparation and thorough characterization of cytotoxic half-sandwich complexes [Ru(η6-pcym(bphen(dca]PF6 (Ru-dca and [Os(η6-pcym(bphen(dca]PF6 (Os-dca containing dichloroacetate(1– (dca as the releasable O-donor ligand bearing its own cytotoxicity; pcym = 1-methyl-4-(propan-2-ylbenzene (p-cymene, bphen = 4,7-diphenyl-1,10-phenanthroline (bathophenanthroline. Complexes Ru-dca and Os-dca hydrolyzed in the water-containing media, which led to the dca ligand release (supported by 1H NMR and electrospray ionization mass spectra. Mass spectrometry studies revealed that complexes Ru-dca and Os-dca do not interact covalently with the model proteins cytochrome c and lysozyme. Both complexes exhibited slightly higher in vitro cytotoxicity (IC50 = 3.5 μM for Ru-dca, and 2.6 μM for Os-dca against the A2780 human ovarian carcinoma cells than cisplatin (IC50 = 5.9 μM, while their toxicity on the healthy human hepatocytes was found to be IC50 = 19.1 μM for Ru-dca and IC50 = 19.7 μM for Os-dca. Despite comparable cytotoxicity of complexes Ru-dca and Os-dca, both the complexes modified the cell cycle, mitochondrial membrane potential, and mitochondrial cytochrome c release by a different way, as revealed by flow cytometry experiments. The obtained results point out the different mechanisms of action between the complexes.

Spectroscopic characterization of some Cu(II) complexes

International Nuclear Information System (INIS)

Singh, Puja; Sharma, S.

2014-01-01

3-hydroxy-4-methoxy benzaldehyde semicarbazone (HMBS) is a biologically active compound which has several potential donor sites. This compound has been used for complexation with Cu(II) ions to synthesize complexes of general formula [Cu(HMBS) 2 X 2 ] where X is Cl − , NO 3 − and CH 3 COO − . Cu(II) is a d 9 system for which 2 D term is generated. Under O h symmetry, this term splits into 2 E g and 2 T 2g . the ground term 2 Eg is doubly degenerate and hence suffers strong Jahn-Teller effect and accordingly the further splitting of terms occur to lower the symmetry from perfect O h . Here, the ligand occupies four planar positions while the two axial positions have been varied by using different ions like Cl − , NO 3 − and CH 3 COO − . These variations on the axial positions also add to the distortion in O h symmetry. Under strong distortion, the electronic spectral band splits into multiplets exhibiting tetragonal distortion in complexes. The extent of distortion has been derived by the derivation of the two radial parameters D s and D t from electronic spectral bands. The ESR spectra of complexes reveal the real position of the only unpaired electron of the d 9 system in complexes

Crystal structure of the C3bot–RalA complex reveals a novel type of action of a bacterial exoenzyme

OpenAIRE

Pautsch, Alexander; Vogelsgesang, Martin; Tränkle, Jens; Herrmann, Christian; Aktories, Klaus

2005-01-01

C3 exoenzymes from bacterial pathogens ADP-ribosylate and inactivate low-molecular-mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP-ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD-glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP-bou...

Invasive Aspergillus niger complex infections in a Belgian tertiary care hospital.

Science.gov (United States)

Vermeulen, E; Maertens, J; Meersseman, P; Saegeman, V; Dupont, L; Lagrou, K

2014-05-01

The incidence of invasive infections caused by the Aspergillus niger species complex was 0.043 cases/10 000 patient-days in a Belgian university hospital (2005-2011). Molecular typing was performed on six available A. niger complex isolates involved in invasive disease from 2010 to 2011, revealing A. tubingensis, which has higher triazole minimal inhibitory concentrations, in five out of six cases. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Proliferative, necrotizing and crescentic immune complex-mediated glomerulonephritis in a cat

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Carolyn Gross

2015-09-01

Full Text Available Case Summary A 5-year-old cat was examined for vomiting and anorexia of 2 days’ duration. Azotemia, hyperphosphatemia and hypoalbuminemia were the main biochemical findings. Serial analyses of the urine revealed isosthenuria, proteinuria and eventual glucosuria. Hyperechoic perirenal fat was detected surrounding the right kidney by ultrasonography. Histopathologic evaluation of ante-mortem ultrasound-guided needle biopsies of the right kidney was consistent with proliferative, necrotizing and crescentic glomerulonephritis with fibrin thrombi, proteinaceous and red blood cell casts, and moderate multifocal chronic-active interstitial nephritis. Owing to a lack of clinical improvement, the cat was eventually euthanized. Post-mortem renal biopsies were processed for light microscopy, transmission electron microscopy and immunofluorescence. This revealed severe focal proliferative and necrotizing glomerulonephritis with cellular crescent formation, podocyte injury and secondary segmental sclerosis. Ultrastructural analysis revealed scattered electron-dense deposits in the mesangium, and immunofluorescence demonstrated positive granular staining for λ light chains, consistent with immune complex-mediated glomerulonephritis. Severe diffuse acute tubular epithelial injury and numerous red blood cell casts were also seen. Relevance and novel information To our knowledge, this is the first report of naturally occurring proliferative, necrotizing and crescentic immune complex glomerulonephritis in a cat.

Exploring the potential relevance of human-specific genes to complex disease

Directory of Open Access Journals (Sweden)

Cooper David N

2011-01-01

Full Text Available Abstract Although human disease genes generally tend to be evolutionarily more ancient than non-disease genes, complex disease genes appear to be represented more frequently than Mendelian disease genes among genes of more recent evolutionary origin. It is therefore proposed that the analysis of human-specific genes might provide new insights into the genetics of complex disease. Cross-comparison with the Human Gene Mutation Database (http://www.hgmd.org revealed a number of examples of disease-causing and disease-associated mutations in putatively human-specific genes. A sizeable proportion of these were missense polymorphisms associated with complex disease. Since both human-specific genes and genes associated with complex disease have often experienced particularly rapid rates of evolutionary change, either due to weaker purifying selection or positive selection, it is proposed that a significant number of human-specific genes may play a role in complex disease.

Joint cross-correlation analysis reveals complex, time-dependent functional relationship between cortical neurons and arm electromyograms

Science.gov (United States)

Zhuang, Katie Z.; Lebedev, Mikhail A.

2014-01-01

Correlation between cortical activity and electromyographic (EMG) activity of limb muscles has long been a subject of neurophysiological studies, especially in terms of corticospinal connectivity. Interest in this issue has recently increased due to the development of brain-machine interfaces with output signals that mimic muscle force. For this study, three monkeys were implanted with multielectrode arrays in multiple cortical areas. One monkey performed self-timed touch pad presses, whereas the other two executed arm reaching movements. We analyzed the dynamic relationship between cortical neuronal activity and arm EMGs using a joint cross-correlation (JCC) analysis that evaluated trial-by-trial correlation as a function of time intervals within a trial. JCCs revealed transient correlations between the EMGs of multiple muscles and neural activity in motor, premotor and somatosensory cortical areas. Matching results were obtained using spike-triggered averages corrected by subtracting trial-shuffled data. Compared with spike-triggered averages, JCCs more readily revealed dynamic changes in cortico-EMG correlations. JCCs showed that correlation peaks often sharpened around movement times and broadened during delay intervals. Furthermore, JCC patterns were directionally selective for the arm-reaching task. We propose that such highly dynamic, task-dependent and distributed relationships between cortical activity and EMGs should be taken into consideration for future brain-machine interfaces that generate EMG-like signals. PMID:25210153

Application of REVEAL-W to risk-based configuration control

International Nuclear Information System (INIS)

Dezfuli, H.; Meyer, J.; Modarres, M.

1994-01-01

Over the past two years, the concept of risk-based configuration control has been introduced to the US Nuclear Regulatory Commission and the nuclear industry. Converting much of the current, deterministically based regulation of nuclear power plants to risk-based regulation can result in lower levels of risk while relieving unnecessary burdens on power plant operators and regulatory staff. To achieve the potential benefits of risk-based configuration control, the risk models developed for nuclear power plants should be (1) flexible enough to effectively support necessary risk calculations, and (2) transparent enough to encourage their use by all parties. To address these needs, SCIENTECH, Inc., has developed the PC-based REVEAL W (formerly known as SMART). This graphic-oriented and user-friendly application software allows the user to develop transparent complex logic models based on the concept of the master plant logic diagram. The logic model is success-oriented and compact. The analytical capability built into REVEAL W is generic, so the software can support different types of risk-based evaluations, such as probabilistic safety assessment, accident sequence precursor analysis, design evaluation and configuration management. In this paper, we focus on the application of REVEAL W to support risk-based configuration control of nuclear power plants. (author)

Revealing effective classifiers through network comparison

Science.gov (United States)

Gallos, Lazaros K.; Fefferman, Nina H.

2014-11-01

The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured, in ways that are otherwise inaccessible to observation. Here, we introduce the n-tangle method to directly compare two networks for structural similarity, based on the distribution of edge density in network subgraphs. We demonstrate that this method can efficiently introduce comparative analysis into network science and opens the road for many new applications. For example, we show how the construction of a “phylogenetic tree” across animal taxa according to their social structure can reveal commonalities in the behavioral ecology of the populations, or how students create similar networks according to the University size. Our method can be expanded to study many additional properties, such as network classification, changes during time evolution, convergence of growth models, and detection of structural changes during damage.

Preparation and structural studies on organotin(IV) complexes with flavonoids

International Nuclear Information System (INIS)

Nagy, L.; Christy, A.A.; Sletten, E.; Andersen, Q.M.; Edelmann, F.T.

1998-01-01

Fourteen complexes of di-n-butyltin(IV) 2+ cations with flavonoid glycosides (rutin, hesperidin, 2',4',3-trihydroxy-5',4-dimetoxychalkone 4-rutinoside) and flavonoid aglycones (quercetin, morin, hesperitin and sorte flavones) were prepared. The composition of the complexes was determined by standard analytical methods. The results showed that complexes containing diorganotin(IV) 2+ moiety and the ligand in 1:1, 2:1 or 3:1 ratio are formed. The FTIR spectra were consistent with the presence of Sn-O (phenol or carbohydrate) vibration in the compounds. The structure of the complexes was measured by Moessbauer spectroscopy. Comparison of the experimental quadrupole splitting with those calculated on the basis of partial quadrupole splitting concept revealed that the complexes are of four types: with the central tin atoms surrounded by donor atoms in a purely trigonal-bipyramidal, octahedral+trigonal-bipyramidal, trigonal-bipyramidal+tetrahedral and octahedral+tetrahedral arrangement. This procedure also distinguished between the different structural isomers of both trigonal-bipyramidal and octahedral complexes. Conclusions could therefore be drawn on the factors determining which of the isomers are formed in the systems. The Moessbauer parameters obtained for organotin(IV)-flavonoid complexes were compared with those measured for organotin(IV)-carbohydrate complexes. (author)

Integrated analysis of multiple data sources reveals modular structure of biological networks

International Nuclear Information System (INIS)

Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

2006-01-01

It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

Immature intra-oceanic arc-type volcanism on the Izanagi Plate revealed by the geochemistry of the Daimaruyama greenstones in the Hiroo Complex, southern Hidaka Belt, central Hokkaido, Japan

Science.gov (United States)

Yamasaki, Toru; Nanayama, Futoshi

2018-03-01

results. Clinopyroxene trace element compositions indicate substantial enrichment of Ba in the magma, reflecting the participation of shallow subduction components such as aqueous fluids. Geochemical investigations reveal that the Daimaruyama greenstones were probably submarine volcanic rocks that formed as a result of the subduction of the Izanagi Plate within the Thalassa Ocean (the Thalassa Ocean was the eastern realm of Panthalassa, and represents the proto-Pacific Ocean) after the Early Cretaceous (Aptian-Albian; 125-101 Ma), and they were eventually accreted onto the Paleo-Kuril arc-trench system at 57-48 Ma to form an allochthonous block as part of the mélange facies of the Hiroo Complex on the landward slope of the trench.

Cytotoxic property of surfactant-cobalt(III) complexes on a human breast cancer cell line.

Science.gov (United States)

Kumar, Rajendran Senthil; Riyasdeen, Anvarbatcha; Dinesh, Mohanakrishnan; Paul, Christo Preethy; Srinag, Suresh; Krishnamurthy, Hanumanthappa; Arunachalam, Sankaralingam; Akbarsha, Mohammad Abdulkadher

2011-07-01

The cancer chemotherapeutic potential of surfactant-cobalt(III) complexes, cis-[Co(bpy)(2)(C(14)H(29)NH(2))Cl](ClO(4))(2)·3 H(2)O (1) and cis-[Co(phen)(2)(C(14)H(29)NH(2))Cl](ClO(4))(2)·3 H(2)O (2) (bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline) on MCF-7 breast cancer cell was determined adopting MTT assay and specific staining techniques. The complexes affected the viability of the cells significantly and the cells succumbed to apoptosis as seen in the changes in the nuclear morphology and cytoplasmic features. Since the complex 2 appeared to be more potent, further assays were carried out on the complex 2. Single-cell electrophoresis indicated DNA damage. The translocation of phosphatidyl serine and loss of mitochondrial potential was revealed by annexin V-Cy3 staining and JC-1 staining respectively. Western blot analysis revealed up-regulation of pro-apoptotic p53 and down-regulation of anti-apoptotic Bcl-2 protein. Taken together, the surfactant-cobalt(III) complex 2 would be a potential candidate for further investigation for application as a chemotherapeutic for cancers in general and estrogen receptor-positive breast cancer in particular. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cumulative trauma and symptom complexity in children: a path analysis.

Science.gov (United States)

Hodges, Monica; Godbout, Natacha; Briere, John; Lanktree, Cheryl; Gilbert, Alicia; Kletzka, Nicole Taylor

2013-11-01

Multiple trauma exposures during childhood are associated with a range of psychological symptoms later in life. In this study, we examined whether the total number of different types of trauma experienced by children (cumulative trauma) is associated with the complexity of their subsequent symptomatology, where complexity is defined as the number of different symptom clusters simultaneously elevated into the clinical range. Children's symptoms in six different trauma-related areas (e.g., depression, anger, posttraumatic stress) were reported both by child clients and their caretakers in a clinical sample of 318 children. Path analysis revealed that accumulated exposure to multiple different trauma types predicts symptom complexity as reported by both children and their caretakers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Oxovanadium (iv) complexes with n/o- and o-donor ligands: their synthesis, characterization, semiempirical study and alkaline phosphatase activity (abstract)

International Nuclear Information System (INIS)

Munawar, K.S.; Ali, S.; Khan, A.N.

2011-01-01

Various N/O- and O-donor ligands and their oxovanadium complexes have been synthesized and characterized by different techniques such as FTIR, elemental analysis, thermogravimetery and conductometry. The IR data show the bidentate nature of the ligands and reveals hexa-coordinated geometry in the solid state which is also confirmed by semi-empirical study. Conductance measurements reveal the non-electrolytic nature of the complexes. These complexes have been checked for their alkaline phosphatase activity in the presence and absence of inhibitor which shows that by the addition of inhibitor the activity of enzyme decreases and at higher concentration it is completely inhibited. (author)

Hierarchy Measure for Complex Networks

Science.gov (United States)

Mones, Enys; Vicsek, Lilla; Vicsek, Tamás

2012-01-01

Nature, technology and society are full of complexity arising from the intricate web of the interactions among the units of the related systems (e.g., proteins, computers, people). Consequently, one of the most successful recent approaches to capturing the fundamental features of the structure and dynamics of complex systems has been the investigation of the networks associated with the above units (nodes) together with their relations (edges). Most complex systems have an inherently hierarchical organization and, correspondingly, the networks behind them also exhibit hierarchical features. Indeed, several papers have been devoted to describing this essential aspect of networks, however, without resulting in a widely accepted, converging concept concerning the quantitative characterization of the level of their hierarchy. Here we develop an approach and propose a quantity (measure) which is simple enough to be widely applicable, reveals a number of universal features of the organization of real-world networks and, as we demonstrate, is capable of capturing the essential features of the structure and the degree of hierarchy in a complex network. The measure we introduce is based on a generalization of the m-reach centrality, which we first extend to directed/partially directed graphs. Then, we define the global reaching centrality (GRC), which is the difference between the maximum and the average value of the generalized reach centralities over the network. We investigate the behavior of the GRC considering both a synthetic model with an adjustable level of hierarchy and real networks. Results for real networks show that our hierarchy measure is related to the controllability of the given system. We also propose a visualization procedure for large complex networks that can be used to obtain an overall qualitative picture about the nature of their hierarchical structure. PMID:22470477

Functional dissection of the proton pumping modules of mitochondrial complex I.

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Stefan Dröse

2011-08-01

Full Text Available Mitochondrial complex I, the largest and most complicated proton pump of the respiratory chain, links the electron transfer from NADH to ubiquinone to the pumping of four protons from the matrix into the intermembrane space. In humans, defects in complex I are involved in a wide range of degenerative disorders. Recent progress in the X-ray structural analysis of prokaryotic and eukaryotic complex I confirmed that the redox reactions are confined entirely to the hydrophilic peripheral arm of the L-shaped molecule and take place at a remarkable distance from the membrane domain. While this clearly implies that the proton pumping within the membrane arm of complex I is driven indirectly via long-range conformational coupling, the molecular mechanism and the number, identity, and localization of the pump-sites remains unclear. Here, we report that upon deletion of the gene for a small accessory subunit of the Yarrowia complex I, a stable subcomplex (nb8mΔ is formed that lacks the distal part of the membrane domain as revealed by single particle analysis. The analysis of the subunit composition of holo and subcomplex by three complementary proteomic approaches revealed that two (ND4 and ND5 of the three subunits with homology to bacterial Mrp-type Na(+/H(+ antiporters that have been discussed as prime candidates for harbouring the proton pumps were missing in nb8mΔ. Nevertheless, nb8mΔ still pumps protons at half the stoichiometry of the complete enzyme. Our results provide evidence that the membrane arm of complex I harbours two functionally distinct pump modules that are connected in series by the long helical transmission element recently identified by X-ray structural analysis.

Bio-softening of mature coconut husk for facile coir recovery.

Science.gov (United States)

Suganya, D S; Pradeep, S; Jayapriya, J; Subramanian, S

2007-06-01

Bio-softening of the mature coconut husk using Basidiomyceteous fungi was attempted to recover the soft and whiter fibers. The process was faster and more efficient in degrading lignin and toxic phenolics. Phanerochaete chrysosporium, Pleurotus eryngii and Ceriporiopsis subvermispora were found to degrade lignin efficiently without any appreciable loss of cellulose, yielding good quality fiber ideal for dyeing.

Interactions of trivalent and tetravalent heavy metal-siderophore complexes with pseudomonas fluorescens

International Nuclear Information System (INIS)

Yoshida, T.; Ozaki, T.; Ohnuki, T.; Francis, A.J.

2004-01-01

We investigated the interactions of the Fe(III)-, Eu(III)-, and Hf(IV)-desferrioxamine B (DFO) complexes with the Gram-negative aerobic bacterium Pseudomonas fluorescens. Potentiometric titration of 1:1 Fe(III)-, Eu(III)-, and Hf(IV)-DFO complexes showed that Hf(IV) formed a strong complex with DFO whose stability was comparable to that of the Fe(III)-DFO complex, while Eu(III) formed a weaker one. DFO in a growth medium was not degraded by P. fluorescens. Contact of P. fluorescens cells with the Fe(III)-, Eu(III)-, and Hf(IV)-DFO complexes at pH 4-9 revealed that there was negligible adsorption of Hf(IV) and Fe(III), whereas Eu(III) was dissociated from DFO and was readily adsorbed by the cells. These results suggest that Fe(III) and Hf(IV) form stable complexes with DFO and are not adsorbed by P. fluorescens cells. Europium(III) forms a weaker complex with DFO than Fe(III) and Hf(IV) do and its DFO complex is readily dissociated in the presence of the cells. (orig.)

Cut Based Method for Comparing Complex Networks.

Science.gov (United States)

Liu, Qun; Dong, Zhishan; Wang, En

2018-03-23

Revealing the underlying similarity of various complex networks has become both a popular and interdisciplinary topic, with a plethora of relevant application domains. The essence of the similarity here is that network features of the same network type are highly similar, while the features of different kinds of networks present low similarity. In this paper, we introduce and explore a new method for comparing various complex networks based on the cut distance. We show correspondence between the cut distance and the similarity of two networks. This correspondence allows us to consider a broad range of complex networks and explicitly compare various networks with high accuracy. Various machine learning technologies such as genetic algorithms, nearest neighbor classification, and model selection are employed during the comparison process. Our cut method is shown to be suited for comparisons of undirected networks and directed networks, as well as weighted networks. In the model selection process, the results demonstrate that our approach outperforms other state-of-the-art methods with respect to accuracy.

Structural insight into the UNC-45–myosin complex

DEFF Research Database (Denmark)

Fratev, Filip; Jonsdottir, Svava Osk; Pajeva, Ilza

2013-01-01

The UNC-45 chaperone protein interacts with and affects the folding, stability, and the ATPase activity of myosins. It plays a critical role in the cardiomyopathy development and in the breast cancer tumor growth. Here we propose the first structural model of the UNC-45–myosin complex using various...... is mainly stabilized by electrostatic interactions. Remarkably, the contact surface area is similar to that of the myosinactin complex. A significant interspecies difference in the myosin binding epitope is observed. Our results reveal the structural basis of MYH7 exons 15–16 hypertrophic cardiomyopathy...... mutations and provide directions for drug targeting. © 2013 Wiley Periodicals, Inc....

The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope.

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Haijiao Xu

Full Text Available The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm -200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.

The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components.

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Lukas Aeberhard

2015-06-01

Full Text Available Chlamydia trachomatis is an important human pathogen that replicates inside the infected host cell in a unique vacuole, the inclusion. The formation of this intracellular bacterial niche is essential for productive Chlamydia infections. Despite its importance for Chlamydia biology, a holistic view on the protein composition of the inclusion, including its membrane, is currently missing. Here we describe the host cell-derived proteome of isolated C. trachomatis inclusions by quantitative proteomics. Computational analysis indicated that the inclusion is a complex intracellular trafficking platform that interacts with host cells' antero- and retrograde trafficking pathways. Furthermore, the inclusion is highly enriched for sorting nexins of the SNX-BAR retromer, a complex essential for retrograde trafficking. Functional studies showed that in particular, SNX5 controls the C. trachomatis infection and that retrograde trafficking is essential for infectious progeny formation. In summary, these findings suggest that C. trachomatis hijacks retrograde pathways for effective infection.

Synthesis, characterization and luminescence studies of gold(I–NHC amide complexes

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Adrián Gómez-Suárez

2013-10-01

Full Text Available A flexible, efficient and straightforward methodology for the synthesis of N-heterocyclic carbene gold(I–amide complexes is reported. Reaction of the versatile building block [Au(OH(IPr] (1 (IPr = 1,3-bis(2,6-diisopropylphenylimidazol-2-ylidene with a series of commercially available (heteroaromatic amines leads to the synthesis of several [Au(NRR’(IPr] complexes in good yields and with water as the sole byproduct. Interestingly, these complexes present luminescence properties. UV–vis and fluorescence measurements have allowed the identification of their excitation and emission wavelengths (λmax. These studies revealed that by selecting the appropriate amine ligand the emission can be easily tuned to achieve a variety of colors, from violet to green.

The complexity of nurses' attitudes toward euthanasia: a review of the literature

OpenAIRE

Berghs, M; d Dierckx,; Gastmans, C

2005-01-01

In this literature review, a picture is given of the complexity of nursing attitudes toward euthanasia. The myriad of data found in empirical literature is mostly framed within a polarised debate and inconclusive about the complex reality behind attitudes toward euthanasia. Yet, a further examination of the content as well as the context of attitudes is more revealing. The arguments for euthanasia have to do with quality of life and respect for autonomy. Arguments against euthanasia have to d...

Co(II) and Cd(II) Complexes Derived from Heterocyclic Schiff-Bases: Synthesis, Structural Characterisation, and Biological Activity

Science.gov (United States)

Ahmed, Riyadh M.; Yousif, Enaam I.; Al-Jeboori, Mohamad J.

2013-01-01

New monomeric cobalt and cadmium complexes with Schiff-bases, namely, N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]furan-2-carbohydrazide (L1) and N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]thiophene-2-carbohydrazide (L2) are reported. Schiff-base ligands L1 and L2 were derived from condensation of 3-hydroxy-4-methoxybenzaldehyde (iso-vanillin) with furan-2-carboxylic acid hydrazide and thiophene-2-carboxylic acid hydrazide, respectively. Complexes of the general formula [M(L)2]Cl2 (where M = Co(II) or Cd(II), L = L1 or L2) have been obtained from the reaction of the corresponding metal chloride with the ligands. The ligands and their metal complexes were characterised by spectroscopic methods (FTIR, UV-Vis, 1H, and 13C NMR spectra), elemental analysis, metal content, magnetic measurement, and conductance. These studies revealed the formation of four-coordinate complexes in which the geometry about metal ion is tetrahedral. Biological activity of the ligands and their metal complexes against gram positive bacterial strain Bacillus (G+) and gram negative bacteria Pseudomonas (G−) revealed that the metal complexes become less resistive to the microbial activities as compared to the free ligands. PMID:24027449

Reactions and mass spectra of complex particles using Aerosol CIMS

Science.gov (United States)

Hearn, John D.; Smith, Geoffrey D.

2006-12-01

Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

Chromatin Remodeling BAF (SWI/SNF Complexes in Neural Development and Disorders

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Godwin Sokpor

2017-08-01

Full Text Available The ATP-dependent BRG1/BRM associated factor (BAF chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.

Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders

Science.gov (United States)

Sokpor, Godwin; Xie, Yuanbin; Rosenbusch, Joachim; Tuoc, Tran

2017-01-01

The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders. PMID:28824374

Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders.

Science.gov (United States)

Sokpor, Godwin; Xie, Yuanbin; Rosenbusch, Joachim; Tuoc, Tran

2017-01-01

The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.

Modeling Air Traffic Situation Complexity with a Dynamic Weighted Network Approach

Directory of Open Access Journals (Sweden)

Hongyong Wang

2018-01-01

Full Text Available In order to address the flight delays and risks associated with the forecasted increase in air traffic, there is a need to increase the capacity of air traffic management systems. This should be based on objective measurements of traffic situation complexity. In current air traffic complexity research, no simple means is available to integrate airspace and traffic flow characteristics. In this paper, we propose a new approach for the measurement of air traffic situation complexity. This approach considers the effects of both airspace and traffic flow and objectively quantifies air traffic situation complexity. Considering the aircraft, waypoints, and airways as nodes, and the complexity relationships among these nodes as edges, a dynamic weighted network is constructed. Air traffic situation complexity is defined as the sum of the weights of all edges in the network, and the relationships of complexity with some commonly used indices are statistically analyzed. The results indicate that the new complexity index is more accurate than traffic count and reflects the number of trajectory changes as well as the high-risk situations. Additionally, analysis of potential applications reveals that this new index contributes to achieving complexity-based management, which represents an efficient method for increasing airspace system capacity.

Chemical genetics analysis of an aniline mustard anticancer agent reveals complex I of the electron transport chain as a target.

Science.gov (United States)

Fedeles, Bogdan I; Zhu, Angela Y; Young, Kellie S; Hillier, Shawn M; Proffitt, Kyle D; Essigmann, John M; Croy, Robert G

2011-09-30

The antitumor agent 11β (CAS 865070-37-7), consisting of a DNA-damaging aniline mustard linked to an androgen receptor (AR) ligand, is known to form covalent DNA adducts and to induce apoptosis potently in AR-positive prostate cancer cells in vitro; it also strongly prevents growth of LNCaP xenografts in mice. The present study describes the unexpectedly strong activity of 11β against the AR-negative HeLa cells, both in cell culture and tumor xenografts, and uncovers a new mechanism of action that likely explains this activity. Cellular fractionation experiments indicated that mitochondria are the major intracellular sink for 11β; flow cytometry studies showed that 11β exposure rapidly induced oxidative stress, mitochondria being an important source of reactive oxygen species (ROS). Additionally, 11β inhibited oxygen consumption both in intact HeLa cells and in isolated mitochondria. Specifically, 11β blocked uncoupled oxygen consumption when mitochondria were incubated with complex I substrates, but it had no effect on oxygen consumption driven by substrates acting downstream of complex I in the mitochondrial electron transport chain. Moreover, 11β enhanced ROS generation in isolated mitochondria, suggesting that complex I inhibition is responsible for ROS production. At the cellular level, the presence of antioxidants (N-acetylcysteine or vitamin E) significantly reduced the toxicity of 11β, implicating ROS production as an important contributor to cytotoxicity. Collectively, our findings establish complex I inhibition and ROS generation as a new mechanism of action for 11β, which supplements conventional DNA adduct formation to promote cancer cell death.

A synthetic NO reduction cycle on a bis(pyrazolato)-bridged dinuclear ruthenium complex including photo-induced transformation.

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Arikawa, Yasuhiro; Hiura, Junko; Tsuchii, Chika; Kodama, Mika; Matsumoto, Naoki; Umakoshi, Keisuke

2018-05-17

A synthetic NO reduction cycle (2NO + 2H+ + 2e- → N2O + H2O) on a dinuclear platform {(TpRu)2(μ-pz)2} (Tp = HB(pyrazol-1-yl)3) was achieved, where an unusual N-N coupling complex was included. Moreover, an interesting photo-induced conversion of the N-N coupling complex to an oxido-bridged complex was revealed.

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics

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Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Chess players' eye movements reveal rapid recognition of complex visual patterns: Evidence from a chess-related visual search task.

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Sheridan, Heather; Reingold, Eyal M

2017-03-01

To explore the perceptual component of chess expertise, we monitored the eye movements of expert and novice chess players during a chess-related visual search task that tested anecdotal reports that a key differentiator of chess skill is the ability to visualize the complex moves of the knight piece. Specifically, chess players viewed an array of four minimized chessboards, and they rapidly searched for the target board that allowed a knight piece to reach a target square in three moves. On each trial, there was only one target board (i.e., the "Yes" board), and for the remaining "lure" boards, the knight's path was blocked on either the first move (the "Easy No" board) or the second move (i.e., "the Difficult No" board). As evidence that chess experts can rapidly differentiate complex chess-related visual patterns, the experts (but not the novices) showed longer first-fixation durations on the "Yes" board relative to the "Difficult No" board. Moreover, as hypothesized, the task strongly differentiated chess skill: Reaction times were more than four times faster for the experts relative to novices, and reaction times were correlated with within-group measures of expertise (i.e., official chess ratings, number of hours of practice). These results indicate that a key component of chess expertise is the ability to rapidly recognize complex visual patterns.

Structural dynamics of a noncovalent charge transfer complex from femtosecond stimulated Raman spectroscopy.

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Fujisawa, Tomotsumi; Creelman, Mark; Mathies, Richard A

2012-09-06

Femtosecond stimulated Raman spectroscopy is used to examine the structural dynamics of photoinduced charge transfer within a noncovalent electron acceptor/donor complex of pyromellitic dianhydride (PMDA, electron acceptor) and hexamethylbenzene (HMB, electron donor) in ethylacetate and acetonitrile. The evolution of the vibrational spectrum reveals the ultrafast structural changes that occur during the charge separation (Franck-Condon excited state complex → contact ion pair) and the subsequent charge recombination (contact ion pair → ground state complex). The Franck-Condon excited state is shown to have significant charge-separated character because its vibrational spectrum is similar to that of the ion pair. The charge separation rate (2.5 ps in ethylacetate and ∼0.5 ps in acetonitrile) is comparable to solvation dynamics and is unaffected by the perdeuteration of HMB, supporting the dominant role of solvent rearrangement in charge separation. On the other hand, the charge recombination slows by a factor of ∼1.4 when using perdeuterated HMB, indicating that methyl hydrogen motions of HMB mediate the charge recombination process. Resonance Raman enhancement of the HMB vibrations in the complex reveals that the ring stretches of HMB, and especially the C-CH(3) deformations are the primary acceptor modes promoting charge recombination.

Organizational changes of the daughter basal complex during the parasite replication of Toxoplasma gondii.

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Ke Hu

2008-01-01

Full Text Available The apicomplexans are a large group of parasitic protozoa, many of which are important human and animal pathogens, including Plasmodium falciparum and Toxoplasma gondii. These parasites cause disease only when they replicate, and their replication is critically dependent on the proper assembly of the parasite cytoskeletons during cell division. In addition to their importance in pathogenesis, the apicomplexan parasite cytoskeletons are spectacular structures. Therefore, understanding the cytoskeletal biogenesis of these parasites is important not only for parasitology but also of general interest to broader cell biology. Previously, we found that the basal end of T. gondii contains a novel cytoskeletal assembly, the basal complex, a cytoskeletal compartment constructed in concert with the daughter cortical cytoskeleton during cell division. This study focuses on key events during the biogenesis of the basal complex using high resolution light microscopy, and reveals that daughter basal complexes are established around the duplicated centrioles independently of the structural integrity of the daughter cortical cytoskeleton, and that they are dynamic "caps" at the growing ends of the daughters. Compartmentation and polarization of the basal complex is first revealed at a late stage of cell division upon the recruitment of an EF-hand containing calcium binding protein, TgCentrin2. This correlates with the constriction of the basal complex, a process that can be artificially induced by increasing cellular calcium concentration. The basal complex is therefore likely to be a new kind of centrin-based contractile apparatus.

Effect of complexing agent on the photoelectrochemical properties of bath deposited CdS thin films

International Nuclear Information System (INIS)

Patil, S.B.; Singh, A.K.

2010-01-01

In the present paper photoelectrochemical (PEC) performance of bath deposited CdS thin films based on complexing agents i.e. ammonia and triethanolamine (TEA) has been discussed. Effect of annealing has also been analyzed. The as-deposited and annealed (at 523 K for 1 h in air) films were characterized by X-ray diffraction (XRD), ultraviolet-visible (UV-vis) absorption spectroscopy, SEM, electrochemical impedance spectroscopy (EIS), and PEC properties. XRD studies revealed that the films were nanocrystalline in nature with mixed hexagonal and cubic phases. TEA complex resulted in better crystallinity. Further improvement in the crystallinity of the films was observed after air annealing. The marigold flower-like structure, in addition to flakes morphology, was observed with TEA complex, whereas for ammonia complex only flakes morphology was observed. The UV-vis absorption studies revealed that the optical absorption edge for the films with ammonia and TEA complex was around 475 nm and 500 nm, respectively. Annealing of the films resulted in red shift in the UV-vis absorption. The PEC cell performance of CdS films was found to be strongly affected by crystallinity and morphology of the films resulted due to complexing agent and annealing. The air annealed film deposited using TEA complex showed maximum short circuit current density (J sc ) and open circuit voltage (V oc ) i.e. 99 μA/cm 2 and 376 mV respectively, under 10 mW/cm 2 of illumination. The films deposited using TEA complex showed good stability under PEC cell conditions.

Structure and reactivity of boron-ate complexes derived from primary and secondary boronic esters.

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Feeney, Kathryn; Berionni, Guillaume; Mayr, Herbert; Aggarwal, Varinder K

2015-06-05

Boron-ate complexes derived from primary and secondary boronic esters and aryllithiums have been isolated, and the kinetics of their reactions with carbenium ions studied. The second-order rate constants have been used to derive nucleophilicity parameters for the boron-ate complexes, revealing that nucleophilicity increased with (i) electron-donating aromatics on boron, (ii) neopentyl glycol over pinacol boronic esters, and (iii) 12-crown-4 ether.

CE-MS fingerprinting of Laurencia complex algae (Rhodophyta).

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Machín-Sánchez, María; Asensio-Ramos, María; Hernández-Borges, Javier; Gil-Rodríguez, María Candelaria

2014-03-01

The use of CE-ESI-MS has been considered as a new chemical strategy for the possible discernment of genera and species of the Laurencia complex. After the selection of the CE-MS and the extraction conditions, a total of 28 specimens of the complex, including different species of four genera (Laurencia, Laurenciella, Palisada, and Osmundea) collected from five intertidal locations on the Island of Tenerife (Canary Islands, Spain) were analyzed. CE-MS fingerprints revealed that CE-MS can be used as a useful tool for these studies in order to assess similarities and differences between them and that it constitutes an important starting point for further studies in the field. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.