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Sample records for isolation structure determination

  1. Isolation and structure determination of oxidative degradation products of atorvastatin.

    PubMed

    Kracun, Matjaz; Kocijan, Andrej; Bastarda, Andrej; Grahek, Rok; Plavec, Janez; Kocjan, Darko

    2009-12-05

    Methods were developed for the preparation and isolation of four oxidative degradation products of atorvastatin. ATV-FX1 was prepared in the alkaline acetonitrile solution of atorvastatin with the addition of hydrogen peroxide. The exposition of aqueous acetonitrile solution of atorvastatin to sunlight for several hours followed by the alkalization of the solution with potassium hydroxide to pH 8-9 gave ATV-FXA. By the acidification of the solution with phosphoric acid to pH 3 ATV-FXA1 and FXA2 were prepared. The isolation of oxidative degradation products was carried out on a reversed-phase chromatographic column Luna prep C18(2) 10 microm applying several separation steps. The liquid chromatography coupled with a mass spectrometer (LC-MS), high resolution MS (HR-MS), 1D and 2D NMR spectroscopy methods were applied for the structure elucidation. All degradants are due to the oxidation of the pyrrole ring. The most probable reaction mechanism is intermediate endoperoxide formation with subsequent rearrangement and nucleophilic attack by the 5-hydroxy group of the heptanoic fragment. ATV-FX1 is 4-[1b-(4-Fluoro-phenyl)-6-hydroxy-6-isopropyl-1a-phenyl-6a-phenylcarbamoyl-hexahydro-1,2-dioxa-5a-aza-cyclopropa[a]inden-3-yl]-3-(R)-hydroxy-butyric acid and has a molecular mass increased by two oxygen atoms with regard to atorvastatin. ATV-FXA is the regioisomeric compound, 4-[6-(4-Fluoro-phenyl)-6-hydroxy-1b-isopropyl-6a-phenyl-1a-phenylcarbamoyl-hexahydro-1,2-dioxa-5a-aza-cyclopropa[a]inden-3-yl]-3-(R)-hydroxy-butyric acid. Its descendants ATV-FXA1 and FXA2 appeared without the atorvastatin heptanoic fragment and are 3-(4-Fluoro-benzoyl)-2-isobutyryl-3-phenyl-oxirane-2-carboxylic acid phenylamide and 4-(4-Fluoro-phenyl)-2,4-dihydroxy-2-isopropyl-5-phenyl-3,6-dioxa-bicyclo[3.1.0]hexane-1-carboxylic acid phenylamide, respectively. Quantitative NMR spectroscopy was employed for the assay determination of isolated oxidative degradation products. The results obtained were used

  2. Isolation, crystal structure determination and cholinesterase inhibitory potential of isotalatizidine hydrate from Delphinium denudatum.

    PubMed

    Ahmad, Hanif; Ahmad, Shujaat; Khan, Ezzat; Shahzad, Adnan; Ali, Mumtaz; Tahir, Muhammad Nawaz; Shaheen, Farzana; Ahmad, Manzoor

    2017-12-01

    Delphinium denudatum Wall (Ranunculaceae) is a rich source of diterpenoid alkaloids and is widely used for the treatment of various neurological disorders such as epilepsy, sciatica and Alzheimer's disease. The present study describes crystal structure determination and cholinesterase inhibitory potential of isotalatazidine hydrate isolated from the aerial part of Delphinium denudatum. Phytochemical investigation of Delphinium denudatum resulted in the isolation of isotalatazidine hydrate in crystalline form. The molecular structure of the isolated compound was established by X-ray diffraction. The structural data (bond length and angles) of the compound were calculated by Density Functional Theory (DFT) using B3LYP/6-31 + G (p) basis set. The cholinesterase inhibitory potential of the isolated natural product was determined at various concentrations (62.5, 125, 250, 500 and 1000 μg/mL) followed by molecular docking to investigate the possible inhibitory mechanism of isotalatazidine hydrate. The compound crystallized in hexagonal unit cell with space group P65. Some other electronic properties such as energies associated with HOMO-LUMO, band gaps, global hardness, global electrophilicity, electron affinity and ionization potential were also calculated by means of B3LYP/6-31 + G (p) basis set. The compound showed competitive type inhibition of both acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with IC50 values of 12.13 μM and 21.41 μM, respectively. These results suggest that isotalatazidine hydrate is a potent dual cholinesterase inhibitor and can be used as a target drug in Alzheimer diseases. This is first report indicating isotalatazidine hydrate with anticholinesterase potential.

  3. Isolation, structure determination and cytotoxicity studies of tryptophan alkaloids from an Australian marine sponge Hyrtios sp.

    PubMed

    Khokhar, Shahan; Feng, Yunjiang; Campitelli, Marc R; Ekins, Merrick G; Hooper, John N A; Beattie, Karren D; Sadowski, Martin C; Nelson, Colleen C; Davis, Rohan A

    2014-08-01

    Mass-guided fractionation of the MeOH extract from a specimen of the Australian marine sponge Hyrtios sp. resulted in the isolation of two new tryptophan alkaloids, 6-oxofascaplysin (2), and secofascaplysic acid (3), in addition to the known metabolites fascaplysin (1) and reticulatate (4). The structures of all molecules were determined following NMR and MS data analysis. Structural ambiguities in 2 were addressed through comparison of experimental and DFT-generated theoretical NMR spectral values. Compounds 1-4 were evaluated for their cytotoxicity against a prostate cancer cell line (LNCaP) and were shown to display IC50 values ranging from 0.54 to 44.9 μM.

  4. Isolation and structure determination of one new metabolite isolated from the red fermented rice of Monascus purpureus.

    PubMed

    Cheng, Ming-Jen; Chen, Jih-Jung; Wu, Ming-Der; Yang, Ping-Shin; Yuan, Gwo-Fang

    2010-06-01

    The n-BuOH-soluble portion of the 95% EtOH extract of red fermented rice fermented with the yellow mutant of the fungus Monascus purpureus BCRC 38113 (Monascaceae) led to the isolation of one new pyran-2-one derivative, namely peroxymonascuspyrone (1), along with nine known compounds, monasfluore A (2), monasfluore B (3), 3-epi-betulinic acid (4), 3-epi-betulinic acid acetate (5), alpha-tocospiro A (6), friedelan-3-one (7), alpha-cadinol (8), anticopalol (9), and spathulenol (10). Interestingly, this is the first report of a naturally occurring pyran-2-one skeleton isolated from Monascus sp. Their structures and relative configurations were elucidated by spectroscopic methods, including 1D- and 2D-NMR ((1)H,(1)H-COSY, HMQC, HMBC and NOESY), as well as low- and high-resolution mass spectrometric analyses. In addition, cytotoxicities against MCF-7, NCI-H460 and SF-268 cancer cell lines were measured in vitro; the results revealed that these metabolites have no cytotoxicity against the selected tumour cells.

  5. Isolation and structure determination of two new constituents from the fruits of Morinda citrifolia Linn.

    PubMed

    Siddiqui, Bina S; Sattar, Fouzia A; Ahmad, Fayaz; Begum, Sabira

    2008-01-01

    Studies on the chemical constituents of the fruits of Morinda citrifolia Linn. have led to the isolation of two new compounds, morinaphthalene (=1,3,6,7-tetrahydroxy-2-hydroxymethyl-1,2,3,4-tetrahydronaphthalene, (1); and morindafurone (=5-hydroxy-1,10b-dihydro-6H-anthra [1,9-bc] furan-6-one, (2); as well as two known constituents, 1,8-dihydroxy-6-methoxy-3-methyl-9-anthrone (3) and 2,4-dimethoxy-9-anthrone (4). Their structures were elucidated by spectral analysis including 2D NMR techniques.

  6. Biologically active glycosides from Asteroidea, 41. Isolation and structure determination of glucocerebrosides from the starfish Linckia laevigata.

    PubMed

    Maruta, Tomoki; Saito, Takeshi; Inagaki, Masanori; Shibata, Osamu; Higuchi, Ryuichi

    2005-10-01

    A new glucocerebroside, linckiacerebroside A (1) and a known glucocerebroside S-2a-3 (2), have been isolated from the cerebroside molecular species obtained from the less polar fraction of the CHCl3/MeOH extract of the starfish Linckia laevigata, together with three pseudo homogeneous glucocerebroside, 3, 4, and 5. The structures of these cerebrosides were determined on the basis of chemical and spectroscopic evidence.

  7. Demographic Histories, Isolation and Social Factors as Determinants of the Genetic Structure of Alpine Linguistic Groups

    PubMed Central

    Coia, Valentina; Capocasa, Marco; Anagnostou, Paolo; Pascali, Vincenzo; Scarnicci, Francesca; Boschi, Ilaria; Battaggia, Cinzia; Crivellaro, Federica; Ferri, Gianmarco; Alù, Milena; Brisighelli, Francesca; Busby, George B. J.; Capelli, Cristian; Maixner, Frank; Cipollini, Giovanna; Viazzo, Pier Paolo; Zink, Albert; Destro Bisol, Giovanni

    2013-01-01

    Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood

  8. Isolation, structural determination, synthesis and quantitative determination of impurities in Intron-A, leached from a silicone tubing.

    PubMed

    Chan, Tze-Ming; Pramanik, Birendra; Aslanian, Robert; Gullo, Vincent; Patel, Mahesh; Cronin, Bart; Boyce, Chris; McCormick, Kevin; Berlin, Mike; Zhu, Xiaohong; Buevich, Alexei; Heimark, Larry; Bartner, Peter; Chen, Guodong; Pu, Haiyan; Hegde, Vinod

    2009-02-20

    Investigation of unexpected levels of impurities in Intron product has revealed the presence of low levels of impurities leached from the silicone tubing (Rehau RAU-SIK) on the Bosch filling line. In order to investigate the effect of these compounds (1a, 1b and 2) on humans, they were isolated identified and synthesized. They were extracted from the tubing by stirring in Intron placebo at room temperature for 72 h and were enriched on a reverse phase CHP-20P column, eluting with gradient aqueous ACN and were separated by HPLC. Structural elucidation of 1a, 1b and 2 by MS and NMR studies demonstrated them to be halogenated biphenyl carboxylic acids. The structures were confirmed by independent synthesis. Levels of extractable impurities in first filled vials of actual production are estimated to be in the range of 0.01-0.55 microg/vial for each leached impurity. Potential toxicity of these extractables does not represent a risk for patients under the conditions of clinical use.

  9. Isolation and structure determination of a sesquiterpene lactone (vernodalinol) from Vernonia amygdalina extracts

    PubMed Central

    Luo, Xuan; Jiang, Yan; Fronczek, Frank R.; Lin, Cuiwu; Izevbigie, Ernest B.; Lee, Ken S.

    2011-01-01

    Context Vernonia amygdalina Del. (VA; Asteraceae or Compositae) is a small tree growing throughout tropical Africa. It is widely used for food and medicinal purposes by local people. It was reported that it had several qualities, including anticancer activity. Objective A sesquiterpene lactone, vernodalinol, was isolated from VA leaves. The first reported source of vernodalinol was in 2009 from a different plant, only 1H NMR spectrum and no detailed structural analysis was carried out. No whole spectroscopic data were provided. Materials and methods VA dried leaves were extracted with 85% ethanol followed by further separation into four fractions by liquid–liquid extraction technique using various solvents: hexane, chloroform, and n-butanol. Vernodalinol was separated from the n-butanol fraction by column chromatography. The biological activity of vernodalinol was evaluated in estrogen receptor-positive (ER+) human breast carcinoma cells (MCF-7) in vitro. Results Results indicated that vernodalinol (25 and 50 μg/mL) inhibited breast cancerous cell growth (DNA synthesis) by 34% (P < 0.025) and 40% (P < 0.025), respectively. It is reasonable to expect an LC50 of 70–75 μg/mL for vernodalinol in MCF-7 cells. Discussion and conclusion Vernodalinol structure was confirmed using a battery of spectroscopic methods, 1D and 2D NMR, high-resolution mass spectrometry (HR-MS), UV, IR, and X-ray. These results suggest that vernodalinol, although it has some biological activity, is likely to work in concert with other ingredients responsible for the anticancer activity exhibited of VA. PMID:21281250

  10. Isolation and Structure Determination of 24-Methylenecycloartanyl Ferulate from Indian Rice Bran and Its Quantitative Analysis

    PubMed Central

    Muthal, Amol P.; Rojatkar, Supada R.; Bodhankar, Subhash Laxmanrao

    2016-01-01

    Background: γ-oryzanol is a major bioactive constituent in rice. Most of the literature reports isolation of 24-methylenecycloartanyl ferulate (24-mCAF) from rice bran oil (RBO) of other than Indian variety. Current research has successfully applied high-performance thin layer chromatography (HPTLC) method for isolation of 24-mCAF from Indian variety (Indrayani) of RBO. Materials and Methods: HPTLC method was developed for standard γ-oryzanol using tinidazole as an internal standard. The proposed HPTLC method was optimized and validated as per the guidelines stated by the International Conference on Harmonization Q2 R1 recommendations. The mobile phase composed of toluene:ethyl acetate:methanol (15.0:1.7:3.3, (v/v/v) was selected because well-resolved peaks were obtained. The optimum wavelength chosen for detection and quantitation was 317 nm. Results: The retention factors for tinidazole, 24-mCAF, and CAF were found to be 0.27 ± 0.02, 0.72 ± 0.02, and 0.79 ± 0.02, respectively. The percent content of 24-mCAF in ethanol fraction was found to be 1.02%. The 24-mCAF was isolated from RBO using HPTLC method. Conclusion: The characterization data of 1D, 2D spectral analysis confirm that the isolated compound 1 is 24-mCAF. SUMMARY HPTLC method was developed for standard γ-oryzanol using tinidazole as an internal standardThe proposed HPTLC method was optimized and validated as per the guidelines stated by the ICH Q2 R1 recommendationsThe characterization data of 1D, 2D spectral analysis confirms that the isolated compound is 24-methylenecycloartanyl ferulateIn this work, high purity 24-mCAF was successfully isolated from crude RBO using HPTLC with a solvent system composed toluene: ethyl acetate: methanol (15.0:1.7:3.3, v/v/v) Abbreviations used: RBO: Rice Bran Oil, CAF: Cycloartenol ferulic acid, 24-mCAF: 24-Methylcycloartenol ferulic acid, HPLC: High-Performance Liquid Chromatography, HPTLC: High-Performance Thin Layer Chromatography, 1H: Proton nuclear magnetic

  11. Isolation from beer and structural determination of a potent stimulant of gastrin release.

    PubMed

    Yokoo, Y; Kohda, H; Kusumoto, A; Naoki, H; Matsumoto, N; Amachi, T; Suwa, Y; Fukazawa, H; Ishida, H; Tsuji, K; Nukaya, H

    1999-01-01

    Beer was subjected to five successive chromatographic procedures to isolate the gastrin release-inducing activity, guided by bioassay of the fractions in anaesthetized Donryu rats. The procedures were: (1) hydrophobic interaction chromatography (aqueous effluent with an HP20 column); (2) weak cation-exchange chromatography (1 M acetic acid eluate with a CM Sephadex C-25 column); (3) gel filtration (methanol eluate with a Sephadex LH-20 column); (4) same as (2); (5) high-performance liquid chromatography (YMC-Pack ODS-AM with 7% acetonitrile-0.01 M HCl). The active component finally isolated had a specific activity approximately 10000 times higher than that of beer. It was identified by means of mass, 1H- and 13C-nuclear magnetic resonance spectral analyses as N-methyltyramine (NMT). The dose of NMT giving maximal gastrin-releasing activity was 25 microg/kg, and the 50% effective dose was approximately 10 microg/kg on oral administration to rats. NMT was isolated and identified as a gastrin release inducer in beer. Its concentration in beer is sufficient to account for most of the activity of beer.

  12. Isolation, pharmacological activity and structure determination of physalin B and 5β,6β-epoxyphysalin B isolated from Congolese Physalis angulata L.

    PubMed

    Mangwala Kimpende, Peter; Lusakibanza, Mariano; Mesia, Kahunu; Tona, Lutete; Tits, Monique; Angenot, Luc; Frédérich, Michel; Van Meervelt, Luc

    2013-12-15

    Physalis angulata L., an annual herb from the Solanaceae family, is widely used in popular medicine in tropical countries to treat a variety of diseases. Two products, (X) and (Y), were isolated from a crude CH2Cl2 extract of dried Congolese Physalis angulata L. plants and crystallized from acetone for structure elucidation. Compound (X) corresponds to a physalin B dimer acetone solvate hydrate (2C28H30O9·C3H6O·0.22H2O), while compound (Y) crystallizes as a mixed crystal containing two physalin B molecules which overlap with 5β,6β-epoxyphysalin B, also known as physalin F, and one acetone molecule in the asymmetric unit (1.332C28H30O9·0.668C28H30O10·C3H6O). Antiplasmodial activity, cytotoxic activity and selectivity indices were determined for crude extracts and the two isolated products (X) and (Y).

  13. Population structure and acquisition of the vanB resistance determinant in German clinical isolates of Enterococcus faecium ST192

    PubMed Central

    Bender, Jennifer K.; Kalmbach, Alexander; Fleige, Carola; Klare, Ingo; Fuchs, Stephan; Werner, Guido

    2016-01-01

    In the context of the global action plan to reduce the dissemination of antibiotic resistances it is of utmost importance to understand the population structure of resistant endemic bacterial lineages and to elucidate how bacteria acquire certain resistance determinants. Vancomycin resistant enterococci represent one such example of a prominent nosocomial pathogen on which nation-wide population analyses on prevalent lineages are scarce and data on how the bacteria acquire resistance, especially of the vanB genotype, are still under debate. With respect to Germany, an increased prevalence of VRE was noted in recent years. Here, invasive infections caused by sequence type ST192 VRE are often associated with the vanB-type resistance determinant. Hence, we analyzed 49 vanB-positive and vanB-negative E. faecium isolates by means of whole genome sequencing. Our studies revealed a distinct population structure and that spread of the Tn1549-vanB-type resistance involves exchange of large chromosomal fragments between vanB-positive and vanB-negative enterococci rather than independent acquisition events. In vitro filter-mating experiments support the hypothesis and suggest the presence of certain target sequences as a limiting factor for dissemination of the vanB element. Thus, the present study provides a better understanding of how enterococci emerge into successful multidrug-resistant nosocomial pathogens. PMID:26902259

  14. Structural determination of the K14 capsular polysaccharide from an ST25 Acinetobacter baumannii isolate, D46.

    PubMed

    Kenyon, Johanna J; Hall, Ruth M; De Castro, Cristina

    2015-11-19

    The structure of the capsular polysaccharide (CPS) recovered from D46, an extensively antibiotic resistant ST25 Acinetobacter baumannii clinical isolate, was elucidated. The structure was resolved on the basis of NMR spectroscopy and chemical analyses, and was found to contain a branched neutral pentasaccharide with a backbone composed of GalpNAc and Galp residues, all d configured, and a d-Glcp side group. The KL14 gene cluster found in the D46 genome includes genes for four glycosyltransferases but no modules for synthesis of complex sugars, and this is consistent with the structure of K14. The K14 structure and KL14 sequence clarify the relationship between the structure and K locus sequence for A. nosocomialis isolate LUH5541. The identity of the first sugar of the K14 repeat unit (K unit), and the functions of the four encoded glycosyltransferases and Wzy polymerase were predicted.

  15. Determination of the chemical structures of tandyukisins B-D, isolated from a marine sponge-derived fungus.

    PubMed

    Yamada, Takeshi; Umebayashi, Yoshihide; Kawashima, Maiko; Sugiura, Yuma; Kikuchi, Takashi; Tanaka, Reiko

    2015-05-21

    Tandyukisins B-D (1-3), novel decalin derivatives, have been isolated from a strain of Trichoderma harzianum OUPS-111D-4 originally derived from the marine sponge Halichondria okadai, and their structures have been elucidated on the basis of spectroscopic analyses using 1D and 2D NMR techniques. In addition, their chemical structures were established by chemical transformation. They exhibited weak cytotoxicity, but selective growth inhibition on panel screening using 39 human cancer cell lines.

  16. Isolation, structure determination, synthesis, and sensory activity of N-phenylpropenoyl-L-amino acids from cocoa (Theobroma cacao).

    PubMed

    Stark, Timo; Hofmann, Thomas

    2005-06-29

    Application of chromatographic separation and taste dilution analyses recently revealed besides procyanidins a series of N-phenylpropenoyl amino acids as the key contributors to the astringent taste of nonfermented cocoa beans as well as roasted cocoa nibs. Because these amides have as yet not been reported as key taste compounds, this paper presents the isolation, structure determination, and sensory activity of these amino acid amides. Besides the previously reported (-)-N-[3',4'-dihydroxy-(E)-cinnamoyl]-3-hydroxy-L-tyrosine (clovamide), (-)-N-[4'-hydroxy-(E)-cinnamoyl]-L-tyrosine (deoxyclovamide), and (-)-N-[3',4'-dihydroxy-(E)-cinnamoyl]-L-tyrosine, seven additional amides, namely, (+)-N-[3',4'-dihydroxy-(E)-cinnamoyl]-L-aspartic acid, (+)-N-[4'-hydroxy-(E)-cinnamoyl]-L-aspartic acid, (-)-N-[3',4'-dihydroxy-(E)-cinnamoyl]-L-glutamic acid, (-)-N-[4'-hydroxy-(E)-cinnamoyl]-L-glutamic acid, (-)-N-[4'-hydroxy-(E)-cinnamoyl]-3-hydroxy-L-tyrosine, (+)-N-[4'-hydroxy-3'-methoxy-(E)-cinnamoyl]-L-aspartic acid, and (+)-N-[(E)-cinnamoyl]-L-aspartic acid, were identified for the first time in cocoa products by means of LC-MS/MS, 1D/2D-NMR, UV-vis, CD spectroscopy, and polarimetry, as well as independent enantiopure synthesis. Using the recently developed half-tongue test, human recognition thresholds for the astringent and mouth-drying oral sensation were determined to be between 26 and 220 micromol/L (water) depending on the amino acid moiety. In addition, exposure to light rapidly converted these [E]-configured N-phenylpropenoyl amino acids into the corresponding [Z]-isomers, thus indicating that analysis of these compounds in food and plant materials needs to be performed very carefully in the absence of light to prevent artifact formation.

  17. Genotypic Diversity and Population Structure of Vibrio vulnificus Strains Isolated in Taiwan and Korea as Determined by Multilocus Sequence Typing.

    PubMed

    Kim, Hye-Jin; Cho, Jae-Chang

    2015-01-01

    The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23-35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer's tests) detected significant evidence of recombination. Tajima's D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus.

  18. Isolation and determination of the primary structure of a lectin protein from the serum of the American alligator (Alligator mississippiensis).

    PubMed

    Darville, Lancia N F; Merchant, Mark E; Maccha, Venkata; Siddavarapu, Vivekananda Reddy; Hasan, Azeem; Murray, Kermit K

    2012-02-01

    Mass spectrometry in conjunction with de novo sequencing was used to determine the amino acid sequence of a 35kDa lectin protein isolated from the serum of the American alligator that exhibits binding to mannose. The protein N-terminal sequence was determined using Edman degradation and enzymatic digestion with different proteases was used to generate peptide fragments for analysis by liquid chromatography tandem mass spectrometry (LC MS/MS). Separate analysis of the protein digests with multiple enzymes enhanced the protein sequence coverage. De novo sequencing was accomplished using MASCOT Distiller and PEAKS software and the sequences were searched against the NCBI database using MASCOT and BLAST to identify homologous peptides. MS analysis of the intact protein indicated that it is present primarily as monomer and dimer in vitro. The isolated 35kDa protein was ~98% sequenced and found to have 313 amino acids and nine cysteine residues and was identified as an alligator lectin. The alligator lectin sequence was aligned with other lectin sequences using DIALIGN and ClustalW software and was found to exhibit 58% and 59% similarity to both human and mouse intelectin-1. The alligator lectin exhibited strong binding affinities toward mannan and mannose as compared to other tested carbohydrates.

  19. Genotypic Diversity and Population Structure of Vibrio vulnificus Strains Isolated in Taiwan and Korea as Determined by Multilocus Sequence Typing

    PubMed Central

    Kim, Hye-Jin; Cho, Jae-Chang

    2015-01-01

    The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23–35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer’s tests) detected significant evidence of recombination. Tajima’s D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus. PMID:26599487

  20. FT-IR and Raman spectroscopies determine structural changes of tilapia fish protein isolate and surimi under different comminution conditions.

    PubMed

    Kobayashi, Yuka; Mayer, Steven G; Park, Jae W

    2017-07-01

    Tilapia proteins refined by pH shift and water washing were chopped under various comminution conditions and their structural changes were investigated using Fourier transform infrared (FT-IR) and Raman spectroscopies. Both techniques revealed the degree of unfolding in protein structure increased when fish protein isolate (FPI) and surimi were chopped at 25°C for 18min compared to samples chopped at 5°C for 6min. Results indicated both hydrophobic interactions and disulfide bonds were significantly enhanced during gelation. FPI and surimi gels prepared at 25°C for 18min exhibited higher β-sheet contents and more chemical bonds such as hydrophobic interactions and disulfide bonds than those at 5°C for 6min. Results suggested that controlling comminution is important to improve gel qualities in FPI and surimi from tropical fish like tilapia. Moreover, FT-IR and Raman spectroscopies are useful complementary tools for elucidating the change in the structure of protein during comminution and gelation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Seismic Behaviour of Vertical Mass Isolated Structures

    SciTech Connect

    Nekooei, M.; Ziyaeifar, M.

    2008-07-08

    In this paper, the seismic behaviour of vertical mass isolated structures against the earthquake is studied. These structures are assumed to be consisted of two subsystems. Mass subsystem possesses low lateral stiffness but carries the major part of mass of the system. Stiffness subsystem, however, controls the deformation of the mass subsystem and attributes with much higher stiffness. The isolator layer is, therefore, located in between the mass and the stiffness subsystems and assumed to be a viscous damper layer. The analytical model used for this investigation is a dual mass-spring model which is an extended form of the three element Maxwell model. In this study, the ability of mass isolation techniques in reducing earthquake effects on buildings with two approaches, parametric and numerical approaches, is shown. In the parametric approach, by definition an isolation factor for structure and determination the dynamic characteristics of system, the relative optimum value of the isolator damping coefficient is obtained. The results provide an insight on role of relative stiffness and mass ratio of the two subsystems. Finally, in the numerical approach, the spectral responses of these structures due to the earthquake are investigated. The results show a noticeable decrease in earthquake input force to vertical mass isolated structures in comparison with non-isolated structures.

  2. Isolation and structure determination of novamethymycin, a new bioactive metabolite of the methymycin biosynthetic pathway in Streptomyces venezuelae.

    PubMed

    Zhang, Q; Sherman, D H

    2001-11-01

    Novamethymycin (9), a novel macrolide antibiotic, was isolated from Streptomyces venezuelae, the producer of methymycin (4) and neomethymycin (5). Spectroscopic analysis of 9 indicated that it is highly related to 4 and 5 but contains hydroxy groups at both C-10 and C-12 on the macrolactone ring. Bioconversion studies using the PikC cytochrome P450 hydroxylase demonstrated that 4 is converted to 9, further broadening the remarkable substrate flexibility of this enzyme.

  3. Isolation, Characterization, Crystal Structure Elucidation of Two Flavanones and Simultaneous RP-HPLC Determination of Five Major Compounds from Syzygium campanulatum Korth.

    PubMed

    Memon, Abdul Hakeem; Ismail, Zhari; Al-Suede, Fouad Saleih Resq; Aisha, Abdalrahim F A; Hamil, Mohammad Shahrul Ridzuan; Saeed, Mohammed Ali Ahmed; Laghari, Madeeha; Majid, Amin Malik Shah Abdul

    2015-08-04

    Two flavanones named (2S)-7-Hydroxy-5-methoxy-6,8-dimethyl flavanone (1), (S)-5,7-dihydroxy-6,8-dimethyl-flavanone (2), along with known chalcone, namely, (E)-2',4'- dihydroxy-6'-methoxy-3',5'-dimethylchalcone (3) and two triterpenoids, namely, betulinic and ursolic acids (4 and 5), were isolated from the leaves of Syzygium campanulatum Korth (Myrtaceae). The structures of compounds (1 and 2) were determined on the basis of UV-visible, FTIR, NMR spectroscopies and LC-EIMS analytical techniques. Furthermore, new, simple, precise, selective, accurate, highly sensitive, efficient and reproducible RP-HPLC method was developed and validated for the quantitative analysis of the compounds (1-5) from S. campanulatum plants of five different age. RP-HPLC method was validated in terms of specificity, linearity (r2 ≤ 0.999), precision (2.0% RSD), and recoveries (94.4%-105%). The LOD and LOQ of these compounds ranged from 0.13-0.38 and 0.10-2.23 μg·mL-1, OPEN ACCESS respectively. Anti-proliferative activity of isolated flavanones (1 and 2) and standardized extract of S. campanulatum was evaluated on human colon cancer (HCT 116) cell line. Compounds (1 and 2) and extract revealed potent and dose-dependent activity with IC50 67.6, 132.9 and 93.4 μg·mL-1, respectively. To the best of our knowledge, this is the first study on isolation, characterization, X-ray crystallographic analysis of compounds (1 and 2) and simultaneous RP-HPLC determination of five major compounds (1-5) from different age of S. campanulatum plants.

  4. Structural Determination of Circulation.

    ERIC Educational Resources Information Center

    Blankenburg, William B.

    1981-01-01

    Analyzes the effects of both structural factors (demographics, economic conditions, and competition) and discretionary factors (content, design, and marketing techniques) and concludes that it is the former that determine a newspaper's circulation. (FL)

  5. Mitochondria: isolation, structure and function.

    PubMed

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-09-15

    Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work.

  6. Mitochondria: isolation, structure and function

    PubMed Central

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-01-01

    Abstract Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work. PMID:21708903

  7. Studies on the minor constituents of the Caribbean gorgonian octocoral Briareum asbestinum Pallas. Isolation and structure determination of the eunicellin-based diterpenoids briarellins E--I.

    PubMed

    Rodríguez, A D; Cóbar, O M

    1995-11-01

    Five new eunicellin-type diterpenoids, briarellins E--I, along with several known diterpenoids of the asbestinane, briarane and eunicellane classes, were isolated from the Caribbean gorgonian octocoral Briareum asbestinum collected in Puerto Rico. The structures of these compounds were established on the basis of spectroscopic evidence.

  8. Novel gene complex structure determination

    SciTech Connect

    Gatewood, J.M.

    1997-08-01

    This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.

  9. Determining structural performance

    NASA Technical Reports Server (NTRS)

    Ernst, Michael A.; Kiraly, Louis J.

    1987-01-01

    An overview is given of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems. Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods are four disciplines that make up the research program at NASA/Lewis Research Center. The Aeroelasticity program develops analytical and experimental methods to minimize flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods have been developed for applications on the turbofan, turbopump, and advanced turboprop. To improve life and performance, the Vibration Control program conceives, analyzes, develops, and demonstrates new methods to control vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The Dynamic Systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. The Computational Structural Methods program uses computer science to improve solutions of structural problems.

  10. Microfabricated structures with electrical isolation and interconnections

    NASA Technical Reports Server (NTRS)

    Clark, William A. (Inventor); Juneau, Thor N. (Inventor); Roessig, Allen W. (Inventor); Lemkin, Mark A. (Inventor)

    2001-01-01

    The invention is directed to a microfabricated device. The device includes a substrate that is etched to define mechanical structures at least some of which are anchored laterally to the remainder of the substrate. Electrical isolation at points where mechanical structures are attached to the substrate is provided by filled isolation trenches. Filled trenches may also be used to electrically isolate structure elements from each other at points where mechanical attachment of structure elements is desired. The performance of microelectromechanical devices is improved by 1) having a high-aspect-ratio between vertical and lateral dimensions of the mechanical elements, 2) integrating electronics on the same substrate as the mechanical elements, 3) good electrical isolation among mechanical elements and circuits except where electrical interconnection is desired.

  11. Determining structural performance

    NASA Technical Reports Server (NTRS)

    Ernst, Michael A. (Editor); Brown, Gerald; Dirusso, Eliseo; Fleming, David; Janetzke, David; Kascak, Albert; Kaza, Krishna; Kielb, Robert; Kiraly, Louis J.; Lawrence, Charles

    1990-01-01

    An overview of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems is presented. Aeroelasticity, vibration control, dynamic systems, and computational structural methods are four disciplines that make up the structural dynamic effort at LeRC. The aeroelasticity program develops analytical and experimental methods for minimizing flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods were developed for applications on the turbofan, turbopump, and advanced turboprop. In order to improve life and performance, the vibration control program conceives, analyzes, develops, and demonstrates new methods for controlling vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The dynamic systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. Work in this field involves the analysis and parametric identification of large, nonlinear, damped, stochastic systems. The computational structural methods program exploits modern computer science as an aid to the solutions of structural problems.

  12. Structural determination of cerebrosides isolated from Asterias amurensis starfish eggs using high-energy collision-induced dissociation of sodium-adducted molecules.

    PubMed

    Park, Taeseong; Park, Young Seung; Rho, Jung-Rae; Kim, Young Hwan

    2011-03-15

    Six cerebrosides were isolated from the eggs of the starfish Asterias amurensis using solvent extraction, silica gel column chromatography, and reversed-phase high-performance liquid chromatography. This study demonstrated that the structures of cerebrosides could be completely characterized, based on their sodium-adducted molecules, using fast atom bombardment (FAB) tandem mass spectrometry. The high-energy collision-induced dissociation of the sodium-adducted molecule, [M + Na](+), of each cerebroside molecular species generated abundant ions, providing information on the compositions of the 2-hydroxy fatty acids and long-chain sphingoid bases, as well as the sugar moiety polar head group. Each homologous ion series along the fatty acid and aliphatic chain of the sphingoid base was useful for locating the double-bond positions of both chains and the methyl branching position of the long-chain base. The N-fatty acyl portions were primarily long-chain saturated or monoenoic acids (C16 to C24) with an α-hydroxy group. The sphingoid long-chain base portions were aliphatic chains (C18 or C22) with two or three degrees of unsaturation and with or without methyl branching. Copyright © 2011 John Wiley & Sons, Ltd.

  13. Structural determinants of glomerular permeability.

    PubMed

    Deen, W M; Lazzara, M J; Myers, B D

    2001-10-01

    Recent progress in relating the functional properties of the glomerular capillary wall to its unique structure is reviewed. The fenestrated endothelium, glomerular basement membrane (GBM), and epithelial filtration slits form a series arrangement in which the flow diverges as it enters the GBM from the fenestrae and converges again at the filtration slits. A hydrodynamic model that combines morphometric findings with water flow data in isolated GBM has predicted overall hydraulic permeabilities that are consistent with measurements in vivo. The resistance of the GBM to water flow, which accounts for roughly half that of the capillary wall, is strongly dependent on the extent to which the GBM surfaces are blocked by cells. The spatial frequency of filtration slits is predicted to be a very important determinant of the overall hydraulic permeability, in keeping with observations in several glomerular diseases in humans. Whereas the hydraulic resistances of the cell layers and GBM are additive, the overall sieving coefficient for a macromolecule (its concentration in Bowman's space divided by that in plasma) is the product of the sieving coefficients for the individual layers. Models for macromolecule filtration reveal that the individual sieving coefficients are influenced by one another and by the filtrate velocity, requiring great care in extrapolating in vitro observations to the living animal. The size selectivity of the glomerular capillary has been shown to be determined largely by the cellular layers, rather than the GBM. Controversial findings concerning glomerular charge selectivity are reviewed, and it is concluded that there is good evidence for a role of charge in restricting the transmural movement of albumin. Also discussed is an effect of albumin that has received little attention, namely, its tendency to increase the sieving coefficients of test macromolecules via steric interactions. Among the unresolved issues are the specific contributions of the

  14. Structural determination of novel sulfated octasaccharides isolated from chondroitin sulfate of shark cartilage and their application for characterizing monoclonal antibody epitopes.

    PubMed

    Deepa, Sarama S; Yamada, Shuhei; Fukui, Shigeyuki; Sugahara, Kazuyuki

    2007-06-01

    Twelve octasaccharide fractions were obtained from chondroitin sulfate C derived from shark cartilage after hyaluronidase digestion. Their sugar and sulfate composition was assigned by matrix-assisted laser desorption ionization time of flight mass spectrometry. The sequences were determined at low picomole amounts by a combination of enzymatic digestions with high-performance liquid chromatography, and were composed of disaccharide building units including O [GlcUAbeta1-3GalNAc], C [GlcUAbeta1-3GalNAc(6S)], A [GlcUAbeta1-3GalNAc(4S)], and/or D [GlcUA(2S)beta1-3GalNAc(6S)], where 2S, 4S, and 6S represent 2-O-, 4-O-, and 6-O-sulfate, respectively. As many as 24 different sequences including minor ones were revealed, exhibiting a high degree of structural diversity reflecting the enormous heterogeneity of the parent polysaccharides. Nineteen of them were novel, with the other four reported previously as unsaturated counterparts obtained after digestion with chondroitinase. Microarrays of these structurally defined octasaccharide fractions were prepared using low picomole amounts of their lipid-derivatives to investigate the binding specificity of four commercial anti-chondroitin sulfate antibodies CS-56, MO-225, 2H6, and LY111. The results revealed that multiple unique sequences were recognized by each antibody, which implies that the common conformation shared by the multiple primary sequences in the intact chondroitin sulfate chains is important as an epitope for each monoclonal antibody. Comparison of the specificity of the tested antibodies indicates that CS-56 and MO-225 specifically recognize octasaccharides containing an A-D tetrasaccharide sequence, whereas 2H6 and LY111 require a hexasaccharide as a minimum size for their binding, and prefer sequences with A- and C-units such as C-C-A-C (2H6) or C-C-A-O, C-C-A-A, and C-C-A-C (LY111) for strong binding but require no D-unit.

  15. Investigating the Web Structure by Isolated Stars

    NASA Astrophysics Data System (ADS)

    Uno, Yushi; Ota, Yoshinobu; Uemichi, Akio

    The link structure of the Web is generally represented by the webgraph, and it is often used for web structure mining that mainly aims to find hidden communities on the Web. In this paper, we identify a common frequent substructure and give it a formal graph definition, which we call an isolated star (i-star), and propose an efficient enumeration algorithm of i-stars. We then investigate the structure of the Web by enumerating i-stars from real web data. As a result, we observed that most i-stars correspond to index structures in single domains, while some of them are verified to be candidates of communities, which implies the validity of i-stars as useful substructure for web structure mining and link spam detecting. We also observed that the distributions of i-star sizes show power-law, which is another new evidence of the scale-freeness of the webgraph.

  16. Isolation and structure determination of a benzofuran and a bis-nor-isoprenoid from Aspergillus niger grown on the water soluble fraction of Morinda citrifolia Linn. leaves.

    PubMed

    Siddiqui, Bina S; Ismail, Fouzia A Sattar; Gulzar, Tahsin; Begum, Sabira

    2003-10-01

    The leaves of Morinda citrifolia, Linn. afforded a new benzofuran and a bis-nor-isoprenoid, blumenol C, hitherto unreported from this source. The structures of these have been elucidated as 5-benzofuran carboxylic acid-6-formyl methyl ester (1) and 4-(3'(R)-hydroxybutyl)-3,5,5, trimethyl-cyclohex-2-en-1-one (2) respectively through spectroscopic studies. The NMR data (including 1D, 2D techniques) and stereochemistry at C-3' of Compound 2 is also being reported for the first time.

  17. Active vibration isolation using smart structures

    NASA Technical Reports Server (NTRS)

    Guigou, C.; Wagstaff, P. R.; Fuller, C. R.

    1991-01-01

    Passive technologies for the isolation of structures from vibrating sources are often inadequate. Using active control inputs applied directly to the source or designing a structure integrating the transducers required for the control inputs and the response measurements are ways of dealing with the problem. Results are given which were obtained on an experimental set up simulating this kind of problem where the form and the position of the transducers could be varied. By measuring the response of the structure integrated over a particular area the effects of particular types of modes could be taken into account to deal with specific types of input or limit particular modes of response more efficiently. Results of using different modes of vibration excitation of the receiving structure with and without control are presented for particular input frequencies. The problems of optimizing the control system to deal with multiple frequency inputs are discussed.

  18. Crystal structure determination of Efavirenz

    SciTech Connect

    Popeneciu, Horea Dumitru, Ristoiu; Tripon, Carmen Borodi, Gheorghe Pop, Mihaela Maria

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  19. Secondary structure determines protein topology

    PubMed Central

    Fleming, Patrick J.; Gong, Haipeng; Rose, George D.

    2006-01-01

    Using a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long-range interactions. It has been a long-standing open question whether such information is sufficient to determine a protein's fold. Indeed, even the far simpler problem of reconstructing the three-dimensional structure of a protein from its exact backbone torsion angles has remained a difficult challenge owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, cause large errors in structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm; the longer the arm, the larger the displacement. Here, correct secondary structure assignments (α-helix, β-strand, β-turn, polyproline II, coil) were used to constrain polypeptide backbone chains devoid of side chains, and the most stable folded conformations were determined, using Monte Carlo simulation. Just three terms were used to assess stability: molecular compaction, steric exclusion, and hydrogen bonding. For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them. PMID:16823044

  20. Structural determination of a 5-acetamido-3,5,7, 9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulos onic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103.

    PubMed Central

    Gil-Serrano, A M; Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Menendez, M; Corzo, J; Ruiz-Sainz, J E; BuendíA-Clavería, A M

    1999-01-01

    The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide. PMID:10477263

  1. Frequency response characteristics and response spectra of base-isolated and un-isolated structures

    SciTech Connect

    Mok, G.C.; Namba, H.

    1995-07-06

    The transmissibility of seismic loads through a linear base-isolation system is analyzed using an impedance method. The results show that the system acts like a {open_quotes}low-pass{close_quotes} filter. It attenuates high-frequency loads but passes through low-frequency ones. The filtering effect depends on the vibration frequencies and damping of the isolated structure and the isolation system. This paper demonstrates the benefits and design principles of base isolation by comparing the transmissibilities and response spectra of isolated and un-isolated structures. Parameters of typical isolated buildings and ground motions of the 1994 Northridge earthquake are used for the demonstration.

  2. Structure determination of enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    2013-02-20

    Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.

  3. Isolation and sequence determination of tetrapeptide from Selaginella bryopteris.

    PubMed

    Prabha, M Rajeswari; Ramachandramurty, B

    2013-09-01

    A simple and inexpensive paper chromatographic method was developed for the isolation of a small peptide from Selaginella bryopteris fronds. The content of peptides is low in most plants and the isolation and purification procedure is troublesome. This method may be used as a first step for the detection of small peptides in the plant extracts. De novo sequence determination by tandem mass spectrometry indicated that the peptide is a tetrapeptide.

  4. Isolation and Structural Determination of the First 8-epi-type Tetrodotoxin Analogs from the Newt, Cynops ensicauda popei, and Comparison of Tetrodotoxin Analogs Profiles of This Newt and the Puffer Fish, Fugu poecilonotus

    PubMed Central

    Kudo, Yuta; Yasumoto, Takeshi; Konoki, Keiichi; Cho, Yuko; Yotsu-Yamashita, Mari

    2012-01-01

    Identification of new tetrodotoxin (TTX) analogs from TTX-possessing animals might provide insight into its biosynthesis and metabolism. In this study, four new analogs, 8-epi-5,6,11-trideoxyTTX, 4,9-anhydro-8-epi-5,6,11-trideoxyTTX, 1-hydroxy-8-epi-5,6,11-trideoxyTTX, and 1-hydroxy-4,4a-anhydro-8-epi-5,6,11-trideoxyTTX, were isolated from the newt, Cynops ensicauda popei, and their structures were determined using spectroscopic methods. These are the first 8-epi-type analogs of TTX that have been found in a natural source. Furthermore, we examined the composition of the TTX analogs in this newt and in the ovary of the puffer fish, Fugu poecilonotus, using LC/MS. The results indicate that TTX and 11-deoxyTTX were present in both sources. However, 6-epiTTX and 8-epi-type analogs were detected only in the newt, while 5,6,11-trideoxyTTX was a specific and major analog in the puffer fish. Such considerable differences among analog compositions might reflect differences in the biosynthesis or metabolism of TTX between these animals. PMID:22611361

  5. Isolation and structural determination of the first 8-epi-type tetrodotoxin analogs from the newt, Cynops ensicauda popei, and comparison of tetrodotoxin analogs profiles of this newt and the puffer fish, Fugu poecilonotus.

    PubMed

    Kudo, Yuta; Yasumoto, Takeshi; Konoki, Keiichi; Cho, Yuko; Yotsu-Yamashita, Mari

    2012-03-01

    Identification of new tetrodotoxin (TTX) analogs from TTX-possessing animals might provide insight into its biosynthesis and metabolism. In this study, four new analogs, 8-epi-5,6,11-trideoxyTTX, 4,9-anhydro-8-epi-5,6,11-trideoxyTTX, 1-hydroxy-8-epi-5,6,11-trideoxyTTX, and 1-hydroxy-4,4a-anhydro-8-epi-5,6,11-trideoxyTTX, were isolated from the newt, Cynops ensicauda popei, and their structures were determined using spectroscopic methods. These are the first 8-epi-type analogs of TTX that have been found in a natural source. Furthermore, we examined the composition of the TTX analogs in this newt and in the ovary of the puffer fish, Fugu poecilonotus, using LC/MS. The results indicate that TTX and 11-deoxyTTX were present in both sources. However, 6-epiTTX and 8-epi-type analogs were detected only in the newt, while 5,6,11-trideoxyTTX was a specific and major analog in the puffer fish. Such considerable differences among analog compositions might reflect differences in the biosynthesis or metabolism of TTX between these animals.

  6. Phase-shifting structures for isolated features

    NASA Astrophysics Data System (ADS)

    Garofalo, Joseph G.; Kostelak, Robert L.; Yang, Tungsheng

    1991-07-01

    The technique for improving optical projection-system resolution by phase-shifting alternate apertures of a periodic grating was introduced in 1982. This halves the frequency content of the image passing through the optics and should therefore double the effective resolution of such patterns. Unfortunately, as feature separation increases, the efficacy of this method diminishes. Previous work applying a similar approach to isolated features involves introducing minute, non-printable, phase-shifted assist slots around the desired feature. The diffraction side-lobes of these slots constructively interfere with the center lobe of the primary aperture. The resolution enhancement afforded be this technique is limited by the printability of the assist slots. This restraint also dictates 1X-size reticle feature dimensions and the employment of high contrast imaging resists. A new approach entails significantly oversizing the desired feature and introducing a phase-shifting region around the periphery. This type of structure affords substantial focus-exposure improvements and may either be fabricated in a single-level, self-aligned scheme or by a two-level exposure with conventional e-beam tools since the phase-shifting regions are on the order of 1 micrometers (reticle dimensions). Extensive modeling of this structure for isolated contact holes and spaces explores the myriad of trade- offs involved in an optimum design. Mask-fabrication tolerances, such as phase-shift uniformity, are also investigated. It is shown that the focus-exposure window enlarges as the overall structure dimensions increase. The degree of enhancement must therefore by weighed against packing density restrictions. Also, the structure suffers, to some degree, from the effect of side-lobes. However, for a given side-lobe intensity, this technique yields enhancements superior to the assist-slot approach. As is typical of phase-shifted systems, performance is improved as the partial coherence ((sigma

  7. Comparison of chitin structures isolated from seven Orthoptera species.

    PubMed

    Kaya, Murat; Erdogan, Sevil; Mol, Abbas; Baran, Talat

    2015-01-01

    Differences in the physichochemical properties of the chitin structure of the exoskeleton of seven species from four genera were investigated in this study. The same method was used to isolate the chitin structure of the seven species. The physicochemical properties of the isolated chitins were revealed by ESEM, FTIR, TGA and XRD analyses. The FTIR, TGA and XRD results from the chitin samples were similar. The surface morphologies of the chitins were investigated by ESEM and interesting results were noted. While the surface morphologies of the chitins isolated from two species within the same genus were quite different, the surface morphologies of chitins isolated from species belonging to different genera showed similarity. It was determined that the dry weight chitin contents of the grasshopper species varied between 5.3% and 8.9%. The results of molecular analysis showed that the chitins from seven Orthoptera species (between 5.2 and 6.8 kDa) have low molecular weights. Considering that these invasive and harmful species are killed with insecticides and go to waste in large amounts, this study suggests that they should be collected and evaluated as an alternative chitin source.

  8. In cellulo structure determination of a novel cypovirus polyhedrin

    SciTech Connect

    Axford, Danny; Ji, Xiaoyun; Stuart, David I.; Sutton, Geoff

    2014-05-01

    The crystal structure of a previously unsolved type of cypovirus polyhedrin has been determined from data collected directly from frozen live insect cells. This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell.

  9. On the structural organization of isolated bovine lens fiber junctions.

    PubMed

    Zampighi, G; Simon, S A; Robertson, J D; McIntosh, T J; Costello, M J

    1982-04-01

    Junctions between fiber cells of bovine lenses have been isolated in milligram quantities, without using detergents or proteases. The structure of the isolated junctions has been studied by thin-section, negative-stain, and freeze-fracture electron microscopy and by x-ray diffraction. The junctions are large and most often have an undulating surface topology as determined by thin sectioning and freeze-fracture. These undulations resemble the tongue-and-groove interdigitations between lens fiber cells previously seen by others (D. H. Dickson and G. W. Crock, 1972, Invest. Ophthalmol. 11:809-815). In sections, the isolated junctions display a pentalamellar structure approximately 13-14 nm in overall thickness, which is significantly thinner than liver gap junctions. Each junctional membrane contains in the plane of the lipid bilayers distinct units arranged in a square lattice with a center-to-center spacing of 6.6 nm. Freeze-fracture replicas of the junctions fractured transversely show that the repeating units extend across the entire thickness of each membrane. Each unit is probably constructed from four identical subunits, with each subunit containing a protein of an apparent molecular weight of 27,000. We conclude that the lens junctions are structurally and chemically, different from gap junctions and could represent a new kind of intercellular contact, not simply another crystalline state of the gap junction protein.

  10. Characterization of integrons and tetracycline resistance determinants in Aeromonas spp. isolated from South African aquaculture systems.

    PubMed

    Jacobs, Liezl; Chenia, Hafizah Y

    2007-03-20

    An increasing incidence of multidrug resistance amongst Aeromonas spp. isolates, which are both fish pathogens and emerging opportunistic human pathogens, has been observed worldwide. This can be attributed to the horizontal transfer of mobile genetic elements, viz.: plasmids and class 1 integrons. The antimicrobial susceptibilities of 37 Aeromonas spp. isolates, from tilapia, trout and koi aquaculture systems, were determined by disc-diffusion testing. The plasmid content of each isolate was examined using the alkaline lysis protocol. Tet determinant type was determined by amplification using two degenerate primer sets and subsequent HaeIII restriction. The presence of integrons was determined by PCR amplification of three integrase genes, as well as gene cassettes, and the qacEDelta1-sulI region. Thirty-seven Aeromonas spp. isolates were differentiated into six species by aroA PCR-RFLP, i.e., A. veronii biovar sobria, A. hydrophila, A. encheleia, A. ichtiosoma, A. salmonicida, and A. media. High levels of resistance to tetracycline (78.3%), amoxicillin (89.2%), and augmentin (86.5%) were observed. Decreased susceptibility to erythromycin was observed for 67.6% of isolates. Although 45.9% of isolates displayed nalidixic acid resistance, majority of isolates were susceptible to the fluoroquinolones. The MAR index ranged from 0.12 to 0.59, with majority of isolates indicating high-risk contamination originating from humans or animals where antibiotics are often used. Plasmids were detected in 21 isolates, with 14 of the isolates displaying multiple plasmid profiles. Single and multiple class A family Tet determinants were observed in 27% and 48.7% of isolates, respectively, with Tet A being the most prevalent Tet determinant type. Class 1 integron and related structures were amplified and carried different combinations of the antibiotic resistance gene cassettes ant(3'')Ia, aac(6')Ia, dhfr1, oxa2a and/or pse1. Class 2 integrons were also amplified, but the

  11. Isolation and determination of absolute configurations of insect-produced methyl-branched hydrocarbons

    PubMed Central

    Bello, Jan E.; McElfresh, J. Steven; Millar, Jocelyn G.

    2015-01-01

    Although the effects of stereochemistry have been studied extensively for volatile insect pheromones, little is known about the effects of chirality in the nonvolatile methyl-branched hydrocarbons (MBCHs) used by many insects as contact pheromones. MBCHs generally contain one or more chiral centers and so two or more stereoisomeric forms are possible for each structure. However, it is not known whether insects biosynthesize these molecules in high stereoisomeric purity, nor is it known whether insects can distinguish the different stereoisomeric forms of MBCHs. This knowledge gap is due in part to the lack of methods for isolating individual MBCHs from the complex cuticular hydrocarbon (CHC) blends of insects, as well as the difficulty in determining the absolute configurations of the isolated MBCHs. To address these deficiencies, we report a straightforward method for the isolation of individual cuticular hydrocarbons from the complex CHC blend. The method was used to isolate 36 pure MBCHs from 20 species in nine insect orders. The absolute stereochemistries of the purified MBCHs then were determined by digital polarimetry. The absolute configurations of all of the isolated MBCHs were determined to be (R) by comparison with a library of synthesized, enantiomerically pure standards, suggesting that the biosynthetic pathways used to construct MBCHs are highly conserved within the Insecta. The development of a straightforward method for isolation of specific CHCs will enable determination of their functional roles by providing pure compounds for bioassays. PMID:25583471

  12. Isolation and determination of absolute configurations of insect-produced methyl-branched hydrocarbons.

    PubMed

    Bello, Jan E; McElfresh, J Steven; Millar, Jocelyn G

    2015-01-27

    Although the effects of stereochemistry have been studied extensively for volatile insect pheromones, little is known about the effects of chirality in the nonvolatile methyl-branched hydrocarbons (MBCHs) used by many insects as contact pheromones. MBCHs generally contain one or more chiral centers and so two or more stereoisomeric forms are possible for each structure. However, it is not known whether insects biosynthesize these molecules in high stereoisomeric purity, nor is it known whether insects can distinguish the different stereoisomeric forms of MBCHs. This knowledge gap is due in part to the lack of methods for isolating individual MBCHs from the complex cuticular hydrocarbon (CHC) blends of insects, as well as the difficulty in determining the absolute configurations of the isolated MBCHs. To address these deficiencies, we report a straightforward method for the isolation of individual cuticular hydrocarbons from the complex CHC blend. The method was used to isolate 36 pure MBCHs from 20 species in nine insect orders. The absolute stereochemistries of the purified MBCHs then were determined by digital polarimetry. The absolute configurations of all of the isolated MBCHs were determined to be (R) by comparison with a library of synthesized, enantiomerically pure standards, suggesting that the biosynthetic pathways used to construct MBCHs are highly conserved within the Insecta. The development of a straightforward method for isolation of specific CHCs will enable determination of their functional roles by providing pure compounds for bioassays.

  13. Isolation and Structure Elucidation of Three New Dolastanes from the Brown Alga Dilophus spiralis

    PubMed Central

    Ioannou, Efstathia; Vagias, Constantinos; Roussis, Vassilios

    2013-01-01

    Three new dolastane diterpenes (1–3) and five previously reported perhydroazulenes were isolated from the organic extracts of the brown alga Dilophus spiralis. The structure elucidation and the assignment of the relative configurations of the isolated natural products were based on extensive analyses of their spectroscopic data, whereas the absolute configuration of metabolite 2 was determined through its chemical conversion to a previously isolated compound of known configuration. PMID:23549282

  14. Structure determination of a siderophore peucechelin from Streptomyces peucetius.

    PubMed

    Kodani, Shinya; Komaki, Hisayuki; Suzuki, Masahiro; Kobayakawa, Fumiya; Hemmi, Hikaru

    2015-10-01

    Previously, Park et al. isolated a new siderophore from Streptomyces peucetius ATCC 27952 based on information of the genome sequence and the structure of the siderophore was deduced to be a cyclic peptide based on MS/MS analysis. To clarify the structure of the siderophore, we cultured S. peucetius with iron deficient medium. Through several chromatographic procedures, the siderophore named peucechelin was isolated with the yield enough to perform NMR experiments. The planar structure of peucechelin was elucidated by the combination of ESI-MS experiment and NMR spectroscopic analyses of the gallium (III) complex. Unlike the previously deduced cyclic structure, the structure was determined to be a linear peptide which was similar to a known siderophore foroxymithine. The stereochemistries of amino acids constituting peucechelin were determined by applying modified Marfey method to the hydrolysate. Since the biosynthetic gene of peucechelin was formerly determined by Park et al. the similar genes were searched using genome data of other streptomycetes. As a result, the similar genes were found in the genome data of S. venezuelae and S. purpureus. Isolation and identification of siderophore was performed from the iron deficient culture of S. venezuelae. The siderophore of S. venezuelae was identified to be known compound foroxymithine by analysis ESI-MS and NMR spectra in the similar manner with peucechelin. Production of foroxymithine was also observed in the iron deficient culture of S. purpureus. Based on the genome data, comparison of the biosynthetic genes of structurally related siderophores peucechelin and foroxymithine was accomplished in discussion.

  15. Determinants of Glycosaminoglycan (GAG) Structure

    PubMed Central

    Prydz, Kristian

    2015-01-01

    Proteoglycans (PGs) are glycosylated proteins of biological importance at cell surfaces, in the extracellular matrix, and in the circulation. PGs are produced and modified by glycosaminoglycan (GAG) chains in the secretory pathway of animal cells. The most common GAG attachment site is a serine residue followed by a glycine (-ser-gly-), from which a linker tetrasaccharide extends and may continue as a heparan sulfate, a heparin, a chondroitin sulfate, or a dermatan sulfate GAG chain. Which type of GAG chain becomes attached to the linker tetrasaccharide is influenced by the structure of the protein core, modifications occurring to the linker tetrasaccharide itself, and the biochemical environment of the Golgi apparatus, where GAG polymerization and modification by sulfation and epimerization take place. The same cell type may produce different GAG chains that vary, depending on the extent of epimerization and sulfation. However, it is not known to what extent these differences are caused by compartmental segregation of protein cores en route through the secretory pathway or by differential recruitment of modifying enzymes during synthesis of different PGs. The topic of this review is how different aspects of protein structure, cellular biochemistry, and compartmentalization may influence GAG synthesis. PMID:26308067

  16. Vibration isolation via a scissor-like structured platform

    NASA Astrophysics Data System (ADS)

    Sun, Xiuting; Jing, Xingjian; Xu, Jian; Cheng, Li

    2014-04-01

    More and more attentions are attracted to the analysis and design of nonlinear vibration control/isolation systems for better isolation performance. In this study, an isolation platform with n-layer scissor-like truss structure is investigated to explore novel design of passive/semi-active/active vibration control/isolation systems and to exploit potential nonlinear benefits in vibration suppression. Due to the special scissor-like structure, the dynamic response of the platform has inherent nonlinearities both in equivalent damping and stiffness characteristics (although only linear components are applied), and demonstrates good loading capacity and excellent equilibrium stability. With the mathematical modeling and analysis of the equivalent stiffness and damping of the system, it is shown that: (a) the structural nonlinearity in the system is very helpful in vibration isolation, (b) both equivalent stiffness and damping characteristics are nonlinear and could be designed/adjusted to a desired nonlinearity by tuning structural parameters, and (c) superior vibration isolation performances (e.g., quasi-zero stiffness characteristics etc.) can be achieved with different structural parameters. This scissor-like truss structure can potentially be employed in different engineering practices for much better vibration isolation or control.

  17. Surface structure determines dynamic wetting

    PubMed Central

    Wang, Jiayu; Do-Quang, Minh; Cannon, James J.; Yue, Feng; Suzuki, Yuji; Amberg, Gustav; Shiomi, Junichiro

    2015-01-01

    Liquid wetting of a surface is omnipresent in nature and the advance of micro-fabrication and assembly techniques in recent years offers increasing ability to control this phenomenon. Here, we identify how surface roughness influences the initial dynamic spreading of a partially wetting droplet by studying the spreading on a solid substrate patterned with microstructures just a few micrometers in size. We reveal that the roughness influence can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. We further identify a criterion to predict if the spreading will be controlled by this surface roughness or by liquid inertia. Our results point to the possibility of selectively controlling the wetting behavior by engineering the surface structure. PMID:25683872

  18. Determination of motility forces on isolated chromosomes with laser tweezers

    PubMed Central

    Khatibzadeh, Nima; Stilgoe, Alexander B.; Bui, Ann A. M.; Rocha, Yesenia; Cruz, Gladys M.; Loke, Vince; Shi, Linda Z.; Nieminen, Timo A.; Rubinsztein-Dunlop, Halina; Berns, Michael W.

    2014-01-01

    Quantitative determination of the motility forces of chromosomes during cell division is fundamental to understanding a process that is universal among eukaryotic organisms. Using an optical tweezers system, isolated mammalian chromosomes were held in a 1064 nm laser trap. The minimum force required to move a single chromosome was determined to be ≈0.8–5 pN. The maximum transverse trapping efficiency of the isolated chromosomes was calculated as ≈0.01–0.02. These results confirm theoretical force calculations of ≈0.1–12 pN to move a chromosome on the mitotic or meiotic spindle. The verification of these results was carried out by calibration of the optical tweezers when trapping microspheres with a diameter of 4.5–15 µm in media with 1–7 cP viscosity. The results of the chromosome and microsphere trapping experiments agree with optical models developed to simulate trapping of cylindrical and spherical specimens. PMID:25359514

  19. Hybrid carrageenans: isolation, chemical structure, and gel properties.

    PubMed

    Hilliou, Loic

    2014-01-01

    Hybrid carrageenan is a special class of carrageenan with niche application in food industry. This polysaccharide is extracted from specific species of seaweeds belonging to the Gigartinales order. This chapter focuses on hybrid carrageenan showing the ability to form gels in water, which is known in the food industry as weak kappa or kappa-2 carrageenan. After introducing the general chemical structure defining hybrid carrageenan, the isolation of the polysaccharide will be discussed focusing on the interplay between seaweed species, extraction parameters, and the hybrid carrageenan chemistry. Then, the rheological experiments used to determine the small and large deformation behavior of gels will be detailed before reviewing the relationships between gel properties and hybrid carrageenan chemistry.

  20. Population structure of Citrus tristeza virus from field Argentinean isolates.

    PubMed

    Iglesias, Néstor G; Gago-Zachert, Selma P; Robledo, Germán; Costa, Norma; Plata, María Inés; Vera, Osmar; Grau, Oscar; Semorile, Liliana C

    2008-02-01

    We studied the genetic variability of three genomic regions (p23, p25 and p27 genes) from 11 field Citrus tristeza virus isolates from the two main citrus growing areas of Argentina, a country where the most efficient vector of the virus, Toxoptera citricida, is present for decades. The pathogenicity of the isolates was determinated by biological indexing, single-strand conformation polymorphism analysis showed that most isolates contained high intra-isolate variability. Divergent sequence variants were detected in some isolates, suggesting re-infections of the field plants. Phylogenetic analysis of the predominant sequence variants of each isolate revealed similar grouping of isolates for genes p25 and p27. The analysis of p23 showed two groups contained the severe isolates. Our results showed a high intra-isolate sequence variability suggesting that re-infections could contribute to the observed variability and that the host can play an important role in the selection of the sequence variants present in these isolates.

  1. Single crystal x-ray structural determination of natural products

    NASA Astrophysics Data System (ADS)

    Fun, Hoong-Kun; Boonnak, Nawong; Chantrapromma, Suchada

    2012-06-01

    Bioactive natural products have been extensively studied worldwide because natural products compounds with their great structural diversity have traditionally provided most of the drugs in use. Nevertheless the most important step in the drug discovery process is the structural characterization of isolated compounds with interesting biological activities. X-ray structure determination is a powerful technique for characterization because this technique is able to provide a lot of informations on stereochemistry and the detailed three-dimension structures made available can be corelated to activities of these structures. The advancement of X-ray crystallography makes the characterization procedure more precise, much easier and less time consumable. Moreover, this technique can directly and easily confirm whether these compounds are enantiomerically pure or racemate. In addition the absolute configuration of a natural products molecule can be easily determined by this technique. This work shall be based on the results from our natural products research. The absolute configuration of 6-Hydroxysalvinolone and Horminone, which were isolated from Premna obtusifolia will be presented. Three racemates, namely Panduratin A, Caged xanthone and Murrayazoline, which were isolated from the natural products sources will also be presented.

  2. Primary Isolation Strain Determines Both Phage Type and Receptors Recognised by Campylobacter jejuni Bacteriophages

    PubMed Central

    Sørensen, Martine C. Holst; Gencay, Yilmaz Emre; Birk, Tina; Baldvinsson, Signe Berg; Jäckel, Claudia; Hammerl, Jens A.; Vegge, Christina S.; Neve, Horst; Brøndsted, Lone

    2015-01-01

    In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated using NCTC12662 as the indicator strain, which may have biased the selection of phages. A large group of C. jejuni phages rely on the highly diverse capsular polysaccharide (CPS) for infection and recent work identified the O-methyl phosphoramidate modification (MeOPN) of CPS as a phage receptor. We therefore chose seven C. jejuni strains each expressing different CPS structures as indicator strains in a large screening for phages in samples collected from free-range poultry farms. Forty-three phages were isolated using C. jejuni NCTC12658, NCTC12662 and RM1221 as host strains and 20 distinct phages were identified based on host range analysis and genome restriction profiles. Most phages were isolated using C. jejuni strains NCTC12662 and RM1221 and interestingly phage genome size (140 kb vs. 190 kb), host range and morphological appearance correlated with the isolation strain. Thus, according to C. jejuni phage grouping, NCTC12662 and NCTC12658 selected for CP81-type phages, while RM1221 selected for CP220-type phages. Furthermore, using acapsular ∆kpsM mutants we demonstrated that phages isolated on NCTC12658 and NCTC12662 were dependent on the capsule for infection. In contrast, CP220-type phages isolated on RM1221 were unable to infect non-motile ∆motA mutants, hence requiring motility for successful infection. Hence, the primary phage isolation strain determines both phage type (CP81 or CP220) as well as receptors (CPS or flagella) recognised by the isolated phages. PMID:25585385

  3. Primary isolation strain determines both phage type and receptors recognised by Campylobacter jejuni bacteriophages.

    PubMed

    Sørensen, Martine C Holst; Gencay, Yilmaz Emre; Birk, Tina; Baldvinsson, Signe Berg; Jäckel, Claudia; Hammerl, Jens A; Vegge, Christina S; Neve, Horst; Brøndsted, Lone

    2015-01-01

    In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated using NCTC12662 as the indicator strain, which may have biased the selection of phages. A large group of C. jejuni phages rely on the highly diverse capsular polysaccharide (CPS) for infection and recent work identified the O-methyl phosphoramidate modification (MeOPN) of CPS as a phage receptor. We therefore chose seven C. jejuni strains each expressing different CPS structures as indicator strains in a large screening for phages in samples collected from free-range poultry farms. Forty-three phages were isolated using C. jejuni NCTC12658, NCTC12662 and RM1221 as host strains and 20 distinct phages were identified based on host range analysis and genome restriction profiles. Most phages were isolated using C. jejuni strains NCTC12662 and RM1221 and interestingly phage genome size (140 kb vs. 190 kb), host range and morphological appearance correlated with the isolation strain. Thus, according to C. jejuni phage grouping, NCTC12662 and NCTC12658 selected for CP81-type phages, while RM1221 selected for CP220-type phages. Furthermore, using acapsular ∆kpsM mutants we demonstrated that phages isolated on NCTC12658 and NCTC12662 were dependent on the capsule for infection. In contrast, CP220-type phages isolated on RM1221 were unable to infect non-motile ∆motA mutants, hence requiring motility for successful infection. Hence, the primary phage isolation strain determines both phage type (CP81 or CP220) as well as receptors (CPS or flagella) recognised by the isolated phages.

  4. Fluid Circulation Determined in the Isolated Bovine Lens

    PubMed Central

    Candia, Oscar A.; Mathias, Richard; Gerometta, Rosana

    2012-01-01

    Purpose. In 1997, a theoretical model was developed that predicted the existence of an internal, Na+-driven fluid circulation from the poles to the equator of the lens. In the present work, we demonstrate with a novel system that fluid movement can be measured across the polar and equatorial surface areas of isolated cow lenses. We have also determined the effects of ouabain and reduced bath [Na+]. Methods. Lenses were isolated in a chamber with three compartments separated by two thin O-rings. Each compartment, anterior (A), equatorial (E), and posterior (P), was connected to a vertical capillary graduated in 0.25 μL. Capillary levels were read every 15 minutes. The protocols consisted of 2 hours in either open circuit or short circuit. The effects of ouabain and low-Na+ solutions were determined under open circuit. Results. In 21 experiments, the E capillary increased at a mean rate of 0.060 μL/min while the A and P levels decreased at rates of 0.044 and 0.037 μL/min, respectively, closely accounting for the increase in E. The first-hour flows under short circuit were approximately 40% larger than those in open-circuit conditions. The first-hour flows were always larger than those during the second hour. Preincubation of lenses with either ouabain or low-[Na+] solutions resulted in reduced rates of fluid transport. When KCl was used to replace NaCl, a transitory stimulation of fluid transport occurred. Conclusions. These experiments support that a fluid circulation consistent with the 1997 model is physiologically active. PMID:22969071

  5. FINE STRUCTURE AND PIGMENT CONVERSION IN ISOLATED ETIOLATED PROPLASTIDS

    PubMed Central

    Klein, Shimon; Poljakoff-Mayber, A.

    1961-01-01

    Proplastids containing a prolamellar body were isolated from leaves of etiolated bean plants. The isolation methods do not necessarily lead to destruction of their submicroscopic structure and most of the isolated proplastids show well preserved outer membranes, lamellar strands, and the prolamellar body. Morphological intactness of the proplastids varies; certain leaf fractions contain single prolamellar bodies as well as proplastids. Since pellets after centrifugation between 350 g and 1000 to 3000 g contain intact proplastids and, as was shown by quantitative experiments, the same fractions show photoconversion of protochlorophyll to chlorophyll, it is supposed that the isolated particles probably retain many of the properties which are characteristic of them in situ. Isolated proplastids may thus be a valuable tool in investigations on the development of the photosynthetic apparatus. PMID:14456780

  6. Determination of carbapenem resistance mechanism in clinical isolates of Pseudomonas aeruginosa isolated from burn patients, in Tehran, Iran.

    PubMed

    Mirsalehian, Akbar; Kalantar-Neyestanaki, Davood; Taherikalani, Morovat; Jabalameli, Fereshteh; Emaneini, Mohammad

    2017-09-01

    Carbapenems are the most important therapeutic options that effect against serious infections caused by multidrug resistant Pseudomonas aeruginosa (MDR-PA) isolates. Carbapenems resistant isolates of P. aeruginosa are increasing worldwide. The aim of this study was to determine the carbapenem resistance mechanisms in clinical P. aeruginosa isolates from burn patients, in Tehran, Iran. A total of 53 non-duplicated isolates of carbapenem-resistant P. aeruginosa were collected from burn patients. The presence of carbapenemase genes were determined by PCR. AmpC overproducer isolates were detected by phenotypic method. The mutation and transcription level of oprD were determined by PCR-sequencing and quantitative Real-time PCR (RT-PCR), respectively. Twenty-seven (50.9%) isolates were positive for carbapenemase (blaVIM=25 and blaIMP=2) and showed high-level resistance to imipenem and meropenem. Twenty-eight isolates were AmpC overproducers. All isolates had a mutation in the oprD gene and down-regulation of oprD was found in 56.6% of MDR-PA isolates. Although the presence of carbapenemase is the common mechanism of resistant to carbapenem, but carbapenem resistance was found by oprD mutation-driven and the AmpC overproducing isolates in Tehran, Iran. Copyright © 2017 Ministry of Health, Saudi Arabia. Published by Elsevier Ltd. All rights reserved.

  7. Conceptual optimization of seismic isolated long span structures

    NASA Astrophysics Data System (ADS)

    Mojolic, Cristian; Petrina, Tudor

    2017-07-01

    This paper presents a conceptual optimization problem for seismic isolated structures with large span roofs. The research proposes that the isolation level should be placed at the top of the columns that support the roof structure. This solution was mainly adopted because of the architectural conception of the model. Three distinct passive isolation systems are proposed in order to reduce the seismic response of the structure. The first case implies the use of Friction Pendulum systems (FP) while the other ones use High Damping Rubber Bearing (HDRB) and Lead Rubber Bearing (LRB) in combination with low friction pot-bearing systems. Using seven sets of accelerograms, the values for the main seismic response parameters are extracted and the efficiency of the system is underlined.

  8. Direct atomic structure determination by the inspection of structural phase.

    PubMed

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  9. Direct atomic structure determination by the inspection of structural phase

    PubMed Central

    Nakashima, Philip N. H.; Moodie, Alexander F.; Etheridge, Joanne

    2013-01-01

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities. PMID:23940343

  10. Determinants of Long Bone Structural Properties

    NASA Technical Reports Server (NTRS)

    Cleek, T. M.; Katz, B.; Whalen, R. T.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The objective of our research is to determine whether a non-invasive determination of long bone cross-sectional areal properties using only the mineral component of bone accurately predicts the true structural properties. In this study section properties of a whole long bone were compared using two methods: (1) special analysis of bone densitometry data, and (2) experimental determination of flexural rigidities from bone surface strain measurements during controlled loading.

  11. Structural determinants of TRIM protein function.

    PubMed

    Esposito, Diego; Koliopoulos, Marios G; Rittinger, Katrin

    2017-02-08

    Tripartite motif (TRIM) proteins constitute one of the largest subfamilies of Really Interesting New Gene (RING) E3 ubiquitin ligases and contribute to the regulation of numerous cellular activities, including innate immune responses. The conserved TRIM harbours a RING domain that imparts E3 ligase activity to TRIM family proteins, whilst a variable C-terminal region can mediate recognition of substrate proteins. The knowledge of the structure of these multidomain proteins and the functional interplay between their constituent domains is paramount to understanding their cellular roles. To date, available structural information on TRIM proteins is still largely restricted to subdomains of many TRIMs in isolation. Nevertheless, applying a combination of structural, biophysical and biochemical approaches has recently allowed important progress to be made towards providing a better understanding of the molecular features that underlie the function of TRIM family proteins and has uncovered an unexpected diversity in the link between self-association and catalytic activity.

  12. Determination of the chemical structure of the capsular polysaccharide of strain B33, a fast-growing soya bean-nodulating bacterium isolated from an arid region of China.

    PubMed Central

    Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Ruiz-Sainz, J E; Buendía-Clavería, A M; Ollero, F J; Yang, S S; Gil-Serrano, A M

    2001-01-01

    We have determined the structure of a polysaccharide from strain B33, a fast-growing bacterium that forms nitrogen-fixing nodules with Asiatic and American soya bean cultivars. On the basis of monosaccharide analysis, methylation analysis, one-dimensional 1H- and 13C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a polymer having the repeating unit -->6)-4-O-methyl-alpha-D-Glcp-(1-->4)-3-O-methyl-beta-D-GlcpA-(1--> (where GlcpA is glucopyranuronic acid and Glcp is glucopyranose). Strain B33 produces a K-antigen polysaccharide repeating unit that does not have the structural motif sugar-Kdx [where Kdx is 3-deoxy-D-manno-2-octulosonic acid (Kdo) or a Kdo-related acid] proposed for different Sinorhizobium fredii strains, all of them being effective with Asiatic soya bean cultivars but unable to form nitrogen-fixing nodules with American soya bean cultivars. Instead, it resembles the K-antigen of S. fredii strain HH303 (rhamnose, galacturonic acid)n, which is also effective with both groups of soya bean cultivars. Only the capsular polysaccharide from strains B33 and HH303 have monosaccharide components that are also present in the surface polysaccharide of Bradyrhizobium elkanii strains, which consists of a 4-O-methyl-D-glucurono-L-rhamnan. PMID:11439101

  13. Seismic Response Analysis and Design of Structure with Base Isolation

    SciTech Connect

    Rosko, Peter

    2010-05-21

    The paper reports the study on seismic response and energy distribution of a multi-story civil structure. The nonlinear analysis used the 2003 Bam earthquake acceleration record as the excitation input to the structural model. The displacement response was analyzed in time domain and in frequency domain. The displacement and its derivatives result energy components. The energy distribution in each story provides useful information for the structural upgrade with help of added devices. The objective is the structural displacement response minimization. The application of the structural seismic response research is presented in base-isolation example.

  14. Active Narrow-Band Vibration Isolation of Large Engineering Structures

    NASA Technical Reports Server (NTRS)

    Rahman, Zahidul; Spanos, John

    1994-01-01

    We present a narrow-band tracking control method using a variant of the Least Mean Squares (LMS) algorithm to isolate slowly changing periodic disturbances from engineering structures. The advantage of the algorithm is that it has a simple architecture and is relatively easy to implement while it can isolate disturbances on the order of 40-50 dB over decades of frequency band. We also present the results of an experiment conducted on a flexible truss structure. The average disturbance rejection achieved is over 40 dB over the frequency band of 5 Hz to 50 Hz.

  15. Active Narrow-Band Vibration Isolation of Large Engineering Structures

    NASA Technical Reports Server (NTRS)

    Rahman, Zahidul; Spanos, John

    1994-01-01

    We present a narrow-band tracking control method using a variant of the Least Mean Squares (LMS) algorithm to isolate slowly changing periodic disturbances from engineering structures. The advantage of the algorithm is that it has a simple architecture and is relatively easy to implement while it can isolate disturbances on the order of 40-50 dB over decades of frequency band. We also present the results of an experiment conducted on a flexible truss structure. The average disturbance rejection achieved is over 40 dB over the frequency band of 5 Hz to 50 Hz.

  16. Protein structure determination from NMR chemical shifts.

    PubMed

    Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M; Vendruscolo, Michele

    2007-06-05

    NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

  17. Isolation and structural determination of C8-vinyl-bacteriochlorophyll d from the bciA and bchU double mutant of the green sulfur bacterium Chlorobaculum tepidum.

    PubMed

    Harada, Jiro; Mizoguchi, Tadashi; Nomura, Kota; Tamiaki, Hitoshi

    2014-07-01

    The mutant lacking enzymes BciA and BchU, that catalyzed reduction of the C8-vinyl group and methylation at the C20 position of bacteriochlorophyll (BChl) c, respectively, in the green sulfur bacterium Chlorobaculum tepidum, were constructed. This mutant accumulated C8-vinyl-BChl d derivatives, and a molecular structure of the major pigment was fully characterized by its NMR, mass, and circular dichroism spectra, as well as by chemical modification: (3(1) R)-8-vinyl-12-ethyl-(R[V,E])BChl d was confirmed as a new BChl d species in the cells. In vitro chlorosome-like self-aggregates of this pigment were prepared in an aqueous micellar solution, and formed more rapidly than those of (3(1) R)-8,12-diethyl-(R[E,E])BChl d isolated from the green sulfur bacterium Chlorobaculum parvum NCIB8327d synthesizing BChl d homologs. Their red-shifted Q y absorption bands were almost the same at 761 nm, and the value was larger than those of in vitro self-aggregates of R[E,E]BChl c (737 nm) and R[V,E]BChl c (726 nm), while the monomeric states of the former gave Q y bands at shorter wavelengths than those of the latter. Red shifts by self-aggregation of the two BChl d species were estimated to be 110 nm and much larger than those by BChls c (75 nm for [E,E] and 64 nm for [V,E]).

  18. Simple approach for ranking structure determining residues.

    PubMed

    Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology.

  19. Simple approach for ranking structure determining residues

    PubMed Central

    Luna-Martínez, Oscar D.; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I.; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N.

    2016-01-01

    Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. PMID:27366642

  20. Distribution of resistance genetic determinants among Vibrio cholerae isolates of 2012 and 2013 outbreaks in IR Iran.

    PubMed

    Rezaie, Niloofar; Bakhshi, Bita; Najar-Peerayeh, Shahin

    2017-03-01

    The objective of this study was to characterize antimicrobial resistance determinants in relation to antimicrobial susceptibility and genotyping profile in 20 clinical isolates of Vibrio cholerae. All of the isolates were resistant to streptomycin. The second most prevalent resistance was observed to trimethoprim (75%), co-trimoxazole (60%), tetracycline (50%), and minocycline (45%). About 50% of the isolates fulfilled the criteria of Multi Drug Resistance (MDR) phenotype. None of the isolates carried tet A, B, C, and, D determinants. This finding shows that tetracycline resistance determinants recognized so far, does not satisfactorily describe the 50% tetracycline resistance phenotype in this study, suggesting the possible contribution of other not yet characterized resistance mechanisms involved. Class 1 integron, widely distributed among enteric bacteria, was not detected among V. cholerae strains under study. Conversely, 100% of the isolates harbored SXT constin(int), among which 70% were positive for dfrA1, strA, and strB genes. The sul1gene was present in 60% of the isolates while none of them contained floR gene. All the isolates uniformly appeared to be identical in fingerprinting profiles expected from outbreak strains. In conclusion, SXT element with its mosaic structure was the exclusive antimicrobial resistance determinant of clonal V. cholerae isolates taken from outbreaks of 2012 and 2013 in Iran. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Isolation, Characterization, Crystal Structure Elucidation, and Anticancer Study of Dimethyl Cardamonin, Isolated from Syzygium campanulatum Korth

    PubMed Central

    Aisha, Abdalrahim F. A.; Al-Suede, Fouad Saleih Resq; Hamil, Mohammad Shahrul Ridzuan; Laghari, Madeeha; Abdul Majid, Amin Malik Shah

    2014-01-01

    Syzygium campanulatum Korth is an equatorial, evergreen, aboriginal shrub of Malaysia. Conventionally it has been used as a stomachic. However, in the currently conducted study dimethyl cardamonin or 2′,4′-dihydroxy-6′-methoxy-3′,5′-dimethylchalcone (DMC) was isolated from S. campanulatum Korth, leaf extract. The structural characterization of DMC was carried out by making use of various techniques including UV, IR, NMR spectral followed by LC-MS, and X-ray crystallographic techniques. For determining the purity of compound, highly effective techniques including TLC, HPLC, and melting point were used. The cytotoxicity of DMC and three different extracts of S. campanulatum was evaluated against human colon cancer cell line (HT-29) by three different assays. DMC and ethanolic extract revealed potent and dose-dependent cytotoxic activity on the cancer cell line with IC50 12.6 and 90.1 µg/mL, respectively. Quite astonishingly to our knowledge, this is the very first report on S. campanulatum as being a rich source (3.5%) of DMC, X-ray crystallography, and anticancer activity on human colon cancer cells. PMID:25530783

  2. Isolation, Characterization, Crystal Structure Elucidation, and Anticancer Study of Dimethyl Cardamonin, Isolated from Syzygium campanulatum Korth.

    PubMed

    Memon, Abdul Hakeem; Ismail, Zhari; Aisha, Abdalrahim F A; Al-Suede, Fouad Saleih Resq; Hamil, Mohammad Shahrul Ridzuan; Hashim, Suzana; Saeed, Mohammed Ali Ahmed; Laghari, Madeeha; Abdul Majid, Amin Malik Shah

    2014-01-01

    Syzygium campanulatum Korth is an equatorial, evergreen, aboriginal shrub of Malaysia. Conventionally it has been used as a stomachic. However, in the currently conducted study dimethyl cardamonin or 2',4'-dihydroxy-6'-methoxy-3',5'-dimethylchalcone (DMC) was isolated from S. campanulatum Korth, leaf extract. The structural characterization of DMC was carried out by making use of various techniques including UV, IR, NMR spectral followed by LC-MS, and X-ray crystallographic techniques. For determining the purity of compound, highly effective techniques including TLC, HPLC, and melting point were used. The cytotoxicity of DMC and three different extracts of S. campanulatum was evaluated against human colon cancer cell line (HT-29) by three different assays. DMC and ethanolic extract revealed potent and dose-dependent cytotoxic activity on the cancer cell line with IC50 12.6 and 90.1 µg/mL, respectively. Quite astonishingly to our knowledge, this is the very first report on S. campanulatum as being a rich source (3.5%) of DMC, X-ray crystallography, and anticancer activity on human colon cancer cells.

  3. Membrane Protein Structure Determination in Membrana

    PubMed Central

    DING, YI; YAO, YONG; MARASSI, FRANCESCA M.

    2014-01-01

    CONSPECTUS The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three

  4. Membrane protein structure determination in membrana.

    PubMed

    Ding, Yi; Yao, Yong; Marassi, Francesca M

    2013-09-17

    The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three-dimensional structure

  5. A structural determinant required for RNA editing

    PubMed Central

    Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng

    2011-01-01

    RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087

  6. Advances on surface structural determination by LEED.

    PubMed

    Soares, Edmar A; de Castilho, Caio M C; de Carvalho, Vagner E

    2011-08-03

    In the last 40 years, low energy electron diffraction (LEED) has proved to be the most reliable quantitative technique for surface structural determination. In this review, recent developments related to the theory that gives support to LEED structural determination are discussed under a critical analysis of the main theoretical approximation-the muffin-tin calculation. The search methodologies aimed at identifying the best matches between theoretical and experimental intensity versus voltage curves are also considered, with the most recent procedures being reviewed in detail.

  7. [Isolation and partial structural characteristics of major toxic components of Latrodectus pallidus venom].

    PubMed

    Charakha, A R; Shevchenko, L V; Molodkin, A K; Pluzhnikov, K A; Volkova, T M; Grishin, E V

    1997-03-01

    Toxic components of the Latrodectus pallidus spider venom were isolated and characterized. The venom was shown to contain a toxin specific for mammals and at least one insectospecific toxin. Partial amino acid sequences of both toxins were determined, and their high structural homology with previously studied alpha-latrotoxin and alpha-latroinsectotoxin from L. mactans tredecimguttatus was found.

  8. Isolation and structural elucidation of chemical constituents from the fruits of Morinda citrifolia Linn.

    PubMed

    Siddiqui, Bina S; Sattar, Fouzia A; Ahmad, Fayaz; Begum, Sabira

    2007-08-01

    The fruits of Morinda citrifolia, Linn. afforded a new constituent, morinaphthalenone (1), and three known constituents, scopoletin (2), 1, 3-dimethoxy-anthraquinone (3) and 1, 2-dihydroxy-anthraquinone (4). The structures of these isolated compounds were determined by spectroscopic methods, including 1D- and 2D-NMR (COSY-45, HMQC, HMBC) techniques, as well as by comparison with published values.

  9. Melanostatin, a new melanin synthesis inhibitor. Production, isolation, chemical properties, structure and biological activity.

    PubMed

    Ishihara, Y; Oka, M; Tsunakawa, M; Tomita, K; Hatori, M; Yamamoto, H; Kamei, H; Miyaki, T; Konishi, M; Oki, T

    1991-01-01

    Melanostatin, a new antibiotic with melanin synthesis inhibitor activity, was isolated from the fermentation broth of Streptomyces clavifer No. N924-2. Its structure was determined by spectral analysis and degradation experiments. Melanostatin strongly inhibited melanin formation in Streptomyces bikiniensis NRRL B-1049 and B16 melanoma cells.

  10. Photoprotein Aequorin Structure Determination by NMR Spectroscopy

    DTIC Science & Technology

    1993-07-09

    AD-A267 066 July 9, 1993 Final Rept. 15 Apr. 1992-31 Dec. 1992 Photoprotein Aequorin Structure Determination by NMR Spectroscopy Grant # N00014-92-J...specific assignments of proteins using homo- and heteronuclear 2D-NMR. Assignments were made for approximately 95% of the 1H and 15N atoms of Bacillus... structure of r-aequorin is included. 028 93-1584993 7 . -,I m!,,•slil Aequorin, bioluminescence, nuclear magnetic reburndie, 3D structure . Unclassified

  11. Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples

    PubMed Central

    Morcatti Coura, Fernanda; Diniz, Soraia de Araújo; Silva, Marcos Xavier; Mussi, Jamili Maria Suhet; Barbosa, Silvia Minharro; Lage, Andrey Pereira; Heinemann, Marcos Bryan

    2015-01-01

    This study analyzes the occurrence and distribution of phylogenetic groups of 391 strains of Escherichia coli isolated from poultry, cattle, and water buffalo. The frequency of the phylogroups was A = 19%, B1 = 57%, B2 = 2.3%, C = 4.6%, D = 2.8%, E = 11%, and F = 3.3%. Phylogroups A (P < 0.001) and F (P = 0.018) were associated with E. coli strains isolated from poultry, phylogroups B1 (P < 0.001) and E (P = 0.002) were associated with E. coli isolated from cattle, and phylogroups B2 (P = 0.003) and D (P = 0.017) were associated with E. coli isolated from water buffalo. This report demonstrated that some phylogroups are associated with the host analyzed and the results provide knowledge of the phylogenetic composition of E. coli from domestic animals. PMID:26421310

  12. Detection of piluslike structures on clinical and environmental isolates of Vibrio vulnificus.

    PubMed Central

    Gander, R M; LaRocco, M T

    1989-01-01

    Twenty clinical isolates of Vibrio vulnificus were compared with 10 environmental strains by using electron microscopy and agglutination assays with human erythrocytes, guinea pig erythrocytes, and Saccharomyces cerevisiae. In addition, the isolates were tested for ability to adhere to the human epithelial cell lines HEp-2 and A549. When examined by electron microscopy, 16 (80%) of the 20 clinical isolates demonstrated the presence of piluslike structures; the composition of the bacterial populations ranged from 0 to 68% piliated cells. In contrast, only 3 (30%) of the 10 environmental isolates were piliated, with a range from 0 to 16% piliated cells. A significant association between the presence of piliated cells and the isolate source was found (P less than 0.05). None of the 30 strains agglutinated erythrocytes or yeast cells. V. vulnificus adherence results obtained with HEp-2 cells showed 10 (50%) of 20 clinical isolates and 0 (0%) of 10 environmental isolates with averages of greater than 10 adherent bacteria per cell, demonstrating a correlation between attachment and the isolate source (P less than 0.05). Selected strains were tested to determine whether methyl alpha-D-mannopyranoside, fructose, or alpha-L-(-)-fucose would inhibit bacterial adherence to HEp-2 cells. Multiple patterns of adherence inhibition were observed. Adherence to A549 cells showed 8 (40%) of 20 clinical isolates and 0 (0%) of 10 environmental strains with averages of greater than 10 adherent bacteria per cell. A statistical association between attachment and the isolate source was demonstrated (P less than 0.05). These data suggest that the presence of piluslike structures and the ability to adhere to human epithelial cell lines may be more closely associated with V. vulnificus isolates from clinical specimens than with environmental strains. Images PMID:2568368

  13. NMR-based identification of the phenolic profile of fruits of Lycium barbarum (goji berries). Isolation and structural determination of a novel N-feruloyl tyramine dimer as the most abundant antioxidant polyphenol of goji berries.

    PubMed

    Forino, Martino; Tartaglione, Luciana; Dell'Aversano, Carmela; Ciminiello, Patrizia

    2016-03-01

    Biological properties of fruits of Lycium barbarum (goji berries) have been ascribed to their high content of nutrients and phenolics. Comprehensive studies aimed at unambiguously identifying the phenolic components in goji berries are still lacking. In this paper, we report on the isolation and NMR-based identification of the major phenolics in commercially available goji berries. Together with already known phenolics, including caffeic acid, p-coumaric acid, rutin, scopoletin, N-trans-feruloyl tyramine, and N-cis-feruloyl tyramine, an unreported N-feruloyl tyramine dimer was characterized as the most abundant polyphenol isolated from the berries. Usually divalent molecules show enhanced biological activities than their corresponding monomers.

  14. Structural investigation of the lipopolysaccharide O-chain isolated from Burkholderia fungorum strain DSM 17061.

    PubMed

    De Felice, Antonia; Di Lorenzo, Flaviana; Scherlach, Kirstin; Ross, Claudia; Silipo, Alba; Hertweck, Christian; Molinaro, Antonio

    2016-10-04

    Gram-negative bacteria exhibit lipopolysaccharides (LPSs) on their outer membrane surface. LPS is considered one of the most potent bacterial virulence factors. Here we report the elucidation of the LPS O-chain structure isolated from Burkholderia fungorum, a bacterium isolated from the white-rot fungus Phanerochaete chrysosporium that can act as a pathogen for plants and domesticated animals. The structure was determined by the employment of detailed chemical and NMR spectroscopy analyses as the following. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Representing Personal Determinants in Causal Structures.

    ERIC Educational Resources Information Center

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  16. Method of fan sound mode structure determination

    NASA Technical Reports Server (NTRS)

    Pickett, G. F.; Sofrin, T. G.; Wells, R. W.

    1977-01-01

    A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.

  17. Crystal structure of meteoritic schreibersites: determination of absolute structure

    NASA Astrophysics Data System (ADS)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  18. Structure determination of molecules of biochemical interest

    NASA Astrophysics Data System (ADS)

    Honzatko, R. B.

    1985-10-01

    In the past year we have established a new laboratory for the determination of macromolecular structure. Currently, facilities are in place for data collection, data processing, molecular modeling and X-ray refinement of structures of up to 100,000 molecular weight in their crystallographic asymmetric unit. In parallel with establishing a new laboratory, we have pursued structure investigations of hemoglobin from the sea lamprey, aspartate carbamoyltransferase from Escherichia coli and p-nitrobenzylidine aminoguanidine, a small molecule which is an acceptor of the adenosine diphosphate ribosyl group in an enzyme mediated reaction. In addition to the structural studies above we have made a theoretical study by techniques of energy minimization of possible modes of aggregation of lamprey hemoglobin and the relationship between aggregate formation and cooperativity expressed in solutions by lamprey hemoglobin.

  19. Structured residual technique for malfunction isolation in interacting systems

    SciTech Connect

    Hardy, C.R.; Miller, D.W.; Hajek, B.K. )

    1992-01-01

    Researchers in the field of fault detection and isolation have presented schemes for diagnosing faults in systems in the presence of unknown input disturbances. These techniques, known collectively as input disturbance decoupling, can be used to isolate a particular system from other systems in a complex process plant. The ability to isolate the operation of a system from systems with which it interacts is desirable when diagnosing faults in complex plants. The diagnosis problem can then be broken down into a set of relatively simple diagnostic tasks and the results evaluated using a knowledge-based approach. One such approach, known as hierarchical classification, has been used for malfunction diagnosis in both nuclear power and chemical plants. Systems that strongly interact are common in nuclear power plants. For example, in the simplified boiling water reactor (BWR) pressure control system (PCS) model of Fig. 1, steam flow from the main steam lines collects in the steam header. The header acts as a source of steam to several plant systems besides the high-pressure turbine. Thus, a change in any one of these auxiliary systems will affect the operation of the PCS. These unmeasured influences complicate the problem of isolating the PCS from the remainder of the plant. The authors have used structured residuals as a disturbance decoupling technique to isolate interacting systems in a BWR model. In this paper, we provide a brief summary of the method and show an example of its application.

  20. Isolation and structural characterization of two new metabolites from monascus.

    PubMed

    Loret, Marie-Odile; Morel, Sandrine

    2010-02-10

    Two new pale yellow metabolites have been isolated from commercially available Chinese food additive Red Monascus Pigment and from Monascus ruber culture broth. They were isolated by successive TLC and semipreparative HPLC. Their structural characterization was elucidated by a variety of spectroscopic techniques (UV, IR, NMR) and mass spectrometry. These two new metabolites present numerous similarities with monascorubrin and rubropunctatin, differing in their structure only by the absence of the lactone ring. High-resolution mass spectrometry indicated the molecular formulas C(20)H(26)O(4) and C(22)H(30)O(4). The new compounds, named monarubrin and rubropunctin, contain a propenyl group on a pyrone ring, an alkyl side chain, but no gamma-lactone ring. The new metabolites have the property of producing strong blue fluorescence at 340 nm.

  1. Isolated structures in two-dimensional optical superlattice

    NASA Astrophysics Data System (ADS)

    Zou, Xin-Hao; Yang, Bao-Guo; Xu, Xia; Tang, Peng-Ju; Zhou, Xiao-Ji

    2017-10-01

    Overlaying commensurate optical lattices with various configurations called superlattices can lead to exotic lattice topologies and, in turn, a discovery of novel physics. In this study, by overlapping the maxima of lattices, a new isolated structure is created, while the interference of minima can generate various "sublattice" patterns. Three different kinds of primitive lattices are used to demonstrate isolated square, triangular, and hexagonal "sublattice" structures in a two-dimensional optical superlattice, the patterns of which can be manipulated dynamically by tuning the polarization, frequency, and intensity of laser beams. In addition, we propose the method of altering the relative phase to adjust the tunneling amplitudes in "sublattices". Our configurations provide unique opportunities to study particle entanglement in "lattices" formed by intersecting wells and to implement special quantum logic gates in exotic lattice geometries.

  2. Oligossacharide structure determination on an ion trap

    SciTech Connect

    Asam, M.R.; Glish, G.L.

    1995-12-31

    Oligosaccharides are important elements in intra- and inter-cellular/molecular recognition mechanisms. Linkage types are part of the information that determine the tertiary structure of oligosaccharides and the tertiary structure is what determines specific recognition, so easily obtained linkage sequences will provide valuable information for computer and other modeling of cellular signaling interactions. Hofmeister et al. have shown that lithium cationized oligosaccharides have specific MS/MS dissociation patterns indicative of the carbohydrate linkage under low energy CID conditions in a hybrid mass spectrometer. The authors have used electrospray ionization on a quadrupole ion trap mass spectrometer to examine MS/MS disaccharide dissociation patterns under ion trap conditions. These studies have concentrated on disaccharides complexed with lithium and sodium.

  3. Requirements for structure determination of aperiodic crystals

    SciTech Connect

    Li, X.; Stern, E.A.; Ma, Y. )

    1991-01-15

    Using computer simulation, we compared the Patterson functions of one-dimensional (1D) randomly packed and quasiperiodic Fibonacci lattices with or without disorder, and a 2D Penrose lattice and random packing of pentagons (icosahedral glass model). Based on these comparisons, we derived some empirical guidelines for distinguishing ideal quasicrystals from aperiodic crystals with disorder using diffraction data. In contrast to periodic crystals, it is essential to include the background to obtain correct Patterson functions of the average structure since the background contains unresolved peaks. In particular, a Bragg peak scattering measurement {ital cannot}, in general, determine the structure of aperiodic crystals. Instead, a diffuse scattering measurement is required, which determines the absolute value of the diffraction background, in addition to the Bragg peaks. We further estimate that, dependent upon the disorder present, it is necessary to include up to 75% of the total diffracted intensity in any analysis.

  4. Distributed structure determination at the JCSG

    PubMed Central

    van den Bedem, Henry; Wolf, Guenter; Xu, Qingping; Deacon, Ashley M.

    2011-01-01

    The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG’s nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in structure refinement. ConsensusModeler exploits complementarities in traces from Xsolve to compute a single optimal model for manual refinement. Xpleo is a powerful robotics-inspired algorithm to build missing fragments and qFit automatically identifies and fits alternate conformations. PMID:21460455

  5. Chemical Structure of Lipid A Isolated from Flavobacterium meningosepticum Lipopolysaccharide

    PubMed Central

    Kato, Hitomi; Haishima, Yuji; Iida, Takatoshi; Tanaka, Akira; Tanamoto, Ken-ichi

    1998-01-01

    The chemical structure of the lipid A of the lipopolysaccharide component isolated from Flavobacterium meningosepticum IFO 12535 was elucidated. Methylation and nuclear magnetic resonance analyses showed that two kinds of hydrophilic backbone exist in the free lipid A: a β (1→6)-linked 2-amino-2-deoxy-d-glucose, which is usually present in enterobacterial lipid A’s, and a 2-amino-6-O-(2,3-diamino-2,3-dideoxy-β-d-glucopyranosyl)-2-deoxy-d-glucose, in a molar ratio of 1.00:0.35. Both backbones were α-glycosidically phosphorylated in position 1, and the hydroxyl groups at positions 4, 4′, and 6′ were unsubstituted. Liquid secondary ion-mass spectrometry revealed a pseudomolecular ion at m/z 1673 [M-H]− as a major monophosphoryl lipid A component carrying five acyl groups. Fatty acid analysis showed that the lipid A contained 1 mol each of amide-linked (R)-3-OH iC17:0, ester-linked (R)-3-OH iC15:0, amide-linked (R)-3-O-(iC15:0)-iC17:0, and both amide- and ester-linked (R)-3-OH C16:0. Fatty acid distribution analyses using several mass spectrometry determinations demonstrated that the former two constituents were distributed on positions 2 and 3 of the reducing terminal unit of the backbones and that the latter two were attached to the 2′ and 3′ positions in the nonreducing terminal residue. PMID:9683486

  6. Structural determinants of sigma receptor affinity

    SciTech Connect

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

  7. Syntheses and Structure Determinations of Calcium Thiolates.

    PubMed

    Chadwick, Scott; Englich, Ulrich; Noll, Bruce; Ruhlandt-Senge, Karin

    1998-09-07

    The exploration of synthetic methodologies toward heavy alkaline-earth chalcogenolates resulted in the preparation and structural characterization of a family of calcium thiolates, including [Ca(SC(6)F(5))(2)(py)(4)], 1 (py = pyridine), the separated ion-triple [Ca(18-crown-6)(NH(3))(3))][SMes](2).2THF, 2 (Mes = 2,4,6-tBu(3)C(6)H(2)), and the contact triple [Ca(18-crown-6)(SMes)(2)].THF, 3. Compound 1 was prepared by treating [Ca(N(SiMe(3))(2))(2)](2) with 4 equiv of HSC(6)F(5) under addition of pyridine. The thiolates 2 and 3 were synthesized by treatment of calcium metal dissolved in dry, liquid NH(3) under addition of 2 equiv of HSMes and crown ether or, alternatively, by the reduction of MesSSMes with calcium metal in dry, liquid ammonia. We also report two reaction products isolated during attempted calcium thiolate syntheses: [CaBr(4)(THF)(2)(&mgr;(2)-Li)(2)(THF)(4)], 4, isolated as the product of a salt elimination reaction between CaBr(2) and 2 equiv of [Li(THF)(n)()S-2,4,6-(i)()Pr(3)C(6)H(2)](m)(). [(NH(4))(py)(SC(6)F(5))], 5, was obtained as the sole product in the reaction of metallic calcium with HSC(6)F(5) in liquid ammonia under addition of pyridine. All compounds were characterized by single-crystal X-ray crystallography in addition to IR and NMR spectroscopy.

  8. Vibration isolation by exploring bio-inspired structural nonlinearity.

    PubMed

    Wu, Zhijing; Jing, Xingjian; Bian, Jing; Li, Fengming; Allen, Robert

    2015-10-08

    Inspired by the limb structures of animals/insects in motion vibration control, a bio-inspired limb-like structure (LLS) is systematically studied for understanding and exploring its advantageous nonlinear function in passive vibration isolation. The bio-inspired system consists of asymmetric articulations (of different rod lengths) with inside vertical and horizontal springs (as animal muscle) of different linear stiffness. Mathematical modeling and analysis of the proposed LLS reveal that, (a) the system has very beneficial nonlinear stiffness which can provide flexible quasi-zero, zero and/or negative stiffness, and these nonlinear stiffness properties are adjustable or designable with structure parameters; (b) the asymmetric rod-length ratio and spring-stiffness ratio present very beneficial factors for tuning system equivalent stiffness; (c) the system loading capacity is also adjustable with the structure parameters which presents another flexible benefit in application. Experiments and comparisons with existing quasi-zero-stiffness isolators validate the advantageous features above, and some discussions are also given about how to select structural parameters for practical applications. The results would provide an innovative bio-inspired solution to passive vibration control in various engineering practice.

  9. Isolated magnetic field structures in Mercury's magnetosheath as possible analogues for terrestrial magnetosheath plasmoids and jets

    NASA Astrophysics Data System (ADS)

    Karlsson, Tomas; Liljeblad, Elisabet; Kullen, Anita; Raines, Jim M.; Slavin, James A.; Sundberg, Torbjörn

    2016-09-01

    We have investigated MESSENGER magnetic field data from the Mercury magnetosheath and near solar wind, to identify isolated magnetic field structures (defined as clear, isolated changes in the field magnitude). Their properties are studied in order to determine if they may be considered as analogues to plasmoids and jets known to exist in Earth's magnetosheath. Both isolated decreases of the magnetic field absolute value ('negative magnetic field structures') and increases ('positive structures') are found in the magnetosheath, whereas only negative structures are found in the solar wind. The similar properties of the solar wind and magnetosheath negative magnetic field structures suggests that they are analogous to diamagnetic plasmoids found in Earth's magnetosheath and near solar wind. The latter have earlier been identified with solar wind magnetic holes. Positive magnetic field structures are only found in the magnetosheath, concentrated to a region relatively close to the magnetopause. Their proximity to the magnetopause, their scale sizes, and the association of a majority of the structures with bipolar magnetic field signatures identify them as flux transfer events (which generally are associated with a decrease of plasma density in the magnetosheath). The positive magnetic field structures are therefore not likely to be analogous to terrestrial paramagnetic plasmoids but possibly to a sub-population of magnetosheath jets. At Earth, a majority of magnetosheath jets are associated with the quasi-parallel bow shock. We discuss some consequences of the findings of the present investigation pertaining to the different nature of the quasi-parallel bow shock at Mercury and Earth.

  10. High Resolution Powder Diffraction and Structure Determination

    SciTech Connect

    Cox, D. E.

    1999-04-23

    It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 {micro}m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis

  11. [Genomic diversity and population structure of Helicobacter pylori isolates in China].

    PubMed

    You, Y H; He, L H; Peng, X H; Sun, L; Zhang, J Z

    2016-10-10

    Objective: To learn about the overall genomic characteristics and population structure of Helicobacter pylori isolated in China. Methods: In this study, we used 10 public available genome sequences of H. pylori strains isolated in China, combined with other H. pylori sequences from GenBank, to analyzed the overall genomic characteristics of H. pylori isolated in China. Core genes and strain specific genes were determined for a further function definition. Results: A total of 1 203 core genes were found among all sequenced China H. pylori isolates. The number of strain specific genes ranged from 19 to 32. These genes mainly encodes hypothetical proteins which might play an important role in adaption to different hosts. Genomic variation regions were mainly in genes encoding type four secretion systems and restriction modification systems. All the China isolates belong to hpEastAsia group, hspEAsia subgroup. Prophages sequences were found in three China H. pylori strains, carrying key elements required for phage assembly. Conclusion: China H. pylori isolates belong to hpEastAsia group, hspEAsia subgroup, and some isolates contain prophages.

  12. Harnessing the Unique Structural Properties of Isolated α-Helices*

    PubMed Central

    Swanson, Carter J.; Sivaramakrishnan, Sivaraj

    2014-01-01

    The α-helix is a ubiquitous secondary structural element that is almost exclusively observed in proteins when stabilized by tertiary or quaternary interactions. However, beginning with the unexpected observations of α-helix formation in the isolated C-peptide in ribonuclease A, there is growing evidence that a significant percentage (0.2%) of all proteins contain isolated stable single α-helical domains (SAH). These SAH domains provide unique structural features essential for normal protein function. A subset of SAH domains contain a characteristic ER/K motif, composed of a repeating sequence of ∼4 consecutive glutamic acids followed by ∼4 consecutive basic arginine or lysine (R/K) residues. The ER/K α-helix, also termed the ER/K linker, has been extensively characterized in the context of the myosin family of molecular motors and is emerging as a versatile structural element for protein and cellular engineering applications. Here, we review the structure and function of SAH domains, as well as the tools to identify them in natural proteins. We conclude with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties, as well as synthetic polypeptides that can be used to monitor and systematically modulate protein interactions within cells. PMID:25059657

  13. ISOLATION AND STRUCTURAL STUDIES ON SYNAPTIC COMPLEXES FROM RAT BRAIN

    PubMed Central

    Cotman, Carl W.; Taylor, Dwan

    1972-01-01

    A fraction enriched in synaptic complexes has been isolated from rat brain. The major structural elements of synaptic complexes after isolation are a sector of pre- and postsynaptic plasma membranes joined together by a synaptic cleft and a postsynaptic density (PSD) located on the inner surface of the postsynaptic membrane. On its outer surface, the postsynaptic membrane has a series of projections which extend about halfway into the cleft and which occur along the entire length of the PSD. Proteolytic enzymes at high concentrations remove the PSD and open the synaptic cleft; at low concentrations the PSD is selectively destroyed. By contrast, the structural integrity of the PSD is resistant to treatment with NaCl, EGTA, and low concentrations of urea. Pre- and postsynaptic membranes also remain joined by the synaptic cleft after NaCl, EGTA, or mild urea treatment. High concentrations of urea cause the partial dissociation of the PSD. We conclude that polypeptides are probably one of the major components of the PSD and that the structural integrity of the PSD depends on polypeptides because disruption of the covalent or hydrophobic bonding of these polypeptides leads to a progressive loss of PSD structure. PMID:4656707

  14. Determination of antimicrobial susceptibilities on infected urines without isolation

    NASA Technical Reports Server (NTRS)

    Picciolo, G. L.; Chappelle, E. W.; Deming, J. W.; Shrock, C. G.; Vellend, H.; Barza, M. J.; Weinstein, L. (Inventor)

    1979-01-01

    A method is described for the quick determination of the susceptibilities of various unidentified bacteria contained in an aqueous physiological fluid sample, particularly urine, to one or more antibiotics. A bacterial adenosine triphosphate (ATP) assay is carried out after the elimination of non-bacterial ATP to determine whether an infection exists. If an infection does exist, a portion of the sample is further processed, including subjecting parts of the portion to one or more antibiotics. Growth of the bacteria in the parts are determined, again by an ATP assay, to determine whether the unidentified bacteria in the sample are susceptible to the antibiotic or antibiotics under test.

  15. Structure Determination of Novel Polydiacetylene Materials.

    NASA Astrophysics Data System (ADS)

    Thakur, Mrinal Kanti

    The major objective of this work has been to synthesize and characterize some novel diacetylene polymers. Monomers of the general type HC(TBOND)C-(CH(,2))(,n)-C(TBOND)CH were oxidatively coupled (Glaser coupling) to synthesize polymers of the form ( (CH(,2))(,n)-C(TBOND)C-C(TBOND)C )(,x). These polymers (n = 5, 6, 8), termed macromonomers, were subsequently exposed to CO('60)-(gamma) radiation to effect the diacetylene polymerization. The resulting materials, called crosspolymerized macromonomers, were composed of regular two-dimensional networks of polydiacetylene and hydrocarbon chains. Crystal structures of macromonomers before and after crosspolymerization were determined essentially by electron diffraction analysis, with supporting information from x-ray fiber diffraction. A detailed investigation of the crosspolymerization reaction was made by C-13 NMR in solid state. A very special type of diacetylene monomer was synthesized by dimerizing 1,11-dodecadiyne through a controlled oxidative coupling. Preliminary characterization of these dimers was accomplished by using GPC, DSC and electron diffraction. Macroscopic single crystals of polymerized dimer were obtained by radiation ((gamma)-radiation) induced polymerization and simultaneous crystallization from solution. X -ray diffraction analysis was employed for the crystal structure determination of this material. The structure was found to be composed of sheets of alternating polydiacetylene and polyacetylene chains. The nearest neighbor distance between a polydiacetylene and a polyacetylene chain was approximately 4(ANGSTROM). The electrical conductivity of this undoped material was measured and found to be reasonably high ((TURN)10('-2) (OMEGA)('-1)cm('-1)). A (pi)-electron band structure calculation indicated that such high conductivity resulted because of significant interchain interaction within the unit cell. A detailed investigation of the consequences of anharmonic interaction on diffraction intensities

  16. RNA Structure Determination Using SAXS Data

    PubMed Central

    Yang, Sichun; Parisien, Marc; Major, François; Roux, Benoît

    2011-01-01

    Exploiting the experimental information from small-angle x-ray solution scattering (SAXS) in conjunction with structure prediction algorithms can be advantageous in the case of ribonucleic acids (RNA), where global restraints on the 3D fold are often lacking. Traditional usage of SAXS data often starts by attempting to reconstruct the molecular shape ab initio, which is subsequently used to assess the quality of model Here, an alternative strategy is explored whereby the models from a very large decoy set are directly sorted according to their fit to the SAXS data is developed. For rapid computation of SAXS patterns, the method developed here makes use of a coarse-grained representation of RNA. It also accounts for the explicit treatment of the contribution to the scattering of water molecules and ions surrounding the RNA. The method, called Fast-SAXS-RNA, is first calibrated using a transfer RNA (tRNA-val) and then tested on the P4-P6 fragment of group I intron (P4-P6). Fast-SAXS-RNA is then used as a filter for decoy models generated by the MC-Fold and MC-Sym pipeline, a suite of RNA 3D all-atoms structure algorithms that encode and exploit RNA 3D architectural principles. The ability of Fast-SAXS-RNA to discriminate native folds is tested against three widely used RNA molecules in molecular modeling benchmarks: the tRNA, the P4-P6, and a synthetic hairpin suspected to assemble into a homodimer. For each molecule, a large pool of decoys are generated, scored, and ranked using Fast-SAXS-RNA. The method is able to identify low-RMSD models among top ranking structures, for both tRNA and P4-P6. For the hairpin, the approach correctly identifies the dimeric state as the solution structure over the monomeric state and alternative secondary structures. The method offers a powerful strategy for recognizing native RNA conformations as well as multimeric assemblies and alternative secondary structures, thus enabling high-throughput RNA structure determination using SAXS

  17. Drug effects on functional structures in isolated perfused pig heart

    NASA Astrophysics Data System (ADS)

    Trinks, Tobias; Rauh, Robert; Hiller, Michael; Kessler, Manfred D.

    2002-06-01

    Until today monitoring of immediate drug tissue interaction in living organs is an unsolved problem. However, for the development of new drugs and the improvement of medical therapy outcome it would be helpful to get new tools to visualize drug effects on tissue directly. With the EMPHO II SSK and a 3D-scanning device we detected changes of functional structures in an isolated perfused pig heart model after adding commonly used drugs like verapamil, nitroglycerin and salviae miltiorrhizae (Chinese herbal drug). In the paper the results are presented.

  18. Isolation and structural elucidation of cyclic tetrapeptides from Onychocola sclerotica.

    PubMed

    Pérez-Victoria, Ignacio; Martín, Jesús; González-Menéndez, Víctor; de Pedro, Nuria; El Aouad, Noureddine; Ortiz-López, Francisco Javier; Tormo, José Rubén; Platas, Gonzalo; Vicente, Francisca; Bills, Gerald F; Genilloud, Olga; Goetz, Michael A; Reyes, Fernando

    2012-06-22

    Three new cyclic tetrapeptides (1-3) have been isolated from the crude fermentation extract of Onychocola sclerotica. The planar structures of 1-3 were elucidated by detailed spectroscopic analyses using one- and two-dimensional NMR experiments and high-resolution mass spectrometry. The absolute configuration of the amino acid residues in each cyclotetrapeptide was established by Marfey's method. Compounds 1-3 displayed activity as cardiac calcium channel blockers (Cav1.2) but did not inhibit the hERG potassium channel and were not cytotoxic. These peptides are the first secondary metabolites ever reported from fungi of the order Arachnomycetales.

  19. Cost of isolation: daily cost of isolation determined and cost avoidance demonstrated from the overuse of personal protective equipment in an acute care facility.

    PubMed

    Verlee, Kerrie; Berriel-Cass, Dorine; Buck, Kristen; Nguyen, Chau

    2014-04-01

    We determined the prevalence and associated cost of isolation precautions. Current census and historic microbiology cultures were assessed for isolation appropriateness following national guidelines. Based on patient assessment and culture data, isolation was discontinued resulting in 4,087 days of isolation and over $141,000 dollars avoided from excess supplies and time.

  20. Structure elucidation and antioxidant activity of (-)-isosilandrin isolated from Silybum marianum L.

    PubMed

    Samu, Zsuzsanna; Nyiredy, Szabolcs; Baitz-Gács, Eszter; Varga, Zsuzsa; Kurtán, Tibor; Dinya, Zoltán; Antus, Sándor

    2004-11-01

    A regioisomer of the known flavanolignan (-)-silandrin (3a), named (-)-isosilandrin (8a), was isolated from the fruits of a white-flowered variant of Silybum marianum L. populated in Hungary. Its structure was established both by spectroscopic methods and total synthesis, and its absolute configuration was determined by means of circular dichroism. This compound showed stronger inhibitory activity on the superoxide anion (O2*-) release by human polymorphonuclear leukocytes (PMNL) than (+)-silybin (1a,b).

  1. [Isolation, biological properties, and spatial structure of an antibiotic loloatin A].

    PubMed

    Krachkovskiĭ, S A; Sobol', A G; Ovchinnikova, T V; Tagaev, A A; Iakimenko, Z A; Azizbekian, R R; Kuznetsova, N I; Shamshina, T N; Arsen'ev, A S

    2002-01-01

    Peptide antibiotic with cyanolytic activity was isolated from the IGM52 strain of the Brevibacillus laterosporus Gram-positive spore-forming bacteria. By 1H NMR spectroscopy, this antibiotic was identified as loloatin A, a cyclic decapeptide cyclo(-Asn-Asp-Tyr-Val-Orn-Leu-DTyr-Pro-Phe-DPhe-). The spatial structure of loloatin A in solution was determined. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 4; see also http://www.maik.ru.

  2. Isolation and structures of new halogenated prostanoids from the Okinawan soft coral Clavularia viridis.

    PubMed

    Watanabe, Kinzo; Sekine, Miyuki; Iguchi, Kazuo

    2003-11-01

    Fifteen new halogenated prostanoids 9-23 were isolated as minor constituents from the Okinawan soft coral Clavularia viridis. Compounds 9-11 were new members of iodovulone, and compounds 12-18 were 12-O-acetyliodovulones, 12-O-acetylbromovulones, and 12-O-acetylchlorovulones. Compounds 19-23 were 10,11-epoxy congeners of iodovulone, bromovulone, and chlorovulone. The structures of these compounds were determined on the basis of spectroscopic analysis and chemical conversion.

  3. Novel Isochroman Dimers from Stachybotrys sp. PH30583: Fermentation, Isolation, Structural Elucidation and Biological Activities.

    PubMed

    Li, Wei; Yang, Ya-Bin; Yang, Xue-Qiong; Xie, Hui-Ding; Shao, Zhi-Hui; Zhou, Hao; Miao, Cui-Ping; Zhao, Li-Xing; Ding, Zhong-Tao

    2017-05-01

    The rare anishidiol and five new isochromans, including three novel dimers with unprecedented skeletons, were isolated from Stachybotrys sp. PH30583. Their structures were determined by spectral analyses. The bioactivities of these compounds were also investigated. The dimers (6-10) inhibited acetylcholinesterase at 50 µM, but the monomers did not. To investigate the biogenesis of the novel dimers, a time-course investigation of metabolite production was undertaken. Georg Thieme Verlag KG Stuttgart · New York.

  4. LC-UV-Guided Isolation and Structure Determination of Lancolide E: A Nortriterpenoid with a Tetracyclo[5.4.0.0(2,4).0(3,7)]undecane-Bridged System from a "Talented" Schisandra Plant.

    PubMed

    Shi, Yi-Ming; Cai, Song-Liang; Li, Xiao-Nian; Liu, Miao; Shang, Shan-Zhai; Du, Xue; Xiao, Wei-Lie; Pu, Jian-Xin; Sun, Han-Dong

    2016-01-04

    Lancolide E (1) featuring a complex tetracyclo[5.4.0.0(2,4).0(3,7)]undecane-bridged system that is constructed by an eight-, a three-, and two five-membered carbon rings in a sterically congested region was obtained in trace amounts from a "talented" schinortriterpenoid producer Schisandra lancifolia. Its structure was fully characterized by combining 2D NMR spectroscopy, theoretical calculations, and X-ray diffraction analysis. The biogenetic pathway of 1 was proposed to involve a Prins cyclization.

  5. Structural Determinants of Misfolding in Multidomain Proteins.

    PubMed

    Tian, Pengfei; Best, Robert B

    2016-05-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.

  6. Structural Determinants of Misfolding in Multidomain Proteins

    PubMed Central

    Tian, Pengfei; Best, Robert B.

    2016-01-01

    Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669

  7. Image-Based Chemical Structure Determination.

    PubMed

    Ofner, Johannes; Brenner, Florian; Wieland, Karin; Eitenberger, Elisabeth; Kirschner, Johannes; Eisenmenger-Sittner, Christoph; Török, Szilvia; Döme, Balazs; Konegger, Thomas; Kasper-Giebl, Anne; Hutter, Herbert; Friedbacher, Gernot; Lendl, Bernhard; Lohninger, Hans

    2017-07-28

    Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50-200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.

  8. Granular structure determined by terahertz scattering

    NASA Astrophysics Data System (ADS)

    Born, Philip; Rothbart, Nick; Sperl, Matthias; Hübers, Heinz-Wilhelm

    2014-05-01

    Light scattering from particles reveals static and dynamical information about the particles and their correlations. Such methods are particularly powerful when the wavelength of the light is chosen similar to the sizes and distances of the particles. To apply scattering to investigate granular matter in particular —or other objects of similar submillimeter size— light of suitable wavelength in the terahertz regime needs to be chosen. By using a quantum cascade laser in a benchtop setup we determine the angle-dependent scattering of spherical particles as well as coffee powder and sugar grains. The scattering from single particles can be interpreted by form factors derived within the Mie theory. In addition, collective correlations can be extracted as static structure factors and compared to recent computer simulations.

  9. Structure of isolated Z-disks from honeybee flight muscle.

    PubMed

    Rusu, Mara; Hu, Zhongjun; Taylor, Kenneth A; Trinick, John

    2017-07-21

    The Z-disk is a complex structure comprising some 40 proteins that are involved in the transmission of force developed during muscle contraction and in important signalling pathways that govern muscle homeostasis. In the Z-disk the ends of antiparallel thin filaments from adjacent sarcomeres are crosslinked by α-actinin. The structure of the Z-disk lattice varies greatly throughout the animal kingdom. In vertebrates the thin filaments form a tetragonal lattice, whereas invertebrate flight muscle has a hexagonal lattice. The width of the Z-disk varies considerably and correlates with the number of α-actinin bridges. A detailed description at a high resolution of the Z-disk lattice is needed in order to better understand muscle function and disease. The molecular architecture of the Z-disk lattice in honeybee (Apis mellifera) is known from plastic embedded thin sections to a resolution of 7 nm, which is not sufficient to dock component protein crystal structures. It has been shown that sectioning is a damaging process that leads to the loss of finer details present in biological specimens. However, the Apis Z-disk is a thin structure (120 nm) suitable for cryo EM. We have isolated intact honeybee Z-disks from indirect flight muscle, thus obviating the need of plastic sectioning. We have employed cryo electron tomography and image processing to investigate the arrangement of proteins within the hexagonal lattice of the Apis Z-disk. The resolution obtained, ~6 nm, was probably limited by damage caused by the harshness of the conditions used to extract the myofibrils and isolate the Z-disks.

  10. Isolation and structure elucidation of cytotoxic polyacetylenes and polyenes from Echinacea pallida.

    PubMed

    Pellati, Federica; Calò, Samuele; Benvenuti, Stefania; Adinolfi, Barbara; Nieri, Paola; Melegari, Michele

    2006-07-01

    Bioassay-guided fractionation of n-hexane extracts of Echinacea pallida (Asteraceae) roots led to the isolation and structure elucidation of two polyacetylenes (1, 3) and three polyenes (2, 4, 5). Two are known hydroxylated compounds, namely 8-hydroxy-pentadeca-(9E)-ene-11,13-diyn-2-one (1) and 8-hydroxy-pentadeca-(9E,13Z)-dien-11-yn-2-one (2). Two dicarbonylic constituents, namely pentadeca-(9E)-ene-11,13-diyne-2,8-dione (3) and pentadeca-(9E,13Z)-dien-11-yne-2,8-dione (4), were isolated and characterized for the first time. Furthermore, the structure elucidation of pentadeca-(8Z,13Z)-dien-11-yn-2-one (5) is described. The structure of the compounds isolated was determined on the basis of UV, IR, NMR (including 1D and 2D NMR experiments, such as 1H-1H gCOSY, gHSQC-DEPT, gHMBC, gNOESY) and MS spectroscopic data. The cytotoxic activity of the isolated constituents against MIA PaCa-2 human pancreatic adenocarcinoma cells was evaluated in the concentration range 1-100 microg/ml. Results show that the hydroxylated compounds (1, 2) have low cytotoxicity, while the more hydrophobic polyacetylenes (3) and polyenes (4, 5) displayed moderate activity.

  11. Isolation and structure of hematoside-type ganglioside from the starfish Linckia laevigata.

    PubMed

    Inagaki, Masanori; Saito, Takeshi; Miyamoto, Tomofumi; Higuchi, Ryuichi

    2009-02-01

    A hematoside-type ganglioside, LLG-1 (1), has been obtained from the polar lipid fraction of the chloroform/methanol extract of the starfish Linckia laevigata. The structure of the ganglioside has been determined on the basis of chemical and spectroscopic evidence as 1-O-[N-glycolyl-alpha-D-neuraminosyl-(2-->3)-beta-D-galactopyranosyl-(1-->4)-beta-D-glucopyranosyl]-ceramide. The ceramide moiety was composed of heterogeneous 2-hydroxy fatty acid and phytosphingosine units. This is the first report on the isolation and structure elucidation of naked hematoside-type ganglioside from echinoderms.

  12. Isolation and structural characterization of dihydrobenzofuran congeners of licochalcone A.

    PubMed

    Simmler, Charlotte; Lankin, David C; Nikolić, Dejan; van Breemen, Richard B; Pauli, Guido F

    2017-09-01

    In an effort to explore the residual complexity of naturally occurring chalcones from the roots of Glycyrrhiza inflata (Fabaceae), two new licochalcone A (LicA) derivatives were isolated as trace metabolites from enriched fractions. Both constituents contain a dihydrofuran moiety linked to carbons C-4 and C-5 of the retrochalcone core. Compound 1 (LicAF1) represents a new chemical entity, whereas compound 2 (LicAF2) has previously been reported as a Lewis acid catalyzed rearrangement of LicA. Evaluation of chirality revealed that both dihydrofuran derivatives existed as a mixture of R and S enantiomers. Interestingly, when solutions were exposed to sunlight, both dihydrofuran retrochalcones, initially isolated as trans isomers, were found to rapidly isomerize yielding trans and cis isomers. Analysis of the 1D (1)H NMR spectra of the photolysis products revealed the presence of two sets of proton resonances ascribed to each of the geometric isomers. An up-field shift of all proton resonances arising from the cis isomer was observed, suggesting that anisotropic shielding effects were introduced through an overall perturbation of the 3-dimensional structure upon photoisomerization. Similar up-field shifts were observed in the (13)C spectrum of the cis isomer, except for the CO, C-α, and C-6 carbons, which experienced downfield shifts. Analogous NMR results were observed for LicA. Hence, the results presented herein encompass the isolation and full characterization of LicAF analogs 1 and 2, and observations of their trans-to-cis photoisomerization through the systematic analysis of their NMR spectra. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Dynamics of the population structure and genetic variability within Iranian isolates of grapevine fanleaf virus: evidence for polyphyletic origin.

    PubMed

    Gholampour, Z; Kargar, M; Zakiaghl, M; Siampour, M; Mehrvar, M; Izadpanah, K

    2017-01-01

    To determine the genetic diversity and population structure of grapevine fanleaf virus (GFLV), the complete nucleotide sequence of the coat protein gene of 41 isolates from different regions in Iran was determined. Phylogenetic analyses of these isolates together with those available in the GenBank revealed two evolutionary divergent lineages, designated GFLV-G and GFLV-Ir that reflect origin of the isolates. Analysis of the genetic variability in the coat protein of these isolates revealed 37 genotype groups in GFLV population. Analyses indicate that GFLV-G and GFLV-Ir clades are significantly differentiated populations of GFLV. Also, geographical subpopulations of the virus in Iran were completely distinct from each other. Examination of nonsynonymous/synonymous nucleotide diversity showed that the CP gene has been under purifying selection. The neutrality tests indicate balancing selection operating within isolates of the northwest of Iran and purifying selection within the other populations.

  14. Genetic diversity of Streptococcus suis isolates as determined by comparative genome hybridization

    PubMed Central

    2011-01-01

    Background Streptococcus suis is a zoonotic pathogen that causes infections in young piglets. S. suis is a heterogeneous species. Thirty-three different capsular serotypes have been described, that differ in virulence between as well as within serotypes. Results In this study, the correlation between gene content, serotype, phenotype and virulence among 55 S. suis strains was studied using Comparative Genome Hybridization (CGH). Clustering of CGH data divided S. suis isolates into two clusters, A and B. Cluster A isolates could be discriminated from cluster B isolates based on the protein expression of extracellular factor (EF). Cluster A contained serotype 1 and 2 isolates that were correlated with virulence. Cluster B mainly contained serotype 7 and 9 isolates. Genetic similarity was observed between serotype 7 and serotype 2 isolates that do not express muramidase released protein (MRP) and EF (MRP-EF-), suggesting these isolates originated from a common founder. Profiles of 25 putative virulence-associated genes of S. suis were determined among the 55 isolates. Presence of all 25 genes was shown for cluster A isolates, whereas cluster B isolates lacked one or more putative virulence genes. Divergence of S. suis isolates was further studied based on the presence of 39 regions of difference. Conservation of genes was evaluated by the definition of a core genome that contained 78% of all ORFs in P1/7. Conclusions In conclusion, we show that CGH is a valuable method to study distribution of genes or gene clusters among isolates in detail, yielding information on genetic similarity, and virulence traits of S. suis isolates. PMID:21736719

  15. Reef structure determined from vertical seismic profiling

    SciTech Connect

    Blackway, C.V.; Keho, T.; Turpening, R.M.; Omnes, G.

    1986-08-01

    MIT has access to a test borehole near a producing (Silurian) reef in Manistee County, Michigan. Data from a multi-offset vertical seismic profiling (VSP) experiment were analyzed and compared to a three-dimensional seismic survey. With the strong reflection at the B-salt/A-2 carbonate interface, they are able to image the reef. The salt and evaporite layers in the A-1 and A-2 formations off the reef give a double reflection that is also used for imaging. The offset VSPs cover three azimuths, two in the direction of the reef and one off the reef, which allow us to compare results on and off the reef. First, a one-dimensional velocity structure was determined from the zero offset VSP data using a waveform inversion. These velocity results compared favorably with the full waveform sonic data. Using these velocities, a model was constructed for VSP migration. The migration algorithm is a Kirchoff migration based on paraxial ray tracing. The reef image from this migration is in good agreement with the three-dimensional seismic survey.

  16. Determination of the structure of HBr DBr

    SciTech Connect

    Chen, Wei; Novick, S.E.; Walker, A.R.H.

    1995-12-31

    The authors have investigated the structure and dynamics of the weakly bound complex of the four bromine isotopomers of HBr DBr using pulsed-jet Fourier transform microwave spectroscopy. In the hydrogen halide dimers, allowed transitions are across the inversion doublet caused by the geared interchange of the donor and acceptor of the hydrogen bond. While in the classic study of (HF){sub 2}{sup 1}, it was observed that this splitting results in an inversion frequency in the microwave region of the spectrum, in (HCl){sub 2} and (HBr){sub 2} the lower inversion barrier results in an inversion frequency in the infrared. In order to investigate the hydrogen bromide dimer with the high precision allowed by an FT microwave experiment, the authors have {open_quotes}quenched{close_quotes} the inversion motion by substituting a deuterium for one of the hydrogens. The Br-Br distance in the complex is 4.136 {Angstrom}. Using measurements of the nuclear quadrupole coupling constants of the bromine nuclei, the wide amplitude bending motions of the hydrogen-bonded deuterium can be determined as can the wide amplitude bending angle of the non-bonding hydrogen atom. Preliminary analysis suggests that the Br---Br-D angle undergoes excursions of 29{degrees} about zero, and that the H-Br--Br angle oscillates 36{degrees} about its 90{degrees} equilibrium angle.

  17. Carotenoids from guava (Psidium guajava l.): isolation and structure elucidation.

    PubMed

    Mercadante, A Z; Steck, A; Pfander, H

    1999-01-01

    Sixteen carotenoids were isolated from the flesh of Brazilian red guavas (Psidium guajava L.). Their structures were established by means of UV-visible, 400 and 500 MHz (1)H NMR, 120 and 125 MHz (13)C NMR, mass, and circular dichroism spectra. The carotenoids were identified as phytofluene, (all-E)-, (9Z)-, (13Z)-, and (15Z)-beta-carotene, (all-E)-gamma-carotene, (all-E)-, (9Z)-, (13Z)-, and (15Z)-lycopene, (all-E,3R)-beta-cryptoxanthin, (all-E, 3R)-rubixanthin, (all-E,3S,5R,8S)-cryptoflavin, (all-E,3R,3'R, 6'R)-lutein, (all-E,3S,5R,6R,3'S,5'R,8'R)-, and (all-E,3S,5R,6R,3'S, 5'R,8'S)-neochrome. Thirteen of the carotenoids identified are reported as guava carotenoids for the first time.

  18. Determination of the prevalence of antimicrobial resistance genes in canine Clostridium perfringens isolates.

    PubMed

    Kather, Elizabeth J; Marks, Stanley L; Foley, Janet E

    2006-03-10

    Clostridium perfringens is a well documented cause of a mild self-limiting diarrhea and a potentially fatal acute hemorrhagic diarrheal syndrome in the dog. A recent study documented that 21% of canine C. perfringens isolates had MIC's indicative of resistance to tetracycline, an antimicrobial commonly recommended for treatment of C. perfringens-associated diarrhea. The objective of the present study was to further evaluate the antimicrobial susceptibility profiles of these isolates by determining the prevalence of specific resistance genes, their expression, and ability for transference between bacteria. One hundred and twenty-four canine C. perfringens isolates from 124 dogs were evaluated. Minimum inhibitory concentrations of tetracycline, erythromycin, tylosin, and metronidazole were determined using the CLSI Reference Agar Dilution Method. All isolates were screened for three tetracycline resistance genes: tetA(P), tetB(P) and tetM, and two macrolide resistance genes: ermB and ermQ, via PCR using primer sequences previously described. Ninety-six percent (119/124) of the isolates were positive for the tetA(P) gene, and 41% (51/124) were positive for both the tetA(P) and tetB(P) genes. No isolates were positive for the tetB(P) gene alone. Highly susceptible isolates (MIC< or = 4 microg/ml) were significantly more likely to lack the tetB(P) gene. One isolate (0.8%) was positive for the ermB gene, and one isolate was positive for the ermQ gene. The tetM gene was not found in any of the isolates tested. Two out of 15 tested isolates (13%) demonstrated transfer of tetracycline resistance via bacterial conjugation. Tetracycline should be avoided for the treatment of C. perfringens-associated diarrhea in dogs because of the relatively high prevalence of in vitro resistance, and the potential for conjugative transfer of antimicrobial resistance.

  19. The population structure of Escherichia coli isolated from subtropical and temperate soils

    USGS Publications Warehouse

    Byappanahalli, Muruleedhara N.; Yan, Tao; Hamilton, Matthew J.; Ishii, Satoshi; Fujioka, Roger S.; Whitman, Richard L.; Sadowsky, Michael J.

    2012-01-01

    While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous

  20. Biosurfactant-producing bacterium, Pseudomonas aeruginosa MA01 isolated from spoiled apples: physicochemical and structural characteristics of isolated biosurfactant.

    PubMed

    Abbasi, Habib; Hamedi, Mir Manochehr; Lotfabad, Tayebe Bagheri; Zahiri, Hossein Shahbani; Sharafi, Hakimeh; Masoomi, Fatemeh; Moosavi-Movahedi, Ali Akbar; Ortiz, Antonio; Amanlou, Massoud; Noghabi, Kambiz Akbari

    2012-02-01

    An extensive investigation was conducted to isolate indigenous bacterial strains with outstanding performance for biosurfactant production from different types of spoiled fruits, food-related products and food processing industries. An isolate was selected from 800 by the highest biosurfactant yield in soybean oil medium and it was identified by 16S rRNA and the two most relevant hypervariable regions of this gene; V3 and V6 as Pseudomonas aeruginosa MA01. The isolate was able to produce 12 g/l of a glycolipid-type biosurfactant and generally less efficient to emulsify vegetable oils compared to hydrocarbons and could emulsify corn and coconut oils more than 50%. However, emulsification index (E(24)) of different hydrocarbons including hexane, toluene, xylene, brake oil, kerosene and hexadecane was between 55.8% and 100%. The surface tension of pure water decreased gradually with increasing biosurfactant concentration to 32.5 mNm(-1) with critical micelle concentration (CMC) value of 10.1mg/l. Among all carbon substrates examined, vegetable oils were the most effective on biosurfactant production. Two glycolipid fractions were purified from the biosurfactant crude extracts, and FTIR and ES-MS were used to determine the structure of these compounds. The analysis indicated the presence of three major monorhamnolipid species: R(1)C(10)C(10), R(1)C(10)C(12:1), and R(1)C(10)C(12); as well as another three major dirhamnolipid species: R(2)C(10)C(10), R(2)C(10)C(12:1), and R(2)C(10)C(12). The strain sweep experiment for measuring the linear viscoelastic of biosurfactant showed that typical behavior characteristics of a weak viscoelastic gel, with storage modulus greater than loss modulus at all frequencies examined, both showing some frequency dependence.

  1. Protein structure determination using metagenome sequence data.

    PubMed

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A; Kim, David E; Kamisetty, Hetunandan; Kyrpides, Nikos C; Baker, David

    2017-01-20

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost. Copyright © 2017, American Association for the Advancement of Science.

  2. Protein Structure Determination using Metagenome sequence data

    PubMed Central

    Ovchinnikov, Sergey; Park, Hahnbeom; Varghese, Neha; Huang, Po-Ssu; Pavlopoulos, Georgios A.; Kim, David E.; Kamisetty, Hetunandan; Kyrpides, Nikos C.; Baker, David

    2017-01-01

    Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families, and that metagenome sequence data more than triples the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact based structure matching and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the PDB. This approach provides the representative models for large protein families originally envisioned as the goal of the protein structure initiative at a fraction of the cost. PMID:28104891

  3. Crystal structure of erioflorin isolated from Podanthus mitiqui (L.)

    PubMed Central

    Paz, Cristian; Schilde, Uwe

    2017-01-01

    The title compound, erioflorin, C19H24O6 [systematic name: (1aR,3S,4Z,5aR,8aR,9R,10aR)-1a,2,3,5a,7,8,8a,9,10,10a-deca­hydro-3-hy­droxy-4,10a-dimethyl-8-methyl­idene-7-oxooxireno[5,6]cyclo­deca­[1,2-b]furan-9-yl methacrylate], is a tricyclic germacrane sesquiterpene lactone, which was isolated from Podanthus mitiqui (L.). The compound crystallizes in the space group P212121, and its mol­ecular structure consists of a methacrylic ester of a ten-membered ring sesquiterpenoid annelated with an epoxide and a butyrolactone. The structure is stabilized by one intramolecular C—H⋯O hydrogen bond. An O—H⋯O hydrogen bond and further C—H⋯O interactions can be observed in the packing. PMID:28316802

  4. Crystal structure of erioflorin isolated from Podanthus mitiqui (L.).

    PubMed

    Paz, Cristian; Ortiz, Leandro; Schilde, Uwe

    2017-03-01

    The title compound, erioflorin, C19H24O6 [systematic name: (1aR,3S,4Z,5aR,8aR,9R,10aR)-1a,2,3,5a,7,8,8a,9,10,10a-deca-hydro-3-hy-droxy-4,10a-dimethyl-8-methyl-idene-7-oxooxireno[5,6]cyclo-deca-[1,2-b]furan-9-yl methacrylate], is a tricyclic germacrane sesquiterpene lactone, which was isolated from Podanthus mitiqui (L.). The compound crystallizes in the space group P212121, and its mol-ecular structure consists of a methacrylic ester of a ten-membered ring sesquiterpenoid annelated with an epoxide and a butyrolactone. The structure is stabilized by one intramolecular C-H⋯O hydrogen bond. An O-H⋯O hydrogen bond and further C-H⋯O interactions can be observed in the packing.

  5. Human seminal alpha inhibins: isolation, characterization, and structure.

    PubMed Central

    Li, C H; Hammonds, R G; Ramasharma, K; Chung, D

    1985-01-01

    Two additional peptides with inhibin-like activity have been isolated from human seminal plasma. One consists of 52 amino acids and the other, 92 amino acids. They are designated alpha-inhibin-52 and alpha-inhibin-92. Sequence analyses show that the NH2-terminal 31 amino acids of alpha-inhibin-52 are identical to the structure of the inhibin-like peptide previously reported [ILP-(1-31), now designated alpha-inhibin-31], and the COOH-terminal 52 amino acids of alpha-inhibin-92 are identical to the structure of alpha-inhibin-52. The amino acid sequence of alpha-inhibin-92 is: (sequence in text) Bioassay data in mouse pituitaries in vitro show that alpha-inhibin-52 is 3.4 times more active and alpha-inhibin-92 is greater than 40 times more active than alpha-inhibin-31 in suppressing follitropin-release. Radioimmunoassay data indicate that alpha-inhibin-52 and alpha-inhibin-92 have only 60% immunoreactivity. PMID:3889920

  6. Mechanical testing of high-damping elastomer materials for determining design parameters of seismic isolation bearings

    SciTech Connect

    Hughes, T.H.; Kulak, R.F.

    1994-06-01

    High-damping steel-laminated elastomeric bearings are one of the devices used for isolating large buildings and structures from earthquake damage. These load-bearing isolators are constructed from alternating layers of high-damping rubber and steel plates. In this paper the mechanical testing of small specimens of some elastomer compounds proposed for the isolation of advanced nuclear reactors is discussed. Variation of shear stiffness and damping with respect to shear strain level (5 % to 300 %), temperature ({minus}40{degrees}C to +50{degrees}C) and frequency (0.002Hz to 5Hz) are reported. Problems involved in obtaining reliable and repeatable results are also discussed.

  7. Molecular Identification of Resistance Determinants, Integrons and Genetic Relatedness of Extensively Drug Resistant Acinetobacter baumannii Isolated From Hospitals in Tehran, Iran

    PubMed Central

    Najar Peerayeh, Shahin; Karmostaji, Afsaneh

    2015-01-01

    Background: Acinetobacter baumannii has emerged as an important nosocomial pathogen. Hospital outbreaks of extensively drug resistant (XDR) A. baumannii are a great concern. Objectives: Aims of this study were to characterize the resistance determinants and genetic relatedness of (XDR) A. baumannii isolates in hospitals in Tehran, Iran. Materials and Methods: During a three-year study, clinical isolates of A. baumannii were collected from two hospitals in Tehran, Iran. Susceptibility testing to antibiotics was performed by disk diffusion method and XDR A. baumannii isolates were identified. Genes’ encoding for carbapenemase production and integrons were identified by PCR. MICs of imipenem and meropenem were determined by agar dilution. Multiple locus variable-number tandem repeat analysis (MLVA) typing was used to determine genetic relationships of XDR isolates. Results: Using PCR for amplification of blaOXA-51, 93.9% (123.131) of isolates were identified as A. baumannii and 24.4% (30.123) were XDR. These isolates were resistant to gentamicin, ciprofloxacin, amikacin, cotrimoxazole, cefepime, cefotaxime, aztreonam and ceftazidime. Thirty percent of the isolates were resistant to tigecycline. All isolates were susceptible to colistin and polymyxin-B, while 93.3% (28.30) possessed blaOXA-23-like and 6.7% (2.30) possessed blaOXA-24-like. All isolates possessed insertion sequence (ISAba1) in the upstream region of the OXA-23-like gene. Almost 96.7% (29.30) of the isolates were positive for class I integron and 43.3% (13.30) for class II. These isolates were also positive for class I. Class III integron was not detected. MLVA typing of XDR isolates showed seven clonally complexes and 16 singletons. Conclusions: The population structure of the A. baumannii isolates in our hospitals was genetically diverse. A significant association between XDR pattern and presence of class 1 integron (P < 0.001) was found indicating that many antibiotic resistance determinants are

  8. Crystallite width determines monolayer hydration across a wide spectrum of celluloses isolated from plants.

    PubMed

    Driemeier, Carlos; Bragatto, Juliano

    2013-01-10

    Relating cellulose structure to its water uptake is a classical problem with many investigations done through measurements of cellulose "crystallinity". However, there is presently a growing consensus that crystallinity measurements are appreciably uncertain, leading to ambiguous interpretations of underlying cellulose organization. In this scenario, this article revisits the relations between cellulose structure and water uptake, moving the emphasis away from degree of crystallinity and directing it toward crystallite width, which is inferred with less ambiguity from the broadening of 200 X-ray diffraction peaks. With this approach, analysis of a wide spectrum of celluloses isolated from plants (preserving cellulose I phase and having variable contents of residual hemicelluloses) reveals a simple linear relation (R(2) = 0.98) between reciprocal crystallite width and monolayer hydration (determined from vapor sorption). The primary role of crystallite width supports that most water-accessible polysaccharides are laterally associated with the crystallites, with a minor fraction in disordered domains along the fibrils. Furthermore, the secondary role left to hemicellulosic contents indicates cellulose being partly decrystallized to complement the disordered amount required to interface the crystallites. Finally, a substantial part of hydration is attributed to polysaccharides in voids left by the imperfect packing of aggregated crystallites.

  9. Structure of an isolated unglycosylated antibody C{sub H}2 domain

    SciTech Connect

    Prabakaran, Ponraj; Vu, Bang K.; Gan, Jianhua; Feng, Yang; Dimitrov, Dimiter S.; Ji, Xinhua

    2008-10-01

    The crystal structure of an isolated unglycosylated antibody C{sub H}2 domain has been determined at 1.7 Å resolution. The C{sub H}2 (C{sub H}3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein–protein interactions with another C{sub H}2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C{sub H}2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody γ1 C{sub H}2 domain was determined at 1.7 Å resolution and compared with corresponding C{sub H}2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C{sub H}2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C{sub H}2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications.

  10. STRUCTURE AS A DETERMINANT OF DEMOCRATIC ADMINISTRATION.

    ERIC Educational Resources Information Center

    COLLINS, CHARLES C.

    THE DEGREE OF OPERATIONAL DEMOCRACY WITHIN A JUNIOR COLLEGE AND, BY EXTENSION, WITHIN ANY SCHOOL OR COLLEGE IS LARGELY DEPENDENT UPON THE KIND OF ORGANIZATIONAL STRUCTURE WHICH IS ESTABLISHED. THE STRUCTURE AND MECHANICS MOST SUPPORTIVE TO THE DEMOCRATIC DEVELOPMENT OF THE COLLEGE AND ITS INSTRUCTIONAL PROGRAM SHOULD HAVE MAXIMAL OPPORTUNITY FOR…

  11. Solution structure of the isolated histone H2A-H2B heterodimer

    PubMed Central

    Moriwaki, Yoshihito; Yamane, Tsutomu; Ohtomo, Hideaki; Ikeguchi, Mitsunori; Kurita, Jun-ichi; Sato, Masahiko; Nagadoi, Aritaka; Shimojo, Hideaki; Nishimura, Yoshifumi

    2016-01-01

    During chromatin-regulated processes, the histone H2A-H2B heterodimer functions dynamically in and out of the nucleosome. Although detailed crystal structures of nucleosomes have been established, that of the isolated full-length H2A-H2B heterodimer has remained elusive. Here, we have determined the solution structure of human H2A-H2B by NMR coupled with CS-Rosetta. H2A and H2B each contain a histone fold, comprising four α-helices and two β-strands (α1–β1–α2–β2–α3–αC), together with the long disordered N- and C-terminal H2A tails and the long N-terminal H2B tail. The N-terminal αN helix, C-terminal β3 strand, and 310 helix of H2A observed in the H2A-H2B nucleosome structure are disordered in isolated H2A-H2B. In addition, the H2A α1 and H2B αC helices are not well fixed in the heterodimer, and the H2A and H2B tails are not completely random coils. Comparison of hydrogen-deuterium exchange, fast hydrogen exchange, and {1H}-15N hetero-nuclear NOE data with the CS-Rosetta structure indicates that there is some conformation in the H2A 310 helical and H2B Lys11 regions, while the repression domain of H2B (residues 27–34) exhibits an extended string-like structure. This first structure of the isolated H2A-H2B heterodimer provides insight into its dynamic functions in chromatin. PMID:27181506

  12. Historical and ecological determinants of genetic structure in arctic canids.

    PubMed

    Carmichael, L E; Krizan, J; Nagy, J A; Fuglei, E; Dumond, M; Johnson, D; Veitch, A; Berteaux, D; Strobeck, C

    2007-08-01

    Wolves (Canis lupus) and arctic foxes (Alopex lagopus) are the only canid species found throughout the mainland tundra and arctic islands of North America. Contrasting evolutionary histories, and the contemporary ecology of each species, have combined to produce their divergent population genetic characteristics. Arctic foxes are more variable than wolves, and both island and mainland fox populations possess similarly high microsatellite variation. These differences result from larger effective population sizes in arctic foxes, and the fact that, unlike wolves, foxes were not isolated in discrete refugia during the Pleistocene. Despite the large physical distances and distinct ecotypes represented, a single, panmictic population of arctic foxes was found which spans the Svalbard Archipelago and the North American range of the species. This pattern likely reflects both the absence of historical population bottlenecks and current, high levels of gene flow following frequent long-distance foraging movements. In contrast, genetic structure in wolves correlates strongly to transitions in habitat type, and is probably determined by natal habitat-biased dispersal. Nonrandom dispersal may be cued by relative levels of vegetation cover between tundra and forest habitats, but especially by wolf prey specialization on ungulate species of familiar type and behaviour (sedentary or migratory). Results presented here suggest that, through its influence on sea ice, vegetation, prey dynamics and distribution, continued arctic climate change may have effects as dramatic as those of the Pleistocene on the genetic structure of arctic canid species.

  13. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  14. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  15. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  16. Structure Elucidation and in Vitro Toxicity of New Azaspiracids Isolated from the Marine Dinoflagellate Azadinium poporum

    PubMed Central

    Krock, Bernd; Tillmann, Urban; Potvin, Éric; Jeong, Hae Jin; Drebing, Wolfgang; Kilcoyne, Jane; Al-Jorani, Ahmed; Twiner, Michael J.; Göthel, Qun; Köck, Matthias

    2015-01-01

    Two strains of Azadinium poporum, one from the Korean West coast and the other from the North Sea, were mass cultured for isolation of new azaspiracids. Approximately 0.9 mg of pure AZA-36 (1) and 1.3 mg of pure AZA-37 (2) were isolated from the Korean (870 L) and North Sea (120 L) strains, respectively. The structures were determined to be 3-hydroxy-8-methyl-39-demethyl-azaspiracid-1 (1) and 3-hydroxy-7,8-dihydro-39-demethyl-azaspiracid-1 (2) by 1H- and 13C-NMR. Using the Jurkat T lymphocyte cell toxicity assay, (1) and (2) were found to be 6- and 3-fold less toxic than AZA-1, respectively. PMID:26528990

  17. Structure of glycopeptides isolated from bovine milk component PP3.

    PubMed

    Girardet, J M; Coddeville, B; Plancke, Y; Strecker, G; Campagna, S; Spik, G; Linden, G

    1995-12-15

    The heat-stable acid-soluble phosphoglycoprotein component PP3 was isolated from the bovine milk proteose peptone fraction by concanavalin A affinity chromatography. Glycopeptides were released by pronase digestion of the milk component PP3 and were subsequently separated by high-pH anion-exchange chromatography on CarboPac PA-1. The primary structures of the glycan and peptide moieties of eight N-glycopeptides have been established by combining methylation analysis, mass spectrometry, 400-MHz 1H-NMR spectroscopy, and peptide sequence analysis. All the analyzed fractions contained biantennary N-acetyllactosamine-type carbohydrate chains, some of them with a GalNAc(beta 1-4)GlcNAc or a NeuAc(alpha 2-6)GalNAc(beta 1-4)GlcNAc group. This particular sequence did or did not replace the Gal(beta 1-4)GlcNAc group usually found in most N-linked glycans. Moreover, the sialylated Gal and GalNAc residues were only found on the Man(alpha 1-3) antenna.

  18. Structure analysis and laxative effects of oligosaccharides isolated from bananas.

    PubMed

    Wang, Juan; Huang, Hui Hua; Cheng, Yan Feng; Yang, Gong Ming

    2012-10-01

    Banana oligosaccharides (BOS) were extracted with water, and then separated and purified using column chromatography. Gel penetration chromatography was used to determine the molecular weights. Thin layer chromatogram and capillary electrophoresis were employed to analyze the monosaccharide composition. The indican bond and structure of the BOS molecule were determined using Fourier transform infrared spectroscopy and nuclear magnetic resonance. Results showed that BOS were probably composed of eight β-D-pyran glucose units linked with 1→6 indican bonds. The laxative effects of BOS were investigated in mice using the method described in "Handbook of Technical Standards for Testing and Assessment of Health Food in China." The length of the small intestine over which a carbon suspension solution advanced in mice treated with low-, middle-, and high-dose BOS was significantly greater than that in the model group, suggesting that BOS are effective in accelerating the movement of the small intestine.

  19. Structural studies of a methyl galacturonosyl-methoxyxylan isolated from the stem of Lagenaria siceraria (Lau).

    PubMed

    Ghosh, Kaushik; Chandra, Krishnendu; Roy, Sadhan K; Mondal, Subhas; Maiti, Debabrata; Das, Debsankar; Ojha, Arnab K; Islam, Syed S

    2008-02-04

    A water-soluble polysaccharide was isolated from the aqueous extract of the stem of Lagenaria siceraria. The polysaccharide was found to be constituted of methyl d-galacturonate, 2-O-methyl-D-xylose, and d-xylose in a ratio of 1:1:1. On the basis of total acid hydrolysis, methylation analysis, periodate oxidation, NMR studies ((1)H, (13)C, 2D-COSY, TOCSY, NOESY, HSQC, and HMBC), and MALDI-TOF MS analysis, the structure of the repeating unit of the polysaccharide is determined as.

  20. Antineoplastic agents. 573. isolation and structure of papilistatin from the papilionid butterfly Byasa polyeuctes termessa.

    PubMed

    Pettit, George R; Ye, Qinghua; Herald, Delbert L; Hogan, Fiona; Pettit, Robin K

    2010-02-26

    Bioassay-guided separation of an extract of the wings from a Taiwan butterfly, Byasa polyeuctes termessa, allowed isolation of a new cancer cell growth inhibitor designated papilistatin (1a). The structure was determined by analysis of 1D and 2D NMR spectra and by HRMS. Against a panel of six human and the murine P388 leukemia cancer cell lines, papilistatin exhibited cancer cell growth inhibition with GI(50)'s of 0.093-3.5 microg/mL. Papilistatin was also found to have antibacterial activity.

  1. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    PubMed

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.

  2. Investigation of olefinic structures in class I resinites by isolation and characterization of soluble polylabdanoids

    SciTech Connect

    Clifford, D.J.; Botto, R.E.; Anderson, K.B.

    1996-10-01

    Resinites derived from labdatriene structures (Class I) are ubiquitous throughout the geosphere. A soluble polylabdanoid material has been isolated by sequential extraction with organic solvents. Solid- and liquid-state NMR spectroscopy, and Py-GC-MS, indicate that at least for immature resinites, the extractable polymer is representative of the insoluble, polylabdanoid material, which constitutes the bulk of most Class I resinites. With increasing maturity, the dominant chemical transformation that occurs in these materials is the {open_quotes}loss{close_quotes} of exomethylene structures and depletion of olefinic character from {approximately}two to {approximately}one olefin per monomer unit. To investigate the fate of olefinic structures and to determine the nature of the residual olefin distribution in these materials, two-dimensional NMR correlation spectroscopies (COSY and HMQC) and nuclear Overhauser experiments (NOESY) have been undertaken. Results from these analyses and their implications to the maturation of Class-I resinites will be discussed.

  3. Protein Structure: Alignment using Mean Field Techniques and Measurement of Isolated Individual Molecules

    SciTech Connect

    Blankenbecler, Richard

    2003-03-13

    Techniques originally developed in High Energy Physics have been applied to selected problems in genetics with promising results. First, this talk will briefly review the importance of protein structure from a physics point of view. Then Mean Field Techniques used in detector track fitting algorithms will be applied to the comparison of protein structures. The practical importance of such comparisons will be discussed. Second, the possibility of measuring the charge structure of ''single'' isolated molecules using the proposed SLAC Free Electron Laser will be outlined. This involves the development of an algorithm that determines the orientation of each of the many targeted identical molecules, constructs the 3-D transform from the many 2-D patterns, and finally performs an inverse fourier transform when only the magnitude of the transform is known, since the phase is not measurable.

  4. Some structural determinants of melody recall.

    PubMed

    Boltz, M

    1991-05-01

    Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme.

  5. Determination of hair structure and shape.

    PubMed

    Schlake, Thomas

    2007-04-01

    The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.

  6. Paramagnetic Structures within a Microfluidic Channel for Enhanced Immunomagnetic Isolation and Surface Patterning of Cells

    PubMed Central

    Sun, Chen; Hassanisaber, Hamid; Yu, Richard; Ma, Sai; Verbridge, Scott S.; Lu, Chang

    2016-01-01

    In this report, we demonstrate a unique method for embedding magnetic structures inside a microfluidic channel for cell isolation. We used a molding process to fabricate these structures out of a ferrofluid of cobalt ferrite nanoparticles. We show that the embedded magnetic structures significantly increased the magnetic field in the channel, resulting in up to 4-fold enhancement in immunomagnetic capture as compared with a channel without these embedded magnetic structures. We also studied the spatial distribution of trapped cells both experimentally and computationally. We determined that the surface pattern of these trapped cells was determined by both location of the magnet and layout of the in-channel magnetic structures. Our magnetic structure embedded microfluidic device achieved over 90% capture efficiency at a flow velocity of 4 mm/s, a speed that was roughly two orders of magnitude faster than previous microfluidic systems used for a similar purpose. We envision that our technology will provide a powerful tool for detection and enrichment of rare cells from biological samples. PMID:27388549

  7. Antibiotic resistance determinants and clonal relationships among multidrug-resistant isolates of Klebsiella pneumoniae.

    PubMed

    Singh, Santosh Kumar; Mishra, Mitali; Sahoo, Minu; Patole, Shashank; Sahu, Suneeta; Misra, Sudhi Ranjan; Mohapatra, Harapriya

    2017-09-01

    In the present study, we performed PCR based screening to determine the presence of antibiotic resistance genes and sequencing to find mutation in QRDR region among fourteen isolates of K. pneumoniae. Association analysis was conducted to detect the co-resistance among the isolates. Multi-locus sequence analysis was carried out to determine the clonal relationship among them. All the K. pneumoniae isolates showed resistance to multiple antibiotics and exhibited cross-resistance to antibiotics. Although few isolates co-harbored variants of β-lactamase genes, others carried qnrB on plasmid and mutations in Quinolone-Resistant Determining Region (QRDR). This study thus indicates that clonally unrelated K. pneumoniae isolates exhibited co-resistance, harboured multiple antibiotic resistance genes present on the chromosome, plasmids and/or integron Therefore, the data from this study can provide guidelines for the prudent use of antibiotics to avert the impending danger of losing out on the available antibiotics for therapeutic use. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Electron Diffraction Determination of Nanoscale Structures

    SciTech Connect

    Parks, Joel H

    2013-03-01

    Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.

  9. Contemporary Methodology for Protein Structure Determination.

    ERIC Educational Resources Information Center

    Hunkapiller, Michael W.; And Others

    1984-01-01

    Describes the nature and capabilities of methods used to characterize protein and peptide structure, indicating that they have undergone changes which have improved the speed, reliability, and applicability of the process. Also indicates that high-performance liquid chromatography and gel electrophoresis have made purifying proteins and peptides a…

  10. Perceptual and Structural Determinants of Youthful Outmigration.

    ERIC Educational Resources Information Center

    Mapstone, James R.

    A sample of 264 high school seniors from a rural environment was used to test some of Everett Lee's theoretic statements on migration, specifically the separate and combined effects of involvement in the institutional structure of place of origin and perception of it as satisfying. To evaluate the relationship of institutional embeddedness to…

  11. Acinetobacter baumannii Isolated from Lebanese Patients: Phenotypes and Genotypes of Resistance, Clonality, and Determinants of Pathogenicity

    PubMed Central

    Dahdouh, Elias; Hajjar, Micheline; Suarez, Monica; Daoud, Ziad

    2016-01-01

    Introduction: Acinetobacter baumannii is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR A. baumannii infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this organism possesses a wide range of virulence factors, whose expression is not yet fully understood. In this study, clinical A. baumannii isolates are characterized in terms of antibiotic resistance, mechanisms of carbapenem resistance, clonality, and virulence. Materials and Methods: A. baumannii clinical isolates (n = 90) where obtained from a tertiary care center in Beirut, Lebanon. API 20NE strips in addition to the amplification of blaOXA−51−like were used for identification. Antibiotic susceptibility testing by disk diffusion was then performed in addition to PCRs for the detection of the most commonly disseminated carbapenemases. Clonality was determined by tri-locus PCR typing and doubling times were determined for isolates with varying susceptibility profiles. Biofilm formation, hemolysis, siderophore production, proteolytic activity, and surface motility was then determined for all the isolates. Statistical analysis was then performed for the determination of associations. Results and Discussion: 81 (90%) of the isolates were resistant to carbapenems. These high rates are similar to other multi-center studies in the country suggesting the need of intervention on a national level. 74 (91.3%) of the carbapenem resistant isolates harbored blaOXA−23−like including two that also harbored blaOXA−24−like. 88.9% of the A. baumannii isolates pertained to ICII and three other international clones were detected, showing the wide dissemination of clones into geographically distinct locations. Virulence profiles were highly diverse and no specific pattern was observed. Nevertheless, an association between

  12. Chromosome-specific segmentation revealed by structural analysis of individually isolated chromosomes.

    PubMed

    Kitada, Kunio; Taima, Akira; Ogasawara, Kiyomoto; Metsugi, Shouichi; Aikawa, Satoko

    2011-04-01

    Analysis of structural rearrangements at the individual chromosomal level is still technologically challenging. Here we optimized a chromosome isolation method using fluorescent marker-assisted laser-capture and laser-beam microdissection and applied it to structural analysis of two aberrant chromosomes found in a lung cancer cell line. A high-density array-comparative genomic hybridization (array-CGH) analysis of DNA samples prepared from each of the chromosomes revealed that these two chromosomes contained 296 and 263 segments, respectively, ranging from 1.5 kb to 784.3 kb in size, derived from different portions of chromosome 8. Among these segments, 242 were common in both aberrant chromosomes, but 75 were found to be chromosome-specific. Sequences of 263 junction sites connecting the ends of segments were determined using a PCR/Sanger-sequencing procedure. Overlapping microhomologies were found at 169 junction sites. Junction partners came from various portions of chromosome 8 and no biased pattern in the positional distribution of junction partners was detected. These structural characteristics suggested the occurrence of random fragmentation of the entire chromosome 8 followed by random rejoining of these fragments. Based on that, we proposed a model to explain how these aberrant chromosomes are formed. Through these structural analyses, it was demonstrated that the optimized chromosome isolation method described here can provide high-quality chromosomal DNA for high resolution array-CGH analysis and probably for massively parallel sequencing analysis. Copyright © 2011 Wiley-Liss, Inc.

  13. A study on association of virulence determinants of verotoxic Escherichia coli isolated from cattle calves

    PubMed Central

    Parul, Singh; Bist, Basanti; Sharma, Barkha; Jain, Udit; Yadav, Janardan K.

    2016-01-01

    Aim: The present study was conducted to find the association among virulence determinants of verotoxic Escherichia coli (VTEC) isolated from cattle calf feces. Materials and Methods: A total of 216 cattle calf fecal samples were collected aseptically and processed under required conditions for the isolation of E. coli. The isolates were further subjected to multiplex polymerase chain reaction (mPCR) for the detection of virulent genes. All the VTEC isolates were serotyped at the Central Research Institute, Kasauli, Himachal Pradesh. The VTEC isolates were observed for the enterohemolysin production on washed sheep blood agar (wSBA). Results: A total of 177 presumptive E. coli were isolated from 216 calf fecal samples revealing an overall prevalence of E. coli to be 81.94%. A total of 32 (14.81%) isolates were detected as VTEC through mPCR. The prevalence of verotoxin genes vt1, vt2, and combination of vt1+vt2 in the VTEC isolates was found to be 12 (37.5%), 14 (43.75%), and 6 (18.75%), respectively. Other virulent genes eaeA and hlyA were found in 6 and 11 VTEC strains with prevalence values of 18.75% and 34.37%, respectively. A total of 13 different O serogroups were revealed in serotyping of 32 VTEC isolates. Out of 32 VTEC strains, only 26 (81.25%) were enterohemolytic on wSBA as they produced the characteristic small, turbid zone of hemolysis around the streaking line. Although enterohemolysin production has been attributed to the presence of hlyA gene, only 11 of 26 enterohemolysin producing VTEC were found to be harboring the hlyA gene (11/26) 42.03%. Conclusion: The present study concludes that there might be an association between the presence of verotoxin genes and enterohemolysin production in VTEC group of E. coli. PMID:27651684

  14. Vascular structure determines pulmonary blood flow distribution

    NASA Technical Reports Server (NTRS)

    Hlastala, M. P.; Glenny, R. W.

    1999-01-01

    Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

  15. Vascular structure determines pulmonary blood flow distribution

    NASA Technical Reports Server (NTRS)

    Hlastala, M. P.; Glenny, R. W.

    1999-01-01

    Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.

  16. Rotational Spectra and Structural Determination of Hccncs

    NASA Astrophysics Data System (ADS)

    Sun, Wenhao; Davis, Rebecca; van Wijngaarden, Jennifer

    2017-06-01

    The ground state of HCCNCS, prepared by high voltage electric discharge of a gas mixture of acetylene and CH_3NCS in neon during supersonic expansion, was studied using both chirped pulse Fourier transform microwave (cp-FTMW) and Balle Flygare FTMW spectrometers. The pure rotational spectra were measured for the parent, ^{34}S, and three ^{13}C isotopologues in natural abundance and the ^{14}N nuclear quadrupole hyperfine structure was resolved. The observed spectra are consistent with a linear or quasilinear ground state of HCCNCS. The corresponding rotational constants were used to derive the substitution (r_{s}) and effective ground state (r_{0}) geometries. Supporting calculations at the MP2/cc-pVQZ and CCSD(T)/cc-pVQZ (expanded basis cc-pV(Q+d)Z for sulfur) levels of theory reveal that the potential energy surface is virtually flat around the minimum and yield an equilibrium structure (r_{e}) that is consistent with experiment.

  17. Diversity of mercury resistance determinants among Bacillus strains isolated from sediment of Minamata Bay.

    PubMed

    Narita, Masaru; Chiba, Kazuyuki; Nishizawa, Hiroshi; Ishii, Hidenori; Huang, Chieh-Chen; Kawabata, Zen'ichiro; Silver, Simon; Endo, Ginro

    2003-06-06

    Thirty mercury-resistant (Hg R) Bacillus strains were isolated from mercury-polluted sediment of Minamata Bay, Japan. Mercury resistance phenotypes were classified into broad-spectrum (resistant to inorganic Hg(2+) and organomercurials) and narrow-spectrum (resistant to inorganic Hg(2+) and sensitive to organomercurials) groups. Polymerase chain reaction (PCR) product sizes and the restriction nuclease site maps of mer operon regions from all broad-spectrum Hg R Bacillus were identical to that of Bacillus megaterium MB1. On the other hand, the PCR products of the targeted merP (extracellular mercury-binding protein gene) and merA (intracellular mercury reductase protein gene) regions from the narrow-spectrum Hg R Bacillus were generally smaller than those of the B. megaterium MB1 mer determinant. Diversity of gene structure configurations was also observed by restriction fragment length polymorphism (RFLP) profiles of the merA PCR products from the narrow-spectrum Hg R Bacillus. The genetic diversity of narrow-spectrum mer operons was greater than that of broad-spectrum ones.

  18. Determination of optimum structure of backpropagation networks

    NASA Astrophysics Data System (ADS)

    Phien, Huynh N.; Sureerattanan, Songyot

    2000-10-01

    The paper proposes the use of the Baysian Information Criterion (BIC), along with an algorithm to systematically select the appropriate structure of the backpropagation (BP) network for a given set of data. Simulation results with hydrological and economic data show that the algorithm performs very satisfactorily. Moreover, it compares with the method of Daqi and Shouyi for one hidden layer network and it is also used for the networks with more than one hidden layer.

  19. Antartic Krill Cohort Determines Dominant Aggregation Structure

    NASA Astrophysics Data System (ADS)

    Bernard, K. S.; Cimino, M. A.; Fraser, W.; Kohut, J. T.; Oliver, M. J.; Patterson-Fraser, D.; Paxton, D.; Raycroft, S.; Statscewich, H.; Steinberg, D. K.; Winsor, P.

    2016-02-01

    Antarctic krill is a key prey item to numerous top predators along the western Antarctic Peninsula. Krill form aggregations of varying size and packing density, found at a wide range of depths within the water column, either sparsely or densely spaced together. Differences in the structure of krill aggregations will impact the availability of krill as prey. The population of Antarctic krill fluctuates over a 5-year period, typically with two strong recruitment years followed by 3 poor recruitment years, resulting in significant variability in the biomass and dominant cohort from year to year. We hypothesized that a shift in the dominant cohort would be accompanied by a shift in the dominant aggregation type. We investigated the aggregation structure of nearshore Antarctic krill over four sequential summers (2011-12 through 2014-15). The summers of 2011-12 and 2012-13 showed strong krill recruitment (juveniles < 30 mm dominated), while 2013-14 and 2014-15 were marked by reduced recruitment (adults > 30 mm dominated). Krill were acoustically mapped (Biosonics DT-X echo sounder) from a Zodiac within a 2-mile radius of Palmer Station. Aggregation parameters (e.g. depth, thickness, length, krill biomass, etc.) were described for each individual aggregation. These were used to group aggregations into similar types using a Principle Components Analysis followed by a Partitioning Around Medoids cluster analysis. Four distinctly different aggregation types were identified and the frequency at which these were observed varied significantly between summers. In particular, in 2011-12, krill aggregations were dominated by those that were near-surface, long and narrow, with high biomass and closely spaced together. Conversely in 2013-14, large, sparsely distributed, near-bottom aggregations, with high biomass dominated. Our results suggest a shift in aggregation structure and, consequently, availability to foraging top predators, with dominant cohort. Understanding inter annual

  20. Enhanced IRES activity by the 3’UTR element determines the virulence of FMDV isolates

    USDA-ARS?s Scientific Manuscript database

    A reverse genetics approach was used to identify viral genetic determinants of the differential virulence displayed by two field foot-and-mouth disease virus (FMDV) strains (A/Arg/00 and A/Arg/01) isolated in Argentina during the 2000-2001 epidemics. A molecular clone of A/Arg/01 strain and viral ch...

  1. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    SciTech Connect

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  2. Determination of antifungal susceptibility patterns among the clinical isolates of Candida species.

    PubMed

    Zomorodian, Kamiar; Rahimi, Mohammad Javad; Pakshir, Kayvan; Motamedi, Marjan; Ghiasi, Moosa Rahimi; Rezashah, Hasanein

    2011-10-01

    Candida species are opportunistic yeasts that cause infections ranging from simple dermatosis to potentially life-threatening fungemia. The emergence of resistance to antifungal drugs has been increased in the past two decades. the present study we determined to find out the susceptibility profiles of clinical isolates of Candida species against four antifungal drugs, including amphotericin B, ketoconazole, fluconazole and itraconazole. Antifungal susceptibility testing of the yeasts was done in accordance with the proposed guidelines for antifungal disk diffusion susceptibility testing of yeasts based on the CLSI document M44-A. A total of 206 yeast isolates were assessed. Among the evaluated Candida species, the highest rates of resistance to ketoconazole were seen in Candida glabrata (16.6%) and Candida albicans (3.2%). Susceptibility and intermediate response to fluconazole were seen in 96.6% and 3.4% of the Candida isolates, respectively. A total of 19 (9.2%) yeast isolates showed petite phenomenon including 11 C. glabrata, 3 C. albicans, 2 Candida dubliniensis and one isolate of each Candida krusei and Candida parapsilosis. The high number of petite mutation in the isolated yeasts should be seriously considered since it may be one of the reasons of antifungal treatment failure.

  3. Living in isolation – population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink)

    PubMed Central

    Putz, Christina M; Schmid, Christoph; Reisch, Christoph

    2015-01-01

    The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential. PMID:26380690

  4. Living in isolation - population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink).

    PubMed

    Putz, Christina M; Schmid, Christoph; Reisch, Christoph

    2015-09-01

    The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential.

  5. Antibiotic Resistance Determinants in a Pseudomonas putida Strain Isolated from a Hospital

    PubMed Central

    Duque, Estrella; Fernández, Matilde; Molina-Santiago, Carlos; Roca, Amalia; Porcel, Mario; de la Torre, Jesús; Segura, Ana; Plesiat, Patrick; Jeannot, Katy; Ramos, Juan-Luis

    2014-01-01

    Environmental microbes harbor an enormous pool of antibiotic and biocide resistance genes that can impact the resistance profiles of animal and human pathogens via horizontal gene transfer. Pseudomonas putida strains are ubiquitous in soil and water but have been seldom isolated from humans. We have established a collection of P. putida strains isolated from in-patients in different hospitals in France. One of the isolated strains (HB3267) kills insects and is resistant to the majority of the antibiotics used in laboratories and hospitals, including aminoglycosides, ß-lactams, cationic peptides, chromoprotein enediyne antibiotics, dihydrofolate reductase inhibitors, fluoroquinolones and quinolones, glycopeptide antibiotics, macrolides, polyketides and sulfonamides. Similar to other P. putida clinical isolates the strain was sensitive to amikacin. To shed light on the broad pattern of antibiotic resistance, which is rarely found in clinical isolates of this species, the genome of this strain was sequenced and analysed. The study revealed that the determinants of multiple resistance are both chromosomally-borne as well as located on the pPC9 plasmid. Further analysis indicated that pPC9 has recruited antibiotic and biocide resistance genes from environmental microorganisms as well as from opportunistic and true human pathogens. The pPC9 plasmid is not self-transmissible, but can be mobilized by other bacterial plasmids making it capable of spreading antibiotic resistant determinants to new hosts. PMID:24465371

  6. Structural determinants of MALT1 protease activity.

    PubMed

    Wiesmann, Christian; Leder, Lukas; Blank, Jutta; Bernardi, Anna; Melkko, Samu; Decock, Arnaud; D'Arcy, Allan; Villard, Frederic; Erbel, Paulus; Hughes, Nicola; Freuler, Felix; Nikolay, Rainer; Alves, Juliano; Bornancin, Frederic; Renatus, Martin

    2012-05-25

    The formation of the CBM (CARD11-BCL10-MALT1) complex is pivotal for antigen-receptor-mediated activation of the transcription factor NF-κB. Signaling is dependent on MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), which not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. It remained unclear how the CBM activates MALT1. Here, we provide biochemical and structural evidence that MALT1 activation is dependent on its dimerization and show that mutations at the dimer interface abrogate activity in cells. The unliganded protease presents itself in a dimeric yet inactive state and undergoes substantial conformational changes upon substrate binding. These structural changes also affect the conformation of the C-terminal Ig-like domain, a domain that is required for MALT1 activity. Binding to the active site is coupled to a relative movement of caspase and Ig-like domains. MALT1 binding partners thus may have the potential of tuning MALT1 protease activity without binding directly to the caspase domain.

  7. Isolation and structure of homotemsirolimuses A, B, and C.

    PubMed

    Kong, Fangming; Zhu, Tianmin; Yu, Ker; Pagano, Thomas G; Desai, Parimal; Radebaugh, Galen; Fawzi, Mahdi

    2011-04-25

    Homotemsirolimuses A, B, and C (2a, 2b, 2c) were found to be minor components of a temsirolimus preparation made from rapamycin. These three temsirolimus analogues are derived from the corresponding rapamycin analogues, homorapamycins A, B, and C (1a, 1b, 1c) produced by the strain Streptomyces hygroscopicus. The structures of homotemsirolimuses A, B, and C were determined by spectroscopic methods. These compounds were tested for mTOR kinase inhibition and in two proliferation assays using LNCap prostate and MDA468 breast cancer cells. The results suggested that the mTOR inhibition and antiproliferation potencies for 2a, 2b, and 2c are comparable to those of rapamycin (1) and temsirolimus (2).

  8. Molecular characterization and determination of antimicrobial resistance of Mycoplasma gallisepticum isolated from chickens.

    PubMed

    Pakpinyo, Somsak; Sasipreeyajan, Jiroj

    2007-11-15

    In this study, three consecutive approaches of molecular characterization, determination of minimum inhibitory concentration (MIC) and antimicrobial tested on Mycoplasma gallisepticum (MG) isolated from chicken farms were investigated. These approaches were conducted between 2004 and 2005 to 134 MG samples collected from five different regions of the intensive farming area of Thailand. Twenty MG isolates and four reference strains including S6, F, ts-11, and 6/85 were classified according to Random Amplification of Polymorphic DNA (RAPD) patterns prior to the antimicrobial tests. These isolates exhibited 5 different genotypes (A-E). Consequently, MG isolates representing each genotype were tested on 11 registered antibiotics. The levels of MIC were determined. Three antibiotics, doxycycline (0.20 microg/ml), tiamulin (0.10 microg/ml), and tylosin (0.33 microg/ml), gave the least MICs among all effective drugs. Break point comparisons of each antimicrobial suggested that the MG isolates were most sensitive to lincomycin, oxytetracycline, tiamulin, and tylosin. Some MG isolates had an intermediate effect on josamycin and were resistant to enrofloxacin and erythromycin. Our results also indicated that MG isolated and collected from the region and nearby districts had similar RAPD patterns showing properties of antimicrobial resistance. The RAPD patterns may imply the frequent use of antibiotics and a resistant strain of MG. This is the first report of genetic characterization using RAPD reflected by the levels of MIC against MG. The information is useful to plan for prophylactic and therapeutic impacts on the poultry industry especially in the area of intensive use of antibiotics.

  9. Plasmid-mediated quinolone resistance determinants among Gram-negative bacteraemia isolates: a hidden threat.

    PubMed

    Margaritis, Athanasios; Galani, Irene; Chatzikonstantinou, Marianthi; Petrikkos, George; Souli, Maria

    2017-03-01

    The aim of the study was to investigate the prevalence of plasmid-mediated quinolone resistance (PMQR) genes in an unselected collection of bloodstream isolates recovered over an 18-month period in a laboratory affiliated to a university hospital in Athens, Greece, and to assess their impact on the in vitro activity of ciprofloxacin and levofloxacin. Eight PMQR genes were screened by PCR and sequencing. All PMQR-positive isolates were submitted to isoelectric focusing for β-lactamase detection, conjugation or transformation, time-kill assays, mutant prevention concentrationand inoculum effect evaluation. PCR and sequencing of gyrA and parC were performed for detection of chromosomal mutations. Among 96 Gram-negative isolates, 7 (7.3 %) carried one or more PMQR genes. qnrS1 was the most prevalent (5.2 %), followed by aac(6')-Ib-cr (4.2 %) and their combination (2 %). Cloning was successful for three isolates. The presence of a single PMQR determinant without any target modification was not associated with quinolone resistance with one exception, Stenotrophomonasmaltophilia carrying qnrS1, which was resistant to norfloxacin and ciprofloxacin, but in this isolate, additional mechanisms of quinolone resistance cannot be excluded. All PMQR-positive isolates showed a significant inoculum effect. The mutant prevention concentrations of ciprofloxacin against the quinolone-susceptible clinical isolates ranged from 0.38 to 32 mg l-1 and those of levofloxacin from 1 to 32 mg l-1. PMQRs compromised the bactericidal activity of ciprofloxacin and levofloxacin when expressed in Enterobactercloacae, S. maltophilia or Klebsiellapneumoniae and when more than one co-existed. PMQR determinants represent an unrecognized threat, capable to compromise the in vitro activity of quinolones if expressed in a favourable genetic environment and to favour selection of resistant mutants by widening the mutant selection window of these agents.

  10. Photoelectron holography applied to surface structural determination

    SciTech Connect

    Petersen, Barry Lee

    1995-05-01

    Photoemitted electron waves are used as coherent source waves for angstrom-scale holographic imaging of local atomic geometry at surfaces. Electron angular distribution patterns are collected above a sample surface and serve as a record of the interference between source wave and waves scattered from surrounding ion cores. Using a mathematical imaging integral transformation, the three-dimensional structural information is obtained directly from these collected patterns. Patterns measured with different electron kinetic energies are phase-summed for image improvement. Pt (111) surface is used as a model system. A pattern 9.6Å-1 (351 eV) is used to generate a full 3-D image of atom locations around an emitter with nearest neighbors within 0.lÅ of the expected bulk positions. Atoms several layers beyond the nearest neighbors are also apparent. Twin-image reduction and artifact suppression is obtained by phase-summing eight patterns measured from 8.8 to 10.2Å-1 (295 to 396 eV). 32 were measured in 0.2Å-1 steps from 6.0 to 12.2Å-1 (137 to 567 eV) are presented here. Simple models of two-slit interference are compared with electron scattering to illuminate understanding of holographic recording of the structural information. This also shows why it sometimes fails due to destructive interferences. Simple theoretical models of electron scattering are compared to experiment to show the origin of the structural information and the differences that result from atomic scattering and from the source wave. Experimental parameters and their relation to imaging is discussed. Comparison is made to the Pt pattern measured at 351 eV using the simple theoretical model. The remaining data set is also modeled, and the eight appropriate theoretical patterns are used to regenerate the multiple-wavenumber experimental result. A clean Cu (001) surface is also measured and imaged.

  11. How Structure Determines Correlations in Neuronal Networks

    PubMed Central

    Pernice, Volker; Staude, Benjamin; Cardanobile, Stefano; Rotter, Stefan

    2011-01-01

    Networks are becoming a ubiquitous metaphor for the understanding of complex biological systems, spanning the range between molecular signalling pathways, neural networks in the brain, and interacting species in a food web. In many models, we face an intricate interplay between the topology of the network and the dynamics of the system, which is generally very hard to disentangle. A dynamical feature that has been subject of intense research in various fields are correlations between the noisy activity of nodes in a network. We consider a class of systems, where discrete signals are sent along the links of the network. Such systems are of particular relevance in neuroscience, because they provide models for networks of neurons that use action potentials for communication. We study correlations in dynamic networks with arbitrary topology, assuming linear pulse coupling. With our novel approach, we are able to understand in detail how specific structural motifs affect pairwise correlations. Based on a power series decomposition of the covariance matrix, we describe the conditions under which very indirect interactions will have a pronounced effect on correlations and population dynamics. In random networks, we find that indirect interactions may lead to a broad distribution of activation levels with low average but highly variable correlations. This phenomenon is even more pronounced in networks with distance dependent connectivity. In contrast, networks with highly connected hubs or patchy connections often exhibit strong average correlations. Our results are particularly relevant in view of new experimental techniques that enable the parallel recording of spiking activity from a large number of neurons, an appropriate interpretation of which is hampered by the currently limited understanding of structure-dynamics relations in complex networks. PMID:21625580

  12. Determining causes of genetic isolation in a large carnivore (Ursus americanus) population to direct contemporary conservation measures

    PubMed Central

    Obbard, Martyn E.; Harnden, Matthew; McConnell, Sabine; Howe, Eric J.; Burrows, Frank G.; White, Bradley N.; Kyle, Christopher J.

    2017-01-01

    The processes leading to genetic isolation influence a population’s local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus) are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP). To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i) a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii) under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been irreversibly modified

  13. Determining causes of genetic isolation in a large carnivore (Ursus americanus) population to direct contemporary conservation measures.

    PubMed

    Pelletier, Agnès; Obbard, Martyn E; Harnden, Matthew; McConnell, Sabine; Howe, Eric J; Burrows, Frank G; White, Bradley N; Kyle, Christopher J

    2017-01-01

    The processes leading to genetic isolation influence a population's local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus) are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP). To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i) a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii) under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been irreversibly modified

  14. Prevalence of tetracycline resistance determinants in broiler isolated Escherichia coli in Iran.

    PubMed

    Seifi, S; Khoshbakht, R

    2016-12-01

    1. Tetracycline resistance determinants are widespread among bacterial species. Resistance to tetracycline occurs by different mechanisms regulated by various genes. 2. The study was conducted to determine the tetracycline resistance and prevalence of tetracycline resistance determinants among Escherichia coli strains isolated from broilers in northern Iran. 3. Minimum inhibitory concentration (MIC) of tetracycline and susceptibility pattern of the isolates were screened using micro-dilution and disk diffusion methods, respectively. The presence of 7 tetracycline resistance genes including tetA, tetB, tetC, tetD, tetE, tetG and tetM was tested using the polymerase chain reaction. 4. Among 100 strains isolated from broilers, 73% were identified as tetracycline resistant. All isolates showed the presence of tetracycline-associated genes. The most prevalent genes were tetA (46%) and tetB (41%) and totally, 17 different genotypes were recognised according to the presence of tetracycline resistance genes. Statistical analysis revealed that concomitant presence of the resistance genes significantly increased the tetracycline MIC and effectiveness of phenotypic characterisation. 5. The results demonstrated a high occurrence of tetracycline-resistant E. coli and related genes among broilers which presents a risk of increasing these strains in human infections associated with food animals.

  15. [Determination of the profiles of secondary metabolites characteristic of Alternaria strains isolated from tomato].

    PubMed

    Benavidez Rozo, Martha Elizabeth; Patriarca, Andrea; Cabrera, Gabriela; Fernández Pinto, Virginia E

    2014-01-01

    Many Alternaria species have been studied for their ability to produce bioactive secondary metabolites, such as tentoxin (TEN), some of which have toxic properties. The main food contaminant toxins are tenuazonic acid, alternariol (AOH), alternariol monomethyl ether (AME), altenuene, and altertoxins i, ii and iii. To determine the profiles of secondary metabolites characteristic of Alternaria strains isolated from tomato for their chemotaxonomic classification. The profiles of secondary metabolites were determined by HPLC MS. The Alternaria isolates obtained from spoiled tomatoes belong, according to their morphological characteristics, to the species groups Alternaria alternata, Alternaria tenuissima and Alternaria arborescens, with A. tenuissima being the most frequent. The most frequent profiles of secondary metabolites belonging to the species groups A. alternata (AOH, AME, TEN), A. tenuissima (AOH, AME, TEN, tenuazonic acid) and A. arborescens (AOH, AME, TEN, tenuazonic acid) were determined, with some isolates of the latter being able to synthesize AAL toxins. Secondary metabolite profiles are a useful tool for the differentiation of small spored Alternaria isolates not easily identifiable by their morphological characteristics. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  16. Prevalence of plasmid-mediated quinolone resistance determinants in Enterobacteriaceae strains isolated in North-East Italy.

    PubMed

    Kocsis, B; Mazzariol, A; Kocsis, E; Koncan, R; Fontana, R; Cornaglia, G

    2013-02-01

    We investigated the prevalence of plasmid-mediated quinolone resistance genes in 756 clinical isolates of Enterobacteriaceae originating from Microbiology Diagnostic Laboratories of North-East Italy. Five point zero two percent of isolates carried a qnr determinant while the aac(6')-Ib-cr determinant was detected in 9·25% of isolates. We also investigated the association between the plasmid-mediated quinolone resistance and the beta-lactamase genes, and characterized the plasmids carrying these determinants of resistance.

  17. Biosynthesis and structural characterization of silver nanoparticles from bacterial isolates

    SciTech Connect

    Zaki, Sahar; El Kady, M.F.; Abd-El-Haleem, Desouky

    2011-10-15

    Graphical abstract: In this study five bacterial isolates belong to different genera were found to be able to biosynthesize silver nanoparticles. Biosynthesis and spectral characterization are reported here. Highlights: {yields} About 300 bacterial isolates were screened for their ability to produce nanosilvers {yields} Five of them were potential candidates for synthesis of silver nanoparticles {yields} Production of silver nanoparticles was examined using UV-Vis, XRD, SEM and EDS. {yields} The presence of nanoparticles with all five bacterial isolates was confirmed. -- Abstract: This study aimed to develop a green process for biosynthesis of silver nanomaterials by some Egyptian bacterial isolates. This target was achieved by screening an in-house culture collection consists of 300 bacterial isolates for silver nanoparticle formation. Through screening process, it was observed that strains belonging to Escherichia coli (S30, S78), Bacillus megaterium (S52), Acinetobacter sp. (S7) and Stenotrophomonas maltophilia (S54) were potential candidates for synthesis of silver nanoparticles. The extracellular production of silver nanoparticles by positive isolates was investigated by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results demonstrated that UV-visible spectrum of the aqueous medium containing silver ion showed a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. Scanning electron microscopy micrograph showed formation of silver nanoparticles in the range of 15-50 nm. XRD-spectrum of the silver nanoparticles exhibited 2{theta} values corresponding to the silver nanocrystal that produce in hexagonal and cubic crystal configurations with different plane of orientation. In addition, the signals of the silver atoms were observed by EDS-spectrum analysis that confirms the presence of silver nanoparticles (Ag

  18. Atmospheric structure determined from satellite data

    NASA Technical Reports Server (NTRS)

    Knight, K. S.; Scoggins, J. R.

    1981-01-01

    The capabilities of the Nimbus 6 satellite sounding data for use in synoptic analysis were considered and interpreted. An evaluation of the ability of the satellite sounding data to detect and depict structural features of the atmosphere was made on the basis of vertical profiles of average difference and standard deviation of differences between satellite and rawinsonde data at nine pressure levels from 850 to 100 mb; and constant pressure charts and cross sections of satellite, rawinsonde and difference values. Results indicate that satellite measurements of temperature as well as the vertical lapse rate and horizontal gradient of temperature are accurate enough to show large scale patterns but not to precisely define fronts or tropopauses; satellite measurements of dew point temperature are smoothed enough to severely reduce contrasts between air masses across fronts; the magnitude of the standard deviation of differences between rawinsonde and satellite data for most variables increases with the synoptic activity in the region; and the most reliable variables to examine from satellite data for depiction of synoptic features are the temperature equivalent potential temperature and mixing ratio.

  19. Structural determinants of criticality in biological networks

    PubMed Central

    Valverde, Sergi; Ohse, Sebastian; Turalska, Malgorzata; West, Bruce J.; Garcia-Ojalvo, Jordi

    2015-01-01

    Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system toward criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality. PMID:26005422

  20. Isolation and nucleotide sequence of the methanol dehydrogenase structural gene from Paracoccus denitrificans.

    PubMed Central

    Harms, N; de Vries, G E; Maurer, K; Hoogendijk, J; Stouthamer, A H

    1987-01-01

    A genomic clone bank of Paracoccus denitrificans DNA has been constructed in the expression vector set pEX1, pEX2, and pEX3. Screening of this clone bank with antibodies raised against P. denitrificans methanol dehydrogenase resulted in the isolation of a clone, pNH3, that synthesized methanol dehydrogenase cross-reactive proteins. The nucleotide sequence of the P. denitrificans DNA fragment inserted in this clone has been determined and shown to contain the full methanol dehydrogenase structural gene. DNA cross-hybridization was found with DNA fragments which have been reported to contain the methanol dehydrogenase structural genes from Methylobacterium sp. strain AM1 and Methylobacterium organophilum. Images PMID:3114231

  1. Language structure is partly determined by social structure.

    PubMed

    Lupyan, Gary; Dale, Rick

    2010-01-20

    Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures--a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in which they are being learned and used. The proposed Linguistic Niche

  2. Structural Determinants of Sleeping Beauty Transposase Activity

    PubMed Central

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-01-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called “sectors”, which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040

  3. Structural Determinants of Sleeping Beauty Transposase Activity.

    PubMed

    Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán

    2016-08-01

    Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.

  4. Isolation blocking voltage of nitrogen ion-implanted AlGaN/GaN high electron mobility transistor structure

    SciTech Connect

    Lo, C. F.; Kang, Tsung Sheng; Liu, L.; Chang, C. Y.; Pearton, S. J.; Kravchenko, Ivan I; Laboutin, O.; Johnson, Wayne J.; Ren, F.

    2010-01-01

    Nitrogen ion-implanted AlGaN/GaN high electron mobility transistor structures showed an isolation blocking voltage of 900 V with a leakage current at 1 A/mm across an implanted isolation-gap of 10 m between two Ohmic pads. The effect of implanted gap distance 1.7, 5, or 10 m between two Ohmic contact pads was evaluated. The isolation current density was determined to be solely dependent on the applied field between the contact pads. A model using a combination of resistive current and Poole Frenkel current is consistent with the experimental data. The resistance of the isolation implantation region significantly decreased after the sample was annealed at temperatures above 600 C.

  5. Determination of antifungal susceptibility patterns among the environmental isolates of Aspergillus fumigatus in Iran

    PubMed Central

    Mohammadi, Faezeh; Dehghan, Parvin; Nekoeian, Shahram; Hashemi, Seyed Jamal

    2016-01-01

    Background: In recent years, triazole-resistant environmental isolates of Aspergillus fumigatus have emerged in Europe and Asia. Azole resistance has been reported in patients who are treated with long-term azole therapy or exposure of the fungus spores to the azole fungicides used in agriculture. To date, a wide range of mutations in A. fumigatus have been described conferring azole-resistance, which commonly involves modifications in the cyp51A gene. We investigated antifungal susceptibility pattern of environmental isolates of A. fumigatus. Materials and Methods: In this study, 170 environmental samples collected from indoors surfaces of three hospitals in Iran. It was used β-tubulin gene to confirm the all of A. fumigatus isolates, which was identified by conventional methods. Furthermore, the antifungal susceptibility of itraconazole, voriconazole, and posaconazole was investigated using broth microdilution test, according to European Committee on Antimicrobial Susceptibility testing reference method. Results: From a total of 158 environmental molds fungi obtained from the hospitals, 58 isolates were identified as A. fumigatus by amplification of expected size of β-tubulin gene (~500 bp). In this study, in vitro antifungal susceptibility testing has shown that there were not high minimum inhibitory concentration values of triazole antifungals in all of the 58 environmental isolates of A. fumigatus. Conclusion: Our findings demonstrated that there was not azole-resistant among environmental isolates of A. fumigatus. Medical triazoles compounds have structural similarity with triazole fungicide compounds in agriculture, therefore, resistance development through exposure to triazole fungicide compounds in the environment is important but it sounds there is not a serious health problem in drug resistance in environmental isolates in Iran. PMID:27656605

  6. Language Structure Is Partly Determined by Social Structure

    PubMed Central

    Lupyan, Gary; Dale, Rick

    2010-01-01

    Background Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. Methodology/Principal Findings We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures— a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. Conclusions/Significance We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in

  7. Leucaena leucocephala (Lam.) de Wit., "subabul" stem lignin: Isolation, structural characterization and thermal properties.

    PubMed

    Yearla, Srinivasa Rao; Padmasree, Kollipara

    2016-06-01

    Lignin is the second most abundant renewable biopolymer on earth after cellulose. It is being used in many industrial applications due to its abundance. In the present study, lignin was isolated from the stems of Leucaena leucocephala (Lam.) de Wit., a high biomass yielding plant using acidic dioxane under N2 atmosphere. Structural characterization of isolated dioxane lignin (DL) was performed by analytical techniques: UV, FT-IR, ¹H NMR and ¹³C NMR. Their monolignol content was determined by nitrobenzene oxidation followed by HPLC-MS/MS analysis. The data was compared with commercial alkali lignin (AL). The results showed that DL is of hardwood guaiacyl-syringyl (GS) type, whereas AL is softwood type with more guaiacyl units and trace amounts of p-hydroxyphenyl units (H). Thermogravimetric analysis (TGA) of DL showed two stage thermal degradation profile similar to AL. The DTGmax for DL and AL were found in the second major loss event of second stage of TGA at 424°C and 404°C, respectively. Differential scanning calorimetry (DSC) study exhibited the glass transition temperatures (Tg) at 132°C and 122°C for DL and AL, respectively. The results from thermal stability studies suggest that dioxane lignin isolated from the "miracle tree" (subabul) can be exploited in various thermoplastic industrial applications.

  8. Determining the Pathogenic Potential of Non-sporulating Molds Isolated from Cutaneous Specimens.

    PubMed

    Jeyaprakasam, Nantha Kumar; Razak, Mohd Fuat Abdul; Ahmad, Noor Azimah Binti; Santhanam, Jacinta

    2016-06-01

    Although non-sporulating molds (NSM) are frequently isolated from patients and have been recognized as agents of pulmonary disease, their clinical significance in cutaneous specimens is relatively unknown. Therefore, this study aimed to identify NSM and to determine the keratinolytic activity of isolates from cutaneous sites. NSM isolates from clinical specimens such as skin, nail, and body fluids were identified based on their ribosomal DNA sequences. Of 17 NSM isolates (7 Ascomycota, 10 Basidiomycota), eleven were identified to species level while five were identified to the genus level. These include Schizophyllum commune, a known human pathogen, Phoma multirostrata, a plant pathogen, and Perenniporia tephropora, a saprophyte. To determine fungal pathogenicity, keratinolytic activity, a major virulence factor, was evaluated ex vivo using human nail samples by measuring dye release from keratin azure, for NSM along with pathogens (Trichophyton mentagrophytes, Trichophyton rubrum, Microsporum canis and Fusarium spp.) and nonpathogenic (endophyte) fungi for comparison. This study showed that pathogenic fungi had the highest keratinolytic activity (7.13 ± 0.552 keratinase units) while the nonpathogenic endophytes had the lowest activity (2.37 ± 0.262 keratinase units). Keratinolytic activity of two Ascomycota NSM (Guignardia mangiferae and Hypoxylon sp.) and one Basidiomycota NSM (Fomitopsis cf. meliae) was equivalent to that of pathogenic fungi, while Xylaria feejeensis showed significantly higher activity (p < 0.05) than nonpathogenic endophytes. These results indicate that the pathogenic ability of NSM is species dependent; clinical isolates, especially more frequently isolated species, may be involved in disease etiology.

  9. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  10. Determination of antimicrobial sensitivities of Campylobacter jejuni isolated from commercial turkey farms in Germany.

    PubMed

    El-Adawy, Hosny; Hotzel, Helmut; Düpre, Sabine; Tomaso, Herbert; Neubauer, Heinrich; Hafez, Hafez M

    2012-12-01

    The emergence of antimicrobial resistance among Campylobacter isolates recovered from turkeys has increased dramatically. Monitoring the progress of this resistance becomes a growing public health issue. The aim of the present study was to provide information of the current status of antibiotic resistance patterns in Campylobacter jejuni from turkeys. Seventy-six C. jejuni isolates were recovered from 67 epidemiologically unrelated meat turkey flocks in different regions of Germany in 2010 and 2011. The isolates were typed by flaA genotyping and were investigated for antimicrobial susceptibility against 12 antibiotics by using a broth microdilution test as well as testing the genetic determination of ciprofloxacin, tetracycline, and erythromycin resistance. All isolates (n = 76) were sensitive to gentamicin and chloramphenicol. The numbers of isolates that were sensitive to streptomycin, erythromycin, neomycin, and amoxicillin were 69 (90.8%), 61 (80.2%), 58 (76.4%), and 44 (57.9%), respectively. Only one isolate was sensitive to all tested antibiotics. The emergence of a high resistance rate and multidrug resistance to three or more classes of antimicrobial agents were observed. The resistance against sulphamethoxazole/trimethoprim, metronidazole, ciprofloxacin, naladixic acid, and tetracycline was 58 (76.3%), 58 (76.3%), 53 (69.7%), 51 (67.1%), and 42 (55.3%), respectively. None of the isolates was resistant to all antibiotics. Multidrug resistance to three or more classes of antimicrobial agents was found and ranged from 3.9% to 40.8%. Replacement of the Thr-86-->Ile in gyrA gene and detection of the tet(O) gene were the main resistance mechanisms for fluoroquinolones and tetracycline, respectively, while the lack of mutation in position 2074 and 2075 on the 23S rRNA gene was responsible for macrolide resistance. The phenotypic and genotypic resistance profiles were compatible in the case of ciprofloxacin and tetracycline but were not completely congruent with

  11. Determination of Ice Characteristics for Marine Hydroengineering Structures

    SciTech Connect

    Kantarzhi, I. G.; Maderich, V. S. Koshebutskii, V. I.

    2016-01-15

    Problems and potential approaches to determining ice characteristics for sea hydroengineering structures design are considered. A system for numerical modeling of ice dynamics is presented. The system may be used to define ice characteristics on approaches to structures with due regard for local hydrometeorological conditions and ice loads on structures. System application examples are presented for determining computational scenarios for ice loads at structures of the Pevek floating nuclear power plant (FNPP), as well as for the breakwater pier under reconstruction in Vanino. A scenario approach is used to determined ice loads.

  12. Structure of catalase determined by MicroED.

    PubMed

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-10-10

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

  13. Structure of catalase determined by MicroED

    PubMed Central

    Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir

    2014-01-01

    MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172

  14. Determinants encoding resistance to several heavy metals in newly isolated copper-resistant bacteria

    SciTech Connect

    Dressler, C.; Kues, U.; Nies, D.H.; Friedrich, B. )

    1991-11-01

    Three copper-resistant, gram-negative bacteria were isolated and characterized. Of the three strains, Alcaligenes dentrificans AH tolerated the highest copper concentration (MIC = 4 mM CuSO{sub 4}). All three strains showed various levels of resistance to other metal ions. A. denitrificans AH contains sequences which cross-hybridized with the mer (mercury resistance) determinant of Tn21 and the czc (cobalt, zinc, and cadmium resistance), cnr (cobalt and nickel resistance), and chr (chromate resistance) determinants of A. eutrophus CH34. DNA-DNA hybridization with probes prepared from A. eutrophus CH34 and Tn21 revealed the presence of chr-, cnr-, and mer-like sequences on the 200-kb plasmid pHG27 and of czc, cnr, and mer homologs located on the chromosomes. The second strain, classified as Alcaligenes sp. strain PW, carries czc, cnr, and mer homologs on the 240-kb plasmid pHG29-c and chr determinant on the 290-kb plasmid pHG29-a; a third plasmid, the 260-kb large plasmid pHG29-b, is cryptic. In contrast to the Alcaligenes strains, which were isolated from metal-contaminated water, Pseudomonas paucimobilis CD was isolated from the air. This strain harbors two cryptic plasmids: the 210-kb large plasmid pHG28-a and the 40-kb plasmid pHG28-b. Southern analysis revealed no homology between the metal ion resistance determinants of A. eutrophus CH34 and P. paucimonilis CD.

  15. Antimicrobial Resistance Determinants in Acinetobacter baumannii Isolates Taken from Military Treatment Facilities

    PubMed Central

    Leski, Tomasz A.; Stockelman, Michael G.; Craft, David W.; Zurawski, Daniel V.; Kirkup, Benjamin C.; Vora, Gary J.

    2014-01-01

    Multidrug-resistant (MDR) Acinetobacter baumannii infections are of particular concern within medical treatment facilities, yet the gene assemblages that give rise to this phenotype remain poorly characterized. In this study, we tested 97 clinical A. baumannii isolates collected from military treatment facilities (MTFs) from 2003 to 2009 by using a molecular epidemiological approach that enabled for the simultaneous screening of 236 antimicrobial resistance genes. Overall, 80% of the isolates were found to be MDR, each strain harbored between one and 17 resistant determinants, and a total of 52 unique resistance determinants or gene families were detected which are known to confer resistance to β-lactam (e.g., blaGES-11, blaTEM, blaOXA-58), aminoglycoside (e.g., aphA1, aacC1, armA), macrolide (msrA, msrB), tetracycline [e.g., tet(A), tet(B), tet(39)], phenicol (e.g., cmlA4, catA1, cat4), quaternary amine (qacE, qacEΔ1), streptothricin (sat2), sulfonamide (sul1, sul2), and diaminopyrimidine (dfrA1, dfrA7, dfrA19) antimicrobial compounds. Importantly, 91% of the isolates harbored blaOXA-51-like carbapenemase genes (including six new variants), 40% harbored the blaOXA-23 carbapenemase gene, and 89% contained a variety of aminoglycoside resistance determinants with up to six unique determinants identified per strain. Many of the resistance determinants were found in potentially mobile gene cassettes; 45% and 7% of the isolates contained class 1 and class 2 integrons, respectively. Combined, the results demonstrate a facile approach that supports a more complete understanding of the genetic underpinnings of antimicrobial resistance to better assess the load, transmission, and evolution of MDR in MTF-associated A. baumannii. PMID:24247131

  16. Antimicrobial resistance determinants in Acinetobacter baumannii isolates taken from military treatment facilities.

    PubMed

    Taitt, Chris Rowe; Leski, Tomasz A; Stockelman, Michael G; Craft, David W; Zurawski, Daniel V; Kirkup, Benjamin C; Vora, Gary J

    2014-01-01

    Multidrug-resistant (MDR) Acinetobacter baumannii infections are of particular concern within medical treatment facilities, yet the gene assemblages that give rise to this phenotype remain poorly characterized. In this study, we tested 97 clinical A. baumannii isolates collected from military treatment facilities (MTFs) from 2003 to 2009 by using a molecular epidemiological approach that enabled for the simultaneous screening of 236 antimicrobial resistance genes. Overall, 80% of the isolates were found to be MDR, each strain harbored between one and 17 resistant determinants, and a total of 52 unique resistance determinants or gene families were detected which are known to confer resistance to β-lactam (e.g., blaGES-11, blaTEM, blaOXA-58), aminoglycoside (e.g., aphA1, aacC1, armA), macrolide (msrA, msrB), tetracycline [e.g., tet(A), tet(B), tet(39)], phenicol (e.g., cmlA4, catA1, cat4), quaternary amine (qacE, qacEΔ1), streptothricin (sat2), sulfonamide (sul1, sul2), and diaminopyrimidine (dfrA1, dfrA7, dfrA19) antimicrobial compounds. Importantly, 91% of the isolates harbored blaOXA-51-like carbapenemase genes (including six new variants), 40% harbored the blaOXA-23 carbapenemase gene, and 89% contained a variety of aminoglycoside resistance determinants with up to six unique determinants identified per strain. Many of the resistance determinants were found in potentially mobile gene cassettes; 45% and 7% of the isolates contained class 1 and class 2 integrons, respectively. Combined, the results demonstrate a facile approach that supports a more complete understanding of the genetic underpinnings of antimicrobial resistance to better assess the load, transmission, and evolution of MDR in MTF-associated A. baumannii.

  17. Development of adaptive seismic isolators for ultimate seismic protection of civil structures

    NASA Astrophysics Data System (ADS)

    Li, Jianchun; Li, Yancheng; Li, Weihua; Samali, Bijan

    2013-04-01

    Base isolation is the most popular seismic protection technique for civil engineering structures. However, research has revealed that the traditional base isolation system due to its passive nature is vulnerable to two kinds of earthquakes, i.e. the near-fault and far-fault earthquakes. A great deal of effort has been dedicated to improve the performance of the traditional base isolation system for these two types of earthquakes. This paper presents a recent research breakthrough on the development of a novel adaptive seismic isolation system as the quest for ultimate protection for civil structures, utilizing the field-dependent property of the magnetorheological elastomer (MRE). A novel adaptive seismic isolator was developed as the key element to form smart seismic isolation system. The novel isolator contains unique laminated structure of steel and MR elastomer layers, which enable its large-scale civil engineering applications, and a solenoid to provide sufficient and uniform magnetic field for energizing the field-dependent property of MR elastomers. With the controllable shear modulus/damping of the MR elastomer, the developed adaptive seismic isolator possesses a controllable lateral stiffness while maintaining adequate vertical loading capacity. In this paper, a comprehensive review on the development of the adaptive seismic isolator is present including designs, analysis and testing of two prototypical adaptive seismic isolators utilizing two different MRE materials. Experimental results show that the first prototypical MRE seismic isolator can provide stiffness increase up to 37.49%, while the second prototypical MRE seismic isolator provides amazing increase of lateral stiffness up to1630%. Such range of increase of the controllable stiffness of the seismic isolator makes it highly practical for developing new adaptive base isolation system utilizing either semi-active or smart passive controls.

  18. Structural and functional effects of social isolation on the hippocampus of rats with traumatic brain injury.

    PubMed

    Khodaie, Babak; Lotfinia, Ahmad Ali; Ahmadi, Milad; Lotfinia, Mahmoud; Jafarian, Maryam; Karimzadeh, Fariba; Coulon, Philippe; Gorji, Ali

    2015-02-01

    Social isolation has significant long-term psychological and physiological consequences. Both social isolation and traumatic brain injury (TBI) alter normal brain function and structure. However, the influence of social isolation on recovery from TBI is unclear. This study aims to evaluate if social isolation exacerbates the anatomical and functional deficits after TBI in young rats. Juvenile male rats were divided into four groups; sham operated control with social contacts, sham control with social isolation, TBI with social contacts, and TBI with social isolation. During four weeks after brain injury in juvenile rats, we evaluated the animal behaviors by T-maze and open-field tests, recorded brain activity with electrocorticograms and assessed structural changes by histological procedures in the hippocampal dentate gyrus, CA1, and CA3 areas. Our findings revealed significant memory impairments and hyperactivity conditions in rats with TBI and social isolation compared to the other groups. Histological assessments showed an increase of the mean number of dark neurons, apoptotic cells, and caspase-3 positive cells in all tested areas of the hippocampus in TBI rats with and without social isolation compared to sham rats. Furthermore, social isolation significantly increased the number of dark cells, apoptotic neurons, and caspase-3 positive cells in the hippocampal CA3 region in rats with TBI. This study indicates the harmful effect of social isolation on anatomical and functional deficits induced by TBI in juvenile rats. Prevention of social isolation may improve the outcome of TBI.

  19. Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus.

    PubMed

    Wang, Qihui; Yang, Huabing; Liu, Xiaoqing; Dai, Lianpan; Ma, Tong; Qi, Jianxun; Wong, Gary; Peng, Ruchao; Liu, Sheng; Li, Junfu; Li, Shihua; Song, Jian; Liu, Jianying; He, Jianhua; Yuan, Hui; Xiong, Ying; Liao, Yong; Li, Jianhua; Yang, Jianping; Tong, Zhou; Griffin, Bryan D; Bi, Yuhai; Liang, Mifang; Xu, Xiaoning; Qin, Chuan; Cheng, Gong; Zhang, Xinzheng; Wang, Peiyi; Qiu, Xiangguo; Kobinger, Gary; Shi, Yi; Yan, Jinghua; Gao, George F

    2016-12-14

    The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and countermeasures are needed to treat and prevent ZIKV infection. We report the isolation of 13 specific human monoclonal antibodies from a single patient infected with ZIKV. Two of the isolated antibodies (Z23 and Z3L1) demonstrated potent ZIKV-specific neutralization in vitro without binding or neutralizing activity against strains 1 to 4 of dengue virus, the closest relative to ZIKV. These two antibodies provided postexposure protection to mice in vivo. Structural studies revealed that Z23 and Z3L1 bound to tertiary epitopes in envelope protein domain I, II, or III, indicating potential targets for ZIKV-specific therapy. Our results suggest the potential of antibody-based therapeutics and provide a structure-based rationale for the design of future ZIKV-specific vaccines.

  20. Further Study of Isolated Electrostatic Structures in the Solar Wind

    NASA Astrophysics Data System (ADS)

    Kellogg, P. J.

    2003-12-01

    A large number of short (sub-millisecond) waveforms has been observed by the Waves Time Domain Sampler on Wind. Similar waveforms have been analyzed by Mangeney et al (1999). They and Lacombe et al (2002) concentrated on double layer-like waveforms having a net potential change, but this study concentrates on electron hole-like waveforms with little potential change. The waveforms are compact, having Debye-length scales. They are often shorter than the X antenna, 100 m tip to tip, and this allows determination of their size and velocity. In many cases they are associated with magnetic discontinuities, and also in many cases occur in close proximity to ion acoustic wave bursts, from which they may evolve. Like the cases analyzed by Mangeney et al, they are quite weak, leading to electric fields of a few tenths of a millivolt per meter. Their structures are generally consistent with electron holes. Lacombe, C., C.Salem, A.Mangeney, D.Hubert, C.Perche, J-L.Bougeret, P.J.Kellogg, K.Goetz, J-M.Bosqued, "Evidence for the interplanetary potential? WIND observations of electrostatic fluctuations", Annales Geophysicae, 20, 609-618, 2002 Mangeney A., C.Salem, C.Lacombe, J-L.Bougeret, C.Perche, R.Manning, P.J.Kellogg, K.Goetz, S.J.Monson, J-M.Bosqued, "WIND observations of coherent electrostatic waves in the solar wind" Annales Geophysicae 17, 307-320, 1999

  1. Sequence determination and anticoagulant and antithrombotic activities of a novel sulfated fucan isolated from the sea cucumber Isostichopus badionotus.

    PubMed

    Chen, Shiguo; Hu, Yaqin; Ye, Xinqian; Li, Guoyun; Yu, Guangli; Xue, Changhu; Chai, Wengang

    2012-07-01

    The aim is to analyze the structure, anticoagulant and antithrombotic activities of a sulfated fucan isolated from sea cucumber Isostichopus badionotus (fucan-Ib). Fucan-Ib was hydrolyzed under mild acid conditions. The oligosaccharide fragments were fractionated by gel-filtration chromatography and the structures were determined by negative-ion electrospray tandem mass spectrometry with collision-induced dissociation and two-dimensional NMR. Anticoagulant activities were measured by activated partial thromboplastin, thrombin and prothrombin times, and by in vitro inhibition experiments with factors IIa and Xa. Antithrombotic activities were determined in vitro by measuring the length and weight of the thrombus generated. The linear polysaccharide sequence of fucan-Ib was deduced from the structures of its oligosaccharide fragments produced by acid hydrolysis. Under mild conditions, the glycosidic bonds between the non-sulfated and 2,4-O-disulfated fucose residues were selectively cleaved and highly ordered oligosaccharide fragments with a tetrasaccharide repeating unit [→3Fuc(2S,4S)α1→3Fuc(2S)α1→3Fuc(2S)α1→3Fucα1→]n were obtained. In in vitro assays fucan-Ib showed good anticoagulant and antithrombotic activities compared with heparin and the fucosylated chondroitin sulfate isolated from the same source (fCS-Ib). The two polysaccharides, fucan-Ib and fCS-Ib, differ in the mechanism of action; the former exhibited activity mainly by potentiation of antithrombin acted on thrombin and factor Xa whereas the latter mainly through heparin cofactor II. Fucan-Ib has a well defined structure with tetrasaccharide tandem repeats and good anticoagulant and antithrombotic activities. GENERAL IMPORTANCE: Fucan-Ib has a well defined structure and can be readily quality-controlled, and therefore has potential therapeutic value as an affective antithrombotic drug with low risk of bleeding. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Phytochemicals of apple peels: isolation, structure elucidation, and their antiproliferative and antioxidant activities.

    PubMed

    He, Xiangjiu; Liu, Rui Hai

    2008-11-12

    Bioactivity-guided fractionation of Red Delicious apple peels was used to determine the chemical identity of bioactive constituents, which showed potent antiproliferative and antioxidant activities. Twenty-nine compounds, including triterpenoids, flavonoids, organic acids and plant sterols, were isolated using gradient solvent fractionation, Diaion HP-20, silica gel, and ODS columns, and preparative HPLC. Their chemical structures were identified using HR-MS and 1D and 2D NMR. Antiproliferative activities of isolated pure compounds against HepG2 human liver cancer cells and MCF-7 human breast cancer cells were evaluated. On the basis of the yields of isolated flavonoids (compounds 18- 23), the major flavonoids in apple peels are quercetin-3-O-beta-D-glucopyranoside (compound 20, 82.6%), then quercetin-3-O-beta-D-galactopyranoside (compound 19, 17.1%), followed by trace amounts of quercetin (compound 18, 0.2%), (-)-catechin (compound 22), (-)-epicatechin (compound 23), and quercetin-3-O-alpha-L-arabinofuranoside (compound 21). Among the compounds isolated, quercetin (18) and quercetin-3-O-beta-D-glucopyranoside (20) showed potent antiproliferative activities against HepG2 and MCF-7 cells, with EC 50 values of 40.9 +/- 1.1 and 49.2 +/- 4.9 microM to HepG2 cells and 137.5 +/- 2.6 and 23.9 +/- 3.9 microM to MCF-7 cells, respectively. Six flavonoids (18-23) and three phenolic compounds (10, 11, and 14) showed potent antioxidant activities. Caffeic acid (10), quercetin (18), and quercetin-3-O-beta-D-arabinofuranoside (21) showed higher antioxidant activity, with EC 50 values of <10 microM. Most tested flavonoids and phenolic compounds had high antioxidant activity when compared to ascorbic acid and might be responsible for the antioxidant activities of apples. These results showed apple peel phytochemicals have potent antioxidant and antiproliferative activities.

  3. Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing.

    PubMed

    Sun, Zhihong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Yu, Jie; Bilige, Menghe; Zhang, Heping; Chen, Yongfu

    2015-05-01

    Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping genes. A total of 108 sequence types were detected, which formed 8 clonal complexes and 27 singletons. Results from Structure, SplitsTree, and ClonalFrame software analyses demonstrated the presence of 3 subpopulations in the L. helveticus isolates used in our study, namely koumiss, kurut-tarag, and panmictic lineages. Most L. helveticus isolates from particular ecological origins had specific population structures.

  4. Determination of extended spectrum beta-lactamases, metallo-beta-lactamases and AmpC-beta-lactamases among carbapenem resistant Pseudomonas aeruginosa isolated from burn patients.

    PubMed

    Neyestanaki, Davood Kalantar; Mirsalehian, Akbar; Rezagholizadeh, Fereshteh; Jabalameli, Fereshteh; Taherikalani, Morovat; Emaneini, Mohammad

    2014-12-01

    Pseudomonas aeruginosa is an important cause of morbidity and mortality in patients with burns. A total of 214 nonduplicated burn wound isolates of P. aeruginosa were recovered from burn patients. Identification of carbapenem resistant isolates and their antimicrobial susceptibility pattern was carried out using the phenotypic methods. The presence of genes encoding extended spectrum beta-lactamases (ESBLs) and metallo-beta-lactamases (MBLs) enzymes were determined by PCR. The genetic relationships between carbapenem resistant isolates were determined by Random Amplified Polymorphic DNA (RAPD)-PCR. Of 214 investigated P. aeruginosa isolates, 100 (46.7%) were carbapenem resistant. All carbapenem resistant P. aeruginosa were resistant to imipenem, meropenem, ertapenem, carbenicillin, aztreonam, gentamicin and ciprofloxacin but susceptible to polymyxin B. Among 100 carbapenem resistant P. aeruginosa isolates, 3%, 65% and 52% were identified as ESBLs, carbapenemase and AmpC overproduction positive isolates respectively. The most prevalent ESBLs and MBLs genes included blaOXA-10 (97%), blaTEM (61%), blaVIM (55%), blaPER (13%), blaIMP (3%) and blaAIM (1%). RAPD analysis yielded 13 distinct profiles among 92 isolates. A dominant RAPD type was designated as A that consisting of 80 isolates. This is the first report of Adelaide IMipenmase (AIM) MBLs producing P. aeruginosa from Iran and also of the high prevalence of AmpC overproduction isolates. According to the results of current study, P. aeruginosa isolates producing OXA-10, TEM, VIM, PER and IMP beta-lactamases are frequent and the population structures of these isolates are highly similar. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

  5. Genetic structure and isolation by distance in a landrace of Thai rice

    PubMed Central

    Pusadee, Tonapha; Jamjod, Sansanee; Chiang, Yu-Chung; Rerkasem, Benjavan; Schaal, Barbara A.

    2009-01-01

    Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans. PMID:19651617

  6. Prevalence and detection of antibiotic-resistant determinant in Salmonella isolated from food-producing animals.

    PubMed

    Igbinosa, Isoken Henrietta

    2015-01-01

    Salmonella spp. infections are considered as the most common food-borne disease globally. The contamination of food products with Salmonella has given rise to severe health and economic challenges. This study assessed the prevalence of Salmonella in the faeces of cows and goats in the Eastern Cape province of South Africa, their antibiotic resistance patterns as well as antibiotic-resistant gene determinant. Antibiotic disc was used for antibiogram profiles while polymerase chain reaction was employed for the detection of antibiotic-resistant genes. A total of 150 Salmonella were isolated from the faecal samples. Eighty two (55%) isolates were recovered from cow faeces while 68 (45%) were isolated from goat faeces. All Salmonella isolates were sensitive to ciprofloxacin (100%) while 95% were sensitive to ofloxacin. Also, a high sensitivity of 93 and 89% was observed against nalidixic acid and ofloxacin, respectively. Salmonella isolates demonstrated moderate sensitivity against cephalothin (70%), chloramphenicol (75%) and minocycline (68%) while 49% were resistant to tetracycline and erythromycin. The prevalence of the antibiotic-resistant genes in Salmonella isolates were detected as follows: integron conserved segment 28% (42/150), bla TEM gene 19.3% (29/150), blapse₁ 7.3% (11/150) and blaampC 4.7% (7/150). The results obtained in the study imply that cow and goat faeces could be potential reservoirs of Salmonella and could possibly cause infections as a result of contamination of food products. There is a need for a surveillance system to track resistance patterns of Salmonella circulating in South Africa.

  7. Comparison of cultural and analytical methods for determination of aflatoxin production by Mississippi Delta Aspergillus isolates.

    PubMed

    Abbas, Hamed K; Zablotowicz, R M; Weaver, M A; Horn, B W; Xie, W; Shier, W T

    2004-03-01

    This study compared cultural and analytical methods for detecting aflatoxin production by Aspergillus species. Aspergillus isolates were obtained from various Mississippi Delta crops (corn, peanut, rice, cotton) and soils. Most of the isolates (99%) were A. flavus and the remainder comprised A. parasiticus and A. nomius. The following three cultural methods were evaluated on potato dextrose agar: fluorescence (FL) on beta-cyclodextrin-containing media (CD), yellow pigment (YP) formation in mycelium and medium, and color change after ammonium hydroxide vapor exposure (AV). Aflatoxins in culture extracts were confirmed by thin-layer chromatography (TLC) and quantified by enzyme-linked immunosorbent assay (ELISA). Of the 517 isolates, 314 produced greater than 20 ng/g of total aflatoxin based on ELISA, and 180 produced greater than 10 000 ng/g of aflatoxin in the medium. Almost all the toxigenic isolates (97%) were confirmed by TLC as producers. Of the toxigenic isolates, as determined by ELISA, 93%, 73%, and 70% gave positive FL, YP, and AV responses, respectively. Of the 203 isolates producing less than 20 ng/g of aflatoxin, 20%, 6%, and 0% of respective FL, YP, and AV methods gave false-positive responses. The 9% false-positive results from TLC fall within this range. This study showed good agreement among all tested cultural methods. However, these cultural techniques did not detect aflatoxin in all cultures that were found to produce aflatoxins by ELISA, LC/MS, and TLC. The best results were obtained when the AV color change and CD fluorescence methods were used together, yielding an overall success rate comparable to TLC but without the need for chemical extraction and the time and expense of TLC.

  8. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  9. Algorithms for Determining Physical Responses of Structures Under Load

    NASA Technical Reports Server (NTRS)

    Richards, W. Lance; Ko, William L.

    2012-01-01

    Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

  10. Virulence and Resistance Determinants of German Staphylococcus aureus ST398 Isolates from Nonhuman Sources▿†

    PubMed Central

    Argudín, M. A.; Tenhagen, B.-A.; Fetsch, A.; Sachsenröder, J.; Käsbohrer, A.; Schroeter, A.; Hammerl, J. A.; Hertwig, S.; Helmuth, R.; Bräunig, J.; Mendoza, M. C.; Appel, B.; Rodicio, M. R.; Guerra, B.

    2011-01-01

    A series of 100 Staphylococcus aureus isolates ascribed to sequence type 398 (ST398) and recovered from different sources (healthy carrier and diseased pigs, dust from pig farms, milk, and meat) in Germany were investigated for their virulence and antimicrobial resistance genetic background. Antimicrobial resistance was determined by the disk diffusion method. Virulence and resistance determinants (37 and 31 genes, respectively) were tested by PCR. Only two virulence profiles, including the accessory gene regulator agrI and three or four hemolysin-encoding genes, were detected. In contrast, 33 resistance profiles were distinguished (only 11 were shown by more than one isolate). Fifty-nine isolates were multiresistant (four or more antimicrobial classes), and 98 were methicillin resistant (mecA positive). All of the ST398 isolates showed resistance to tetracycline [encoded by tet(M) alone or together with tet(K) and/or tet(L)]. In addition, 98% were resistant to other antimicrobials, including macrolide-lincosamine-streptogramin B (70%, encoded by ermA, ermB, and ermC, alone or in combination), trimethoprim (65%, mostly due to dfrK and dfrG), kanamycin and gentamicin [29% and 14%, respectively, mainly related to aac(6′)-Ie-aph(2″)-Ia and/or ant(4′)-Ia but also to aph(3′)-IIIa], chloramphenicol (9%, fexA or cfr), quinupristin-dalfopristin (9%), ciprofloxacin (8%), and trimethoprim-sulfamethoxazole (4%). The heterogeneity of the resistance profiles underlines the ability of the ST398 clone to acquire multiple antimicrobial resistance genes. However, the virulence gene content of the tested isolates was low. Continuous surveillance is needed to clarify whether its pathogenicity potential for animals and humans will increase over time. PMID:21378035

  11. Structural determination of two new steroidal saponins from Smilax china.

    PubMed

    Huang, Hui-Lian; Liu, Rong-Hua; Shao, Feng

    2009-09-01

    Two new steroidal saponins (1 and 2) were isolated from the BuOH fraction of the 70% EtOH extract of the tubes of Smilax china, together with four known analogues, 3-6. The structures of the new compounds were elucidated by means of chemical evidence and spectroscopic analyses, including HR-MS, IR, (1)H- and (13)C-NMR, and 2D experiments ((1)H-(1)H COSY, HSQC and HMBC).

  12. Target selection and determination of function in structural genomics.

    PubMed

    Watson, James D; Todd, Annabel E; Bray, James; Laskowski, Roman A; Edwards, Aled; Joachimiak, Andrzej; Orengo, Christine A; Thornton, Janet M

    2003-01-01

    The first crucial step in any structural genomics project is the selection and prioritization of target proteins for structure determination. There may be a number of selection criteria to be satisfied, including that the proteins have novel folds, that they be representatives of large families for which no structure is known, and so on. The better the selection at this stage, the greater is the value of the structures obtained at the end of the experimental process. This value can be further enhanced once the protein structures have been solved if the functions of the given proteins can also be determined. Here we describe the methods used at either end of the experimental process: firstly, sensitive sequence comparison techniques for selecting a high-quality list of target proteins, and secondly the various computational methods that can be applied to the eventual 3D structures to determine the most likely biochemical function of the proteins in question.

  13. Engine isolation for structural-borne interior noise reduction in a general aviation aircraft

    NASA Technical Reports Server (NTRS)

    Unruh, J. F.; Scheidt, D. C.

    1981-01-01

    Engine vibration isolation for structural-borne interior noise reduction is investigated. A laboratory based test procedure to simulate engine induced structure-borne noise transmission, the testing of a range of candidate isolators for relative performance data, and the development of an analytical model of the transmission phenomena for isolator design evaluation are addressed. The isolator relative performance test data show that the elastomeric isolators do not appear to operate as single degree of freedom systems with respect to noise isolation. Noise isolation beyond 150 Hz levels off and begins to decrease somewhat above 600 Hz. Coupled analytical and empirical models were used to study the structure-borne noise transmission phenomena. Correlation of predicted results with measured data show that (1) the modeling procedures are reasonably accurate for isolator design evaluation, (2) the frequency dependent properties of the isolators must be included in the model if reasonably accurate noise prediction beyond 150 Hz is desired. The experimental and analytical studies were carried out in the frequency range from 10 Hz to 1000 Hz.

  14. [Study on the structure of defatted wheat germ protein isolate under ultrasonic treatment].

    PubMed

    Liu, Bin; Ma, Hai-Le; Li, Shu-Jun; Tian, Wan-Min; Wu, Ben-Gang

    2011-08-01

    The structure changes of defatted wheat germ protein Isolate (DWGP) treated by ultrasonic was determined by FTIR and fluorescence spectra, and the effect of its structure changes on the high-efficient enzymatic hydrolysis was studied. Research showed that the efficiency of hydrolysate could be improved by ultrasonic treatment. Compared with control group, inhibitory activity of the hydrolysate was increased by 23.96% after the treatment of 600 W for 10 min. The fluorescence intensity of DWGP after ultrasonic treatment was found discovered to be changed. An appropriate ultrasonic treatment can unfold the protein molecule and make the chromogenic groups uncovered, which contribute to the acquirement of the higher-activity inhibitory peptide. The effects of various ultrasonic power and time on the secondary structure of DWGP were quantitatively determined via analysis of the amide I changes of infrared spectra using curve fitting method. Content of beta-sheet was decreased and beta-turn was increased after ultrasonic treatment, which could be the main factor to make the prepared inhibitory peptides high efficient. The results provide a theoretical basis for the mechanism research of enzymatic hydrolysis of ultrasonic treated protein.

  15. Application of adaptive trusses to vibration isolation in flexible structures

    NASA Technical Reports Server (NTRS)

    Clark, William W.; Robertshaw, Harry H.

    1992-01-01

    It is shown through analysis that force feedback can be used to provide complete vibration isolation in two directions. Simultations were carried out to demonstrate the use of two control methods applied to an adaptive truss as an active mount. The first technique was simple force feedback with a gain. This method has the potential to provide excellent vibration isolation performance. It requires no model of the system and no knowledge of the applied disturbance, and is easily implemented in an adaptive truss. There is some question as to how high the gain can be allowed to go but the experimental results have shown performance advantages over passive techniques even for small gains. The second technique presented is the LQR method, with disturbance modeling. A method is presented for using the LQR method for vibration isolation with the intention of achieving performance with guaranteed stability and relatively lower loop gains. The overhead for those benefits is an accurate system model. It was shown analytically that this method works; however, the performance is not as good as expected. It is believed that the difference in performance is partly due to an increase in active damping which is inadvertently provided by the LQR method.

  16. Structural Requirements for the Action of Neurohypophyseal Hormones upon the Isolated Amphibian Urinary Bladder

    PubMed Central

    Rasmussen, Howard; Schwartz, Irving L.; Young, Richard; Marc-Aurele, Julien

    1963-01-01

    The response of the isolated amphibian urinary bladder to thirty-four structural analogs of arginine vasotocin was determined in an effort to define the physiological significance of specific structural groups on the hormone molecule. All but one of the analogs tested possessed full intrinsic activity in this system but varied greatly in their affinity for the receptor site. An analysis of the effect of changes in hydrogen ion concentration upon the response of the bladder to oxytocin was performed in order to determine the number and nature of the ionizable groups involved in hormone receptor interaction. Two ionizable groups with apparent pK's of 7.1 and 7.75 were found to be important in determining the magnitude of the hormonal response. On the basis of the results it was postulated that hormone-receptor interaction can be considered a two-step process: (a) The binding or attachment of hormone to receptor site through ionic, hydrogen, and hydrophobic bonds and (b) a disulfide interchange reaction between hormonal disulfide and receptor sulfhydryl. The latter step is considered to be the reaction which initiates the chain of events leading to the observed change in permeability. PMID:14042998

  17. Nature's Anti-Alzheimer's Drug: Isolation and Structure Elucidation of Galantamine from "Leucojum Aestivum"

    ERIC Educational Resources Information Center

    Halpin, Catherine M.; Reilly, Ciara; Walsh, John J.

    2010-01-01

    The discovery that galantamine penetrates the blood-brain barrier has led to its clinical use in the treatment of choline-deficiency conditions in the brain, such as Alzheimer's disease. This experiment involves the isolation and structure elucidation of galantamine from "Leucojum aestivum". Isolation of the alkaloid constituents in "L. aestivum"…

  18. Nature's Anti-Alzheimer's Drug: Isolation and Structure Elucidation of Galantamine from "Leucojum Aestivum"

    ERIC Educational Resources Information Center

    Halpin, Catherine M.; Reilly, Ciara; Walsh, John J.

    2010-01-01

    The discovery that galantamine penetrates the blood-brain barrier has led to its clinical use in the treatment of choline-deficiency conditions in the brain, such as Alzheimer's disease. This experiment involves the isolation and structure elucidation of galantamine from "Leucojum aestivum". Isolation of the alkaloid constituents in "L. aestivum"…

  19. Population Structure of Blueberry Mosaic Associated Virus: Evidence of Genetic Exchange in Geographically Distinct Isolates

    USDA-ARS?s Scientific Manuscript database

    The population structure of blueberry mosaic associated virus (BlMaV), a putative member of the family Ophioviridae, was examined using 59 isolates collected from North America and Slovenia. The studied isolates displayed low genetic diversity in the movement and nucleoprotein regions and low ratios...

  20. The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Mills, A. L.

    2005-01-01

    To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial

  1. Isolation and characterization of structural components of Aloe vera L. leaf pulp.

    PubMed

    Ni, Y; Turner, D; Yates, K M; Tizard, I

    2004-12-20

    The clear pulp, also known as inner gel, of Aloe vera L. leaf is widely used in various medical, cosmetic and nutraceutical applications. Many beneficial effects of this plant have been attributed to the polysaccharides present in the pulp. However, discrepancies exist regarding the composition of pulp polysaccharide species and an understanding of pulp structure in relation to its chemical composition has been lacking. Thus, we examined pulp structure, isolated structural components and determined their carbohydrate compositions along with analyzing a partially purified pulp-based product (Acemannan hydrogel) used to make Carrisyn hydrogel wound dressing. Light and electron microscopy showed that the pulp consisted of large clear mesophyll cells with a diameter as large as 1000 microm. These cells were composed of cell walls and cell membranes along with a very limited number of degenerated cellular organelles. No intact cellular organelles were found in mesophyll cells. Following disruption of pulp by homogenization, three components were isolated by sequential centrifugation. They were thin clear sheets, microparticles and a viscous liquid gel, which corresponded to cell wall, degenerated cellular organelles and liquid content of mesophyll cells based on morphological and chemical analysis. These three components accounted for 16.2% (+/-3.8), 0.70% (+/-0) and 83.1% of the pulp on a dry weight basis. The carbohydrate composition of each component was distinct; liquid gel contained mannan, microparticles contained galactose-rich polysaccharide(s) and cell walls contained an unusually high level of galacturonic acid (34%, w/w; Gal A). The same three components were also found in Acemannan Hydrogel with mannan as the predominant component. Thus, different pulp structural components are associated with different polysaccharides and thus may potentially be different functionally. These findings may help lay a basis for further studies and development of better

  2. Nutritional milieu of isolated stromal vascular cells determines their proliferative, adipogenic, and lipogenic capacity in vitro

    PubMed Central

    Kadegowda, Anil K G; Wright, Asher; Duckett, Susan K

    2014-01-01

    The objective was to determine the effect of nutritional milieu of isolated stromal vascular (SV) cells on proliferative capacity of preadipocytes, and adipogenic and lipogenic capacity in adipocytes in vitro. Proliferation of the preadipocytes increased over time with 48 and 72 h being greater than 24 h; however, preadipocytes from steers supplemented with corn (LC) had lower proliferation rates compared with those without corn grain supplementation (L) at 72 h. Adipocyte cultures isolated from LC group had higher mean diameter on d 4 and 6, and higher mean volume on d 0, 4, 6, and 12 of culture. Adipocytes from steers supplemented with corn grain (LC) had lower expression of key adipogenic genes during extended days in culture. The results show that prior nutritional treatment of the donor animal used to isolate SV cultures alters their proliferative, adipogenic, and lipogenic capacity in culture. These differences may be related to lower induction/expression of AP2 gene in the adipose cultures from corn supplemented group. Corn grain supplementation to steers grazing legumes could have stimulated more active adipogenic progenitor cells to differentiate, which would leave fewer behind in the SV pool for subsequent isolation. PMID:26317055

  3. Submicrometer Single Crystal Diffractometry for Highly Accurate Structure Determination

    SciTech Connect

    Yasuda, Nobuhiro; Fukuyama, Yoshimitsu; Kimura, Shigeru; Toriumi, Koshiro; Takata, Masaki

    2010-06-23

    Submicrometer single crystal diffractometry for highly accurate structure determination was developed using the extremely stable and highly brilliant synchrotron radiation from SPring-8. This was achieved using a microbeam focusing system and the submicrometer precision low-eccentric goniometer system. We demonstrated the structure analyses with 2x2x2 {mu}m{sup 3} cytidine, 600x600x300 nm{sup 3} BaTiO{sub 3}, and 1x1x1 {mu}m{sup 3} silicon. The observed structure factors of the silicon crystal were in agreement with the structure factors determined by the Pendelloesung method and do not require absorption and extinction corrections.

  4. H-point curve isolation method for determination of catechol in complex unknown mixtures

    NASA Astrophysics Data System (ADS)

    Hasani, Masoumeh; Mohammadi, Masoumeh; Shariati-Rad, Masoud; Abdollahi, Hamid

    2012-10-01

    In this work, the combination of H-point curve isolation method (HPCIM) and H-point standard additions method (HPSAM) was used for determination of catechol in the presence of phenolic interferents. Spectrophotometric multivariate calibration data constructed by successive standard additions of an analyte in an unknown matrix was used by the method. A cumulative spectrum for interferents in sample was extracted by HPCIM and then HPSAM is used for determination of the catechol concentration by obtained cumulative interferents spectrum. The method was tested with simulated data set. The spectrum obtained from applying HPCIM to the simulated data well agrees with the cumulative spectra of the interferents. The method was applied to the determination of catechol in the presence of highly overlapping interferents in synthetic ternary mixtures using spectrophotometric data. Moreover, the proposed method was successfully used for determination of catechol in real complicated matrices of tea and urine samples. Percent recoveries were between 95.4 and 113.6.

  5. H-point curve isolation method for determination of catechol in complex unknown mixtures.

    PubMed

    Hasani, Masoumeh; Mohammadi, Masoumeh; Shariati-Rad, Masoud; Abdollahi, Hamid

    2012-10-01

    In this work, the combination of H-point curve isolation method (HPCIM) and H-point standard additions method (HPSAM) was used for determination of catechol in the presence of phenolic interferents. Spectrophotometric multivariate calibration data constructed by successive standard additions of an analyte in an unknown matrix was used by the method. A cumulative spectrum for interferents in sample was extracted by HPCIM and then HPSAM is used for determination of the catechol concentration by obtained cumulative interferents spectrum. The method was tested with simulated data set. The spectrum obtained from applying HPCIM to the simulated data well agrees with the cumulative spectra of the interferents. The method was applied to the determination of catechol in the presence of highly overlapping interferents in synthetic ternary mixtures using spectrophotometric data. Moreover, the proposed method was successfully used for determination of catechol in real complicated matrices of tea and urine samples. Percent recoveries were between 95.4 and 113.6.

  6. Reduction of structural response to near fault earthquakes by seismic isolation columns and variable friction dampers

    NASA Astrophysics Data System (ADS)

    Ribakov, Y.

    2010-03-01

    This paper focuses on the investigation of a hybrid seismic isolation system with passive variable friction dampers for protection of structures against near fault earthquakes. The seismic isolation can be implemented by replacing the conventional columns fixed to the foundations by seismic isolating ones. These columns allow horizontal displacement between the superstructure and the foundations and decouple the building from the damaging earthquake motion. As a result, the forces in the structural elements decrease and damage that may be caused to the building by the earthquake significantly decreases. However, this positive effect is achieved on account of displacements occurring in the isolating columns. These displacements become very large when the structure is subjected to a strong earthquake. In this case, impact may occur between the parts of the isolating column yielding their damage or collapse. In order to limit the displacements in the isolating columns, it is proposed to add variable friction dampers. A method for selecting the dampers’ properties is proposed. It is carried out using an artificial ground motion record and optimal active control algorithm. Numerical simulation of a sevenstory structure shows that the proposed method allows efficient reduction in structural response and limits the displacements at the seismic isolating columns.

  7. Seismic Performance of a Base Isolated Structure by Shake Table Tests

    SciTech Connect

    Yenidogan, Cem; Uckan, Eren

    2008-07-08

    A 1/4 scaled model structure has been tested on a shake table to investigate the effectiveness of a passive-hybrid isolation system for a three-storey mass concentric steel structure. The isolation system consists of two high damping rubber bearings (HDRB) and four flat sliding bearings (PTFE), which are located below the central and corner columns, respectively. To maintain dynamic similitude, each earthquake record was compressed in time by a factor of two. Measurements were taken at structural points and at the bearings. Two different type of HDRB's were tested. A numerical model for the structure was developed and calibrated by the data from the experimental studies. The effectiveness of the hybrid isolation system is verified by comparing the results obtained from both isolated and fixed base models.

  8. Structural design of active seismic isolation floor with a charging function

    NASA Astrophysics Data System (ADS)

    Nakakoji, Hayato; Miura, Nanako

    2016-04-01

    This study shows an optimum structure of a seismic isolation floor against horizontal ground motions. Although a seismic isolation floor is effective with vibration reduction, the response of the floor becomes larger when excited by long-period ground motions. It is shown that caster equipment move and suffer damage in a seismic isolation structure by an experiment. Moreover, the permissible displacement of the floor is limited. Therefore, the focus is on an active seismic isolation. About active control, the system cannot operate without power supply. To solve these problems an energy regeneration is considered in our previous study. These studies only analyze simple model and did not choose the suitable structure for active control and energy regeneration. This research propose a new structure which has regenerated energy exceeds the energy required for the active control by numerical simulation.

  9. Structures of wall heterogalactomannans isolated from three genera of entomopathogenic fungi.

    PubMed

    Bernabé, Manuel; Salvachúa, Davinia; Jiménez-Barbero, Jesús; Leal, Juan Antonio; Prieto, Alicia

    2011-09-01

    O-linked heterogalactomannans with similar structural features have been purified from the fungal walls of the entomopathogenic fungi Lecanicillium muscarium, Beauveria bassiana, Beauveriabrongniartii, and Cordyceps sphingum. Their composition and structure have been determined using acid hydrolysis, methylation analysis, gas-liquid chromatography-mass spectrometry (GC-MS) and Nuclear magnetic resonance spectroscopy (NMR). All structures have an α-(1→6)-mannose backbone, but one of the two strains of L. muscarium included in this study contained an acidic heterogalactomannan instead of the neutral polysaccharide isolated in the rest of the species analyzed. Sequence analysis of the internal transcribed spacer (ITS) region of this strain indicated that it belongs to the related genus Simplicillium, displaying low identity (83%) with the closest Lecanicillium species. This is a new demonstration of the structural diversity of fungal wall heteromannans and validates their interest as chemotaxonomic markers. The production of a pullulan-like extracellular polysaccharide in strain CBS 413.70C of L. muscarium is also reported. Copyright © 2011 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  10. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    SciTech Connect

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  11. Spatial and temporal determinants of genetic structure in Gentianella bohemica

    PubMed Central

    Königer, Julia; Rebernig, Carolin A; Brabec, Jiří; Kiehl, Kathrin; Greimler, Josef

    2012-01-01

    The biennial plant Gentianella bohemica is a subendemic of the Bohemian Massif, where it occurs in seminatural grasslands. It has become rare in recent decades as a result of profound changes in land use. Using amplified fragment length polymorphisms (AFLP) fingerprint data, we investigated the genetic structure within and among populations of G. bohemica in Bavaria, the Czech Republic, and the Austrian border region. The aim of our study was (1) to analyze the genetic structure among populations and to discuss these findings in the context of present and historical patterns of connectivity and isolation of populations, (2) to analyze genetic structure among consecutive generations (cohorts of two consecutive years), and (3) to investigate relationships between intrapopulational diversity and effective population size (Ne) as well as plant traits. (1) The German populations were strongly isolated from each other (pairwise FST= 0.29–0.60) and from all other populations (FST= 0.24–0.49). We found a pattern of near panmixis among the latter (FST= 0.15–0.35) with geographical distance explaining only 8% of the genetic variance. These results were congruent with a principal coordinate analysis (PCoA) and analysis using STRUCTURE to identify genetically coherent groups. These findings are in line with the strong physical barrier and historical constraints, resulting in separation of the German populations from the others. (2) We found pronounced genetic differences between consecutive cohorts of the German populations (pairwise FST= 0.23 and 0.31), which can be explained by local population history (land use, disturbance). (3) Genetic diversity within populations (Shannon index, HSh) was significantly correlated with Ne (RS= 0.733) and reflected a loss of diversity due to several demographic bottlenecks. Overall, we found that the genetic structure in G. bohemica is strongly influenced by historical periods of high connectivity and isolation as well as by marked

  12. Demographic structure and microevolution of an Italian alpine isolated population.

    PubMed

    Sella, G; Marin, A; Santovito, A; Girotti, M; Cervella, P; Delpero, M

    2010-08-01

    The isonymic method has been generally accepted in population genetic studies and surnames have been successfully used to investigate human populations as if they were genetic markers associated to the Y chromosome. In this study we analysed the microevolution dynamics of Postua, a mountain village of North Western Italy, by means of demographic methods. The uniqueness of this community is due to its past geographical and cultural isolation and to the high frequency of marriage between relatives. During the study period considered (1640-1989) the population underwent several fluctuations in size and other demographic parameters such as the endogamy, isonimy and consanguinity rates. Until the first half of the XIX century Postua appears to be a village characterised by a closed and isolated community, with high endogamy (80-90%) and isonimy (up to 34.4%). Only at the beginning of the XX century, when the population started to be subjected to significant immigration fluxes, data show a progressive reduction of the isolation. The population showed two demographic peaks, the first around the second half of the XVIII century (1639 inhabitants) and the second at the end of the XIX century (1464 inhabitants). The S/Nratio was low (0.2-0.3) and relatively constant until the beginning of the last century, and only in the last three decades of the XX century, when the population was subjected to immigration, Postua showed a significant increase in the S/Nratio values (to about 0.9). The surname frequency was constant until the 1850 when almost all surnames were the same as those already present in the XVII century. From the first half of the XIX century, the founder surnames decreased, whereas new surnames started to increase and became persistent in the population.

  13. Determining the surface and interface structure of nanomaterials

    SciTech Connect

    Van Hove, Michel A.

    2004-06-14

    This paper informally speculates on the challenges of determining the atomic-scale surface and interface structure of nanomaterials. The relative capabilities of different techniques are compared. This includes discussion of theoretical methods needed to interpret experimental techniques.

  14. Isolation, subunit structure, and proteolytic modification of bovine factor VIII.

    PubMed

    Legaz, M E; Weinstein, M J; Heldebrant, C M; Davie, E W

    1975-01-20

    A new method has been described for the isolation of factor VIII. The method results in a high yield of factor VIII that is homogeneous by several different criteria. The purified protein is very stable and is not dissociated in the presence of 1 M NaCl or 0.25 M CaCl2. The highly purified protein is readily activated and inactivated by various proteolytic enzymes, such as thrombin, plasmin, and trypsin. The molecular events that lead to the activation reaction, however, have not been established.

  15. Isolation, Structure Elucidation and Total Synthesis of Lajollamide A from the Marine Fungus Asteromyces cruciatus

    PubMed Central

    Gulder, Tobias A. M.; Hong, Hanna; Correa, Jhonny; Egereva, Ekaterina; Wiese, Jutta; Imhoff, Johannes F.; Gross, Harald

    2012-01-01

    The marine-derived filamentous fungus Asteromyces cruciatus 763, obtained off the coast of La Jolla, San Diego, USA, yielded the new pentapeptide lajollamide A (1), along with the known compounds regiolone (2), hyalodendrin (3), gliovictin (4), 1N-norgliovicitin (5), and bis-N-norgliovictin (6). The planar structure of lajollamide A (1) was determined by Nuclear Magnetic Resonance (NMR) spectroscopy in combination with mass spectrometry. The absolute configuration of lajollamide A (1) was unambiguously solved by total synthesis which provided three additional diastereomers of 1 and also revealed that an unexpected acid-mediated partial racemization (2:1) of the L-leucine and L-N-Me-leucine residues occurred during the chemical degradation process. The biological activities of the isolated metabolites, in particular their antimicrobial properties, were investigated in a series of assay systems. PMID:23342379

  16. Structure and bioactivity of steroidal saponins isolated from the roots of Chamaelirium luteum (false unicorn).

    PubMed

    Challinor, Victoria L; Stuthe, Julia M U; Parsons, Peter G; Lambert, Lynette K; Lehmann, Reginald P; Kitching, William; De Voss, James J

    2012-08-24

    Phytochemical investigation of Chamaelirium luteum ("false unicorn") resulted in the isolation of 15 steroidal glycosides. Twelve of these (1, 2, 4-9, 11-13, and 15) are apparently unique to this species, and eight of these (6-9, 11-13, and 15) are previously unreported compounds; one (15) possesses a new steroidal aglycone. In addition, the absolute configuration of (23R,24S)-chiograsterol A (10) was defined, and its full spectroscopic characterization is reported for the first time. The structures and configurations of the saponins were determined using a combination of multistage mass spectrometry (MS(n)), 1D and 2D NMR experiments, and chemical degradation. The antiproliferative activity of nine compounds obtained in the present work, and eight related compounds generated in previous work, was compared in six human tumor cell lines, with aglycones 3 and 10 and related derivatives 16, 17, 19, and 20 all displaying significant antiproliferative activity.

  17. Isolation and structural elucidation of two impurities from a diacerein bulk drug.

    PubMed

    Ashok, Chaudhari; Golak, Maikap; Adwait, Deo; Krishna, Vivek; Himani, Agrawal; Umesh, Peshawe; Amol, Gawande; Srinivas, Sompalli; Sharad, Mane; Deepali, Jadhav; Atul, Chaudhari

    2009-02-20

    Two impurities were found in the crude sample of diacerein. The level of these impurities 1.14% and 1.24% were detected by isocratic reverse-phase high performance liquid chromatography (HPLC). The molecular weights of the impurities were determined by liquid chromatography-mass spectroscopy (LC-MS) analysis. These impurities were isolated from crude sample of diacerein by reverse-phase preparative liquid chromatography. These impurities were characterized as 5-acetoxy-4-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (Impurity-1) and 4-acetoxy-5-hydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (Impurity-2) respectively. Structural elucidation of both the impurities were carried out by (1)H NMR, (13)C NMR, DEPT, 1D NOESY, MS and IR spectroscopy.

  18. Structure Determination of Membrane Proteins in Five Easy Pieces

    PubMed Central

    Marassi, Francesca M.; Das, Bibhuti B.; Lu, George J.; Nothnagel, Henry J.; Park, Sang Ho; Son, Woo Sung; Tian, Ye; Opella, Stanley J.

    2011-01-01

    A general method for determining the structures of membrane proteins in phospholipid bilayers under physiological conditions is described. Membrane proteins are high priority targets for structure determination, and are challenging for the existing experimental methods. Because membrane proteins reside in a liquid crystalline phospholipid bilayer membranes it is important to study them in this type of environment. The approach we have developed can be summarized in five steps, and incorporates methods of molecular biology, biochemistry, sample preparation, construction and modification of NMR instrumentation, the development and execution of NMR experiments, and structure calculations. It relies on solid-state NMR spectroscopy to obtain high-resolution spectra and residue-specific structural restraints for membrane proteins which undergo rotational diffusion around the membrane normal, but whose mobility is otherwise restricted by interactions with the membrane phospholipids. The spectra of membrane proteins alone and in complex with other proteins and ligands set the stage for structure determination and functional studies. PMID:21964394

  19. Ambiguity of structure determination from a minimum of diffraction intensities.

    PubMed

    Al-Asadi, Ahmed; Leggas, Dimitri; Tsodikov, Oleg V

    2014-07-01

    Although the ambiguity of the crystal structures determined directly from diffraction intensities has been historically recognized, it is not well understood in quantitative terms. Bernstein's theorem has recently been used to obtain the number of one-dimensional crystal structures of equal point atoms, given a minimum set of diffraction intensities. By a similar approach, the number of two- and three-dimensional crystal structures that can be determined from a minimum intensity data set is estimated herein. The ambiguity of structure determination from the algebraic minimum of data increases at least exponentially fast with the increasing structure size. Substituting lower-resolution intensities by higher-resolution ones in the minimum data set has little or no effect on this ambiguity if the number of such substitutions is relatively small.

  20. Structure of an isolated unglycosylated antibody C(H)2 domain.

    PubMed

    Prabakaran, Ponraj; Vu, Bang K; Gan, Jianhua; Feng, Yang; Dimitrov, Dimiter S; Ji, Xinhua

    2008-10-01

    The C(H)2 (C(H)3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein-protein interactions with another C(H)2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C(H)2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody gamma1 C(H)2 domain was determined at 1.7 A resolution and compared with corresponding C(H)2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C(H)2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C(H)2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications.

  1. Structure of an isolated unglycosylated antibody C[subscript H]2 domain

    SciTech Connect

    Prabakaran, Ponraj; Vu, Bang K.; Gan, Jianhua; Feng, Yang; Dimitrov, Dimiter S.; Ji, Xinhua

    2009-01-15

    The C{sub H}2 (C{sub H}3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein-protein interactions with another C{sub H}2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C{sub H}2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody gamma1 C{sub H}2 domain was determined at 1.7 A resolution and compared with corresponding C{sub H}2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C{sub H}2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C{sub H}2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications.

  2. Rapid Screening Tests for Determining In Vitro Susceptibility of Herpes Simplex Virus Clinical Isolates

    PubMed Central

    de la Iglesia, Pedro; Melón, Santiago; López, Beatriz; Rodriguez, Mercedes; Blanco, Maria I.; Mellado, Purificación; de Oña, Maria

    1998-01-01

    The susceptibility of human herpes simplex virus (HSV) to acyclovir (ACV) was determined with the use of a single dose of the drug (1 and 2 μg of ACV per ml for HSV-1 and HSV-2, respectively) in two rapid assays: a rapid cytopathic effect inhibitory assay (Rapid CIA) and a rapid dye uptake assay (Rapid DUA). These tests allow the simultaneous determination of virus titer and susceptibility to ACV at a determined viral concentration (100 50% tissue culture infective doses and 100 50% dye uptake units). These tests were compared with a conventional susceptibility assay (dye uptake assay) and showed similar results. Indeterminate results with the Rapid CIA appeared in 3 of 30 samples. With the use of both Rapid CIA and Rapid DUA, we were able to determine the susceptibility of 100% of the isolates. The rapid tests, unlike conventional assays, are able to provide susceptibility results within 3 days after the virus has been isolated from a clinical specimen and could thus play a direct role in therapeutic decisions. PMID:9666034

  3. Rapid screening tests for determining in vitro susceptibility of herpes simplex virus clinical isolates.

    PubMed

    de la Iglesia, P; Melón, S; López, B; Rodriguez, M; Blanco, M I; Mellado, P; de Oña, M

    1998-08-01

    The susceptibility of human herpes simplex virus (HSV) to acyclovir (ACV) was determined with the use of a single dose of the drug (1 and 2 micrograms of ACV per ml for HSV-1 and HSV-2, respectively) in two rapid assays: a rapid cytopathic effect inhibitory assay (Rapid CIA) and a rapid dye uptake assay (Rapid DUA). These tests allow the simultaneous determination of virus titer and susceptibility to ACV at a determined viral concentration (100 50% tissue culture infective doses and 100 50% dye uptake units). These tests were compared with a conventional susceptibility assay (dye uptake assay) and showed similar results. Indeterminate results with the Rapid CIA appeared in 3 of 30 samples. With the use of both Rapid CIA and Rapid DUA, we were able to determine the susceptibility of 100% of the isolates. The rapid tests, unlike conventional assays, are able to provide susceptibility results within 3 days after the virus has been isolated from a clinical specimen and could thus play a direct role in therapeutic decisions.

  4. Latency is the major determinant of UDP-glucuronosyltransferase activity in isolated hepatocytes.

    PubMed

    Bánhegyi, G; Garzó, T; Fulceri, R; Benedetti, A; Mandl, J

    1993-08-09

    The glucuronidation of p-nitrophenol was measured in intact, saponin- and alamethicin-treated isolated mouse hepatocytes. In saponin-permeabilized cells the elevation of extrareticular UDP-glucuronic acid concentration enhanced the rate of glucuronidation threefold. When intracellular membranes were also permeabilized by alamethicin, a further tenfold increase in the glucuronidation of p-nitrophenol was present. Parallel measurements of the ER mannose 6-phosphatase activity revealed that saponin selectively permeabilized the plasma membrane, whereas alamethicin permeabilized both plasma membrane and ER membranes. The inhibition of p-nitrophenol glucuronidation by dbcAMP in intact hepatocytes was still present in saponin-treated cells and disappeared in alamethicin-permeabilized hepatocytes. It is suggested that the permeability of the endoplasmic reticulum membrane is a major determinant of glucuronidation not only in microsomes but in isolated hepatocytes as well.

  5. Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase

    SciTech Connect

    Hall, R.S.; Swaminathan, S.; Agarwal, R.; Hitchcock, D.; Sauder, J. M.; Burley, S. K.; Raushel, F. M.

    2010-05-25

    Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a (gi|44585104) and NYSGXRC-9236b (gi|44611670), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 {angstrom} resolution (Protein Data Bank entry 2PAJ). This protein folds as a distorted ({beta}/{alpha}){sub 8} barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s{sup -1}, 8.0 {micro}M, and 1.3 x 10{sup 5} M{sup -1} s{sup -1} (k{sub cat}, K{sub m}, and k{sub cat}/K{sub m}, respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site

  6. Formalism for the determination of structural isotope effects with neutrons

    SciTech Connect

    Neuefeind, Joerg C; Benmore, Chris J

    2009-01-01

    In general the analysis of neutron isotopic substitution experiments in terms of partial structure factors and partial pair distribution functions is based on the assumption that the structure of isotopic variants of a molecule is identical. This assumption is clearly only an approximation especially in the case of hydrogen bonding molecular liquids like liquid water and structural isotope effects have been measured with X-rays for more than 20 years. A analysis method of neutron isotope data is presented that avoids the necessity to assume structural equality and allows the determination of the isotope effect in the hydrogen-hydrogen partial structure factor of liquid water from neutron data. It is shown that a combination of X-ray and neutron scattering measurements allows in principle the determination of the isotope effects on all all partials structure factors of liquid water.

  7. Evaluation of structural issues related to isolation of the 100-KE/100-KW discharge chute

    SciTech Connect

    Winkel, B.V.; Hyde, L.L.

    1995-03-10

    The issue of excessive post-seismic leakage in the discharge chute of the K East and K West fuel storage basins was resolved by designing isolation barriers to maintain basin water levels if the discharge chute should drain. This report addresses the structural issues associated with isolation of the discharge chute. The report demonstrates the structural adequacy of the components associated with chute isolation for normal and seismic loading. Associated issues, such as hardware drop accidents and seismic slosh heights are also addressed.

  8. Introducing Chemists to X-Ray Structure Determination.

    ERIC Educational Resources Information Center

    Enemark, John H.

    1988-01-01

    Presents the organization of a one-semester graduate course in structural chemistry including lectures and problems. Discusses the coverage of diffraction from real crystals and structure determination. Summarizes experiments on real crystals conducted by students in the X-ray laboratory. (CW)

  9. Introducing Chemists to X-Ray Structure Determination.

    ERIC Educational Resources Information Center

    Enemark, John H.

    1988-01-01

    Presents the organization of a one-semester graduate course in structural chemistry including lectures and problems. Discusses the coverage of diffraction from real crystals and structure determination. Summarizes experiments on real crystals conducted by students in the X-ray laboratory. (CW)

  10. A 6DOF passive vibration isolator using X-shape supporting structures

    NASA Astrophysics Data System (ADS)

    Wu, Zhijing; Jing, Xingjian; Sun, Bo; Li, Fengming

    2016-10-01

    A novel 6 degree of freedom (6-DOF) passive vibration isolator is studied theoretically and validated with experiments. Based on the Stewart platform configuration, the 6-DOF isolator is constructed by 6 X-shape structures as legs, which can realize very good and tunable vibration isolation performance in all 6 directions with a passive manner. The mechanic model is established for static analysis of the working range, static stiffness and loading capacity. Thereafter, the equation of motion of the isolator is derived with the Hamilton principle. The equivalent stiffness and the displacement transmissibility in the six decoupled DOFs direction are then discussed with experimental results for validation. The results reveal that (a) by designing the structure parameters, the system can possess flexible stiffness such as negative, quasi-zero and positive stiffness, (b) due to the combination of the Stewart platform and the X-shape structure, the system can have very good vibration isolation performance in all the 6 directions and in a passive manner, and (c) compared with the simplified linear-stiffness legs, the nonlinearity of the X-shape structures enhance the passive isolator to have much better vibration isolation performance.

  11. Fast native-SAD phasing for routine macromolecular structure determination.

    PubMed

    Weinert, Tobias; Olieric, Vincent; Waltersperger, Sandro; Panepucci, Ezequiel; Chen, Lirong; Zhang, Hua; Zhou, Dayong; Rose, John; Ebihara, Akio; Kuramitsu, Seiki; Li, Dianfan; Howe, Nicole; Schnapp, Gisela; Pautsch, Alexander; Bargsten, Katja; Prota, Andrea E; Surana, Parag; Kottur, Jithesh; Nair, Deepak T; Basilico, Federica; Cecatiello, Valentina; Pasqualato, Sebastiano; Boland, Andreas; Weichenrieder, Oliver; Wang, Bi-Cheng; Steinmetz, Michel O; Caffrey, Martin; Wang, Meitian

    2015-02-01

    We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

  12. Labor Market Structure and Salary Determination among Professional Basketball Players.

    ERIC Educational Resources Information Center

    Wallace, Michael

    1988-01-01

    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  13. Labor Market Structure and Salary Determination among Professional Basketball Players.

    ERIC Educational Resources Information Center

    Wallace, Michael

    1988-01-01

    The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)

  14. Crystal structure of a bioactive sesquiterpene isolated from Artemisia reticulata.

    PubMed

    Bauri, A K; Foro, Sabine; Do, Nhu Quynh Nguyen

    2016-04-01

    The title compound, C15H24O2 {systematic name: 1-[6-hy-droxy-7-(propan-2-yl)-4-methyl-idene-2,3,3a,4,5,6,7,7a-octa-hydro-1H-inden-1-yl]ethanone} was iso-la-ted from A. reticulata by column chromatography over silica gel by gradient solvent elution. The mol-ecule comprises a bi-cyclo-[4.3.0]nonane ring bearing acet-oxy, hy-droxy and isopropyl substituents, and an exocyclic double bond on the cyclo-hexane ring. In the bicyclic skeleton, the cyclo-hexane ring adopts a chair conformation ring and the cyclo-pentane ring is in an envelope conformation. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds, forming chains along [010]. These chains are cross-linked by C-H⋯O hydrogen bonds.

  15. Biosynthetic thiolase from Zoogloea ramigera. III. Isolation and characterization of the structural gene.

    PubMed

    Peoples, O P; Masamune, S; Walsh, C T; Sinskey, A J

    1987-01-05

    The gene coding for the biosynthetic thiolase from Zoogloea ramigera has been isolated by using antibody screening methods to detect its expression in Escherichia coli under the transcriptional control of the lac promoter. We have located and determined the nucleotide sequence of the gene. The structural gene is 1173 nucleotides long and codes for a polypeptide of 391 amino acids; 282 nucleotides 5' and 58 nucleotides 3' to the coding sequence are also reported. By comparing the amino acid sequence data predicted from the gene with data determined experimentally, we have derived the complete primary structure of thiolase. A catalytically essential cysteine is located at residue 89. The DNA sequence presented has a very high G/C content, 66.2%, typical of the Z. ramigera genome. In the coding region, this increases to 68.2% and is strongly reflected in the codon usage which demonstrates a strong preference for G or C in the third position. Examination of the 5'-flanking sequence establishes that the NH2-terminal methionine is specified by an ATG codon, 7 nucleotides downstream from a Shine-Dalgarno sequence.

  16. Structure Based In Silico Analysis of Quinolone Resistance in Clinical Isolates of Salmonella Typhi from India

    PubMed Central

    Sharma, Priyanka; Sharma, Sujata; Singh, Tej P.; Kapil, Arti; Kaur, Punit

    2015-01-01

    Enteric fever is a major cause of morbidity in several parts of the Indian subcontinent. The treatment for typhoid fever majorly includes the fluoroquinolone group of antibiotics. Excessive and indiscriminate use of these antibiotics has led to development of acquired resistance in the causative organism Salmonella Typhi. The resistance towards fluoroquinolones is associated with mutations in the target gene of DNA Gyrase. We have estimated the Minimum Inhibitory Concentration (MIC) of commonly used fluoroquinolone representatives from three generations, ciprofloxacin, ofloxacin, levofloxacin and moxifloxacin, for 100 clinical isolates of Salmonella Typhi from patients in the Indian subcontinent. The MICs have been found to be in the range of 0.032 to 8 μg/ml. The gene encoding DNA Gyrase was subsequently sequenced and point mutations were observed in DNA Gyrase in the quinolone resistance determining region comprising Ser83Phe/Tyr and Asp87Tyr/Gly. The binding ability of these four fluoroquinolones in the quinolone binding pocket of wild type as well as mutant DNA Gyrase was computationally analyzed by molecular docking to assess their differential binding behaviour. This study has revealed that mutations in DNA Gyrase alter the characteristics of the binding pocket resulting in the loss of crucial molecular interactions and consequently decrease the binding affinity of fluoroquinolones with the target protein. The present study assists in understanding the underlying molecular and structural mechanism for decreased fluoroquinolone susceptibility in clinical isolates as a consequence of mutations in DNA Gyrase. PMID:25962113

  17. Isolation and structural elucidation of cyclopentynafil and N-octylnortadalafil found in a dietary supplement.

    PubMed

    Hasegawa, Takashi; Takahashi, Kazunaga; Saijo, Masaaki; Ishii, Toshiyasu; Nagata, Tomoko; Kurihara, Masaaki; Haishima, Yuji; Goda, Yukihiro; Kawahara, Nobuo

    2009-02-01

    A new sildenafil analogue, cyclopentynafil (1) and a new tadalafil analogue, N-octylnortadalafil (2) were isolated from a dietary supplement illegally marketed for erectile dysfunction. The structures of the sildenafil and tadalafil analogues were elucidated by using HPLC-photodiode array (PDA), LC-MS, high-resolution MS, NMR and circular dichroism (CD). These compounds were determined to be 5-[2-ethoxy-5-(4-cyclopentylpiperazin-1-ylsulfonyl)phenyl]-1-methyl-3-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one and (6R,12aR)-2-octyl-6-(1,3-benzodioxol-5-yl)-2,3,6,7,12,12a-hexahydropyrazino[1',2':1,6]pyrido[3,4-b]indole-1,4-dione, respectively. Recently, a large number of phosphodiesterase-5 (PDE-5) inhibitors, including their analogues, have been isolated from dietary supplements, while cyclopentynafil and N-octylnortadalafil are the first compounds reported to be new sildenafil and tadalafil analogues, respectively. Quantitative HPLC analysis showed that the contents of 1 and 2 in the product were about 130 mg/tablet (301 microg/mg) and about 27 mg/tablet (64.1 microg/mg), respectively.

  18. Isolation of fucoidan from Sargassum polycystum brown algae: Structural characterization, in vitro antioxidant and anticancer activity.

    PubMed

    Palanisamy, Subramanian; Vinosha, Manoharan; Marudhupandi, Thangapandi; Rajasekar, Periyannan; Prabhu, Narayanan Marimuthu

    2017-09-01

    In this study antioxidant and anticancer effect of fucoidan isolated from brown seaweed Sargassum polycystum was investigated. The total yield of fucoidan was 4.51±0.24%, of these, 46.8% of fucose and 22.35±0.23% of sulphate respectively. The structural characteristic of fucoidan was analyzed by Fourier transform infrared spectroscopy and nuclear magnetic resonance. The antioxidant properties were determined by DPPH scavenging, reducing power and total antioxidant assays. The maximum DPPH scavenging activity (61.2±0.33%), reducing ability (67.56±0.26%) and total antioxidant activity (65.3±0.66%) were obtained at 1000μg/ml of fucoidan. The cytotoxicity effect of fucoidan showed a higher percentage (90.4±0.25%) of inhibition against the MCF-7 cell line at 150μg/ml with an estimated IC50 at 50μg/ml. Further, cytomorphological and apoptosis changes of fucoidan treated cells were observed under inverted light microscope and confocal laser scanning microscope (CLSM). The results demonstrated that the isolated fucoidan from S. polycystum possessed potent antioxidant and anticancer properties. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Structure based in silico analysis of quinolone resistance in clinical isolates of Salmonella Typhi from India.

    PubMed

    Kumar, Manoj; Dahiya, Sushila; Sharma, Priyanka; Sharma, Sujata; Singh, Tej P; Kapil, Arti; Kaur, Punit

    2015-01-01

    Enteric fever is a major cause of morbidity in several parts of the Indian subcontinent. The treatment for typhoid fever majorly includes the fluoroquinolone group of antibiotics. Excessive and indiscriminate use of these antibiotics has led to development of acquired resistance in the causative organism Salmonella Typhi. The resistance towards fluoroquinolones is associated with mutations in the target gene of DNA Gyrase. We have estimated the Minimum Inhibitory Concentration (MIC) of commonly used fluoroquinolone representatives from three generations, ciprofloxacin, ofloxacin, levofloxacin and moxifloxacin, for 100 clinical isolates of Salmonella Typhi from patients in the Indian subcontinent. The MICs have been found to be in the range of 0.032 to 8 μg/ml. The gene encoding DNA Gyrase was subsequently sequenced and point mutations were observed in DNA Gyrase in the quinolone resistance determining region comprising Ser83Phe/Tyr and Asp87Tyr/Gly. The binding ability of these four fluoroquinolones in the quinolone binding pocket of wild type as well as mutant DNA Gyrase was computationally analyzed by molecular docking to assess their differential binding behaviour. This study has revealed that mutations in DNA Gyrase alter the characteristics of the binding pocket resulting in the loss of crucial molecular interactions and consequently decrease the binding affinity of fluoroquinolones with the target protein. The present study assists in understanding the underlying molecular and structural mechanism for decreased fluoroquinolone susceptibility in clinical isolates as a consequence of mutations in DNA Gyrase.

  20. Accurate determination of reference materials and natural isolates by means of quantitative (1)h NMR spectroscopy.

    PubMed

    Frank, Oliver; Kreissl, Johanna Karoline; Daschner, Andreas; Hofmann, Thomas

    2014-03-26

    A fast and precise proton nuclear magnetic resonance (qHNMR) method for the quantitative determination of low molecular weight target molecules in reference materials and natural isolates has been validated using ERETIC 2 (Electronic REference To access In vivo Concentrations) based on the PULCON (PULse length based CONcentration determination) methodology and compared to the gravimetric results. Using an Avance III NMR spectrometer (400 MHz) equipped with a broad band observe (BBO) probe, the qHNMR method was validated by determining its linearity, range, precision, and accuracy as well as robustness and limit of quantitation. The linearity of the method was assessed by measuring samples of l-tyrosine, caffeine, or benzoic acid in a concentration range between 0.3 and 16.5 mmol/L (r(2) ≥ 0.99), whereas the interday and intraday precisions were found to be ≤2%. The recovery of a range of reference compounds was ≥98.5%, thus demonstrating the qHNMR method as a precise tool for the rapid quantitation (~15 min) of food-related target compounds in reference materials and natural isolates such as nucleotides, polyphenols, or cyclic peptides.

  1. [Genetic determinants of pathogenicity of opportunistic enterobacteria isolated from children with acute intestinal infections].

    PubMed

    Anganova, E V; Dukhanina, A V; Savilov, E D

    2012-01-01

    Detection of nucleotide sequences of genes controlling synthesis of pathogenicity factors in clinical strains of opportunistic enterobacteria isolated from children with acute intestinal infections (AII), as well as their association with resistance to antibiotics and the course of the infectious process. 175 clinical strains obtained from children with AII undergoing treatment in Irkutsk state infectious diseases hospital (2007-2010) were studied. Primers to a number of genes detected in Escherichia coli pathogenicity islands, controlling type S and type 1 adhesion; formation of hemolysins; iron-regulatory protein synthesis; capsule formation were used in the study. PCR products analysis was performed by agar gel electrophoresis. Genetic determinants of pathogenicity were detected in bacteria genera Klebsiella, Citrobacter, Enterobacter, Proteus, Kluyvera, Morganella, Pantoea, Serratia. Fragments of hlyA and hlyB genes (hemolysin production) were detected more frequently; less frequently--sfaA, sfaG, fimA (adhesion), as well as irp-2 gene (synthesis of iron-regulatory protein). The largest set of genetic determinants of pathogenicity was noted in clinical strains of Klebsiella spp. Cultures with DNA fragments specific to genes of E. coli pathogenicity clusters were obtained predominately from children aged up to 3 years, had multiple antibiotic resistance and were isolated significantly more frequently in severe forms of AII when compared with strains in which these determinants were not detected. The studies performed showed that clinical strains of opportunistic bacteria isolated from patients with AII have a certain pathogenic potential, as evidenced by the presence of genetic pathogenicity markers in them.

  2. Structural determination of intact proteins using mass spectrometry

    DOEpatents

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  3. Structure Determination of Natural Products by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Biemann, Klaus

    2015-07-01

    I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.

  4. The progress made in determining the Mycobacterium tuberculosis structural proteome

    PubMed Central

    Hecker, Michael

    2011-01-01

    Mycobacterium tuberculosis is a highly infectious pathogen that is still responsible for millions of deaths annually. Effectively treating this disease typically requires a course of antibiotics, most of which were developed decades ago. These drugs are, however, not effective against persistent tubercle bacilli and the emergence of drug-resistant stains threatens to make many of them obsolete. The identification of new drug targets, allowing the development of new potential drugs, is therefore imperative. Both proteomics and structural biology have important roles to play in this process, the former as a means of identifying promising drug targets and the latter allowing understanding of protein function and protein–drug interactions at atomic resolution. The determination of M. tuberculosis protein structures has been a goal of the scientific community for the last decade, who have aimed to supply a large amount of structural data that can be used in structure-based approaches for drug discovery and design. Only since the genome sequence of M. tuberculosis has been available has the determination of large numbers of tuberculosis protein structures been possible. Currently, the molecular structures of 8.5% of all the pathogen's protein-encoding ORFs have been determined. In this review, we look at the progress made in determining the M. tuberculosis structural proteome and the impact this has had on the development of potential new drugs, as well as the discovery of the function of crucial mycobaterial proteins. PMID:21674801

  5. [Isolation, extractive concentration, and determination of caffeine in the studies of blood plasma].

    PubMed

    Korenman, Ia I; Shormanov, V K; Mokshina, N Ia; Krivosheeva, O A; Golubitskiĭ, G B

    2012-01-01

    The optimal conditions for the isolation of caffeine from human blood by means of acetone extraction are described with special reference to the peculiarities of extraction from aqueous solutions. The possibility of concentration and purification of caffeine from blood plasma using acetone and aceton-chlorophorm mixture (2:8) as the solvents is illustrated. In addition, purification by silica-gel thin layer chromatography is discussed. Thin layer chromatography, UV-spectrophotometry, and high performance liquid chromatography are considered as potential methods for the identification and quantitative determination of caffeine.

  6. Sequence Determination of a Novel Tripeptide Isolated from the Young Leaves of Azadirachta indica A. Juss

    PubMed Central

    Rajeswari Prabha, M.; Ramachandramurty, B.

    2013-01-01

    The neem tree has long been recognized for its unique properties, both against insects and in improving human health. Every part of the tree has been used as a traditional medicine for household remedy against various human ailments, from antiquity. Although the occurrence of various phytochemicals in neem has been studied, we have identified the presence of a novel tripeptide in the young leaves of neem using a simple and inexpensive paper chromatographic method, detected by Cu(II)-ninhydrin reagent. The peptide nature of the isolated compound is confirmed by spectral studies. The sequence of the peptide is determined using de novo sequencing by tandem MS after purification. PMID:23509470

  7. Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

    SciTech Connect

    Lamb, Kristen; Lokesh, G.L.; Sherman, Michael; Watowich, Stanley

    2010-10-25

    Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to the mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.

  8. Complete genome sequence of a novel Plum pox virus strain W isolate determined by 454 pyrosequencing.

    PubMed

    Sheveleva, Anna; Kudryavtseva, Anna; Speranskaya, Anna; Belenikin, Maxim; Melnikova, Natalia; Chirkov, Sergei

    2013-10-01

    The near-complete (99.7 %) genome sequence of a novel Russian Plum pox virus (PPV) isolate Pk, belonging to the strain Winona (W), has been determined by 454 pyrosequencing with the exception of the thirty-one 5'-terminal nucleotides. This region was amplified using 5'RACE kit and sequenced by the Sanger method. Genomic RNA released from immunocaptured PPV particles was employed for generation of cDNA library using TransPlex Whole transcriptome amplification kit (WTA2, Sigma-Aldrich). The entire Pk genome has identity level of 92.8-94.5 % when compared to the complete nucleotide sequences of other PPV-W isolates (W3174, LV-141pl, LV-145bt, and UKR 44189), confirming a high degree of variability within the PPV-W strain. The isolates Pk and LV-141pl are most closely related. The Pk has been found in a wild plum (Prunus domestica) in a new region of Russia indicating widespread dissemination of the PPV-W strain in the European part of the former USSR.

  9. Thermal morphing anisogrid smart space structures: thermal isolation design and linearity evaluation

    NASA Astrophysics Data System (ADS)

    Phoenix, Austin A.

    2017-04-01

    To meet the requirements for the next generation of space missions, a paradigm shift is required from current structures that are static, heavy and stiff, toward innovative structures that are adaptive, lightweight, versatile, and intelligent. A novel morphing structure, the thermally actuated anisogrid morphing boom, can be used to meet the design requirements by making the primary structure actively adapt to the on-orbit environment. The anisogrid structure is able to achieve high precision morphing control through the intelligent application of thermal gradients. This active primary structure improves structural and thermal stability performance, reduces mass, and enables new mission architectures. This effort attempts to address limits to the author's previous work by incorporating the impact of thermal coupling that was initially neglected. This paper introduces a thermally isolated version of the thermal morphing anisogrid structure in order to address the thermal losses between active members. To evaluate the isolation design the stiffness and thermal conductivity of these isolating interfaces need to be addressed. This paper investigates the performance of the thermal morphing system under a variety of structural and thermal isolation interface properties.

  10. Comparison of seismic response of ordinary and base-isolated structures

    SciTech Connect

    Kuroda, T.; Kobatake, M. ); Seidensticker, R.W.; Chang, Y.W. )

    1992-01-01

    Seismic isolation is growing rapidly worldwide as a cost-effective and reliable design strategy for a wide range of critical and important facilities (e.g., hospitals, computer centers, etc.) Shimizu Corporation of Japan has a test facility at Tohoku University in Sendai, Japan. The test facility was constructed in 1986 and has two buildings: one is base isolated and the other is conventionally founded. The buildings are full-size, three-story reinforced concrete structures. The dimensions and construction of the superstructures are identical. For the past several years, Shimizu Corporation has installed a number of different isolation systems in the isolated building at the test facility to study the response of base isolation systems to actual earthquake motions. Argonne National Laboratory (ANL) has been deeply involved in the development of seismic isolation for use in nuclear facilities for the past decade. Using the funding and direction of the US Department of Energy (USDOE), ANL has been developing methodology needed to evaluate the usefulness and effectiveness of seismic isolation for advanced liquid metal-cooled reactors (LMRs). This paper compares the seismic responses of ordinary and base-isolated buildings. Earthquake records of significant importance from April 1989 to September 1991, after the installation of bearings have been analyzed. Numerical simulations of the building responses have been performed and correlated with earthquake observation data. It is hoped that the results of this study will provide guidelines for the future use of isolator bearings for mitigation of earthquake damages.

  11. Comparison of seismic response of ordinary and base-isolated structures

    SciTech Connect

    Kuroda, T.; Kobatake, M.; Seidensticker, R.W.; Chang, Y.W.

    1992-04-01

    Seismic isolation is growing rapidly worldwide as a cost-effective and reliable design strategy for a wide range of critical and important facilities (e.g., hospitals, computer centers, etc.) Shimizu Corporation of Japan has a test facility at Tohoku University in Sendai, Japan. The test facility was constructed in 1986 and has two buildings: one is base isolated and the other is conventionally founded. The buildings are full-size, three-story reinforced concrete structures. The dimensions and construction of the superstructures are identical. For the past several years, Shimizu Corporation has installed a number of different isolation systems in the isolated building at the test facility to study the response of base isolation systems to actual earthquake motions. Argonne National Laboratory (ANL) has been deeply involved in the development of seismic isolation for use in nuclear facilities for the past decade. Using the funding and direction of the US Department of Energy (USDOE), ANL has been developing methodology needed to evaluate the usefulness and effectiveness of seismic isolation for advanced liquid metal-cooled reactors (LMRs). This paper compares the seismic responses of ordinary and base-isolated buildings. Earthquake records of significant importance from April 1989 to September 1991, after the installation of bearings have been analyzed. Numerical simulations of the building responses have been performed and correlated with earthquake observation data. It is hoped that the results of this study will provide guidelines for the future use of isolator bearings for mitigation of earthquake damages.

  12. Isolation, antimicrobial activities, and primary structures of hamster neutrophil defensins.

    PubMed Central

    Mak, P; Wójcik, K; Thogersen, I B; Dubin, A

    1996-01-01

    Hamster (Mesocricetus auratus) neutrophil granules contain at least four microbicidal peptides belonging to the defensin family. These compounds were purified from granule acid extracts by reverse-phase chromatography and termed HaNP-1 to -4 (hamster neutrophil peptide). HaNP-1 and HaNP-3 revealed the most bactericidal activity, with a 50% inhibitory concentration of 0.3 to 0.8 microg/ml for Staphylococcus aureus and Streptococcus pyogenes strains. The HaNP-4 was always isolated in concentrations exceeding about 10 times the concentrations of other hamster peptides, but its antibacterial activity as well as that of HaNP-2 was relatively lower, probably as a result of conserved Arg residue substitutions. Other microorganisms were also tested, and generally, hamster defensins exhibited less potency against gram-negative bacteria. The amino acid sequence of hamster defensins showed a high percentage of identity to the sequence of mouse enteric defensins, reaching about 60% identical residues in the case of HaNP-3 and cryptdin 3. PMID:8890190

  13. Integrated framework for jitter analysis combining disturbance, structure, vibration isolator and optical model

    NASA Astrophysics Data System (ADS)

    Lee, Dae-Oen; Yoon, Jae-San; Han, Jae-Hung

    2012-04-01

    Micro-vibration induced by actuating components of the satellite can severely degrade the optical performance of high precision observation satellites. In this paper, an integrated analysis framework combining disturbance, structure, vibration isolator and optical system model is developed for evaluating the performance of optical payloads in the presence of micro-vibration, and the effectiveness of using a vibration isolator for performance enhancement. Reaction wheel generated disturbance, usually the largest anticipated disturbance, is modeled including the disturbances' interaction with the structural modes of the wheel. For structure modeling, a finite element program is used to solve for eigenvalues and eigenvectors of a structure model which are then used to create a state space model in modal form. A vibration isolator model capturing dynamics of an active isolator utilizing piezoelectric based actuator and load cell for feedback control is included to reduce the transmission of reaction wheel disturbances to the base structure. Dynamic response of the structure to reaction wheel disturbances is calculated with and without vibration isolator. The resulting jitter is used to obtain modulation transfer function (MTF) of diffraction limited optical system model, and the obtained MTF is used as spatial frequency filter for image simulation.

  14. Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton.

    PubMed

    Naman, C Benjamin; Li, Jie; Moser, Arvin; Hendrycks, Jeffery M; Benatrehina, P Annécie; Chai, Heebyung; Yuan, Chunhua; Keller, William J; Kinghorn, A Douglas

    2015-06-19

    Melanodiol 4″-O-protocatechuate (1) and melanodiol (2) represent novel flavonoid derivatives isolated from a botanical dietary supplement ingredient, dried black chokeberry (Aronia melanocarpa) fruit juice. These noncrystalline compounds possess an unprecedented fused pentacyclic core with two contiguous hemiketals. Due to having significant hydrogen deficiency indices, their structures were determined using computer-assisted structure elucidation software. The in vitro hydroxyl radical-scavenging and quinone reductase-inducing activity of each compound are reported, and a plausible biogenetic scheme is proposed.

  15. Computer-Assisted Structure Elucidation of Black Chokeberry (Aronia melanocarpa) Fruit Juice Isolates with a New Fused Pentacyclic Flavonoid Skeleton

    PubMed Central

    Naman, C. Benjamin; Li, Jie; Moser, Arvin; Hendrycks, Jeffery M.; Benatrehina, P. Annécie; Chai, Heebyung; Yuan, Chunhua; Keller, William J.; Kinghorn, A. Douglas

    2015-01-01

    Melanodiol 4″-O-protocatechuate (1) and melanodiol (2) represent novel flavonoid derivatives isolated from a botanical dietary supplement ingredient, dried black chokeberry (Aronia melanocarpa) fruit juice. These non-crystalline compounds possess an unprecedented fused pentacyclic core with two contiguous hemiketals. Due to having significant hydrogen deficiency indices, their structures were determined using computer-assisted structure elucidation software. The in vitro hydroxyl radical-scavenging and quinone reductase-inducing activity of each compound are reported, and a plausible biogenetic scheme is proposed PMID:26030740

  16. Determination of Proanthocyanidin A2 Content in Phenolic Polymer Isolates by Reversed-Phase High Performance Liquid Chromatography

    USDA-ARS?s Scientific Manuscript database

    This article summarizes the development of an analytical method for the determination of proanthocyanidin (PAC) A2 in phenolic polymer isolates following acid-catalyzed degradation in the presence of excess phloroglucinol. Isolates from cranberry juice concentrate (CJC) were extensively characterize...

  17. Isolation, Characterization and Quantity Determination of Aristolochic Acids, Toxic Compounds in Aristolochia bracteolata L.

    PubMed Central

    Abdelgadir, Abdelgadir A.; Ahmed, Elhadi M.; Eltohami, Mahgoub Sharif

    2011-01-01

    Background: Aristolochic Acids (AAs) are major components of plants in Aristolochia and have been found to be nephrotoxic, carcinogenic and mutagenic. Herein reported are the isolation, identification and quantity determination methods of Aristolochic Acid-I (AA-I) and Aristolochic Acid-II (AA-II) toxic compounds of Aristolochia bracteolata indigenous to Central Sudan and medicinally used in diverse biological functions including analgesic and diuretic effects, treatment of tumors, malaria and/or fevers. Methods and results: AAs mixture was extracted with methanol from the defatted material of Aristolochia bracteolata whole plant at room temperature and was isolated from the aqueous methanol extract by chloroform. Moreover, Silica-gel column chromatography and Preparative Thin Layer Chromatography (PTLC) using chloroform/methanol gradient mixtures were used to isolate AAs mixtures as a yellow crystalline solid. A preliminary detection of AAs was made by Thin Layer Chromatography (silica-gel, chloroform: methanol (6:1)). The Rf value of the acids mixture was 0.43–0.46. The presence of AAs in plant sample was confirmed by High Performance Liquid Chromatography/Ultraviolet (HPLC/UV) analysis using 1% acetic acid and methanol (40:60) as mobile phase and maximum absorption wave length of 250 nm. Quantitative determination of AA-II (49.03 g/kg) and AA-I (12.98 g/kg) was also achieved by HPLC/UV. Recommendation: It is recommended that the use of Aristolochia bracteolata as a medicinal plant should be extremely limited or strictly prohibited. The chromatograms obtained in this study can serve as fingerprints to identify AAs in plant samples. PMID:21487531

  18. Isolation and amino-acid sequence determination of monkey insulin and proinsulin.

    PubMed

    Naithani, V K; Steffens, G J; Tager, H S; Buse, G; Rubenstein, A H; Steiner, D F

    1984-05-01

    Insulin has been isolated and purified from rhesus monkey pancreas by means of acid-ethanol extraction, gel filtration and ion exchange chromatography. The complete amino-acid sequence of the hormone has been determined by amino-acid analysis of the oxidized A- and B-chains, by end group determination, by the identification of the C-terminal residues (AsnA21 and ThrB30) by carboxypeptidase A digestion and by Edman degradation of the S-carboxymethylated A- and B-chains. The 51-residue monkey insulin was shown to be identical to human insulin. From the known insulin and C-peptide sequence the primary sequence of monkey proinsulin has been proposed.

  19. Study of sequential optimal control algorithm smart isolation structure based on Simulink-S function

    NASA Astrophysics Data System (ADS)

    Liu, Xiaohuan; Liu, Yanhui

    2017-01-01

    The study of this paper focuses on smart isolation structure, a method for realizing structural vibration control by using Simulink simulation is proposed according to the proposed sequential optimal control algorithm. In the Simulink simulation environment, A smart isolation structure is used to compare the control effect of three algorithms, i.e., classical optimal control algorithm, linear quadratic gaussian control algorithm and sequential optimal control algorithm under the condition of sensor contaminated with noise. Simulation results show that this method can be applied to the simulation of sequential optimal control algorithm and the proposed sequential optimal control algorithm has a good ability of resisting the noise and better control efficiency.

  20. Mounting Systems for Structural Members, Fastening Assemblies Thereof, and Vibration Isolation Systems Including the Same

    NASA Technical Reports Server (NTRS)

    Young, Ken (Inventor); Hindle, Timothy (Inventor); Barber, Tim Daniel (Inventor)

    2016-01-01

    Mounting systems for structural members, fastening assemblies thereof, and vibration isolation systems including the same are provided. Mounting systems comprise a pair of mounting brackets, each clamped against a fastening assembly forming a mounting assembly. Fastening assemblies comprise a spherical rod end comprising a spherical member having a through opening and an integrally threaded shaft, first and second seating members on opposite sides of the spherical member and each having a through opening that is substantially coaxial with the spherical member through opening, and a partially threaded fastener that threadably engages each mounting bracket forming the mounting assembly. Structural members have axial end portions, each releasably coupled to a mounting bracket by the integrally threaded shaft. Axial end portions are threaded in opposite directions for permitting structural member rotation to adjust a length thereof to a substantially zero strain position. Structural members may be vibration isolator struts in vibration isolation systems.

  1. Genetic Resistance Determinants for Cefixime and Molecular Analysis of Gonococci Isolated in Italy.

    PubMed

    Carannante, Anna; Vacca, Paola; Ghisetti, Valeria; Latino, Maria Agnese; Cusini, Marco; Matteelli, Alberto; Vocale, Caterina; Prignano, Grazia; Leli, Christian; Ober, Patrizia; Antonetti, Raffaele; Poletti, Federica; Stefanelli, Paola

    2017-03-01

    A strictly defined subset of gonococci (n = 65) isolated in Italy from 2011 to 2014 was characterized by antimicrobial susceptibility for cefixime (CFM) and ceftriaxone (CRO) and by sequencing of resistance determinant genes (penA, mtrR, porB1b, ponA) for extended-spectrum cephalosporins and Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST). The penA mosaic alleles XXXIV and XXXV were found in all resistant (R) and decreased susceptibility (DS) gonococci to CFM, except for one. They were associated with an adenine deletion in the mtrR promoter plus amino acid substitutions, H105Y or G45D, in the coding region and ponA L421P. The penA mosaic allele XXXIV, and one variant, was found exclusively among genogroup (G) 1407 and its closely related sequence types (STs), as in CFM-DS as well as in CFM-R isolates. Single or combined mutation patterns in penA, mtrR, porB1b, and ponA genes were associated with different CFM susceptibility patterns and NG-MAST STs. Genotyping and antimicrobial resistance (AMR) determinant analyses can be valuable to enhance the gonococcal AMR surveillance.

  2. Isolation and structure elucidation of new phthalide and phthalane derivatives, isolated as antimicrobial agents from Emericella sp. IFM57991.

    PubMed

    Saito, Tetsuya; Itabashi, Takeshi; Wakana, Daigo; Takeda, Hisashi; Yaguchi, Takashi; Kawai, Ken-ichi; Hosoe, Tomoo

    2016-02-01

    Three new phthalide derivatives, emefuranones A1, A2 and B (1-3); six new phthalane derivatives, emefuran A, B1, B2, C1, C2 and D (4-9); three new farnesylated phthalide derivatives, farnesylemefuranones A-C (10-12); xylarinol C (13); and emericelloxide (14), along with four known compounds (dustanin, sorbicillin, aspergillodiol and xylarinol A), were isolated from the culture extracts of Emericella sp. IFM57991. Structures of 1-14 were elucidated on the basis of spectroscopic analysis and chemical evidence. Compounds 4-7 and 13 showed moderate antibacterial activities against Bacillus subtilis.

  3. Compounds from Ageratum conyzoides: isolation, structural elucidation and insecticidal activity.

    PubMed

    Moreira, Márcio D; Picanço, Marcelo C; Barbosa, Luiz Cláudio A; Guedes, Raul Narciso C; Barros, Emerson C; Campos, Mateus R

    2007-06-01

    This work aimed at identifying plant compounds with insecticidal activity against Diaphania hyalinata (L.) (Lepidoptera: Pyralidae), Musca domestica (L.) (Diptera: Muscidae), Periplaneta americana (L.) (Blattodea: Blattidae) and Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae). The plant species used were: basil (Ocimum selloi Benth.), rue (Ruta graveolens L.), lion's ear (Leonotis nepetaefolia L.), Jimson weed (Datura stramonium L.), 'baleeira' herb (Cordia verbenaceae L.), mint (Mentha piperita L.), wild balsam apple (Mormodica charantia L.) and billy goat weed (Ageratum conyzoides L.). Firstly, the insecticidal activities of hexane and ethanol plant extracts were evaluated against adults of R. dominica. Among them, only the hexane extract of A. conyzoides showed insecticidal activity. The hexane extract of this plant species was therefore fractionated by silica gel column chromatography to isolate and purify its bioactive chemical constituents. Three compounds were identified using IR spectra, (1)H NMR, (13)C NMR, HMBC and NOE after gel chromatography: 5,6,7,8,3', 4', 5'-heptamethoxyflavone, 5,6,7,8,3'-pentamethoxy-4', 5'-methylenedioxyflavone and coumarin. The complete assignment of (13)C NMR to 5,6,7,8,3'-pentamethoxy-4', 5'-methylenedioxyflavone was successfully made for the first time. 5,6,7,8,3'-Pentamethoxy-4', 5'-methylenedioxyflavone did not show any insecticidal activity against the four insect species tested. 5,6,7,8,3', 4', 5'-Heptamethoxyflavone showed low activity against D. hyalinata and R. dominica and was not toxic to M. domestica or P. americana. In contrast, coumarin showed insecticidal activity against all four insect pest species tested, with the following order of susceptibility: R. dominica < P. americana < D. hyalinata < M. domestica after 24 h exposure. Copyright 2007 Society of Chemical Industry.

  4. Isolation, structures, and structure - cytotoxic activity relationships of withanolides and physalins from Physalis angulata.

    PubMed

    Damu, Amooru G; Kuo, Ping-Chung; Su, Chung-Ren; Kuo, Tsung-Hsiao; Chen, Tzu-Hsuan; Bastow, Kenneth F; Lee, Kuo-Hsiung; Wu, Tian-Shung

    2007-07-01

    Phytochemical investigation of Physalis angulata was initiated following primary biological screening. Fractionation of CHCl3 and n-BuOH solubles of the MeOH extract from the whole plant was guided by in vitro cytotoxic activity assay using cultured HONE-1 and NUGC cells and led to the isolation of seven new withanolides, withangulatins B-H (1-7), and a new minor physalin, physalin W (8), along with 14 known compounds, including physaprun A, withaphysanolide, dihydrowithanolide E, physanolide A, withaphysalin A, and physalins B, D, F, G, I, J, T, U, and V. New compounds (1-8) were fully characterized by a combination of spectroscopic methods (1D and 2D NMR and MS) and the relative stereochemical assignments based on NOESY correlations and analysis of coupling constants. Biological evaluation of these compounds against a panel of human cancer cell lines showed broad cytotoxic activity. Withangulatin B (1) and physalins D (10) and F (11) displayed potent cytotoxic activity against a panel of human cancer cell lines with EC50 values ranging from 0.2 to 1.6 microg/mL. Structure-activity relationship analysis indicated that withanolides and physalins with 4beta-hydroxy-2-en-1-one and 5beta,6beta-epoxy moieties are potential cytotoxic agents.

  5. Structural characterization of neutral oligosaccharides with blood-group A and H activity isolated from bovine submaxillary mucin.

    PubMed Central

    Savage, A V; D'Arcy, S M; Donoghue, C M

    1991-01-01

    In this study we investigated the structures of 11 neutral oligosaccharides released from bovine submaxillary mucin by alkaline borohydride treatment and isolated by h.p.l.c. One hexa-, one penta-, three tetra-, four tri- and two di-saccharides containing core types 1, 2, 3 or 4 were obtained. We report their structures, determined by a combination of one- and two-dimensional 1H n.m.r. spectroscopy at 270 MHz and methylation analysis involving g.l.c.-m.s., along with their approximate molar ratios. Only three of these oligosaccharides have previously been reported in this source. Of the new oligosaccharides, one contains the blood-group-A antigenic determinant, two contain the blood-group-H type 2 determinant, while another contains the blood-group-H type 3 determinant. The oligosaccharide GlcNAc beta (1----6)[GlcNAc beta (1----3)]GalNAcol, although previously found as a core structure, has been isolated here as a novel trisaccharide. PMID:1718265

  6. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

    One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based on these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.

  7. Mashed potatoes enriched with soy protein isolate and inulin: chemical, rheological and structural basis.

    PubMed

    Alvarez, M D; Olivares, M D; Blanch, M; Canet, W

    2013-10-01

    Soy protein isolate is typical vegetable protein with health-enhancing activities. Inulin, a prebiotic no digestible carbohydrate, has functional properties. A mashed potato serving of 200 g with added soy protein isolate and/or inulin concentrations of 15-60 g/kg provides from 3 to 12 g of soy protein isolate and/or inulin, respectively. Currently, no information is available about the possible texture-modifying effect of this non-ionizable polar carbohydrate in different soy-based food systems. In this study, the effect of the addition of soy protein isolate and inulin blends at different soy protein isolate: inulin ratios on the degree of inulin polymerization and the rheological and structural properties of fresh mashed and frozen/thawed mashed potatoes were evaluated. The inulin chemical structure remained intact throughout the various treatments, and soy protein isolate did not affect inulin composition being a protein compatible with this fructan. Small-strain rheology showed that both ingredients behaved like soft fillers. In the frozen/thawed mashed potatoes samples, addition of 30 : 30 and 15 : 60 blend ratios significantly increased elasticity (G' value) compared with 0 : 0 control, consequently reducing the freeze/thaw stability conferred by the cryoprotectants. Inulin crystallites caused a significant strengthening effect on soy protein isolate gel. Micrographs revealed that soy protein isolate supports the inulin structure by building up a second fine-stranded network. Thereby, possibility of using soy protein isolate and inulin in combination with mashed potatoes to provide a highly nutritious and healthy product is promising.

  8. Arbutin: Isolation, X-ray structure and computional studies

    NASA Astrophysics Data System (ADS)

    Nycz, Jacek E.; Malecki, Grzegorz; Morag, Monika; Nowak, Gerard; Ponikiewski, Lukasz; Kusz, Joachim; Switlicka, Anna

    2010-09-01

    Arbutin, an active component originated from Serratula quinquefolia for skin-whitening use and treating skin related allergic inflammation, was characterized by microanalysis, FTIR, UV-Vis, multinuclear NMR spectroscopy, and single crystal X-ray diffraction method. The geometries of the studied compound were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. Electronic spectra were calculated by TDDFT method. In general, the predicted bond lengths and angles are in a good agreement with the values based on the X-ray crystal structure data.

  9. Isolation and structural characterization of anthocyanin-furfuryl pigments.

    PubMed

    Sousa, André; Mateus, Nuno; Silva, Artur Manuel Soares; Vivas, Nicolas; Nonier, Marie-Françoise; Pianet, Isabelle; de Freitas, Victor

    2010-05-12

    Condensation reactions of malvidin-3-glucoside with two representative oak wood furanic aldehydes (furfural and methylfurfural) were conducted in wine-like model solutions. Methylfurfural led to the formation of malvidin-3-glucoside-methylfurfural (603 m/z), whereas furfural led to the formation of malvidin-3-glucoside-furfural (589 m/z). The latter was structurally characterized by 1D and 2D NMR, allowing an elucidation of the formation mechanism of these anthocyanin-furanic aldehyde adducts in the absence of flavanols.

  10. Widely distributed and regionally isolated! Drivers of genetic structure in Gammarus fossarum in a human-impacted landscape.

    PubMed

    Weiss, Martina; Leese, Florian

    2016-07-29

    The actual connectivity between populations of freshwater organisms is largely determined by species biology, but is also influenced by many area- and site-specific factors, such as water pollution and habitat fragmentation. Therefore, the prediction of effective gene flow, even for well-studied organisms, is difficult. The amphipod crustacean Gammarus fossarum is a key invertebrate in freshwater ecosystems and contains many cryptic species. One of these species is the broadly distributed G. fossarum clade 11 (type B). In this study, we tested for factors driving the genetic structure of G. fossarum clade 11 in a human-impacted landscape at local and regional scales. To determine population structure, we analyzed the mitochondrial cytochrome c oxidase 1 (CO1) gene of 2,086 specimens from 54 sampling sites and microsatellite loci of 420 of these specimens from ten sites. We detected strong overall genetic differentiation between populations at regional and local scales with both independent marker systems, often even within few kilometers. Interestingly, we observed only a weak correlation of genetic distances with geographic distances or catchment boundaries. Testing for factors explaining the observed population structure revealed, that it was mostly the colonization history, which has influenced the structure rather than any of the chosen environmental factors. Whereas the number of in-stream barriers did not explain population differentiation, the few large water reservoirs in the catchment likely act as dispersal barriers. We showed that populations of Gammarus fossarum clade 11 are strongly isolated even at local scales in the human-impacted region. The observed genetic structure was best explained by the effects of random genetic drift acting independently on isolated populations after historical colonization events. Genetic drift in isolated populations was probably further enhanced by anthropogenic impacts, as G. fossarum is sensitive to many anthropogenic

  11. Determination of antibiotic resistance pattern and bacteriocin sensitivity of Listeria monocytogenes strains isolated from different foods in turkey

    USDA-ARS?s Scientific Manuscript database

    This study aimed to determine the antibiotic resistance pattern and bacteriocin sensitivity of Listeria monocytogenes strains isolated from animal derived foods. With disc diffusion assay, all fourteen L. monocytogenes strains were susceptible to the antibiotics, including penicillin G, vancomycin, ...

  12. Isolation of translating ribosomes containing peptidyl-tRNAs for functional and structural analyses.

    PubMed

    Shirole, Nitin; Balasubramanian, Sreeram; Yanofsky, Charles; Cruz-Vera, Luis

    2011-02-25

    RNA sequences are stalled at the stop codon region, due to the absence of the RF2 protein, which normally accomplishes translation termination. Stalled ribosomes containing the newly synthesized peptidyl-tRNA are isolated and removed from the translation reactions using SMB and an MF. These beads only bind biotin-containing messages. The isolated, translational complexes, can be used to analyze the structural and functional features of wild type or mutant ribosomal components, or peptidyl-tRNA sequences, as well as determining ribosome interaction with antibiotics or other molecular factors. To examine the function of these isolated ribosome complexes, peptidyl-transferase assays can be performed in the presence of the antibiotic puromycin. To study structural changes in translational complexes, well established procedures can be used, such as i) crosslinking to specific amino acids and/or ii) alkylation protection assays.

  13. Composition, structure and functional properties of protein concentrates and isolates produced from walnut (Juglans regia L.).

    PubMed

    Mao, Xiaoying; Hua, Yufei

    2012-01-01

    In this study, composition, structure and the functional properties of protein concentrate (WPC) and protein isolate (WPI) produced from defatted walnut flour (DFWF) were investigated. The results showed that the composition and structure of walnut protein concentrate (WPC) and walnut protein isolate (WPI) were significantly different. The molecular weight distribution of WPI was uniform and the protein composition of DFWF and WPC was complex with the protein aggregation. H(0) of WPC was significantly higher (p < 0.05) than those of DFWF and WPI, whilst WPI had a higher H(0) compared to DFWF. The secondary structure of WPI was similar to WPC. WPI showed big flaky plate like structures; whereas WPC appeared as a small flaky and more compact structure. The most functional properties of WPI were better than WPC. In comparing most functional properties of WPI and WPC with soybean protein concentrate and isolate, WPI and WPC showed higher fat absorption capacity (FAC). Emulsifying properties and foam properties of WPC and WPI in alkaline pH were comparable with that of soybean protein concentrate and isolate. Walnut protein concentrates and isolates can be considered as potential functional food ingredients.

  14. Composition, Structure and Functional Properties of Protein Concentrates and Isolates Produced from Walnut (Juglans regia L.)

    PubMed Central

    Mao, Xiaoying; Hua, Yufei

    2012-01-01

    In this study, composition, structure and the functional properties of protein concentrate (WPC) and protein isolate (WPI) produced from defatted walnut flour (DFWF) were investigated. The results showed that the composition and structure of walnut protein concentrate (WPC) and walnut protein isolate (WPI) were significantly different. The molecular weight distribution of WPI was uniform and the protein composition of DFWF and WPC was complex with the protein aggregation. H0 of WPC was significantly higher (p < 0.05) than those of DFWF and WPI, whilst WPI had a higher H0 compared to DFWF. The secondary structure of WPI was similar to WPC. WPI showed big flaky plate like structures; whereas WPC appeared as a small flaky and more compact structure. The most functional properties of WPI were better than WPC. In comparing most functional properties of WPI and WPC with soybean protein concentrate and isolate, WPI and WPC showed higher fat absorption capacity (FAC). Emulsifying properties and foam properties of WPC and WPI in alkaline pH were comparable with that of soybean protein concentrate and isolate. Walnut protein concentrates and isolates can be considered as potential functional food ingredients. PMID:22408408

  15. Determinants of Market Structure and the Airline Industry

    NASA Technical Reports Server (NTRS)

    Raduchel, W.

    1972-01-01

    The general economic determinants of market structure are outlined with special reference to the airline industry. Included are the following facets: absolute size of firms; distributions of firms by size; concentration; entry barriers; product and service differentiation; diversification; degrees of competition; vertical integration; market boundaries; and economies of scale. Also examined are the static and dynamic properties of market structure in terms of mergers, government policies, and economic growth conditions.

  16. Microgram-scale protein structure determination by NMR.

    PubMed

    Aramini, James M; Rossi, Paolo; Anklin, Clemens; Xiao, Rong; Montelione, Gaetano T

    2007-06-01

    Using conventional triple-resonance nuclear magnetic resonance (NMR) experiments with a 1 mm triple-resonance microcoil NMR probe, we determined near complete resonance assignments and three-dimensional (3D) structure of the 68-residue Methanosarcina mazei TRAM protein using only 72 mug (6 microl, 1.4 mM) of protein. This first example of a complete solution NMR structure determined using microgram quantities of protein demonstrates the utility of microcoil-probe NMR technologies for protein samples that can be produced in only limited quantities.

  17. Optimizing an emperical scoring function for transmembrane protein structure determination.

    SciTech Connect

    Young, Malin M.; Sale, Kenneth L.; Gray, Genetha Anne; Kolda, Tamara Gibson

    2003-10-01

    We examine the problem of transmembrane protein structure determination. Like many other questions that arise in biological research, this problem cannot be addressed by traditional laboratory experimentation alone. An approach that integrates experiment and computation is required. We investigate a procedure which states the transmembrane protein structure determination problem as a bound constrained optimization problem using a special empirical scoring function, called Bundler, as the objective function. In this paper, we describe the optimization problem and some of its mathematical properties. We compare and contrast results obtained using two different derivative free optimization algorithms.

  18. Organizational Structure as a Determinant of Job Burnout.

    PubMed

    Bilal, Atif; Ahmed, Hafiz Mushtaq

    2017-03-01

    This exploratory study determined the impact of organizational structure, particularly participation in decision making, instrumental communication, formalization, integration, and promotional opportunity, on burnout among Pakistani pediatric nurses. Data were collected from pediatric nurses working for Punjab's largest state-run hospital. The findings revealed that participation in decision making, instrumental communication, and promotional opportunity prevented burnout. Formalization contributed to burnout but integration was not related to burnout. Quite interestingly, except for supervisory status, most control variables for this study were not significantly related to emotional burnout. Hence, the hypothesis that organizational structure is a determinant of job burnout was accepted.

  19. AFLP analysis reveals high genetic diversity but low population structure in Coccidioides posadasii isolates from Mexico and Argentina

    PubMed Central

    2013-01-01

    Background Coccidioides immitis and C. posadasii cause coccidioidomycosis, a disease that is endemic to North and South America, but for Central America, the incidence of coccidioidomycosis has not been clearly established. Several studies suggest genetic variability in these fungi; however, little definitive information has been discovered about the variability of Coccidioides fungi in Mexico (MX) and Argentina (AR). Thus, the goals for this work were to study 32 Coccidioides spp. isolates from MX and AR, identify the species of these Coccidioides spp. isolates, analyse their phenotypic variability, examine their genetic variability and investigate the Coccidioides reproductive system and its level of genetic differentiation. Methods Coccidioides spp. isolates from MX and AR were taxonomically identified by phylogenetic inference analysis using partial sequences of the Ag2/PRA gene and their phenotypic characteristics analysed. The genetic variability, reproductive system and level of differentiation were estimated using AFLP markers. The level of genetic variability was assessed measuring the percentage of polymorphic loci, number of effective allele, expected heterocygosity and Index of Association (IA). The degree of genetic differentiation was determined by AMOVA. Genetic similarities among isolates were estimated using Jaccard index. The UPGMA was used to contsruct the corresponding dendrogram. Finally, a network of haplotypes was built to evaluate the genealogical relationships among AFLP haplotypes. Results All isolates of Coccidioides spp. from MX and AR were identified as C. posadasii. No phenotypic variability was observed among the C. posadasii isolates from MX and AR. Analyses of genetic diversity and population structure were conducted using AFLP markers. Different estimators of genetic variability indicated that the C. posadasii isolates from MX and AR had high genetic variability. Furthermore, AMOVA, dendrogram and haplotype network showed a small

  20. Isolation and further structural characterization of lignins from the valonea of Quercus variabilis.

    PubMed

    Yang, Lina; Wang, Dongmei; Zhou, Dan; Zhang, Yawei; Yang, Tingting

    2017-04-01

    The isolation process of alkali lignin (AL) from the valonea of Quercus variabilis Blume was optimized (liquid/solid ratio, 12.21; isolation time, 4.21h; isolation temperature, 42.21°C; and alkali concentration, 0.85mol/L) using the response surface method (RSM), with the highest isolation rate obtained being 22.67%. Then, the apparent structures of AL, enzymatic hydrolysis lignin (CEL) and milled wood lignin (MWL) were studied by scanning electron microscopy (SEM), which indicated that the isolation processes of AL and CEL caused some damage to the apparent structure of lignin. The comprehensive structure characteristics of lignin samples was studied using (1)H, (13)C and 2D-HSQC techniques based on former studies. It was found that (1) three lignins were GSH-type; (2) the relative content of β-O-4' linkages in CEL (75.91%) was lower than those in AL (91.57%) and MWL (83.23%), suggesting that the β-O-4' linkages were largely cleaved during the CEL isolation process. In addition, the existence of phenylcoumarane, ferulic acid, p-coumarates and p-hydroxycinnamyl alcohol end groups can be found; (3) The S/G ratios were estimated to be 8.72, 1.30 and 0.98 for AL, MWL and CEL, respectively, suggesting that the lignin fragment rich in S-units was easily released under the alkali conditions.

  1. NMR structural determination of unique invertebrate glycosaminoglycans endowed with medical properties.

    PubMed

    Pomin, Vitor H

    2015-09-02

    Glycosaminoglycans (GAGs) are sulfated polysaccharides of complex structure endowed with numerous biomedical functions. Although ubiquitously distributed in vertebrates, GAGs can also occur in certain terrestrial or marine invertebrates. Solution nuclear magnetic resonance (NMR) spectroscopy has been the analytical technique mostly employed in structural characterization of GAGs from any source. This review aims at illustrating the application of NMR in structural determination of few representative invertebrate GAG examples of unique structures and endowed with therapeutic actions. They are the holothurian fucosylated chondroitin sulfate, the acharan sulfate isolated from the snail Achatina fulica, the dermatan sulfates with distinct sulfation patterns extracted from ascidian species, the sulfated glucuronic acid-containing heparan sulfate isolated from the gastropode Nodipecten nodosum, and the hybrid heparin/heparan sulfate molecule obtained from the shrimp Litopenaeus vannamei. These invertebrate GAGs exhibit distinct structures when compared to those extracted from mammalian GAGs. The distinct structures of the invertebrate GAGs lead also to different mechanisms of actions as compared to the mammalian GAG standards. Invertebrate GAGs comprise promising therapeutic candidates in fights against diseases. Solution NMR has been playing a pivotal role in this carbohydrate-based drug research, discovery and development.

  2. Structural and Electronic Properties of Isolated Nanodiamonds: A Theoretical Perspective

    SciTech Connect

    Raty, J; Galli, G

    2004-09-09

    Nanometer sized diamond has been found in meteorites, proto-planetary nebulae and interstellar dusts, as well as in residues of detonation and in diamond films. Remarkably, the size distribution of diamond nanoparticles appears to be peaked around 2-5 nm, and to be largely independent of preparation conditions. Using ab-initio calculations, we have shown that in this size range nanodiamond has a fullerene-like surface and, unlike silicon and germanium, exhibit very weak quantum confinement effects. We called these carbon nanoparticles bucky-diamonds: their atomic structure, predicted by simulations, is consistent with many experimental findings. In addition, we carried out calculations of the stability of nanodiamond which provided a unifying explanation of its size distribution in extra-terrestrial samples, and in ultra-crystalline diamond films. Here we present a summary of our theoretical results and we briefly outline work in progress on doping of nanodiamond with nitrogen.

  3. Detection of the plasmid-mediated quinolone resistance determinants in clinical isolates of Acinetobacter baumannii in China.

    PubMed

    Yang, Haifei; Hu, Lifen; Liu, Yanyan; Ye, Ying; Li, Jiabin

    2016-10-01

    We examined the prevalence of plasmid-mediated quinolone resistance (PMQR) determinants among Acinetobacter baumannii in Anhui, China. And β-lactamase genes and mutations in quinolone resistance-determining regions (QRDRs) were also investigated among the PMQR-positive isolates. Among the 39 A. baumannii isolates, 3 (7.7%) isolates harbored qnrB and 1 (2.6%) harbored qnrS. Mutations in the QRDRs of gyrA were identified in 2 isolates amongst the 4 PMQR-positive isolates. Quinolone resistance could be transferred by conjugation from all 4 PMQR-positive donors. In conclusion, more attention should be taken to prevent the transmission of PMQR genes among A. baumannii.

  4. Molecular Characterization of Multidrug Resistant Hospital Isolates Using the Antimicrobial Resistance Determinant Microarray

    PubMed Central

    Leski, Tomasz A.; Vora, Gary J.; Barrows, Brian R.; Pimentel, Guillermo; House, Brent L.; Nicklasson, Matilda; Wasfy, Momtaz; Abdel-Maksoud, Mohamed; Taitt, Chris Rowe

    2013-01-01

    Molecular methods that enable the detection of antimicrobial resistance determinants are critical surveillance tools that are necessary to aid in curbing the spread of antibiotic resistance. In this study, we describe the use of the Antimicrobial Resistance Determinant Microarray (ARDM) that targets 239 unique genes that confer resistance to 12 classes of antimicrobial compounds, quaternary amines and streptothricin for the determination of multidrug resistance (MDR) gene profiles. Fourteen reference MDR strains, which either were genome, sequenced or possessed well characterized drug resistance profiles were used to optimize detection algorithms and threshold criteria to ensure the microarray's effectiveness for unbiased characterization of antimicrobial resistance determinants in MDR strains. The subsequent testing of Acinetobacter baumannii, Escherichia coli and Klebsiella pneumoniae hospital isolates revealed the presence of several antibiotic resistance genes [e.g. belonging to TEM, SHV, OXA and CTX-M classes (and OXA and CTX-M subfamilies) of β-lactamases] and their assemblages which were confirmed by PCR and DNA sequence analysis. When combined with results from the reference strains, ∼25% of the ARDM content was confirmed as effective for representing allelic content from both Gram-positive and –negative species. Taken together, the ARDM identified MDR assemblages containing six to 18 unique resistance genes in each strain tested, demonstrating its utility as a powerful tool for molecular epidemiological investigations of antimicrobial resistance in clinically relevant bacterial pathogens. PMID:23936031

  5. Molecular characterization of multidrug resistant hospital isolates using the antimicrobial resistance determinant microarray.

    PubMed

    Leski, Tomasz A; Vora, Gary J; Barrows, Brian R; Pimentel, Guillermo; House, Brent L; Nicklasson, Matilda; Wasfy, Momtaz; Abdel-Maksoud, Mohamed; Taitt, Chris Rowe

    2013-01-01

    Molecular methods that enable the detection of antimicrobial resistance determinants are critical surveillance tools that are necessary to aid in curbing the spread of antibiotic resistance. In this study, we describe the use of the Antimicrobial Resistance Determinant Microarray (ARDM) that targets 239 unique genes that confer resistance to 12 classes of antimicrobial compounds, quaternary amines and streptothricin for the determination of multidrug resistance (MDR) gene profiles. Fourteen reference MDR strains, which either were genome, sequenced or possessed well characterized drug resistance profiles were used to optimize detection algorithms and threshold criteria to ensure the microarray's effectiveness for unbiased characterization of antimicrobial resistance determinants in MDR strains. The subsequent testing of Acinetobacter baumannii, Escherichia coli and Klebsiella pneumoniae hospital isolates revealed the presence of several antibiotic resistance genes [e.g. belonging to TEM, SHV, OXA and CTX-M classes (and OXA and CTX-M subfamilies) of β-lactamases] and their assemblages which were confirmed by PCR and DNA sequence analysis. When combined with results from the reference strains, ~25% of the ARDM content was confirmed as effective for representing allelic content from both Gram-positive and -negative species. Taken together, the ARDM identified MDR assemblages containing six to 18 unique resistance genes in each strain tested, demonstrating its utility as a powerful tool for molecular epidemiological investigations of antimicrobial resistance in clinically relevant bacterial pathogens.

  6. Applications of model structure determination to flight test data

    NASA Technical Reports Server (NTRS)

    Batterson, J. G.; Klein, V.

    1984-01-01

    Several statistical and information criteria need to be considered when selecting an adequate model. Incorrect stability and control derivates result from inadequate aerodynamic model structure. Stepwise regression is used to determine the structure for an adequate model. Flight data which covers a nonlinear aerodynamic model range may be analyzed as a single data set or partitioned into several distinct sets. Stepwise regression for model structure detemination and parameter estimation was successfully applied to three aircraft types (single engine general aviation, unaugmented modern jet fighter, jet transport).

  7. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

    PubMed Central

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

    2013-01-01

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

  8. High-resolution protein structure determination by serial femtosecond crystallography.

    PubMed

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  9. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins.

    PubMed

    Brookes, David H; Head-Gordon, Teresa

    2016-04-06

    We develop a Bayesian approach to determine the most probable structural ensemble model from candidate structures for intrinsically disordered proteins (IDPs) that takes full advantage of NMR chemical shifts and J-coupling data, their known errors and variances, and the quality of the theoretical back-calculation from structure to experimental observables. Our approach differs from previous formulations in the optimization of experimental and back-calculation nuisance parameters that are treated as random variables with known distributions, as opposed to structural or ensemble weight optimization or use of a reference ensemble. The resulting experimental inferential structure determination (EISD) method is size extensive with O(N) scaling, with N = number of structures, that allows for the rapid ranking of large ensemble data comprising tens of thousands of conformations. We apply the EISD approach on singular folded proteins and a corresponding set of ∼25 000 misfolded states to illustrate the problems that can arise using Boltzmann weighted priors. We then apply the EISD method to rank IDP ensembles most consistent with the NMR data and show that the primary error for ranking or creating good IDP ensembles resides in the poor back-calculation from structure to simulated experimental observable. We show that a reduction by a factor of 3 in the uncertainty of the back-calculation error can improve the discrimination among qualitatively different IDP ensembles for the amyloid-beta peptide.

  10. Equilibration kinetics in isolated and membrane-bound photosynthetic reaction centers upon illumination: a method to determine the photoexcitation rate.

    PubMed

    Manzo, Anthony J; Goushcha, Alexander O; Barabash, Yuri M; Kharkyanen, Valery N; Scott, Gary W

    2009-07-01

    Kinetics of electron transfer, following variation of actinic light intensity, for photosynthetic reaction centers (RCs) of purple bacteria (isolated and membrane-bound) were analyzed by measuring absorbance changes in the primary photoelectron donor absorption band at 865 nm. The bleaching of the primary photoelectron donor absorption band in RCs, following a sudden increase of illumination from the dark to an actinic light intensity of I(exp), obeys a simple exponential law with the rate constant alphaI(exp) + k(rec), in which alpha is a parameter relating the light intensity, measured in mW/cm(2), to a corresponding theoretical rate in units of reciprocal seconds, and k(rec) is the effective rate constant of the charge recombination in the photosynthetic RCs. In this work, a method for determining the alpha parameter value is developed and experimentally verified for isolated and membrane-bound RCs, allowing for rigorous modeling of RC macromolecule dynamics under varied photoexcitation conditions. Such modeling is necessary for RCs due to alterations of the forward photoexcitation rates and relaxation rates caused by illumination history and intramolecular structural dynamics effects. It is demonstrated that the classical Bouguer-Lambert-Beer formalism can be applied for the samples with relatively low scattering, which is not necessarily the case with strongly scattering media or high light intensity excitation.

  11. Population Genetic Structure of Clinical and Environmental Isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers ▿ †

    PubMed Central

    Meece, Jennifer K.; Anderson, Jennifer L.; Fisher, Matthew C.; Henk, Daniel A.; Sloss, Brian L.; Reed, Kurt D.

    2011-01-01

    Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. PMID:21705544

  12. Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

    USGS Publications Warehouse

    Meece, J.K.; Anderson, J.L.; Fisher, M.C.; Henk, D.A.; Sloss, Brian L.; Reed, K.D.

    2011-01-01

    Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

  13. Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis based on 27 polymorphic microsatellite markers

    USGS Publications Warehouse

    Meece, Jennifer K.; Anderson, Jennifer L.; Fisher, Matthew C.; Henk, Daniel A.; Sloss, Brian L.; Reed, Kurt D.

    2011-01-01

    Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.

  14. Novel genetic algorithm search procedure for LEED surface structure determination.

    PubMed

    Viana, M L; dos Reis, D D; Soares, E A; Van Hove, M A; Moritz, W; de Carvalho, V E

    2014-06-04

    Low Energy Electron Diffraction (LEED) is one of the most powerful experimental techniques for surface structure analysis but until now only a trial-and-error approach has been successful. So far, fitting procedures developed to optimize structural and nonstructural parameters-by minimization of the R-factor-have had a fairly small convergence radius, suitable only for local optimization. However, the identification of the global minimum among the several local minima is essential for complex surface structures. Global optimization methods have been applied to LEED structure determination, but they still require starting from structures that are relatively close to the correct one, in order to find the final structure. For complex systems, the number of trial structures and the resulting computation time increase so rapidly that the task of finding the correct model becomes impractical using the present methodologies. In this work we propose a new search method, based on Genetic Algorithms, which is able to determine the correct structural model starting from completely random structures. This method-called here NGA-LEED for Novel Genetic Algorithm for LEED-utilizes bond lengths and symmetry criteria to select reasonable trial structures before performing LEED calculations. This allows a reduction of the parameter space and, consequently of the calculation time, by several orders of magnitude. A refinement of the parameters by least squares fit of simulated annealing is performed only at some intermediate stages and in the final step. The method was successfully tested for two systems, Ag(1 1 1)(4 × 4)-O and Au(1 1 0)-(1 × 2), both in theory versus theory and in theory versus experiment comparisons. Details of the implementation as well as the results for these two systems are presented.

  15. Recent Research and Application on Seismic Isolation, Energy Dissipation and Control for Structures in China

    SciTech Connect

    Zhou Fulin; Tan Ping; Cui Jie; Xian Qiaoling; Wei Lushun; Huang Dongyang

    2008-07-08

    This paper briefly introduces the recent research, testing analysis, design and application on seismic isolation, energy dissipation, tuned mass damper and active control for buildings and bridges in mainland China. Paper introduces some typical researches, testing and analysis, including the mechanical tests for bearings and control devices, and the shaking table tests for structural models with different control systems. Paper also introduces the Chinese design codes for structures with seismic isolation and energy dissipation. Paper describes the recent application status and typical examples, especially introduces the largest isolation buildings group in the world, and the using passive and semi active control for structures. Also the paper makes discussion some problems existed on passive and active control technique now and the tendency of development on seismic control in future.

  16. Seismic response analyses of base isolated structures with high damping elastomeric bearings

    SciTech Connect

    Wang, C.Y.; Tang, Y.; Chang, Y.W.; Seidensticker, R.W. ); Marchertas, A.H. )

    1991-01-01

    Seismic response analysis of base-isolated structures with high damping elastomeric bearings is described. Emphasis is placed on the adaptation of a nonlinear constitutive model for the isolation bearing together with the treatment of foundation embedment for the soil-structure-interaction analysis. The constitutive model requires six input parameters derived from bearing experimental data under sinusoidal loading. The characteristic behavior of bearing, such as the variation of shear modulus and material damping with the change of maximum shear deformation, can be captured closely by the formulation. In the treatment of soil embedment a spring method is utilized to evaluate the foundation input motion as well as soil stiffness and damping. The above features have been incorporated into a three-dimensional system response program, SISEC, developed at Argonne National Laboratory. Sample problems are presented to illustrate the relative response of isolated and unisolated structures. 11 refs., 12 figs.

  17. Effect of removal of phenolic compounds on structural and thermal properties of sunflower protein isolate.

    PubMed

    Malik, M A; Sharma, H K; Saini, C S

    2016-09-01

    The present study evaluated the effect of removal of polyphenols on the structural properties of protein isolates extracted from sunflower seed and kernel. The structural and thermal changes in protein upon phenolic interaction were studied using circular dichroism, differential scanning calorimetry, thermal gravimetric analysis, X-ray diffraction, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), and Fourier Transform Infrared (FT-IR) spectroscopy. Presence of phenolic compounds in proteins decreased the ordered structure content with parallel increase in unordered structure content. Denaturation temperature was higher for protein isolates with phenolic compounds while, enthalpy decreased upon phenolic interaction. In the presence of phenolic compounds, higher mass loss was observed upon heating. Crystalinity and crystal size got increased after removal of phenolic compounds. Protein isolates from kernels had higher percentage of crystalinity and crystal size as compared to seed protein isolates. Higher molecular weights were observed for protein isolates with phenolic compounds. Presence of polyphenols reduced the hydrophobicity as well the sulfhydryl content and increased the particle size of proteins.

  18. Determining the Cognitive Structures of Geography Teacher Candidates on "Earthquake"

    ERIC Educational Resources Information Center

    Kaya, Bastürk; Aladag, Caner

    2017-01-01

    The objective of this study is to determine the cognitive structures of the students of geography teaching department by identifying their conceptual frameworks about the concept of earthquake. A case study design from qualitative research approaches was used in this research. Sample group of the study constitutes 155 students from the Department…

  19. Determining modulus of elasticity of ancient structural timber

    Treesearch

    Houjiang Zhang; Lei Zhu; Yanliang Sun; Xiping Wang; Haicheng Yan

    2011-01-01

    During maintenance of ancient timber architectures, it is important to determine mechanical properties of the wood component materials non-destructively and effectively, so that degraded members may be replaced or repaired to avoid structural failure. Experimental materials are four larch (Larix principis-rupprechtii Mayr.) components, which were taken down from the...

  20. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  1. A Laboratory Exercise in the Determination of Carbohydrate Structures.

    ERIC Educational Resources Information Center

    White, Bernard J.; Robyt, John F.

    1988-01-01

    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  2. A Laboratory Exercise in the Determination of Carbohydrate Structures.

    ERIC Educational Resources Information Center

    White, Bernard J.; Robyt, John F.

    1988-01-01

    Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

  3. Determination of the neutron spin-structure function

    SciTech Connect

    Petratos, G.G.; SLAC E-142 Collaboration

    1993-10-01

    The neutron spin-structure function g{sub 1}{sup n} has been determined by measuring the asymmetry in deep inelastic scattering of polarized electrons off a polarized {sup 3}He target. The results are interpreted in the quark-parton model and used, in conjuction with earlier proton results, to test the Bjorken sum rule.

  4. Birthday Cake Activity Structured Arrangement for Helping Children Determining Quantities

    ERIC Educational Resources Information Center

    Mariana, Neni

    2010-01-01

    Few researches have been concerned about relation between children's spatial thinking and number sense. Narrowing for this small research, we focused on one component of spatial thinking, that is structuring objects, and one component of number senses, that is cardinality by determining quantities. This study focused on a design research that was…

  5. Determination of permissible applied load stress in structural elements

    NASA Technical Reports Server (NTRS)

    Loy, R. E.; Posever, F. C.

    1969-01-01

    Graphic method is used to select allowable stresses in thermally loaded structures. Equations are used for determining the mode of failure for specific materials in order to plot a range of stress curves. Linear assumption and iterative calculations are eliminated resulting in comparatively high accuracy.

  6. From bacterial to human dihydrouridine synthase: automated structure determination

    SciTech Connect

    Whelan, Fiona Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-06-30

    The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a T. maritima enzyme, has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template. The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr-rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer.

  7. Structures and serospecificity of threonine-containing O polysaccharides of two clinical isolates belonging to the genus Proteus and their classification into O11 subserogroups.

    PubMed

    Drzewiecka, Dominika; Arbatsky, Nikolay P; Kondakova, Anna N; Shashkov, Alexander S; Knirel, Yuriy A

    2016-11-01

    Two clinical isolates from Polish patients, Proteus mirabilis 9B-m and Proteus genomospecies 3J-r, were found to be serologically related to P mirabilis O11. However, serological studies involving ELISA and Western blotting methods, using lipopolysaccharides (LPSs) extracted from the strains as antigens and native or adsorbed rabbit polyclonal O antisera, specific to the studied strains, revealed slight differences in the cross-reactivity and specificity of the two studied Proteus isolates, when compared to P. mirabilis O11. Two different O polysaccharides containing N-(d-galacturonoyl)-l-threonine were isolated from the LPSs of the isolates. Their structures were determined by chemical analysis and NMR spectroscopy and found to be related to the P. mirabilis O11 antigen structure established earlier, the 9B-m structure differing in the absence of the lateral glucose residue and the 3J-r structure in non-stoichiometric O-acetylation of the threonine residue only. Thus, the Proteus O11 serogroup should be divided into two subgroups: O11a, represented by the 9B-m isolate and O11a, b possessing the additional b epitope, containing the lateral residue of glucose and formed by the 3J-r isolate as well as P. mirabilis 25/57 belonging to O11 serogroup so far. O11a is the sixth new serotype found in Proteus spp. strains recently isolated from patients in central Poland.

  8. Polyclonal population structure of Streptococcus pneumoniae isolates in Spain carrying mef and mef plus erm(B).

    PubMed

    de la Pedrosa, Elia Gómez G; Morosini, María-Isabel; van der Linden, Mark; Ruiz-Garbajosa, Patricia; Galán, Juan Carlos; Baquero, Fernando; Reinert, Ralf René; Cantón, Rafael

    2008-06-01

    The population structure (serotypes, pulsed-field gel electrophoresis [PFGE] types, and multilocus sequencing types) of 45 mef-positive Streptococcus pneumoniae isolates [carrying mef alone (n = 17) or with the erm(B) gene n = 28)] were studied. They were selected from among all erythromycin-resistant isolates (n = 244) obtained from a collection of 712 isolates recovered from different Spanish geographic locations in the prevaccination period from 1999 to 2003. The overall rates of resistance (according to the criteria of the CLSI) among the 45 mef-positive isolates were as follows: penicillin G, 82.2%; cefotaxime, 22.2%; clindamycin, 62.2%; and tetracycline, 68.8% [mainly in isolates carrying erm(B) plus mef(E); P < 0.001]. No levofloxacin or telithromycin resistance was found. Macrolide resistance phenotypes (as determined by the disk diffusion approximation test) were 37.7% for macrolide resistance [with all but one due to mef(E)] and 62.2% for constitutive macrolide-lincosamide-streptogramin B resistance [cMLS(B); with all due to mef(E) plus erm(B)]. Serotypes 14 (22.2%), 6B (17.7%), 19A (13.3%), and 19F (11.1%) were predominant. Twenty-five different DNA patterns (PFGE types) were observed. Our mef-positive isolates were grouped (by eBURST analysis) into four clonal complexes (n = 18) and 19 singleton clones (n = 27). With the exception of clone Spain(9V)-3, all clonal complexes (clonal complexes 6B, Spain(6B)-2, and Sweden(15A)-25) and 73.6% of singleton clones carried both the erm(B) and the mef(E) genes. The international multiresistant clones Spain(23F)-1 and Poland(6B)-20 were represented as singleton clones. A high proportion of mef-positive S. pneumoniae isolates presented the erm(B) gene, with all isolates expressing the cMLS(B) phenotype. A polyclonal population structure was demonstrated within our Spanish mef-positive S. pneumoniae isolates, with few clonal complexes overrepresented within this collection.

  9. Does the genetic type of collagen determine fibril structure

    SciTech Connect

    Eikenberry, E.; Brodsky, B.; Cassidy, K.

    1980-10-01

    A number of genetic types of collagen, all triple-helical but with significant variations in their amino acid sequences, have been found and the distribution of these genetic types is tissue specific. For example, tendon is composed only of type I collagen, while cartilage contains largely type II collagen. Skin contains a large amount of type I, but has a significant fraction, approx. 15%, of type III. Each of these types can form fibrils, but it is not known whether they form distinctive fibril structures that are important in determining tissue organization. We are using x-ray diffraction to analyze a variety of tissues with different collagen genetic types to compare the fibril structures and thus investigate whether genetic type is an important determinant of this structure.

  10. The Shake-and-Bake structure determination of triclinic lysozyme.

    PubMed

    Deacon, A M; Weeks, C M; Miller, R; Ealick, S E

    1998-08-04

    The crystal structure of triclinic lysozyme, comprised of 1,001 non-H protein atoms and approximately 200 bound water molecules, has been determined ab initio (using native data alone) by the "Shake-and-Bake" method by using the computer program SnB. This is the largest structure determined so far by the SnB program. Initial experiments, using default SnB parameters derived from studies of smaller molecules, were unsuccessful. In fact, such experiments produced electron density maps dominated by a single large peak. This problem was overcome by considering the choice of protocol used during the parameter-shift phase refinement. When each phase was subjected to a single shift of +/-157.5 degrees during each SnB cycle, an unusually high percentage of random trials (approximately 22%) yielded correct solutions within 750 cycles. This success rate is higher than that typically observed, even for much smaller structures.

  11. Determination of the Absolute Configuration of a Monoglyceride Antibolting Compound and Isolation of Related Compounds from Radish Leaves (Raphanus sativus).

    PubMed

    Ogihara, Tsuyoshi; Amano, Naruki; Mitsui, Yuki; Fujino, Kaien; Ohta, Hiroyuki; Takahashi, Kosaku; Matsuura, Hideyuki

    2017-04-28

    A monoglyceride (1) has been reported to possess an antibolting effect in radish (Raphanus sativus), but its absolute configuration at the C-2 position was not determined earlier. In this work, the absolute configuration of 1 was determined to be (2S), and it was also accompanied by one new (2) and two known monoglycerides (3 and 4). The chemical structure of 2 was determined as β-(7'Z,10'Z,13'Z)-hexadecatrienoic acid monoglyceride (β-16:3 monoglyceride). Qualitative and quantitative analytical methods for compounds 1-4 were developed, using two deuterium-labeled compounds (8 and 9) as internal standards. The results revealed a broader range of distribution of 1-4 in several annual winter crops. It was also found that these isolated compounds have an inhibitory effect on the root elongation of Arabidopsis thaliana seedlings at concentrations of 25 and 50 μM in the medium. However, the inhibitory effect of 1 was not dependent on coronatin-insensitive 1 (COI1) protein, which may suggest the involvement of an unidentified signaling system other than jasmonic acid signaling.

  12. Antimicrobial susceptibility, virulence determinant carriage and molecular characteristics of Staphylococcus aureus isolates associated with skin and soft tissue infections.

    PubMed

    Yu, Fangyou; Liu, Yunling; Lv, Jinnan; Qi, Xiuqin; Lu, Chaohui; Ding, Yu; Li, Dan; Liu, Huanle; Wang, Liangxing

    2015-01-01

    A better understanding of the antimicrobial susceptibility, carriage of virulence determinants and molecular characteristics of Staphylococcus aureus isolates associated with skin and soft tissue infections (SSTIs) may provide further insights related to clinical outcomes with these infections. From January 2012 to September 2013, a total of 128 non-duplicate S. aureus isolates were recovered from patients with SSTIs. All 128 S. aureus SSTI isolates carried at least five virulence genes tested. Virulence genes detected among at least 70% of all tested isolates included hld (100%), hla (95.3%), icaA (96.9%), clf (99.2%), sdrC (79.7%), sdrD (70.3%), and sdrE (72.7%). The prevalence of MRSA isolates with 10 virulence genes tested (54.4%, 31/56) was significantly higher than that among MSSA isolates (35.2%, 25/71) (p<0.05). The positive rates of seb, sen, sem, sdrE and pvl among MRSA isolates were significantly higher than among MSSA isolates (p<0.05). ST7 and ST630 accounting for 10.9% were found to be the predominant STs. The most prevalent spa type was t091 (8.6%). MRSA-ST59-SCCmec IV was the most common clone (12.3%) among MRSA isolates whereas among MSSA isolates the dominant clone was MSSA-ST7 (15.5%). Six main clonal complexes (CCs) were found, including CC5 (52.3%), CC7 (11.7%), CC59 (8.6%), CC88 (6.3%), CC398 (4.7%), and CC121 (3.1%). A higher carriage of seb and sec was found among CC59 isolates. In comparison to CC5 and CC7 isolates, those with the highest carriage rates (>80.0%) of sdrC and sdrD, CC59 isolates had lower prevalence of these two virulence genes. All CC59 isolates were susceptible to gentamicin and trimethoprim/sulfamethoxazole, while CC5 and CC7 isolates had resistance rates to these two antimicrobials of 25.4% and 20.9%, and 40.0% and 40.0%, respectively. The resistance rates for tetracycline, clindamycin, and erythromycin among CC5 isolates were lower than among CC7 and CC59 isolates. In conclusion, the molecular typing of S. aureus SSTI

  13. Spectroscopic study of the n-hexanol cluster structure, isolated in an argon matrix

    NASA Astrophysics Data System (ADS)

    Doroshenko, I. Yu.

    2017-06-01

    Infrared absorption spectra of n-hexanol isolated in an argon matrix are recorded at temperatures varying between 20 and 50 K. The temperature evolution of the recorded spectra across several spectral regions is analyzed. The experimental data are interpreted using the results of quantum-chemical modeling [DFT/B3LYP/6-31G (d,p)] of the structure and the vibrational spectra of chain and cyclic clusters that included between one and four hexanol molecules. It is shown that as the temperature of the isolating matrix is increased, there is a gradual transformation of the hexanol cluster structure.

  14. Antimicrobial resistance determinant microarray for analysis of multi-drug resistant isolates

    NASA Astrophysics Data System (ADS)

    Taitt, Chris Rowe; Leski, Tomasz; Stenger, David; Vora, Gary J.; House, Brent; Nicklasson, Matilda; Pimentel, Guillermo; Zurawski, Daniel V.; Kirkup, Benjamin C.; Craft, David; Waterman, Paige E.; Lesho, Emil P.; Bangurae, Umaru; Ansumana, Rashid

    2012-06-01

    The prevalence of multidrug-resistant infections in personnel wounded in Iraq and Afghanistan has made it challenging for physicians to choose effective therapeutics in a timely fashion. To address the challenge of identifying the potential for drug resistance, we have developed the Antimicrobial Resistance Determinant Microarray (ARDM) to provide DNAbased analysis for over 250 resistance genes covering 12 classes of antibiotics. Over 70 drug-resistant bacteria from different geographic regions have been analyzed on ARDM, with significant differences in patterns of resistance identified: genes for resistance to sulfonamides, trimethoprim, chloramphenicol, rifampin, and macrolide-lincosamidesulfonamide drugs were more frequently identified in isolates from sources in Iraq/Afghanistan. Of particular concern was the presence of genes responsible for resistance to many of the last-resort antibiotics used to treat war traumaassociated infections.

  15. Protein structure determination using a database of interatomic distance probabilities.

    PubMed Central

    Wall, M. E.; Subramaniam, S.; Phillips, G. N.

    1999-01-01

    The accelerated pace of genomic sequencing has increased the demand for structural models of gene products. Improved quantitative methods are needed to study the many systems (e.g., macromolecular assemblies) for which data are scarce. Here, we describe a new molecular dynamics method for protein structure determination and molecular modeling. An energy function, or database potential, is derived from distributions of interatomic distances obtained from a database of known structures. X-ray crystal structures are refined by molecular dynamics with the new energy function replacing the Van der Waals potential. Compared to standard methods, this method improved the atomic positions, interatomic distances, and side-chain dihedral angles of structures randomized to mimic the early stages of refinement. The greatest enhancement in side-chain placement was observed for groups that are characteristically buried. More accurate calculated model phases will follow from improved interatomic distances. Details usually seen only in high-resolution refinements were improved, as is shown by an R-factor analysis. The improvements were greatest when refinements were carried out using X-ray data truncated at 3.5 A. The database potential should therefore be a valuable tool for determining X-ray structures, especially when only low-resolution data are available. PMID:10631988

  16. Virulence determinants invA and spvC in salmonellae isolated from poultry products, wastewater, and human sources.

    PubMed Central

    Swamy, S C; Barnhart, H M; Lee, M D; Dreesen, D W

    1996-01-01

    The presence of two virulence foci, invA and spvC, in Salmonella isolates obtained from poultry, wastewater, and human sources was determined. All isolates (n = 245) were positive for the invA gene sequence. Differences in degree of invasiveness were apparent with the Madin Darby canine kidney cell line, as only 79 of 159 randomly selected isolates (49.7%) tested were invasive at > 0.1% of the inoculum. 25% were invasive between 0.1 and 1.0% of the inoculum, and 24.5% were invasive at > 1.0% of the inoculum. There was a significant correlation between degree of invasion and source from which the isolate was recovered but no correlation between geographic origin of poultry isolates and degree of invasion. Only 37 of 245 isolates (15.1%) hybridized with the spvC DNA probe. All isolates that were recovered from a commercial egg production environment and chicken eggs and whose sequences exhibited homology with the spvC gene sequence were determined to be either Salmonella enteritidis PT 23 or PT 13. The sequences of few isolates from ceca and none from wastewater or humans demonstrated homology with the spvC gene. PMID:8837432

  17. Crystallization, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes

    DTIC Science & Technology

    1998-07-01

    COOPERATIVE AGREEMENT NUMBER DAMD17-95-2-5007 TITLE: Crystallization, X-ray Structure Determination and Structure-Based Drug Design for...approach for the develpment of anti-malarial agent using structure-based drug design . This technique will enable us to identify active site inhibitors...based drug design project high resolution three domensional structure of the enzyme - inhibitor complex provides the basis for further modifications

  18. Isolation of Francisella tularensis and Yersinia pestis from Blood Cultures by Plasma Purification and Immunomagnetic Separation Accelerates Antibiotic Susceptibility Determination

    PubMed Central

    Aloni-Grinstein, Ronit; Schuster, Ofir; Yitzhaki, Shmuel; Aftalion, Moshe; Maoz, Sharon; Steinberger-Levy, Ida; Ber, Raphael

    2017-01-01

    The early symptoms of tularemia and plague, which are caused by Francisella tularensis and Yersinia pestis infection, respectively, are common to other illnesses, resulting in a low index of suspicion among clinicians. Moreover, because these diseases can be treated only with antibiotics, rapid isolation of the bacteria and antibiotic susceptibility testing (AST) are preferable. Blood cultures of patients may serve as a source for bacteria isolation. However, due to the slow growth rates of F. tularensis and Y. pestis on solid media, isolation by plating blood culture samples on proper agar plates may require several days. Thus, improving the isolation procedure prior to antibiotic susceptibility determination is a major clinically relevant need. In this study, we developed a rapid, selective procedure for the isolation of F. tularensis and Y. pestis from blood cultures. We examined drop-plating and plasma purification followed by immunomagnetic separation (IMS) as alternative isolation methods. We determined that replacing the classical isolation method with drop-plating is advantageous with respect to time at the expense of specificity. Hence, we also examined isolation by IMS. Sub-localization of F. tularensis within blood cultures of infected mice has revealed that the majority of the bacteria are located within the extracellular fraction, in the plasma. Y. pestis also resides within the plasma. Therefore, the plasma fraction was isolated from blood cultures and subjected to an IMS procedure using polyclonal anti-F. tularensis live vaccine strain (LVS) or anti-Y. pestis antibodies conjugated to 50-nm nano-beads. The time required to reach an inoculum of sufficient bacteria for AST was shortest when using the plasma and IMSs for both bacteria, saving up to 2 days of incubation for F. tularensis and 1 day for Y. pestis. Our isolation procedure provides a proof of concept for the clinical relevance of rapid isolation for AST from F. tularensis- and Y. pestis

  19. Comparative study of fine structure in samples of isolated and paired early-type galaxies

    NASA Astrophysics Data System (ADS)

    Reduzzi, L.; Longhetti, M.; Rampazzo, R.

    1996-09-01

    Fine structure in early-type galaxies is considered to be among the more robust indicators of a past merging or acquisition event, although growing evidence from numerical simulations suggests that fine structure may be also interpreted in a `weak interaction' framework. We present a morphological study of a sample composed of 61 `isolated' early-type galaxies addressed to the detection of fine structure. This sample has been selected in order to be statistically comparable to a set of 54 early-type galaxies, members of pairs analysed by Reduzzi & Rampazzo with a similar technique. The rate of occurrence of fine structure detected in the `isolated' galaxy sample is significantly higher than that found for the pairs. In particular, the fraction of isolated early-type galaxies exhibiting shells is 16.4 per cent, a percentage similar to that found by Malin & Carter for RC2 isolated objects in the southern sky, while the fraction of early-type galaxies in pairs is ~=4 per cent. We discuss the comparison between the two samples in the context of the merger versus the weak interaction origin of fine structures. Concerning the formation of shells, although the merger origin cannot be ruled out, the observed difference is more naturally explained within the weak interaction framework.

  20. Third Structure Determination by Powder Diffractometery Round Robin (SDPDRR-3)

    SciTech Connect

    Le Bail, A.; Cranswick, L; Adil, K; Altomare, A; Avdeev, M; Cerny, R; Cuocci, C; Giacovazzo, C; Halasz, I; et al.

    2009-01-01

    The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solving a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.

  1. Determinants of oligomeric structure in the chicken liver glycoprotein receptor.

    PubMed Central

    Verrey, F; Drickamer, K

    1993-01-01

    The oligomeric state of the chicken liver receptor (chicken hepatic lectin), which mediates endocytosis of glycoproteins terminating with N-acetylglucosamine, has been investigated using physical methods as well as chemical cross-linking. Receptor isolated from liver and from transfected rat fibroblasts expressing the full-length polypeptide is a homotrimer immediately following solubilization in non-ionic detergent, but forms the previously observed hexamer during purification. These results are most consistent with the presence of a trimer of receptor polypeptides in liver membranes and in transfected cells. Analysis of truncated receptors reveals that the C-terminal extracellular portion of this type-II transmembrane protein does not form stable oligomers when isolated from the membrane anchor and cytoplasmic tail. The behaviour of chimeric receptors, in which the cytoplasmic tail of the glycoprotein receptor is replaced with the corresponding segments of rat liver asialoglycoprotein receptor or the beta-subunit of Na+,K(+)-ATPase, or with unrelated sequences from globin, indicates that the cytoplasmic tail influences oligomer stability. Replacement of N-terminal portions of the receptor with corresponding segments of influenza virus neuraminidase results in formation of tetramers, suggesting that the membrane anchor and flanking sequences are important determinants of oligomer formation. Images Figure 1 Figure 3 PMID:8503842

  2. Isolation, folding and structural investigations of the amino acid transporter OEP16

    SciTech Connect

    Ni, Da Qun; Zook, James; Klewer, Douglas A.; Nieman, Ronald A.; Soll, J.; Fromme, Petra

    2011-12-01

    Membrane proteins compose more than 30% of all proteins in the living cell. However, many membrane proteins have low abundance in the cell and cannot be isolated from natural sources in concentrations suitable for structure analysis. The overexpression, reconstitution, and stabilization of membrane proteins are complex and remain a formidable challenge in membrane protein characterization. Here we describe a novel, in vitro folding procedure for a cation-selective channel protein, the outer envelope membrane protein 16 (OEP16) of pea chloroplast, overexpressed in Escherichia coli in the form of inclusion bodies. The protein is purified and then folded with detergent on a Ni-NTA affinity column. Final concentrations of reconstituted OEP16 of up to 24 mg/ml have been achieved, which provides samples that are sufficient for structural studies by NMR and crystallography. Reconstitution of OEP16 in detergent micelles was monitored by circular dichroism, fluorescence, and NMR spectroscopy. Tryptophan fluorescence spectra of heterologous expressed OEP16 in micelles are similar to spectra of functionally active OEP16 in liposomes, which indicates folding of the membrane protein in detergent micelles. CD spectroscopy studies demonstrate a folded protein consisting primarily of a-helices. 15N-HSQC NMR spectra also provide evidence for a folded protein. We present here a convenient, effective and quantitative method to screen large numbers of conditions for optimal protein stability by using microdialysis chambers in combination with fluorescence spectroscopy. Recent collection of multidimensional NMR data at 500, 600 and 800 MHz demonstrated that the protein is suitable for structure determination by NMR and stable for weeks during data collection.

  3. Prevalence of plasmid-mediated quinolone resistance determinants among Escherichia coli isolated from food animals in Korea.

    PubMed

    Tamang, Migma Dorji; Nam, Hyang-Mi; Chae, Myung Hwa; Kim, Su-Ran; Gurung, Mamata; Jang, Geum-Chan; Jung, Suk-Chan; Lim, Suk-Kyung

    2012-12-01

    The aim of this study was to investigate the prevalence of plasmid-mediated quinolone resistance (PMQR) determinants in Escherichia coli isolated from food-producing animals and to characterize the PMQR-positive isolates. A total of 365 E. coli isolates which were either nalidixic acid resistant and ciprofloxacin susceptible (NAL(R)-CIP(S); n=185), or nalidixic acid and ciprofloxacin resistant (NAL(R)-CIP(R); n=180) were assessed for the presence of PMQR determinants by polymerase chain reaction. PMQR-positive isolates were further characterized by mutation analysis within the quinolone resistance-determining region (QRDR) of gyrA, gyrB, parC, and parE, phylogenetic group analysis, and pulsed-field gel electrophoresis (PFGE). Fourteen NAL(R)-CIP(S) (n=8) and NAL(R)-CIP(R) (n=6) E. coli isolates were positive for PMQR genes. Among them, qnrB4, qnrS1, and aac(6')-Ib-cr genes were detected in two (0.5%), eight (2.2%), and four (1.1%) isolates, respectively. None of the isolates harbored qnrA, qnrC, qnrD, and qepA genes. All but one PMQR-positive isolates harbored one or more point mutations in the QRDR of gyrA, and five of these isolates had additional mutations in the parC gene. Furthermore, one isolate each had additional substitutions in gyrB and parE genes, respectively. The most prevalent mutation was Ser83-Leu within the QRDR of gyrA. Phylogenetic analysis identified three major phylogenetic lineages, with phylogroups A (n=7) and D (n=4) being the most common phylogroups. None of the isolates belonged to virulent phylogroup B2. PFGE demonstrated that a combination of clonal and horizontal gene transmission is disseminating PMQR genes among the veterinary E. coli isolates in Korea. To our knowledge, this is the first report of occurrence of qnrB, qnrS, and aac(6')-Ib-cr genes in E. coli isolated from food-producing animals in Korea. Isolation of PMQR genes from food animals is a matter of concern since they could be transmitted to humans via food animals.

  4. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  5. Uncertainties in the use of periodate oxidation for determination of dextran structure.

    PubMed

    Leonard, G J

    1975-05-01

    A glucan of high molecular weight isolated from stale sugar-cane, and previously shown to have a marked effect on sucrose crystallisation processes-1, is a relatively linear dextran. Approximately 96-97% of its D-glucose residues are involved in (1 yields 6)-alpha-D linkages and constitute the linear backbone of the polymer. The remaining 3-4% of D-glucose residues form branch-points by (1 yields 3)-alpha-D linkages. The periodate-oxidation technique, which has been extensively used by other workers to determine dextran structure, gave erroneous results when applied to the dextran from stale sugar-cane.

  6. Regional mechanics determine collagen fiber structure in healing myocardial infarcts.

    PubMed

    Fomovsky, Gregory M; Rouillard, Andrew D; Holmes, Jeffrey W

    2012-05-01

    Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal directions and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities.

  7. DNA Nanotubes for NMR Structure Determination of Membrane Proteins

    PubMed Central

    Bellot, Gaëtan; McClintock, Mark A.; Chou, James J; Shih, William M.

    2013-01-01

    Structure determination of integral membrane proteins by solution NMR represents one of the most important challenges of structural biology. A Residual-Dipolar-Coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size, however, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for weak alignment of membrane proteins was severely limited. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400nm-long six-helix bundles each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, towards collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes via counter ions and small DNA binding molecules. This detergent-resistant liquid-crystal media offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility, and structural programmability. Production of sufficient nanotubes for 4–5 NMR experiments can be completed in one week by a single individual. PMID:23518667

  8. Isolation and determination of anthocyanins in seed coats of black soybean (Glycine max (L.) Merr.).

    PubMed

    Choung, M G; Baek, I Y; Kang, S T; Han, W Y; Shin, D C; Moon, H P; Kang, K H

    2001-12-01

    Anthocyanin pigments in seed coats of black soybean (Glycine max (L.) Merr.) were extracted with 1% HCl-CH(3)OH, and the crude anthocyanin extract was purified by Shepadex LH-20 and Lichroprep RP-18 open-column chromatography. Three major anthocyanins were isolated, and their chemical structures were identified by spectroscopic methods (UV-visible, FABMS, (1)H and (13)C NMR, and by TLC). The complete structures of these anthocyanins were elucidated as delphinidin-3-glucoside, cyanidin-3-glucoside, and petunidin-3-glucoside. Among them, petunidin-3-glucoside was identified as a new anthocyanin in black soybeans. On the basis of RP-HPLC with a UV-vis detector, the contents of delphinidin-3-glucoside, cyanidin-3-glucoside, petunidin-3-glucoside, and total anthocyanins in seed coats of 10 black soybeans were found in the ranges of 0-3.71, 0.94-15.98, 0-1.41, and 1.58-20.18 mg/g, respectively. The results obtained in this study imply that the seed coats of black soybean can be used as a good source for cyanidin-3-glucoside and delphinidin-3-glucoside.

  9. Sarcomere length uniformity determined from three-dimensional reconstructions of resting isolated heart cell striation patterns.

    PubMed Central

    Roos, K P

    1987-01-01

    A- and I-band striation positions have been obtained, three-dimensionally reconstructed, and statistically analyzed from the volumes of resting isolated heart cells. Striation patterns from optically discrete subvolumes are imaged along the length of these myocytes with a computer-interfaced optical microscope imaging system. Planar striation maps are reconstructed by the computer from sequentially obtained striation pattern images displaced across the width or depth of the cell in controlled steps. Multiple planar maps are combined to form full three-dimensional (3-D) reconstructions that illustrate the sarcomeric structure and ordering throughout the volume of the cell. These reconstructions demonstrate a high degree of striation registration throughout most regions of cardiac cells. The striation registration is often slightly (less than 10 degrees) skewed across the width or depth of nearly every cell and is occasionally disrupted between adjacent groups of sarcomeres. These disruptions in registration are always associated with the locations of the nuclei. Rigorous statistical analyses indicate small volumetric regions of the cell delineated by these disruptions can have significantly (0.014-0.113 micron) shorter or longer average sarcomere length periodicities. Unlike skeletal muscle "fibrillenstruktur," these data from cardiac cells exhibit no evidence of helical packing schemes for sarcomere order. These observations suggest that the relatively large nuclei displace and disrupt the normal registration of the sarcomeres, which is probably mediated by internal cytoskeletal structures. Images FIGURE 2 PMID:3663835

  10. Observation and Structure Determination of an Oxide Quasicrystal Approximant

    NASA Astrophysics Data System (ADS)

    Förster, S.; Trautmann, M.; Roy, S.; Adeagbo, W. A.; Zollner, E. M.; Hammer, R.; Schumann, F. O.; Meinel, K.; Nayak, S. K.; Mohseni, K.; Hergert, W.; Meyerheim, H. L.; Widdra, W.

    2016-08-01

    We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 32 .4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO3 clusters, leading to a fundamental edge length of the tiling 6.7 Å.

  11. One-day pulsed-field gel electrophoresis protocol for rapid determination of emetic Bacillus cereus isolates.

    PubMed

    Kaminska, Paulina S; Fiedoruk, Krzysztof; Jankowska, Dominika; Mahillon, Jacques; Nowosad, Karol; Drewicka, Ewa; Zambrzycka, Monika; Swiecicka, Izabela

    2015-04-01

    Bacillus cereus, the Gram-positive and spore-forming ubiquitous bacterium, may cause emesis as the result of food intoxication with cereulide, a heat-stable emetic toxin. Rapid determination of cereulide-positive B. cereus isolates is of highest importance due to consequences of this intoxication for human health and life. Here we present a 1-day pulsed-field gel electrophoresis for emetic B. cereus isolates, which allows rapid and efficient determination of their genomic relatedness and helps determining the source of intoxication in case of outbreaks caused by these bacilli.

  12. Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure

    PubMed Central

    González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo‐Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin

    2016-01-01

    Abstract Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C5‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383

  13. A METHOD FOR DETERMINING TOTAL PROTEIN OF ISOLATED CELLULAR ELEMENTS AND CORRESPONDING TRITIUM RADIOACTIVITY

    PubMed Central

    Koenig, Edward

    1968-01-01

    A method is described for the microanalysis of protein, obtained from isolated tissue elements, in the range of 500 µµg-500 mµg. The method entails solubilization of cellular protein with phosphoric acid and heat after extraction of acid-soluble compounds, lipids, and RNA. A procedure for the extraction and recovery of cellular RNA by the use of 40% trichloroacetic acid is presented. The solubilized protein, in the form of a microdroplet, is photomicrographed with monochromatic light at 230 mµ. Total density in the microdroplet is determined from calibrated photographic plates by microdensitometry, and is converted to protein mass by using an experimentally determined average specific absorbance value. A solubilized protein labeled with tritium can be recovered after photomicrography, combusted, and reduced to generate tritiated gas for high-efficiency tritium radiometry. Total protein was analyzed in (a) nerve cells of three different sizes from Deiters' nucleus of the rabbit; and the whole rod cell and rod cell nucleus of the rabbit retina. PMID:5664225

  14. The gp120 Protein Is a Second Determinant of Decreased Neurovirulence of Indian HIV-1C Isolates Compared to Southern African HIV-1C Isolates

    PubMed Central

    Rao, Vasudev R.; Neogi, Ujjwal; Eugenin, Eliseo; Prasad, Vinayaka R.

    2014-01-01

    Regional differences in neurovirulence have been documented among subtype/clade-C HIV-1 isolates in India and Southern Africa. We previously demonstrated that a C31S substitution in Clade-C Tat dicysteine motif reduces monocyte recruitment, cytokine induction and direct neurotoxicity. Therefore, this polymorphism is considered to be a causative factor for these differences in neurovirulence. We previously reported on the genotypic differences in Tat protein between clade-C and rest of the clades showing that approximately 90% of clade-C HIV-1 Tat sequences worldwide contained this C31S polymorphism, while 99% of non-clade C isolates lacked this Tat polymorphism at C31 residue (Ranga et al. (2004) J Virol 78∶2586–2590). Subsequently, we documented intra-clade-C differences in the frequency of Tat dicysteine variants between India and Southern Africa, as the basis for differential disease severity and showed the importance of the Tat dicysteine motif for neuropathogenesis using small animal models. We have now examined if determinants of neurovirulence besides Tat are different between the clade-C HIV-1 isolates from Southern Africa and India. Envelope glycoprotein gp120 is a well-documented contributor to neurotoxicity. We found that gp120 sequences of HIV-1 isolates from these two regions are genetically distinct. In order to delineate the contribution of gp120 to neurovirulence, we compared direct in vitro neurotoxicity of HIV-infected supernatants of a representative neurovirulent US clade-B isolate with two isolates each from Southern Africa and India using primary human neurons and SH-SY5Y neuroblastoma cells. Immunodepletion of gp120 of both US clade B and the Southern African clade C isolates revealed robust decreases in neurotoxicity, while that of the Indian isolates showed minimal effect on neurotoxicity. The gp120 as a cause of differential neurotoxicity was further confirmed using purified recombinant gp120 from HIV isolates from these regions. We

  15. Method of Determining Specification for Transmissibility of Vibration Isolator for ASTRO-H Soft X-Ray Spectrometer (SXS

    NASA Astrophysics Data System (ADS)

    Yasuda, Susumu; Ishimura, Kosei

    2014-06-01

    The ASTRO-H is an X-ray astronomy satellite scheduled for launch in 2015. One of the key instruments on board is the Soft X-ray Spectrometer (SXS). The SXS engineering model test revealed that the micro-vibration of cryocoolers affects the energy resolution of the detector. We presume that the micro- vibration produces considerable heat which disturbs temperature of the detector. In response, one of the measures taken was installing a passive vibration isolator between the SXS Dewar and cryocoolers to reduce the level of micro-vibration transmitted. In this case, the isolator must be soft enough to avoid disrupting the detector and stiff enough to withstand the launch load. To meet these mutually exclusive requirements, we must find a compromise when designing an isolator. To determine the relevant requirements, tests were contrived and performed, the results of which were used to determine the requirements and start designing the flight hardware of vibration isolators.

  16. Nature's Migraine Treatment: Isolation and Structure Elucidation of Parthenolide from "Tanacetum parthenium"

    ERIC Educational Resources Information Center

    Walsh, Emma L.; Ashe, Siobhan; Walsh, John J.

    2012-01-01

    The purpose of this experiment is to provide students with the essential skills and knowledge required to perform the extraction, isolation, and structural elucidation of parthenolide from "Tanacetum parthenium" or feverfew. Students are introduced to a background of the traditional medicinal uses of parthenolide, while more modern applications of…

  17. Nature's Migraine Treatment: Isolation and Structure Elucidation of Parthenolide from "Tanacetum parthenium"

    ERIC Educational Resources Information Center

    Walsh, Emma L.; Ashe, Siobhan; Walsh, John J.

    2012-01-01

    The purpose of this experiment is to provide students with the essential skills and knowledge required to perform the extraction, isolation, and structural elucidation of parthenolide from "Tanacetum parthenium" or feverfew. Students are introduced to a background of the traditional medicinal uses of parthenolide, while more modern applications of…

  18. Effect of structural flexibility on the design of vibration-isolating mounts for aircraft engines

    NASA Technical Reports Server (NTRS)

    Phillips, W. H.

    1984-01-01

    Previous analyses of the design of vibration-isolating mounts for a rear-mounted engine to decouple linear and rotational oscillations are extended to take into account flexibility of the engine-mount structure. Equations and curves are presented to allow the design of mount systems and to illustrate the results for a range of design conditions.

  19. Structure of complex cell wall polysaccharides isolated from Trichoderma and Hypocrea species.

    PubMed

    Prieto, A; Leal, J A; Poveda, A; Jiménez-Barbero, J; Gómez-Miranda, B; Domenech, J; Ahrazem, O; Bernabé, M

    1997-11-28

    The structure of fungal polysaccharides isolated from the cell wall of Trichoderma reesei, T. koningii, and Hypocrea psychrophila, have been investigated by means of chemical analyses and 1D and 2D NMR spectroscopy. The polysaccharides have an irregular structure, idealized as follows: [formula: see text] The proportions of the different side chains vary from a species to another, being n above some three times larger in H. psychrophila than in T. reesei or T. koningii.

  20. Team Assembly Mechanisms Determine Collaboration Network Structure and Team Performance

    PubMed Central

    Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Nunes Amaral, Luís A.

    2007-01-01

    Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields. PMID:15860629

  1. Membrane Proteins in Four Acts: Function Precedes Structure Determination

    PubMed Central

    Cramer, W. A.; Zakharov, S. D.; Hasan, S. Saif; Zhang, H.; Baniulis, D.; Zhalnina, M. V.; Soriano, G. M.; Sharma, O.; Rochet, J. C.; Ryan, C.; Whitelegge., J.; Kurisu, G.; Yamashita, E.

    2011-01-01

    Studies on four membrane protein systems, which combine information derived from crystal structures and biophysical studies have emphasized, as a precursor to crystallization, demonstration of functional activity. These assays have relied on sensitive spectrophotometric, electrophysiological, and microbiological assays of activity to select purification procedures that lead to functional complexes and with greater likelihood to successful crystallization: (I), Hetero-oligomeric proteins involved in electron transport/ proton translocation). (1) Crystal structures of the eight subunit heterooligomeric trans-membrane dimeric cytochrome b6f complex were obtained from cyanobacteria using a protocol that allowed an analysis of the structure and function of internal lipids at specific intra-membrane, intra-protein sites. Proteolysis and monomerization that inactivated the complex and prevented crystallization was minimized through the use of filamentous cyanobacterial strains that seem to have a different set of membrane-active proteases. (2) An NADPH-quinone oxido-reductase isolated from cyanobacteria contains an expanded set of seventeen monotopic and polytopic hetero-subunits. (II) β-barrel outer membrane proteins (OMPs). High resolution structures of the vitamin B12 binding protein, BtuB, solved in meso and in surfo, provide the best example of the differences in such structures that were anticipated in the first application of the lipid cubic phase to membrane proteins (1). A structure of the complex of BtuB with the colicin E3 and E2 receptor binding domain established a “fishing pole” model for outer membrane receptor function in cellular import of nuclease colicins. (III) A modified faster purification procedure contributed to significantly improved resolution (1.83 Å) of the universal porin, OmpF, the first membrane protein for which meaningful 3D crystals have been obtained (2). A crystal structure of the N-terminal translocation domain of colicin E3

  2. Virulence determinants, phylogenetic groups and fluoroquinolone resistance in Escherichia coli isolated from cystitis and pyelonephritis.

    PubMed

    Ferjani, S; Saidani, M; Ennigrou, S; Hsairi, M; Ben Redjeb, S

    2012-10-01

    The aim of this study is to assess the relation between virulence genotype, phylogenetic group and susceptibility to fluoroquinolones and the urinary tract infection type including pyelonephritis and cystitis due to Escherichia coli. Between 2006 and 2007, 129 non-duplicate E. coli isolates from pyelonephritis (n=56) and cystitis (n=73) were prospectively collected. The antibiotic susceptibility was done by disk diffusion method. The phylogenetic groups, A, B1, B2 and D and 18 virulence genes were determined by multiplex PCR. Statistical analysis was done with the Pearson χ2 test, Mann-Whitney U-test, Kruskal-Wallis test and stepwise multivariable logistic regression analysis, P values below 0.05 were considered statistically significant. For the pyelonephritis group, sex ratio was 0.3, the median age for women was 30 years and for men it was 54 years. For the cystitis group, sex ratio was 0.4, the median age for women was 41.5 years and for men it was 67.8 years. Significant statistical correlations were found between pyelonephritis isolates and susceptibility to ciprofloxacin (P=4 10(-5)), papG allele II (P=2 10(-6)), hlyA (P=10(-03)), iroN (P=0.04), iha (P=0.03) and ompT (P=0.03) virulence genes, high virulence score (P=0.008) and B2 phylogenetic group (P=0.03). In multivariate logistic regression analysis, papG II as predictor of pyelonephritis, no correlation could be established for the cystitis group. Our findings argue for a direct link between pyelonephritis, virulence factors, susceptibility to fluroquinolones and B2 phylogenetic group among uropthogenic E. coli. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  3. Investigation of the La{sub 2}O{sub 3}–Nb{sub 2}O{sub 5}–WO{sub 3} ternary phase diagram: Isolation and crystal structure determination of the original La{sub 3}NbWO{sub 10} material

    SciTech Connect

    Vu, T.D.; Barre, M.; Adil, K.; Jouanneaux, A.; Suard, E.; Goutenoire, F.

    2015-09-15

    In the course of the exploration of the La{sub 2}O{sub 3}–WO{sub 3}–Nb{sub 2}O{sub 5} ternary phase diagram, a new compound with the formula La{sub 3}NbWO{sub 10} was discovered. Its structure was determined from a combination of powder X-ray and neutron diffraction data. It crystallizes in the tetragonal space group P4{sub 2}/nmc (no. 137) with the lattice parameters: a=10.0807(1) Å; c=12.5540(1) Å. The structure is built up from infinite ribbons of octahedra (W/Nb)O{sub 5} which are perpendicular to each other, lanthanum ions being distributed around these ribbons. The electrical properties of this compound were investigated on sintered pellets by means of complex impedance spectroscopy. - Graphical abstract: Projection along the c-axis of cationic and anionic positions of a La{sub 3}NbWO{sub 10} unit cell. - Highlights: • The structure of La{sub 3}NbWO{sub 10} was resolved from the XRD and ND data. • The structure was described in many ways. • The ionic conduction property was studied.

  4. Determination and Distribution of cry-Type Genes of Bacillus thuringiensis Isolates from Taiwan

    PubMed Central

    Chak, K.-F.; Chao, D.-C.; Tseng, M.-Y.; Kao, S.-S.; Tuan, S.-J.; Feng, T.-Y.

    1994-01-01

    Using PCR with a set of specific oligonucleotide primers to detect cryI-type genes, we were able to screen the cry-type genes of 225 Bacillus thuringiensis soil isolates from Taiwan without much cost in time or labor. Some combinations of cry genes (the cry-type profile) in a single isolate were unique. We identified five distinct profiles of crystal genes from the B. thuringiensis soil isolates from Taiwan. The cry genes included cryIA(a), cryIA(b), cryIA(c), cryIC, cryID, and cryIV. Interestingly, 501 B. thuringiensis isolates (93.5% of the total number that we identified) were isolated from areas at high altitudes. The profiles of cry-type genes were distinct in all isolation areas. The distribution of cry-type genes of our isolates therefore depended on geography. Using PCR footprinting to detect cryIC-type genes, we identified two distinct cryIC footprints from some of our isolates, indicating that these isolates may contain novel cryIC-type genes. B. thuringiensis isolates containing cryIA(a)-, cryIA(b)-, and cryIA(c)-type genes exhibited much greater activity against Plutella xylostella than did other isolates, indicating that multiple cry-type genes may be used as markers for the prediction of insecticidal activities. Images PMID:16349324

  5. Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments.

    PubMed

    Carnelli, Alessandro; Mauri, Federica; Demarta, Antonella

    2017-03-02

    Aeromonas spp. and fecal coliforms, two abundant and cultivable bacterial populations that can be found in water ecosystems, might substantially contribute to the spread of antibiotic resistance. We investigated the presence and spread of transposons (elements that can move from one location to another in the genome), integrons (structures able to capture and incorporate gene cassettes) and resistance plasmids in strains isolated from polluted and unpolluted water. We recovered 231 Aeromonas and 250 fecal coliforms from water samplings with different degrees of pollution (hospital sewage, activated sludge of a wastewater treatment plant, river water before and after treatment and water from an alpine lake). Sixteen Aeromonas spp. and 22 fecal coliforms carried intI, coding for the site-specific integrase of class 1 integrons, while 22 Aeromonas spp. and 14 fecal coliforms carried tnpA, the transposase gene of the Tn3-family of replicative transposons. The majority of intI and tnpA-positive strains were phenotypically resistant to at least four antibiotics. Integrons and transposons were mainly located on mobilizable plasmids. Our results did not detect common mobile structures in the two populations and therefore relativize the role played by Aeromonas spp. as vectors of antimicrobial resistance determinants between water and commensal gut bacteria.

  6. Diversity of Fusarium species isolated from UK forage maize and the population structure of F. graminearum from maize and wheat.

    PubMed

    Basler, Ryan

    2016-01-01

    Pre-harvest contamination of forage maize by mycotoxin producing Fusarium species was investigated in the UK in 2011 and 2012. A total of 15 Fusarium species were identified from a collection of 1,761 Fusarium isolates recovered from maize stalks and kernels. This study characterized the diversity of Fusarium species present in forage maize in the UK. The predominant species detected were F. graminearum (32.9%) and F. culmorum (34.1%). Along with those species; F. avenacem, F. cerealis, F. equiseti, F. langsethiae, F. napiforme, F. oxysporum, F. poae, F. proliferatum, F. scripi, F. solani, F. subglutinans, F. tricinctum and, F. verticillioides were occasionally isolated. The trichothecene genotypes for F. graminearum were determined to be 84.9% deoxynivalenol (DON) and 15.0% nivalenol (NIV) while F. culmorum isolates were determined to have 24.9% DON and 75.1% NIV genotypes. A Bayesian model-based clustering method with nine variable number of tandem repeat markers was used to evaluate the population genetic structure of 277 F. graminearum isolates from the maize and wheat in the UK. There were three genetic clusters detected which were DON in maize, NIV in maize and DON in wheat. There were high admixture probabilities for 14.1% of the isolates in the populations. In conclusion, increased maize production in the UK and the high admixture rates in a significant portion of F. graminearum populations in maize and wheat will contribute to a new pathogen population which will further complicate breeding strategies for tolerance or resistance to this pathogen in both crops.

  7. Diversity of Fusarium species isolated from UK forage maize and the population structure of F. graminearum from maize and wheat

    PubMed Central

    2016-01-01

    Pre-harvest contamination of forage maize by mycotoxin producing Fusarium species was investigated in the UK in 2011 and 2012. A total of 15 Fusarium species were identified from a collection of 1,761 Fusarium isolates recovered from maize stalks and kernels. This study characterized the diversity of Fusarium species present in forage maize in the UK. The predominant species detected were F. graminearum (32.9%) and F. culmorum (34.1%). Along with those species; F. avenacem, F. cerealis, F. equiseti, F. langsethiae, F. napiforme, F. oxysporum, F. poae, F. proliferatum, F. scripi, F. solani, F. subglutinans, F. tricinctum and, F. verticillioides were occasionally isolated. The trichothecene genotypes for F. graminearum were determined to be 84.9% deoxynivalenol (DON) and 15.0% nivalenol (NIV) while F. culmorum isolates were determined to have 24.9% DON and 75.1% NIV genotypes. A Bayesian model-based clustering method with nine variable number of tandem repeat markers was used to evaluate the population genetic structure of 277 F. graminearum isolates from the maize and wheat in the UK. There were three genetic clusters detected which were DON in maize, NIV in maize and DON in wheat. There were high admixture probabilities for 14.1% of the isolates in the populations. In conclusion, increased maize production in the UK and the high admixture rates in a significant portion of F. graminearum populations in maize and wheat will contribute to a new pathogen population which will further complicate breeding strategies for tolerance or resistance to this pathogen in both crops. PMID:27366645

  8. The potential for biological structure determination with pulsed neutrons

    SciTech Connect

    Wilson, C.C.

    1994-12-31

    The potential of pulsed neutron diffraction in structural determination of biological materials is discussed. The problems and potential solutions in this area are outlined, with reference to both current and future sources and instrumentation. The importance of developing instrumentation on pulsed sources in emphasized, with reference to the likelihood of future expansion in this area. The possibilities and limitations of single crystal, fiber and powder diffraction in this area are assessed.

  9. Determination of the Basin Structure Beneath European Side of Istanbul

    NASA Astrophysics Data System (ADS)

    Karabulut, Savas; Cengiz Cinku, Mulla; Thomas, Michael; Lamontagne, Maurice

    2016-04-01

    Istanbul (near North Anatolian Fault Zone:NAFZ, Turkey) is located in northern part of Sea of Marmara, an area that has been influenced by possible Marmara Earthquakes. The general geology of Istanbul divided into two stratigraphic unit such as sedimentary (from Oligocene to Quaternary Deposits) and bedrock (Paleozoic and Eocene). The bedrock units consists of sand stone, clay stone to Paleozoic age and limestone to Eocene age and sedimentary unit consist of sand, clay, mil and gravel from Oligocene to Quaternary age. Earthquake disaster mitigation studies divided into two important phases, too. Firstly, earthquake, soil and engineering structure problems identify for investigation area, later on strategic emergency plan can prepare for these problems. Soil amplification play important role the disaster mitigation and the site effect analysis and basin structure is also a key parameter for determining of site effect. Some geophysical, geological and geotechnical measurements are requeired to defined this relationship. Istanbul Megacity has been waiting possible Marmara Earthquake and their related results. In order to defined to possible damage potential related to site effect, gravity measurements carried out for determining to geological structure, basin geometry and faults in Istanbul. Gravity data were collected at 640 sites by using a Scientrex CG-5 Autogravity meter Standard corrections applied to the gravity data include those for instrumental drift, Earth tides and latitude, and the free-air and Bouguer corrections. The corrected gravity data were imported into a Geosoft database to create a grid and map of the Bouguer gravity anomaly (grid cell size of 200 m). As a previously results, we determined some lineminants, faults and basins beneath Istanbul City. Especially, orientation of faults were NW-SE direction and some basin structures determined on between Buyukcekmece and Kucukcekmece Lake.

  10. Isolation, structural elucidation and immunomodulatory activity of fructans from aged garlic extract.

    PubMed

    Chandrashekar, Puthanapura M; Prashanth, Keelara V Harish; Venkatesh, Yeldur P

    2011-02-01

    Traditionally, garlic (Allium sativum) is known to be a significant immune booster. Aged garlic extract (AGE) possesses superior immunomodulatory effects than raw garlic; these effects are attributed to the transformed organosulfur compounds. AGE is also known to contain fructans; the amount of fructans in AGE represents a small fraction (0.22%) of the total fructans in raw garlic. In order to evaluate the biological activity of fructans present in AGE, both high molecular weight (>3.5 kDa; HF) and low molecular weight (<3 kDa; LF) fructans were isolated. The structures of purified HF and LF from AGE determined by (1)H NMR and (13)C NMR spectroscopy revealed that both have (2→1) β-D-fructofuranosyl bonds linked to a terminal glucose at the non-reducing end and β-D-fructofuranosyl branching on its backbone. Biological activity of fructans was assessed by immunostimulatory activity using murine lymphocytes and peritoneal exudate cells (source of macrophages). Both HF and LF displayed mitogenic activity and activation of macrophages including phagocytosis. These activities were comparable to that of known polysaccharide immunomodulators such as zymosan and mannan. This study clearly demonstrates that garlic fructans also contribute to the immunomodulatory properties of AGE, and is the first such study on the biological effects of garlic fructans.

  11. Isolation and structural elucidation of antioxidant peptides from oyster (Saccostrea cucullata) protein hydrolysate.

    PubMed

    Umayaparvathi, S; Meenakshi, S; Vimalraj, V; Arumugam, M; Balasubramanian, T

    2014-01-01

    Protein derived from the oyster (Saccostrea cucullata) was hydrolyzed using protease from Bacillus cereus SU12 for isolation of antioxidant peptides. The oyster hydrolysate exhibited a strong antioxidant potential in DPPH (85.7±0.37%) followed by Hydrogen peroxide radical scavenging activity (81.6±0.3%), Hydroxyl radical-scavenging activity (79.32±0.6%), Reducing power assay (2.63±0.2 OD at 700nm). Due to the high antioxidant potential, hydrolysate was fractionated in Sephadex G-25 gel filtration chromatography. The active peptide fraction was further purified by UPLC-MS. Totally 7 antioxidant peptides were collected. Among 7 peptides (SCAP 1-7), 3 peptides (SCAP 1, 3 and 7) had highest scavenging ability on DPPH radicals. The amino acid sequence and molecular mass of purified antioxidant peptides (SCAP1, SCAP3 and SCAP7) were determined by Q-TOF ESI mass spectroscopy and structures of the peptides were Leu-Ala-Asn-Ala-Lys (MW=515.29Da), Pro-Ser-Leu-Val-Gly-Arg-Pro-Pro-Val-Gly-Lys-Leu-Thr-Leu (MW=1432.89Da) and Val-Lys-Val-Leu-Leu-Glu-His-Pro-Val-Leu (MW=1145.75Da), respectively. The unique amino acid composition and sequence in the peptides might play an important role in expression of their antioxidant activity. The results of this study suggest that oyster protein hydrolysate is good source of natural antioxidants.

  12. The effect of detergent on the structure and composition of chlorosomes isolated from Chloroflexus aurantiacus.

    PubMed

    Miller, M; Simpson, D; Redlinger, T E

    1993-03-01

    Isolated chlorosomes, treated with the detergent lithium dodecyl sulfate (LDS), can be separated into two green fractions by agarose gel electrophoresis. One fraction contains chlorosomes with a full complement of proteins and antenna BChl c absorbing at 740 nm, but with a more spherical form than the normal ellipsoid shape observed in control chlorosomes. The second fraction was completely devoid of proteins but had a similar absorption spectrum. Electron micrographs of the protein-free fraction indicated the presence of stain-excluding spheres with overall dimensions resembling those of intact chlorosomes (40-100 nm). These spheres are probably micelles of BChl c liberated from the chlorosomes during the detergent treatment, since similar structures could be produced when purified BChl c, dissolved in 1-hexanol, was dispersed in buffer, producing an aggregate absorbing at 742 nm. These results suggest that the chlorosome proteins are not required to produce an arrangement of BChl c chromophores which gives rise to a 740 nm absorption peak resembling that of intact chlorosomes. It seems probable, however, that proteins have a role in determining the overall shape of the chlorosome. Treatment with cross-linking reagents did not prevent the detergent-induced changes in chlorosome morphology.

  13. Optimization, purification and structural characterization of a dextran produced by L. mesenteroides isolated from Chinese sauerkraut.

    PubMed

    Du, Renpeng; Xing, Hanwen; Yang, Yanping; Jiang, Hanji; Zhou, Zhijiang; Han, Ye

    2017-10-15

    A higher yield of dextran strain Leuconstoc mesenteroides TDS2-19 was isolated from Chinese sauerkraut juice. Effects of the three main factors on exopolysaccharide (EPS) yield were investigated by central composite design (CCD) and the optimum composition was sucrose 117.48g/L, sodium acetate 4.10g/L, and initial pH 6.88. Optimum results showed that EPS yield was increased to 71.23±2.25g/L in 48h fermentation, 31.24% higher than before. The molecular weight (Mw) of ESP was 8.79×10(7)Da, as determined by high-performance size-exclusion chromatography (HPSEC). Fourier transform infrared spectra (FT-IR) and nuclear magnetic resonance spectra (NMR) showed that the polysaccharide synthesized by L. mesenteroides TDS2-19 in the MRS medium was dextran with a peak, a linear backbone composed of consecutive α-(1→6)-linked d-glucopyranose units. No branching was observed in the dextran structure. The present study suggested that L. mesenteroides TDS2-19 might be used for the industrial-scale production of linear dextran. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Physicochemical, digestibility and structural characteristics of starch isolated from banana cultivars.

    PubMed

    Agama-Acevedo, Edith; Nuñez-Santiago, Maria C; Alvarez-Ramirez, José; Bello-Pérez, Luis A

    2015-06-25

    Banana starches from diverse varieties (Macho, Morado, Valery and Enano Gigante) were studied in their physicochemical, structural and digestibility features. X-ray diffraction indicated that the banana starches present a B-type crystallinity pattern, with slight difference in the crystallinity level. Macho and Enano Gigante starches showed the highest pasting temperatures (79 and 78°C, respectively), whilst Valery and Morado varieties presented a slight breakdown and higher setback than the formers. Morado starch presented the highest solubility value and Valery starch the lowest one. The swelling pattern of the banana starches was in agreement with their pasting profile. All banana starches showed a shear-thinning profile. The resistant starch (RS) fraction was the main fraction in the uncooked banana starches. Morado variety showed the highest amount of slowly digestible starch (SDS) and the lowest RS content reported until now in banana starches. Banana starch cooked samples presented an important amount of SDS and RS. Molecular weight and gyration radius of the four banana starches ranged between 2.88-3.14×10(8)g/mol and 286-302nm, respectively. The chain-length distributions of banana amylopectin showed that B1 chains (DP 13-24) is the main fraction, and an important amount of long chains (DP≥37) are present. The information generated from this study can be useful to determine banana varieties for starch isolation with specific functionality.

  15. Structure Determination Algorithms in Computational X-Ray Crystallography.

    NASA Astrophysics Data System (ADS)

    Chang, Chun-Shi

    This dissertation focuses on the development and implementation of practical algorithms for solving the phase problem of X-ray crystallography. We based our strategies on the Shake-and-Bake method of structure determination which alternates phase refinement in reciprocal space with density modification in real space. The strategies we consider include variants of Shake-and-Bake which incorporate optimization techniques based on parameter shift, genetic algorithms, tangent formula, and one based on special properties of space group P1. These four approaches have been implemented on a variety of parallel and sequential machines, including a Thinking Machine Corporation CM-5, an Intel iPSC/860, and a network of SGI Indigo workstations. Experimental results show that the tangent formula approach is the most cost-effective means for solving structures of small size, while the parameter shift variant is better for medium -size or larger structures. The P1 approach appears to be promising for structures in certain space groups. We show that the tangent formula approach can be successfully applied to the CRAMBIN structure, which contains approximately 400 atoms in the asymmetric unit cell. This represents the first successful application of a tangent formula-based approach to solve the CRAMBIN structure.

  16. Structural analysis of a new cryptic plasmid pAR67 isolated from Ruminococcus albus AR67.

    PubMed

    Ohara, H; Miyagi, T; Kaneichi, K; Karita, S; Kobayashi, Y; Kimura, T; Sakka, K; Ohmiya, K

    1998-01-01

    The complete nucleotide sequence of a new cryptic plasmid pAR67 isolated from a rumen bacterium Ruminococcus albus AR67 has been determined. The plasmid pAR67 was 3419 bp in size with a 45% GC content. Two open reading frames, ORF1 and ORF2, encoding potential polypeptides of 285 and 165 amino acids, with limited sequence similarity to replication and mobilization proteins, respectively, were identified within the sequence. The region upstream of ORF1 had an AT-rich (80%) segment followed by four 19-bp direct repeats, which is similar to the structural organization characteristic of replication origins of some bacterial plasmids.

  17. PC-766B, a new macrolide antibiotic produced by Nocardia brasiliensis. II. Isolation, physico-chemical properties and structure elucidation.

    PubMed

    Kumagai, K; Fukui, A; Tanaka, S; Ikemoto, M; Moriguchi, K; Nabeshima, S

    1993-07-01

    A new macrolide antibiotic, PC-766B, was isolated from the cells of Nocardia brasiliensis SC-4710 by acetone extraction, and purified by gel filtration, silica gel chromatography, HPLC and TLC. The structure of PC-766B was determined by NMR spectral analysis to be a new class of the hygrolidin family antibiotics. PC-766B had a 16-membered macrocyclic lactone ring, a 6-membered hemiketal ring and a 2-deoxy-D-rhamnose moiety. DL-alpha-Tocopherol, known as an antioxidant agent, significantly improved the stability of PC-766B and prevented the decomposition of PC-766B during the storage of the antibiotic.

  18. MOTIVATION INTERNALIZATION AND SIMPLEX STRUCTURE IN SELF-DETERMINATION THEORY.

    PubMed

    Ünlü, Ali; Dettweiler, Ulrich

    2015-12-01

    Self-determination theory, as proposed by Deci and Ryan, postulated different types of motivation regulation. As to the introjected and identified regulation of extrinsic motivation, their internalizations were described as "somewhat external" and "somewhat internal" and remained undetermined in the theory. This paper introduces a constrained regression analysis that allows these vaguely expressed motivations to be estimated in an "optimal" manner, in any given empirical context. The approach was even generalized and applied for simplex structure analysis in self-determination theory. The technique was exemplified with an empirical study comparing science teaching in a classical school class versus an expeditionary outdoor program. Based on a sample of 84 German pupils (43 girls, 41 boys, 10 to 12 years old), data were collected using the German version of the Academic Self-Regulation Questionnaire. The science-teaching format was seen to not influence the pupils' internalization of identified regulation. The internalization of introjected regulation differed and shifted more toward the external pole in the outdoor teaching format. The quantification approach supported the simplex structure of self-determination theory, whereas correlations may disconfirm the simplex structure.

  19. Determination of the stretch tensor for structural transformations

    NASA Astrophysics Data System (ADS)

    Chen, Xian; Song, Yintao; Tamura, Nobumichi; James, Richard D.

    2016-08-01

    Structural transformations in crystalline solids are increasingly the basis of the functional behavior of materials. Recently, in diverse alloy systems, both low hysteresis and reversibility of phase transformations have been linked to the satisfaction of the nongeneric conditions of compatibility between phases. According to the Cauchy-Born rule, these conditions are expressed as properties of transformation stretch tensor. The transformation stretch tensor is difficult to measure directly due to the lack of knowledge about the exact transforming pathway during the structural change, and the complicating effects of microstructure. In this paper we give a rigorous algorithmic approach for determining the transformation stretch tensor from X-ray measurements of structure and lattice parameters. For some traditional and emerging phase transformations, the results given by the algorithm suggest unexpected transformation mechanisms.

  20. Local magnetic structure determination using polarized neutron holography

    NASA Astrophysics Data System (ADS)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-05-01

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  1. Local magnetic structure determination using polarized neutron holography

    SciTech Connect

    Szakál, Alex Markó, Márton Cser, László

    2015-05-07

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  2. Structural properties for determining mechanisms of toxic action

    SciTech Connect

    Bradbury, S.P.; Lipnick, R.L.

    1989-01-01

    The results of a workshop co-sponsored by EPA through the Health and Environmental Review Division, Office of Toxic Substances and the Environmental Research Laboratory-Duluth, of the Office of Research and Development are briefly summarized as an introduction to a series of manuscripts dealing with the structural properties of chemicals that determine their toxic mechanisms. Results of the workshop are intended to be incorporated in an expert system to predict mechanisms from chemical structure and aid in predictive toxicology applications in the Agency. The goal of the workshop was to review current understanding of fundamental mechanisms, and develop an initial knowledge base on chemical features and properties from which toxic mechanisms could be predicted from structure. Areas addressed included general anesthesia, or narcosis, oxidative phosphorylation uncoupling, electrophile and free-radical reactivity, and a variety of pesticide-based mechanisms.

  3. Structural Determinants and Mechanism of HIV-1 Genome Packaging

    PubMed Central

    Lu, Kun; Heng, Xiao; Summers, Michael F.

    2011-01-01

    Like all retroviruses, the Human Immunodeficiency Virus (HIV) selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer mediated recombination during reverse transcription – a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid (NC) domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5′-untranslated region (5′-UTR) of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions remain open regarding the RNA structures, and potentially the structural changes, that are responsible for dimeric genome selection. Here we review efforts that have been made to identify the molecular determinants and mechanism of HIV-1 genome packaging. PMID:21762803

  4. Structure determination of membrane proteins by NMR spectroscopy

    PubMed Central

    Opella, S.J.; Nevzorov, A.; Mesleh, M.F.; Marassi, F.M.

    2012-01-01

    Current strategies for determining the structures of membrane proteins in lipid environments by NMR spectroscopy rely on the anisotropy of nuclear spin interactions, which are experimentally accessible through experiments performed on weakly and completely aligned samples. Importantly, the anisotropy of nuclear spin interactions results in a mapping of structure to the resonance frequencies and splittings observed in NMR spectra. Distinctive wheel-like patterns are observed in two-dimensional 1H–15N heteronuclear dipolar/15N chemical shift PISEMA (polarization inversion spin-exchange at the magic angle) spectra of helical membrane proteins in highly aligned lipid bilayer samples. One-dimensional dipolar waves are an extension of two-dimensional PISA (polarity index slant angle) wheels that map protein structures in NMR spectra of both weakly and completely aligned samples. Dipolar waves describe the periodic wave-like variations of the magnitudes of the heteronuclear dipolar couplings as a function of residue number in the absence of chemical shift effects. Since weakly aligned samples of proteins display these same effects, primarily as residual dipolar couplings, in solution NMR spectra, this represents a convergence of solid-state and solution NMR approaches to structure determination. PMID:12440700

  5. From bacterial to human dihydrouridine synthase: automated structure determination

    PubMed Central

    Whelan, Fiona; Jenkins, Huw T.; Griffiths, Samuel C.; Byrne, Robert T.; Dodson, Eleanor J.; Antson, Alfred A.

    2015-01-01

    The reduction of uridine to dihydrouridine at specific positions in tRNA is catalysed by dihydrouridine synthase (Dus) enzymes. Increased expression of human dihydrouridine synthase 2 (hDus2) has been linked to pulmonary carcinogenesis, while its knockdown decreased cancer cell line viability, suggesting that it may serve as a valuable target for therapeutic intervention. Here, the X-ray crystal structure of a construct of hDus2 encompassing the catalytic and tRNA-recognition domains (residues 1–340) determined at 1.9 Å resolution is presented. It is shown that the structure can be determined automatically by phenix.mr_rosetta starting from a bacterial Dus enzyme with only 18% sequence identity and a significantly divergent structure. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel β-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain–domain interactions. The structure may inform the development of novel therapeutic approaches in the fight against lung cancer. PMID:26143927

  6. Inner structural vibration isolation method for a single control moment gyroscope

    NASA Astrophysics Data System (ADS)

    Zhang, Jingrui; Guo, Zixi; Zhang, Yao; Tang, Liang; Guan, Xin

    2016-01-01

    Assembling and manufacturing errors of control moment gyros (CMG) often generate high frequency vibrations which are detrimental to spacecrafts with high precision pointing requirement. In this paper, some design methods of vibration isolation between CMG and spacecraft is dealt with. As a first step, the dynamic model of the CMG with and without supporting isolation structures is studied and analyzed. Subsequently, the frequency domain analysis of CMG with isolation system is performed and the effectiveness of the designed system is ascertained. Based on the above studies, an adaptive design suitable with appropriate design parameters are carried out. A numerical analysis is also performed to understand the effectiveness of the system and the comparison made. The simulation results clearly indicate that when the ideal isolation structure was implemented in the spacecraft, the vibrations generated by the rotor were found to be greatly reduced, while the capacity of the output torque was not lost, which means that the isolation system will not affect the performance of attitude control.

  7. [Characteristics of microbial community structure during isolation of electrical active bacteria].

    PubMed

    Wang, Min; Zhao, Yang- Guo; Lu, Shan-Shan

    2014-10-01

    To investigate the effect of selective culturing on microorganisms and functional role of electrical active bacteria in biofilm, some exoelectrogens were isolated from microbial fuel cell (MFC) anodic biofilm using Hungate roll-tube technique with iron oxide as indicator. At the same time, the dynamics of the microbial community structure was monitored during the pure culture isolation. The results show that maximum voltages of MFCs feeding with lactic acid, acetic acid and steroid wastewater are 0.57, 0.60 and 0.40 V respectively. The dominant bacteria isolated from seed sludge and anodic films feeding with acetate and lactate belong to phylum Proteobacteria; while steroid wastewater contains relative high diversity of bacteria, i. e. Proteobacteria, Firmicutes and Bacteroidetes. After enriching and culturing, two bacteria were consequently obtained, which shared the highest similarity with Enterobacter ludwigii and Citrobacter freundii respectively. When inoculated in MFC with lactic acid as the substrate, they produced maximum voltage of 0.10 and 0.17 V individually. This study shows that electrical active bacteria can be isolated from the MFC anodic biofilm using anaerobic gradient dilution culture techniques with iron oxide as indicator. Microbial community structure presents markedly shifting during the bacteria isolation owing to its selectivity.

  8. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  9. Structural Analysis to Determine the Core of Hypoxia Response Network

    PubMed Central

    Heiner, Monika; Sriram, K.

    2010-01-01

    The advent of sophisticated molecular biology techniques allows to deduce the structure of complex biological networks. However, networks tend to be huge and impose computational challenges on traditional mathematical analysis due to their high dimension and lack of reliable kinetic data. To overcome this problem, complex biological networks are decomposed into modules that are assumed to capture essential aspects of the full network's dynamics. The question that begs for an answer is how to identify the core that is representative of a network's dynamics, its function and robustness. One of the powerful methods to probe into the structure of a network is Petri net analysis. Petri nets support network visualization and execution. They are also equipped with sound mathematical and formal reasoning based on which a network can be decomposed into modules. The structural analysis provides insight into the robustness and facilitates the identification of fragile nodes. The application of these techniques to a previously proposed hypoxia control network reveals three functional modules responsible for degrading the hypoxia-inducible factor (HIF). Interestingly, the structural analysis identifies superfluous network parts and suggests that the reversibility of the reactions are not important for the essential functionality. The core network is determined to be the union of the three reduced individual modules. The structural analysis results are confirmed by numerical integration of the differential equations induced by the individual modules as well as their composition. The structural analysis leads also to a coarse network structure highlighting the structural principles inherent in the three functional modules. Importantly, our analysis identifies the fragile node in this robust network without which the switch-like behavior is shown to be completely absent. PMID:20098728

  10. Method and apparatus for determining material structural integrity

    DOEpatents

    Pechersky, Martin

    1996-01-01

    A non-destructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis techniques to determine the damping loss factor of a material. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity as a function of time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method. If an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the amount of coil current used in vibrating the magnet. If a reciprocating transducer is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by a force gauge in the reciprocating transducer. Using known vibrational analysis methods, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity measurements. The damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

  11. Method and apparatus for determining material structural integrity

    DOEpatents

    Pechersky, M.J.

    1994-01-01

    Disclosed are a nondestructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis to determine the damping loss factor. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity vs time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method: if an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the coil current. If a reciprocating transducer is used, the vibrational force is determined by a force gauge in the transducer. Using vibrational analysis, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity data. Damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

  12. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy.

    PubMed

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu

    2017-01-23

    An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by (129) Xe NMR spectroscopy. The high sensitivity of the (129) Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

  13. Comparison of structural features of dissolved organic matter isolated from rainwater with those of aquatic humic substances

    NASA Astrophysics Data System (ADS)

    Santos, P.; Santos, E.; Duarte, A.

    2012-04-01

    The complexity of rainwater dissolved organic matter (DOM), a large percentage of which remains uncharacterized, has made difficult to determine the role of rainwater DOM in regional and global carbon budgets. Recent studies have focused on determining the structural characteristics of the bulk DOM in rainwater, reporting the prevalence of DOM with characteristics resembling those of natural humic substances due to its polyacidic nature. However, it is important to investigate the structural features of humic-like DOM isolated from rainwater and to evaluate whether such features differ from those found in aquatic humic substances, namely in what concerns the relative content of aliphacity and aromaticity. In this work, rainwater samples were collected for about one year, in Aveiro (Portugal). Humic-like DOM was extracted from rainwater by a procedure based on adsorption onto DAX-8 resin. The International Humic Substance Society (IHSS) (http://www.ihss.gatech.edu) operationally defined dissolved humic substances (HSs) on the base of adsorption onto a XAD-8 like resin. The isolation and extraction procedure adopted in the present work for the extraction of DOM from rainwater was slightly modified from the procedure recommended by the IHSS as suggested by Santos et al. (2009). Then, humic-like DOM isolated from rainwater was analysed by 1H NMR spectroscopy. Due to the small amounts of DOM extracted from rainwater, the DOM fractions extracted from rainwater samples were combined for each sampling season, and the 1H NMR results were compared between seasons and also with spectra of aquatic humic substances from available literature. Similar structural characteristics were observed for extracted DOM from the different seasons: high content of aliphatic structures, of hydroxy and alkoxy groups, of carbonyl groups and unsaturated carbon atoms, and low content in aromatic structures when compared with aliphatic structures. Moreover, results suggest that the DOM extracted

  14. Determination of Acquired Resistance Profiles of Pseudomonas aeruginosa Isolates and Characterization of an Effective Bacteriocin-Like Inhibitory Substance (BLIS) Against These Isolates

    PubMed Central

    Shokri, Dariush; Rabbani Khorasgani, Mohammad; Zaghian, Saeideh; Fatemi, Seyed Masih; Mohkam, Milad; Ghasemi, Younes; Taheri-Kafrani, Asghar

    2016-01-01

    Background The emergence of pan-drug resistant strains (PDR) of Pseudomonas aeruginosa has led to renewed efforts to identify alternative agents, such as bacteriocins and bacteriocin-like inhibitory substances (BLISs). Objectives The aims of this study were to determine the acquired resistance profiles of multidrug-resistant (MDR), extensively drug-resistant (XDR), and PDR P. aeruginosa isolates based on the revised definitions of the CDC and ECDC and to screen and characterize effective BLISs against these isolates. Patients and Materials In a cross-sectional study, 96 P. aeruginosa strains were isolated during a 12-month period. The resistance profiles of these isolates were determined as MDR, XDR, and PDR, and the data were analyzed using WHONET5.6 software. A BLIS against the P. aeruginosa strains was characterized based on its physicochemical properties, size, growth curves, and production profiles. Results Among the 96 isolates of P. aeruginosa, 2 (2.1%), 94 (97.9%), and 63 (65.6%) were non-MDR, MDR, and XDR, respectively, and 1 (1.1%) was PDR. The most effective antibiotics against these isolates were polymyxins and fosfomycin. A BLIS isolated from the P. aeruginosa DSH22 strain had potent activity against 92 (95.8%) of the 96 isolates. The BLIS was heat stable, (up to 100°C for 10 min), UV stable, and active within a pH range of 3 - 9. The activity of BLIS disappeared when treated with trypsin, proteinase K, and pepsin, indicating its proteinous nature. Based on its size (25 kDa), the BLIS may belong to the large colicin-like bacteriocin family. BLIS production started in the midexponential phase of growth, and the maximum level (2700 AU/mL) occurred in the late-stationary phase after 25 hours of incubation at 30°C. Conclusions This BLIS with broad-spectrum activity may be a potential agent for the treatment or control of drug-resistant strains of P. aeruginosa infection. PMID:27800131

  15. A physicochemical characterization of fully acetylated chitin structure isolated from two spider species: with new surface morphology.

    PubMed

    Kaya, Murat; Seyyar, Osman; Baran, Talat; Erdoğan, Sevil; Kar, Musa

    2014-04-01

    Spiders are a huge group which includes more than 44,000 species. But there has been no study of the chitin structure of spiders. In this study we physicochemically characterized chitin structure of two common spider species (Geolycosa vultuosa and Hogna radiata). Chitin content was determined as 8-8.5% for G. vultuosa and 6.5-7% for H. radiata. FTIR, TGA and XRD results showed that the chitin structures are in α-form. Environmental scanning electron microscopy (ESEM) revealed that the surface morphology of each species is different. Chitin yielded from G. vultuosa has two different pore structures. The type one pore is rarely sequenced and its size ranges between 190 and 240 nm, while the type two pore is tightly sequenced and its size ranges between 11 and 32 nm. There is no information in previous studies about the chitin structure with two different pore morphologies. A new chitin surface morphology has been determined in G. vultuosa. The chitin isolated from H. radiata, has classic morphology: nanofibre structures (10-17 nm) and 195-260 nm sized pores. Acetylation degree of the chitin samples was calculated as 97% for G. vultuosa and 99% for H. radiata in accordance with elemental analysis results.

  16. Isolation of II-alcohol dehydrogenase of human liver: Is it a determinant of alcoholism?

    PubMed Central

    Li, Ting-Kai; Bosron, William F.; Dafeldecker, Werner P.; Lange, Louis G.

    1977-01-01

    Human liver alcohol dehydrogenase (alcohol: NAD+ oxidoreductase, EC 1.1.1.1), homogeneous by physicochemical criteria, has been available in quantity only recently [Lange, L. G. & Vallee, B. L. (1976) Biochemistry 15, 4681-4686]. Until now, the biochemical basis of human alcohol metabolism had to be extrapolated from the properties and behavior of enzymes from other species, primarily horses and yeast. The biological determinants of human alcoholism have remained obscure, although recent evidence indicates a genetic predisposition, requiring delineation. A functionally distinct form of human liver alcohol dehydrogenase (ADH), which we have designated II-ADH, is provocative since, thus far, it seems to be unique to human beings. It has a high Km for ethanol and is remarkably insensitive (apparent KI, 500 μM) to pyrazole and its derivatives, which are usually potent ADH inhibitors (KI, 1 μM), a property that is the basis for the isolation of II-ADH. The affinity resin 4-[3-(N-6-aminocaproyl)aminopropyl]pyrazole-Sepharose binds all other known forms of ADH but not II-ADH, thereby separating it selectively by affinity chromatography. In turn, this has led to the establishment of its identity with that enzyme form which was previously known as the anodic band and characterized by a high Km for ethanol (20 mM at pH 7.5). The remarkable insensitivity of II-ADH to pyrazole inhibition has also permitted quantitation of its role in hepatic ethanol oxidation. At 5 mM ethanol, a saturating concentration for virtually all other forms of ADH, II-ADH contributes less than 15% to total ethanol oxidation. However, at intoxicating concentrations, e.g., 60 mM, it can account for as much as 40% of the total ethanol oxidation rate of liver, indicating a seemingly unique role for this enzyme form in ethanol elimination. Thus far, we have found the amount of II-ADH varies from liver to liver of individuals and is considerably more labile than the other molecular forms, phenomena whose

  17. Isolation and immunizations with hepatitis A viral structural proteins: induction of antiprotein, antiviral, and neutralizing responses.

    PubMed

    Hughes, J V; Stanton, L W

    1985-08-01

    An immune affinity purification procedure for hepatitis A virus (HAV) was designed which yielded milligram quantities of the virus with greater than 95% purity. The major structural proteins VP-1, VP-2, and VP-3 were isolated from the purified virus by electroelution from sodium dodecyl sulfate-polyacrylamide gels and used to immunize Lewis rats (three to four doses, 10 to 15 micrograms per dose). The two Lewis rats immunized with VP-1 developed a strong antibody response to VP-1, as determined by Western blot analysis and immune precipitation of the denatured protein. These animals also developed a good antibody response to the whole virus, as demonstrated by a positive response in a competitive radioimmunoassay (HAV antibody test) and by precipitation of the whole virus. In addition, both animals developed a low titer neutralizing antibody to HAV, as demonstrated by an in vitro cell culture assay. While the two rats receiving VP-2 developed only minimal responses to the protein and to the virus by the same assays described above, one of the two developed a significant neutralizing antibody to HAV. The immunization of one Lewis rat with VP-3 induced a good antibody response to both denatured protein and the whole virus. This serum sample was also demonstrated to neutralize the viral infectivity. Finally, two rabbits that had received inoculations of sodium dodecyl sulfate and heat-disrupted HAV (containing 20 to 30 micrograms of each protein per dose) developed good antiprotein responses to all of the proteins and good antiviral responses, including a consistently significant neutralizing activity. The neutralizing antibody responses suggest that the structural proteins of HAV, or a portion of them, could provide the basis for a subunit vaccine for HAV.

  18. Probing the factor structure of metabolic syndrome in Sardinian genetic isolates.

    PubMed

    Graziano, F; Grassi, M; Sacco, S; Concas, M P; Vaccargiu, S; Pirastu, M; Biino, G

    2015-06-01

    Owing to the multiplicity of the key components of metabolic syndrome (MetS), its diagnosis is very complex. The lack of a unique definition is responsible for the prevalence variability observed among studies; therefore, a definition based on continuous variables was recommended. The aim of this study was to compare competing models of the MetS factor structure for selecting the one that explains the best clustering pattern and to propose an algorithm for computing MetS as a continuous variable. Data were from isolated Sardinian populations (n = 8102). Confirmatory factor analysis (CFA) and two-group CFA by gender were performed to evaluate the sex-specific factor structure of MetS. After selecting the best model, an algorithm was obtained using factor loadings/residual variances. The quality of the MetS score was evaluated by the receiver operating characteristics curve and the area under the curve. Cross-validation was performed to validate the score and to determine the best cut point. The best fit model was a bifactor one with a general factor (MetS) and three specific factors (f1: obesity/adiposity trait; f2: hypertension/blood pressure trait; and f3: lipid trait). Gender-specific algorithms were implemented to obtain MetS scores showing a good diagnostic performance (0.80 specificity and 0.80 sensitivity for the cut point). Furthermore, cross-validation confirmed these results. These analyses suggested that the bifactor model was the most representative one. In addition, they provided a score and a cut point that are both clinically accessible and interpretable measures for MetS diagnosis and likely useful for evaluating the association with adverse cardiovascular disease and diabetes and for investigating the MetS genetic component. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Isolation and primary structure of a cellulase from the Japanese sea urchin Strongylocentrotus nudus.

    PubMed

    Nishida, Yukiko; Suzuki, Ken-ichi; Kumagai, Yuya; Tanaka, Hiroyuki; Inoue, Akira; Ojima, Takao

    2007-08-01

    Glycoside-hydrolase-family 9 (GHF9) cellulases are known to be widely distributed in metazoa. These enzymes have been appreciably well investigated in protostome invertebrates such as arthropods, nematodes, and mollusks but have not been characterized in deuterostome invertebrates such as sea squirts and sea urchins. In the present study, we isolated the cellulase from the Japanese purple sea urchin Strongylocentrotus nudus and determined its enzymatic properties and primary structure. The sea urchin enzyme was extracted from the acetone-dried powder of digestive tract of S. nudus and purified by conventional chromatographies. The purified enzyme, which we named SnEG54, showed a molecular mass of 54kDa on SDS-PAGE and exhibited high hydrolytic activity toward carboxymethyl cellulose with an optimum temperature and pH at 35 degrees C and 6.5, respectively. SnEG54 degraded cellulose polymer and cellooligosaccharides larger than cellotriose producing cellotriose and cellobiose but not these small cellooligosaccharides. From a cDNA library of the digestive tract we cloned 1822-bp cDNA encoding the amino-acid sequence of 444 residues of SnEG54. This sequence showed 50-57% identity with the sequences of GHF9 cellulases from abalone, sea squirt, and termite. The amino-acid residues crucial for the catalytic action of GHF9 cellulases are completely conserved in the SnEG54 sequence. An 8-kbp structural gene fragment encoding SnEG54 was amplified by PCR from chromosomal DNA of S. nudus. The positions of five introns are consistent with those in other animal GHF9 cellulase genes. Thus, we confirmed that the sea urchin produces an active GHF9 cellulase closely related to other animal cellulases.

  20. Isolation and structural characterization of glycosphingolipids of in vitro propagated human umbilical vein endothelial cells.

    PubMed

    Müthing, J; Duvar, S; Heitmann, D; Hanisch, F G; Neumann, U; Lochnit, G; Geyer, R; Peter-Katalinic, J

    1999-05-01

    To investigate in detail the expression of glycosphingolipids (GSLs) on endothelial cells, 4.85 x 10(9) human umbilical vein endothelial cells (HUVECs) were cultivated in a 2 l bioreactor using microcarriers as a support for anchorage dependent growing cells. Neutral GSLs and gangliosides were isolated and their structures were determined by TLC immunostaining, fast atom bombardment-mass spectrometry (FAB-MS) of the native GSLs, and gas chromatography-electron impact mass spectrometry (GC-EIMS) of partially methylated alditol acetates. GbOse4Cer, GbOse3Cer, and LacCer, all carrying mainly C24- and C16-fatty acid beside C18-sphingosine, were detected as the major neutral GSLs (36%, 23%, and 15% of the total orcinol stain, respectively); GlcCer, nLcOse4Cer, and nLcOse6Cer were expressed to substantial minor amounts (9%, 12%, and 5% of the total orcinol stain, respectively). TLC immunostaining revealed the presence of lipid bound Lewisx antigen, whereas the isomeric Lewisa structure was detectable only in very low quantities. GM3(Neu5Ac) with C18-sphingosine was the major ganglioside constituting about 90% of the whole ganglioside fraction. The fatty acid composition was determined by GC-MS of fatty acid methyl esters, indicating the predominance of C24- and C16-substituted GM3(Neu5Ac), followed by C18- and C22-substituted species. Terminally alpha2-3 sialylated neolacto-series ganglioside IV3Neu5Ac-nLcOse4Cer was the second most abundant ganglioside in HUVECs (8% of the total resorcinol stain), and IV6Neu5Ac-nLcOse4Cer and VI3Neu5Ac-nLcOse6Cer (together less than 2% of total resorcinol stain) were found in minor quantities. Lipid bound sialyl Lewisx antigen with poly-N-acetyllactosaminyl chains, and traces of gangliotetraose-type gangliosides GM1 and GD1a were identified by TLC immunostaining. The expression of dominant neutral GSLs LacCer, GbOse3Cer, and GbOse4Cer, and of ganglioside GM3(Neu5Ac) was assayed by indirect immunofluorescence microscopy of cell layers

  1. Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments

    PubMed Central

    Chakshusmathi, G.; Ratnaparkhi, Girish S.; Madhu, P. K.; Varadarajan, R.

    1999-01-01

    Ordered protein complexes are often formed from partially ordered fragments that are difficult to structurally characterize by conventional NMR and crystallographic techniques. We show that concentration-dependent hydrogen exchange studies of a fragment complex can provide structural information about the solution structures of the isolated fragments. This general methodology can be applied to any bimolecular or multimeric system. The experimental system used here consists of Ribonuclease S, a complex of two fragments of Ribonuclease A. Ribonuclease S and Ribonuclease A have identical three-dimensional structures but exhibit significant differences in their dynamics and stability. We show that the apparent large dynamic differences between Ribonuclease A and Ribonuclease S are caused by small amounts of free fragments in equilibrium with the folded complex, and that amide exchange rates in Ribonuclease S can be used to determine corresponding rates in the isolated fragments. The studies suggest that folded RNase A and the RNase S complex exhibit very similar dynamic behavior. Thus cleavage of a protein chain at a single site need not be accompanied by a large increase in flexibility of the complex relative to that of the uncleaved protein. PMID:10393919

  2. Filament wound composite thermal isolator structures for cryogenic dewars and instruments

    SciTech Connect

    Morris, E.E.

    1982-01-01

    Studies showing high tensile strength, low thermal conductivity, and adequate fatigue strength capabiliies in conjunction with low resin outgassing properties of S-90 fiber glass with SCI REZ 080 and 081 epoxy resins has resulted in use of filament wound tension straps, struts, and conical shells as thermal isolators in several high-performance cryogenic applications. These thermal isolator structures and their use in the following cryogenic systems are discussed in this paper: hydrogen and oxygen dewars for space shuttle, helium tank for the infra-red astronomy satellite, spacecraft refrigerators, and infrared telescope. Mechanical and thermo-physical properties of the composite laminates are presented.

  3. Isolation and structure elucidation of anhydroluteins from cooked sorrel (Rumex rugosus Campd.).

    PubMed

    Molnár, Péter; Osz, Erzsébet; Zsila, Ferenc; Deli, József

    2005-07-01

    Anhydrolutein I (= (all-E,3R,6'R)-3',4'-didehydro-beta,gamma-caroten-3-ol; 2) and anhydrolutein II (= (all-E, 3R,6'S)-2',3'-didehydro-beta,epsilon-caroten-3-ol; 3) have been isolated and characterized from the extract of steam-cooked sorrel. The presence of these compounds in cooked vegetable is postulated to be due to acid-catalyzed dehydration of lutein (1; Scheme). The structures of the isolated anhydroluteins were established by UV/VIS, CD, and 1H-NMR spectroscopy, and mass spectrometry.

  4. Methods for SAXS-Based Structure Determination of Biomolecular Complexes

    SciTech Connect

    Yang, Sichun

    2014-05-30

    Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, we describe current and recent SAXS-driven developments, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules can adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.

  5. Methods for SAXS-Based Structure Determination of Biomolecular Complexes

    DOE PAGES

    Yang, Sichun

    2014-05-30

    Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, we describe current and recent SAXS-driven developments, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules canmore » adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.« less

  6. Databases of Conformations and NMR Structures of Glycan Determinants.

    PubMed

    Sarkar, Anita; Drouillard, Sophie; Rivet, Alain; Perez, Serge

    2015-12-01

    The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Meeting Report: Structural Determination of Environmentally Responsive Proteins

    PubMed Central

    Reinlib, Leslie

    2005-01-01

    The three-dimensional structure of gene products continues to be a missing lynchpin between linear genome sequences and our understanding of the normal and abnormal function of proteins and pathways. Enhanced activity in this area is likely to lead to better understanding of how discrete changes in molecular patterns and conformation underlie functional changes in protein complexes and, with it, sensitivity of an individual to an exposure. The National Institute of Environmental Health Sciences convened a workshop of experts in structural determination and environmental health to solicit advice for future research in structural resolution relative to environmentally responsive proteins and pathways. The highest priorities recommended by the workshop were to support studies of structure, analysis, control, and design of conformational and functional states at molecular resolution for environmentally responsive molecules and complexes; promote understanding of dynamics, kinetics, and ligand responses; investigate the mechanisms and steps in posttranslational modifications, protein partnering, impact of genetic polymorphisms on structure/function, and ligand interactions; and encourage integrated experimental and computational approaches. The workshop participants also saw value in improving the throughput and purity of protein samples and macromolecular assemblies; developing optimal processes for design, production, and assembly of macromolecular complexes; encouraging studies on protein–protein and macromolecular interactions; and examining assemblies of individual proteins and their functions in pathways of interest for environmental health. PMID:16263521

  8. The structure and immunoreactivity of exopolysaccharide isolated from Lactobacillus johnsonii strain 151.

    PubMed

    Górska-Frączek, Sabina; Sandström, Corine; Kenne, Lennart; Paściak, Mariola; Brzozowska, Ewa; Strus, Magdalena; Heczko, Piotr; Gamian, Andrzej

    2013-08-30

    The exopolysaccharide (EPS) structure from Lactobacillus johnsonii strain 151 isolated from the intestinal tract of mice was investigated. Sugar and methylation analyses together with (1)H and (13)C NMR spectroscopy, including two-dimensional (1)H,(1)H COSY, TOCSY, NOESY, and (1)H,(13)C HSQC, HMBC experiments, revealed that the repeating unit of the EPS is the linear pentasaccharide: →6)-α-d-Galp-(1→6)-α-d-Glcp-(1→3)-β-d-Galf-(1→3)-α-d-Glcp-(1→2)-β-d-Galf-(1→ The immunoreactivity of two structurally different exopolysaccharides isolated from L. johnsonii, 151 and 142 (Carbohydr. Res. 2010, 345, 108-114), was compared. Both EPSs differed in their reactivity with antisera. EPS from L. johnsonii 151 reacted with anti-Lactobacillus polyclonal sera against cells of five different strains, while EPS from L. johnsonii 142 was found to react only with its own antiserum. The broader specificity and higher reactivity of EPS from 151 strain than EPS from 142 strain were also observed with human sera. The physiological antibodies recognizing polysaccharide antigens were present in both adults and umbilical cord blood sera. A highly specific EPS 142 bearing strain was isolated from experimentally induced inflammatory bowel disease (IBD) mice, while a strain with EPS 151 isolated from the intestinal tract of healthy mice is characterized by a broad immune reactivity common structure.

  9. Plant antimutagenic agents, 4. Isolation and structure elucidation of maesol, an inactive constituent of Maesa spp.

    PubMed

    Wall, M E; Wani, M C; Gaetano, K; Manikumar, G; Taylor, H; McGivney, R

    1988-01-01

    Maesol, a novel dimeric phenol, was isolated from seeds of Maesa montana and Maesa indica. Maesol was shown to have the formula C28H42O4 with structure 1, a dimeric, symmetrical 1,12-bis(3,3'-dihydroxy-4,4'-dimethyl-5,5'-dimethoxyphenyl)dodecane. It is the first compound with such structure to be isolated from plant material. Structure elucidation was based largely on 1H- and 13C-nmr techniques and comparison with a known synthetic isomeric dimer 3. Although crude extracts showed strong inhibition of 2-aminoanthracene activity against Salmonella typhimurium (T-98), the pure compound was inactive when tested for inhibition of the mutagenic activity of several mutagens.

  10. Single Nanotube Spectral Imaging To Determine Molar Concentrations of Isolated Carbon Nanotube Species.

    PubMed

    Galassi, Thomas V; Jena, Prakrit V; Roxbury, Daniel; Heller, Daniel A

    2017-01-17

    Electronic and biological applications of carbon nanotubes can be highly dependent on the species (chirality) of nanotube, purity, and concentration. Existing bulk methods, such as absorbance spectroscopy, can quantify sp(2) carbon based on spectral bands, but nanotube length distribution, defects, and carbonaceous impurities can complicate quantification of individual particles. We present a general method to relate the optical density of a photoluminescent nanotube sample to the number of individual nanotubes. By acquiring 3-dimensional images of nanotubes embedded in a gel matrix with a reducing environment, we quantified all emissive nanotubes in a volume. Via spectral imaging, we assessed structural impurities and precisely determined molar concentrations of the (8,6) and (9,4) nanotube species. We developed an approach to obtain the molarity of any structurally enriched semiconducting single-walled carbon nanotube preparation on a per-nanotube basis.

  11. Finite element prediction of seismic response modification of monumental structures utilizing base isolation

    NASA Astrophysics Data System (ADS)

    Spanos, Konstantinos; Anifantis, Nikolaos; Kakavas, Panayiotis

    2015-05-01

    The analysis of the mechanical behavior of ancient structures is an essential engineering task concerning the preservation of architectural heritage. As many monuments of classical antiquity are located in regions of earthquake activity, the safety assessment of these structures, as well as the selection of possible restoration interventions, requires numerical models capable of correctly representing their seismic response. The work presented herein was part of a research project in which a better understanding of the dynamics of classical column-architrave structures was sought by means of numerical techniques. In this paper, the seismic behavior of ancient monumental structures with multi-drum classical columns is investigated. In particular, the column-architrave classical structure under strong ground excitations was represented by a finite element method. This approach simulates the individual rock blocks as distinct rigid blocks interconnected with slidelines and incorporates seismic isolation dampers under the basement of the structure. Sliding and rocking motions of individual stone blocks and drums are modeled utilizing non-linear frictional contact conditions. The seismic isolation is modeled through the application of pad bearings under the basement of the structure. These pads are interpreted by appropriate rubber and steel layers. Time domain analyses were performed, considering the geometric and material non-linear behavior at the joints and the characteristics of pad bearings. The deformation and failure modes of drum columns subject to seismic excitations of various types and intensities were analyzed. The adverse influence of drum imperfections on structural safety was also examined.

  12. Antifungal Susceptibility in Serum and Virulence Determinants of Candida Bloodstream Isolates from Hong Kong

    PubMed Central

    Seneviratne, Chaminda J.; Rajan, Suhasini; Wong, Sarah S. W.; Tsang, Dominic N. C.; Lai, Christopher K. C.; Samaranayake, Lakshman P.; Jin, Lijian

    2016-01-01

    Candida bloodstream infections (CBI) are one of the most common nosocomial infections globally, and they account for a high mortality rate. The increasing global prevalence of drug-resistant Candida strains has also been posing a challenge to clinicians. In this study, we comprehensively evaluated the biofilm formation and production of hemolysin and proteinase of 63 CBI isolates derived from a hospital setting in Hong Kong as well as their antifungal susceptibility both in the presence and in the absence of human serum, using standard methodology. Candida albicans was the predominant species among the 63 CBI isolates collected, and non-albicans Candida species accounted for approximately one third of the isolates (36.5%). Of them, Candida tropicalis was the most common non-albicans Candida species. A high proportion (31.7%) of the CBI isolates (40% of C. albicans isolates, 10% of C. tropicalis isolates, 11% of C. parapsilosis isolates, and 100% of C. glabrata isolates) were found to be resistant to fluconazole. One of the isolates (C. tropicalis) was resistant to amphotericin B. A rising prevalence of drug-resistance CBI isolates in Hong Kong was observed with reference to a previous study. Notably, all non-albicans Candida species, showed increased hemolytic activity relative to C. albicans, whilst C. albicans, C. tropicalis, and C. parapsilosis exhibited proteinase activities. Majority of the isolates were capable of forming mature biofilms. Interestingly, the presence of serum distorted the yeast sensitivity to fluconazole, but not amphotericin B. Taken together, our findings demonstrate that CBI isolates of Candida have the potential to express to varying extent their virulence attributes (e.g., biofilm formation, hemolysin production, and proteinase activity) and these, together with perturbations in their antifungal sensitivity in the presence of serum, may contribute to treatment complication in candidemia. The effect of serum on antifungal activity

  13. Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?

    PubMed

    Hylton, Rebecca K; Tizzard, Graham J; Threlfall, Terence L; Ellis, Amy L; Coles, Simon J; Seaton, Colin C; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L

    2015-09-02

    Mandelic acids are prototypic chiral molecules where the sensitivity of crystallized forms (enantiopure/racemic compound/polymorphs) to both conditions and substituents provides a new insight into the factors that may allow chiral separation by crystallization. The determination of a significant number of single crystal structures allows the analysis of 13 enantiopure and 30 racemic crystal structures of 21 (F/Cl/Br/CH3/CH3O) substituted mandelic acid derivatives. There are some common phenyl packing motifs between some groups of racemic and enantiopure structures, although they show very different hydrogen-bonding motifs. The computed crystal energy landscape of 3-chloromandelic acid, which has at least two enantiopure and three racemic crystal polymorphs, reveals that there are many more possible structures, some of which are predicted to be thermodynamically more favorable as well as slightly denser than the known forms. Simulations of mandelic acid dimers in isolation, water, and toluene do not differentiate between racemic and enantiopure dimers and also suggest that the phenyl ring interactions play a major role in the crystallization mechanism. The observed crystallization behavior of mandelic acids does not correspond to any simple "crystal engineering rules" as there is a range of thermodynamically feasible structures with no distinction between the enantiopure and racemic forms. Nucleation and crystallization appear to be determined by the kinetics of crystal growth with a statistical bias, but the diversity of the mandelic acid crystallization behavior demonstrates that the factors that influence the kinetics of crystal nucleation and growth are not yet adequately understood.

  14. Determination of lytic enzyme activities of indigenous Trichoderma isolates from Pakistan.

    PubMed

    Asad, Saeed Ahmad; Tabassum, Ayesha; Hameed, Abdul; Hassan, Fayyaz Ul; Afzal, Aftab; Khan, Sabaz Ali; Ahmed, Rafiq; Shahzad, Muhammad

    2015-01-01

    This study investigated lytic enzyme activities in three indigenous Trichoderma strains namely, Trichoderma asperellum, Trichoderma harzianum and Trichoderma sp. Native Trichoderma strains and a virulent strain of Rhizoctonia solani isolated from infected bean plants were also included in the study. Enzyme activities were determined by measuring sugar reduction by dinitrosalicylic acid (DNS) method using suitable substrates. The antagonists were cultured in minimal salt medium with the following modifications: medium A (1 g of glucose), medium B (0.5 g of glucose + 0.5 g of deactivated R. solani mycelia), medium C (1.0 g of deactivated respective antagonist mycelium) and medium D (1 g of deactivated R. solani mycelia). T asperellum showed presence of higher amounts of chitinases, β-1, 3-glucanases and xylanases in extracellular protein extracts from medium D as compared to medium A. While, the higher activities of glucosidases and endoglucanses were shown in medium D extracts by T. harzianum. β-glucosidase activities were lower compared with other enzymes; however, activities of the extracts of medium D were significantly different. T. asperellum exhibited maximum inhibition (97.7%). On the other hand, Trichoderma sp. did not show any effect on mycelia growth of R. solani on crude extract.

  15. An approach toward optimization of the influential growth determinants of opportunistic yeast isolate Pichia guilliermondii.

    PubMed

    Mukherjee, Suprabhat; Mukherjee, Niladri; Roy, Priya; Saini, Prasanta; Sinha Babu, Santi P

    2016-07-03

    The present study reports statistical optimization of growth conditions of an opportunistic fungal strain Pichia guilliermondii, isolated from the blood of patients suffering from bancroftian filariasis. Seven key determinants, namely, primary inoculums size (%), volume (mL) and pH of media, serum proportion, temperature (°C), incubation time (hr), and agitation speed (rpm) that influence in vitro growth of the pathogen were optimized statistically using response surface methodology (RSM). RSM with seven factors and two-level Box-Behnken design was employed for designing experimental run, prediction of case statistics, suitable exploration of quadratic response surfaces, and constructing a second-order polynomial equation. Analysis of variance (ANOVA) showed that primary inoculums size, volume of culture media, temperature, incubation time, and agitation speed exert most significant influence over fungal growth. The RSM study predicted that optimum fungal growth can be obtained using 10% primary inoculums size in 100 mL culture media with pH 6.0, 6.28% serum, 32.5°C temperature, and 24 hr of incubation, alongside agitation speed at 400 rpm. The desirability of the optimized growth model for P. guilliermondii is 99.123%, which indicated its accuracy and acceptability. Finally, the optimized growth module illustrated in the study could be useful in improving in vitro growth of clinically important P. guilliermondii.

  16. Structure determination of bisacetylenic oxylipins in carrots (Daucus carota L.) and enantioselective synthesis of falcarindiol.

    PubMed

    Schmiech, Ludger; Alayrac, Carole; Witulski, Bernhard; Hofmann, Thomas

    2009-11-25

    Although bisacetylenic oxylipins have been demonstrated to exhibit diverse biological activities, the chemical structures of many representatives of this class of phytochemicals still remain elusive. As carrots play an important role in our daily diet and are known as a source of bisacetylenes, an extract made from Daucus carota L. was screened for bisacetylenic oxylipins, and, after isolation, their structures were determined by means of LC-MS and 1D/2D NMR spectroscopy. Besides the previously reported falcarinol, falcarindiol, and falcarindiol 3-acetate, nine additional bisacetylenes were identified, among which six derivatives are reported for the first time in literature and three compounds were previously not identified in carrots. To determine the absolute stereochemistry of falcarindiol in carrots, the (3R,8R)-, (3R,8S)-, (3S,8R)-, and (3S,8S)-stereoisomers of falcarindiol were synthesized according to a novel 10-step total synthesis involving a Cadiot-Chodkiewicz cross-coupling reaction of (S)- and (R)-trimethylsilanyl-4-dodecen-1-yn-3-ol and (R)- and (S)-5-bromo-1-penten-4-yn-3-ol, respectively. Comparative chiral HPLC analysis of the synthetic stereoisomers with the isolated phytochemical led to the unequivocal assignment of the (Z)-(3R,8S)-configuration for falcarindiol in carrot extracts from Daucus carota L.

  17. Probing ion-molecule structure and dynamics in isolated molecular clusters and proteins

    NASA Astrophysics Data System (ADS)

    Abate, Yohannes

    Ion-molecule interactions in isolated molecular clusters and proteins are studied in this work using experimental and theoretical methods. Photodissociation spectroscopy and chemical dynamics of several metal ion-molecule clusters are studied. The experimental tool used for these studies is an Angular Reflectron Time Of Flight Mass Spectrometer (ARTOFMS). The experimental work is supported by ab initio electronic structure calculations on the Gaussian and GAMESS platforms. This work also describes a computational study of the interaction of protonated histidine with other aromatic residues in proteins. We have studied the photodissociation spectroscopy of weakly bound Zn +(H2O) and Zn+(D2O) bimolecular complexes. We assign two molecular absorption bands in the near UV correlating to Zn+ (4s-4p)-metal centered transitions, and identify vibrational progressions associated with both intermolecular and intramolecular vibrational modes of the cluster. Partially resolved rotational structure is consistent with a C2 V equilibrium complex geometry. The photodissociation spectroscopy and chemical dynamics of Zn +-formaldehyde and Zn+-acetaldehyde clusters are investigated in the near UV spectral range. The work is also supported by ab initio electronic structure calculations to study the ground-state bonding and interactions in the low-lying doublet excited states. We identify absorption bands corresponding to photoinduced charge transfer, Zn+(4s-4p)-based transitions, and aldehyde-based excitations. We propose a reaction mechanism for the reactive dissociation that proceeds via H-atom abstraction on the charge-transfer surface. This work shows important differences with results from earlier experiments on Mg+- and Ca+-aldehyde complexes despite the similar valence character for these metal ions. In the study of Mg+-acetic acid we observe three distinct absorption bands, two red-shifted and one blue-shifted from the Mg +(3s ← 3p) resonance at 280 nm (35714 cm-1). We

  18. X-ray structure determination and deuteration of nattokinase

    PubMed Central

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-01-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis. PMID:24121331

  19. X-ray structure determination and deuteration of nattokinase.

    PubMed

    Yanagisawa, Yasuhide; Chatake, Toshiyuki; Naito, Sawa; Ohsugi, Tadanori; Yatagai, Chieko; Sumi, Hiroyuki; Kawaguchi, Akio; Chiba-Kamosida, Kaori; Ogawa, Megumi; Adachi, Tatsumi; Morimoto, Yukio

    2013-11-01

    Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.

  20. Life determination of riveted aircraft structure by holographic NDE

    NASA Astrophysics Data System (ADS)

    Baird, John P.; Heslehurst, Rikard B.; Williamson, Hugh M.; Clark, Robert K.; Hollamby, Derek

    1996-11-01

    In a project funded by the Federal Aviation Administration's (FAA) Aging Aircraft Program, a Portable Holographic Inspection System (PHITS) has been further developed. The technique involves taking a double exposure white light reflection hologram of aircraft structures. Each exposure is taken at a slightly different load state, and the resulting interferogram shows the deformations that occur between the two load states. Results showed that the rivets in a simple lap joint, designed to simulate the longitudinal lap splice on a Boeing 737, behaved in two distinct and easily recognizable modes. The first mode occurred at low loads and was an indication that friction forces between the two sheets of the lap joint dominated the load transfer mechanism. Indications were that the second mode related to higher loads for which the friction forces played a much lesser role. The load at which the changeover begins to occur has been called the critical load. Preliminary experiments showed that structures with a high value of critical load had a fatigue life of order ten times that of a normally fastened splice. Critical load can be readily determined in the field using the PHITS system. Research designed to establish the relationship between fatigue life and critical load is continuing. An understanding of that relationship could lead to a technique capable of fatigue life determination in typical aircraft structures.

  1. Tackling the crystallographic structure determination of the COP9 signalosome

    PubMed Central

    Bunker, Richard D.

    2016-01-01

    The COP9 signalosome (CSN) is an essential multi-protein complex in eukaryotes. CSN is a master regulator of intracellular protein degradation, controlling the vast family of cullin–RING ubiquitin (E3) ligases (CRLs). Important in many cellular processes, CSN has prominent roles in DNA repair, cell-cycle control and differentiation. The recent crystal structure of human CSN provides insight into its exquisite regulation and functionality [Lingaraju et al. (2014 ▸), Nature (London), 512, 161–165]. Structure determination was complicated by low-resolution diffraction from crystals affected by twinning and rotational pseudo-symmetry. Crystal instability and non-isomorphism strongly influenced by flash-cooling, radiation damage and difficulty in obtaining heavy-atom derivatives, were overcome. Many different subunits of the same fold class were distinguished at low resolution aided by combinatorial selenomethionine labelling. As an example of how challenging projects can be approached, the structure determination of CSN is described as it unfolded using cluster-compound MIRAS phasing, MR-SAD with electron-density models and cross-crystal averaging exploiting non-isomorphism among unit-cell variants of the same crystal form. PMID:26960120

  2. Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations

    NASA Astrophysics Data System (ADS)

    Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.

    2001-12-01

    Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations

  3. DNA Hybridization Probe for Use in Determining Restricted Nodulation among Bradyrhizobium japonicum Serocluster 123 Field Isolates

    PubMed Central

    Sadowsky, Michael J.; Cregan, Perry B.; Keyser, Harold H.

    1990-01-01

    Several soybean plant introduction (PI) genotypes have recently been described which restrict nodulation of Bradyrhizobium japonicum serocluster 123 in an apparently serogroup-specific manner. While PI 371607 restricts nodulation of strains in serogroup 123 and some in serogroup 127, those in serogroup 129 are not restricted. When DNA regions within and around the B. japonicum I-110 common nodulation genes were used as probes to genomic DNA from the serogroup strains USDA 123, USDA 127, and USDA 129, several of the probes differentially hybridized to the nodulation-restricted and -unrestricted strains. One of the gene regions, cloned in plasmid pMJS12, was subsequently shown to hybridize to 4.6-kilobase EcoRI fragments from DNAs from nodulation-restricted strains and to larger fragments in nodulation-unrestricted strains. To determine if the different hybridization patterns could be used to predict nodulation restriction, we hybridized pMJS12 to EcoRI-digested genomic DNAs from uncharacterized serocluster 123 field isolates. Of the 36 strains examined, 15 were found to have single, major, 4.6-kilobase hybridizing EcoRI fragments. When tested for nodulation, 80% (12 of 15) of the strains were correctly predicted to be restricted for nodulation of the PI genotypes. In addition, hybridization patterns obtained with pMJS12 and nodulation phenotypes on PI 371607 indicated that there are at least three types of serogroup 127 strains. Our results suggest that the pMJS12 gene probe may be useful in selecting compatible host-strain combinations and in determining the suitability of field sites for the placement of soybean genotypes containing restrictive nodulation alleles. Images PMID:16348217

  4. The morphology of islets within the porcine donor pancreas determines the isolation result: successful isolation of pancreatic islets can now be achieved from young market pigs.

    PubMed

    Krickhahn, Mareike; Bühler, Christoph; Meyer, Thomas; Thiede, Arnulf; Ulrichs, Karin

    2002-01-01

    Clinical islet allotransplantation has become an increasingly efficient "routine" therapy in recent years. Shortage of human donor organs leads to porcine pancreatic islets as a potential source for islet xenotransplantation. Yet it is still very difficult to isolate sufficient numbers of intact porcine islets, particularly from young market pigs. In the following study islets were successfully isolated from retired breeders [4806 +/- 720 islet equivalents per gram organ (IEQ/g); n = 25; 2-3 years old; RB] and also from young hybrid pigs [2868 +/- 260 IEQ/g; n = 65; 4-6 months old; HY] using LiberasePI and a modified version of Ricordi's digestion-filtration technique. As expected, isolations from RB showed significantly better results (p < 0.002). A retrospective histological analysis of almost all donor pancreases showed that the majority of organs from RB (80%) contained mainly large islets (diameter > 200 microm), in contrast to only 35% of all pancreases from HY. Remarkably, the islet size in situ, regardless whether detected in RB or HY, strongly determined the isolation result. A donor organ with predominantly large islets resulted in significantly higher numbers of IEQs compared with a donor organ with predominantly small islets [RB(Large Islets): 5680 +/- 3,318 IEQ/g (n= 20); RB(Small Islets): 1353 +/- 427 IEQ/g (n = 5); p < 0.02]. In addition, isolation results were strongly influenced by the quality of the LiberasePI batch, and therefore single batch testing is invariably required. Purification was performed using Ficoll or OptiPrep density gradient centrifugation manually or in the COBE cell processor. Although islet purity was highest when OptiPrep was used, final islet yields did not differ between the different purification methods. Our study demonstrates that islet size in situ is an extremely critical parameter for highly successful islet isolation; consequently, we are now performing a morphological screening of each donor organ prior to the

  5. Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain

    SciTech Connect

    Mortenson, David E.; Kreitler, Dale F.; Yun, Hyun Gi; Gellman, Samuel H. Forest, Katrina T.

    2013-12-01

    Two structures of a small protein with a defined tertiary fold, the isolated Pin1 WW domain, have been determined via racemic crystallization with small-molecule additives. These additives, which are either racemic or achiral, appear to stabilize a dynamic loop region of the structure. The human Pin1 WW domain is a small autonomously folding protein that has been useful as a model system for biophysical studies of β-sheet folding. This domain has resisted previous attempts at crystallization for X-ray diffraction studies, perhaps because of intrinsic conformational flexibility that interferes with the formation of a crystal lattice. Here, the crystal structure of the human Pin1 WW domain has been obtained via racemic crystallization in the presence of small-molecule additives. Both enantiomers of a 36-residue variant of the Pin1 WW domain were synthesized chemically, and the l- and d-polypeptides were combined to afford diffracting crystals. The structural data revealed packing interactions of small carboxylic acids, either achiral citrate or a d,l mixture of malic acid, with a mobile loop region of the WW-domain fold. These interactions with solution additives may explain our success in crystallization of this protein racemate. Molecular-dynamics simulations starting from the structure of the Pin1 WW domain suggest that the crystal structure closely resembles the conformation of this domain in solution. The structural data presented here should provide a basis for further studies of this important model system.

  6. A vibration isolation system in low frequency excitation region using negative stiffness structure for vehicle seat

    NASA Astrophysics Data System (ADS)

    Le, Thanh Danh; Ahn, Kyoung Kwan

    2011-12-01

    This paper designs and fabricates a vibration isolation model for improving vibration isolation effectiveness of the vehicle seat under low excitation frequencies. The feature of the proposed system is to use two symmetric negative stiffness structures (NSS) in parallel to a positive stiffness structure. Here, theoretical analysis of the proposed system is clearly presented. Then, the design procedure is derived so that the resonance peak of frequency-response curve drifts to the left, the load support capacity of the system is maintained, the total size of the system is reduced for easy practical application and especially, the bending of the frequency-response curve is minimized. Next the dynamic equation of the proposed system is set up. Then, the harmonic balance (HB) method is employed to seek the characteristic of the motion transmissibility of the proposed system at the steady state for each of the excitation frequency. From this characteristic, the curves of the motion transmission are predicted according to the various values of the configurative parameters of the system. Then, the time responses to the sinusoidal, multi frequency and random excitations are also investigated by simulation and experiment. In addition, the isolation performance comparison between the system with NSS and system without NSS is realized. The simulation results reveal that the proposed system has larger frequency region of isolation than that of the system without NSS. The experimental results confirm also that with a random excitation mainly spreading from 0.1 to 10 Hz, the isolation performance of the system with NSS is greatly improved, where the RMS values of the mass displacement may be reduced to 67.2%, whereas the isolation performance of the system without NSS is bad. Besides, the stability of the steady-state response is also studied. Finally, some conclusions are given.

  7. A modified Kelvin impact model for pounding simulation of base-isolated building with adjacent structures

    NASA Astrophysics Data System (ADS)

    Ye, Kun; Li, Li; Zhu, Hongping

    2009-09-01

    Base isolation can effectively reduce the seismic forces on a superstructure, particularly in low- to medium-rise buildings. However, under strong near-fault ground motions, pounding may occur at the isolation level between the base-isolated building (BIB) and its surrounding retaining walls. To effectively investigate the behavior of the BIB pounding with adjacent structures, after assessing some commonly used impact models, a modified Kelvin impact model is proposed in this paper. Relevant parameters in the modified Kelvin model are theoretically derived and numerically verified through a simple pounding case. At the same time, inelasticity of the isolated superstructure is introduced in order to accurately evaluate the potential damage to the superstructure caused by the pounding of the BIB with adjacent structures. The reliability of the modified Kelvin impact model is validated through numerical comparisons with other impact models. However, the difference between the numerical results from the various impact analytical models is not significant. Many numerical simulations of BIBs are conducted to investigate the influence of various design parameters and conditions on the peak inter-story drifts and floor accelerations during pounding. It is shown that pounding can substantially increase floor accelerations, especially at the ground floor where impacts occur. Higher modes of vibration are excited during poundings, increasing the inter-story drifts instead of keeping a nearly rigid-body motion of the superstructure. Furthermore, higher ductility demands can be imposed on lower floors of the superstructure. Moreover, impact stiffness seems to play a significant role in the acceleration response at the isolation level and the inter-story drifts of lower floors of the superstructure. Finally, the numerical results show that excessive flexibility of the isolation system used to minimize the floor accelerations may cause the BIB to be more susceptible to pounding

  8. Solving a generalized distance geometry problem for protein structure determination.

    PubMed

    Sit, Atilla; Wu, Zhijun

    2011-12-01

    We propose a new approach to the problem of determining an ensemble of protein structures with a set of interatomic distance bounds in NMR protein modeling. Similarly to X-ray crystallography, we assume that the protein has an equilibrium structure and the atoms fluctuate around their equilibrium positions. Then, the problem can be formulated as a generalized distance geometry problem, to find the equilibrium positions and maximal possible fluctuation radii for the atoms in the protein, subject to the condition that the fluctuations should be within the given distance bounds. We describe the scientific background of the work, the motivation of the new approach and the formulation of the problem. We develop a geometric buildup algorithm for an approximate solution to the problem and present some preliminary test results as a first step concept proofing. We also discuss related theoretical and computational issues and potential impacts of this work in NMR protein modeling.

  9. Structure Determination of Natural Products by Nuclear Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Du.

    High-field NMR experiments were used to determine the full structures of six new natural products extracted from plants. These are: four saponins (PT-2, P1, P2 and P3) from the plant Alphitonia zizyphoides found in Samoa; one sesquiterpene (DF-4) from Douglas fir and one diterpene derivative (E-2) from a Chinese medicinal herb. By concerted use of various 1D and 2D NMR techniques, the structures of the above compounds were established and complete resonance assignments were achieved. The 2D INADEQUATE technique coupled with a computerized spectral analysis was extensively used. When carried out on concentrations as low as 60 mg of sample, this technique provided absolute confirmation of the assignments for 35 of the possible 53 C-C bonds for PT-2. On 30 mg of sample of E-21, it revealed 22 of 28 possible C-C bonds.

  10. Theoretical challenge to the experimentally determined geometrical structure of dimethylsilaethylene

    SciTech Connect

    Yoshioka, Yasunori; Goddard, John D.; Schaefer, III, Henry F.

    1981-05-01

    The equilibrium geometries of (CH3)2Si=CH2 and H{2Si=CH2 have been determined at the self-consistent-field level of electronic structure theory using a double zeta basis set augmented with d functions on all heavy atoms. For the parent silaethylene, large scale configuration interaction (6920 configurations) demonstrates that electron correlation effects do not qualitatively alter the predicted structure. Because of this, it is concluded that the experimental electron diffraction geometry of Mahaffy, Gutowsky, and Montgomery is likely to be seriously incorrect. Specifically the theoretical prediction for the dimethylsilaethylene Si=C distance is 1.692 Å, while the range of experimental values presented was 1.815 - 1.835 Å.

  11. Multilocus Sequence Analysis of Housekeeping Genes and Antigenic Determinant Genes in Bordetella pertussis Strains Isolated in Korea

    PubMed Central

    Jung, Sang-Oun; Moon, Yu Mi; Kim, So-Hyeon; Sung, Hwa Young; Kwon, Seung-Jik; Kang, Yeon Ho; Yu, Jae Yon

    2011-01-01

    Objectives To confirm genotype diversities of clinical isolates of Bordetella pertussis and to evaluate the risk of pertussis outbreak in Korea. Methods Seven housekeeping genes and 10 antigenic determinant genes from clinical B. pertussis isolates were analyzed by Multilocus sequence typing (MLST). Results More variant pattern was observed in antigenic determinant genes. Especially, PtxS1 gene was the most variant gene; five genotypes were observed from eight global genotypes. In the bacterial type, the number of observed sequence types in the isolates was seven and the most frequent form was type 1 (79.6%). This major sequence type also showed a time-dependent transition pattern. Older isolates (1968 and 1975) showed type 1 and 6 in housekeeping genes and antigenic determinant genes, respectively. However, these were changed to type 2 and 1 in isolates 1999–2008. This transition was mainly attributed to genotype change of PtxS1 and Fim3 gene; the tendency of genotype change was to avoid vaccine-derived genotype. In addition, there was second transition in 2009. In this period, only the sequence type of antigenic determinant genes was changed to type 2. Based Upon Related Sequence Types (BURST) analysis confirmed that there were two clonal complexes (ACCI and ACCII) in the Korean isolates. Moreover, the recently increased sequence type was revealed as AST2 derived from AST 3 in ACCI. Conclusions Genotype changes in Korean distributing strains are still progressing and there was a specific driving force in antigenic determinant genes. Therefore continuous surveillance of genotype change of the distributing strains should be performed to confirm interrelationship of genotype change with vaccine immunity. PMID:24159461

  12. A use of Ramachandran potentials in protein solution structure determinations.

    PubMed

    Bertini, Ivano; Cavallaro, Gabriele; Luchinat, Claudio; Poli, Irene

    2003-08-01

    A strategy is developed to use database-derived phi-psi constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived phi-psi constraints are enforced for all amino acids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the phi-psi values for each residue are examined. In the second and final run, the database-derived phi-psi constraints are enforced only for those residues which in the first run have ended in one and the same favored phi-psi region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.

  13. Computational determination of radiation damage effects on DNA structure

    NASA Astrophysics Data System (ADS)

    Pinak, Miroslav

    2003-03-01

    Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

  14. The Phenix software for automated determination of macromolecular structures.

    PubMed

    Adams, Paul D; Afonine, Pavel V; Bunkóczi, Gábor; Chen, Vincent B; Echols, Nathaniel; Headd, Jeffrey J; Hung, Li-Wei; Jain, Swati; Kapral, Gary J; Grosse Kunstleve, Ralf W; McCoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert D; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C; Zwart, Peter H

    2011-09-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.

  15. Detection of antibiotic resistance, virulence gene determinants and biofilm formation in Aeromonas species isolated from cattle.

    PubMed

    Igbinosa, Isoken H; Igbinosa, Etinosa O; Okoh, Anthony I

    2015-11-01

    This study aimed to assess the antibiogram of Aeromonas strains recovered from cattle faeces and the potential pathogenic status of the isolates. The antibiogram of the Aeromonas isolates demonstrated total resistance to clindamycin oxacillin, trimethoprim, novobiocin and ticarcillin. However, Aeromonas strains were sensitive to cefotaxime, oxytetracycline and tobramycin. The Aeromonas strains from Lovedale and Fort Cox farms were found to possess some virulence genes. The percentage distribution was aer 71.4%, ast 35.7%, fla 60.7%, lip 35.7% and hlyA 25% for Lovedale farm and aer 63.1%, alt 10.5%, ast 55.2%, fla 78.9%, lip 21% and hlyA 35.9% for Fort Cox farm. Class 1 integron was present in 27% of Aeromonas isolates; the bla TEM gene was present in 34.8%, while the blaP1 class A β-lactamase gene was detected in 12.1% of the isolates. Approximately 86% of the isolates formed a biofilm on microtitre plates. The presence of multiple antibiotic resistance and virulence genes in Aeromonas isolates from cattle faeces reveals the pathogenic and infectious importance of these isolates and is of great significance to public health. The possession of a biofilm-forming capability by such isolates may lead to difficulty during the management of infection related to Aeromonas species.

  16. Structural Characterization of Actinomycin D Using Multiple Ion Isolation and Electron Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Wills, Rebecca H.; O'Connor, Peter B.

    2013-12-01

    Non-ribosomal peptides are bio synthesized using a range of enzymes that allow much more structural variability compared with "normal" peptides. Deviations from the standard amino acid structures are common features of this diverse class of natural products, making sequencing a challenging process. FTICR mass spectrometry, specifically the complementary tandem mass spectrometry techniques collision activated dissociation (CAD) and electron induced dissociation (EID), have been used to reveal structural information on the non-ribosomal peptide actinomycin D. EID was also combined with a multiple ion isolation method in order to provide an accurate (sub-ppm) internal calibration for the product ions. EID has been found to produce more detailed, complementary data than CAD for actinomycin D, with additional information being provided through fragmentation of the sodium and lithium adducts. Furthermore, the use of isolation in the FTICR cell was found to increase product ion intensities relative to the precursor ion, enabling significantly more peaks to be detected than when using EID alone. The combination of multiple ion isolation with EID, therefore, enables an accurate internal calibration of the fragment ions to be made (average mass uncertainty of <0.3 ppm), as well as increasing the degree of fragmentation of the compound, resulting in detailed structural information.

  17. Chromatographic analysis and structure determination of biliverdins and bilirubins.

    PubMed

    Heirwegh, K P; Fevery, J; Blanckaert, N

    1989-11-10

    Recent applications of thin-layer chromatographic (TLC) and high-performance liquid chromatographic (HPLC) procedures has revealed an unexpected wide variety of naturally occurring unconjugated and conjugated bilirubins. Biliverdins seems to occur only in unconjugated forms, mainly as the IX alpha isomer. Several synthetic biliverdins and bilirubins present interesting models for biochemical and metabolic studies. Owing to recent recognition of the astounding heterogeneity of natural bilirubins and to the various artifactual changes that bile pigments can undergo, considerable confusion has existed, and still exists, with regard to the nomenclature of the bile pigments and their derivatives. To set a background for further discussion, the present review starts with a brief discussion of nomenclature and of the various characteristic forms of lability of the bile pigments. TLC and HPLC procedures for preparation and analysis of unconjugated biliverdins and bilirubins and their methyl ester and sugar ester conjugates, as well as procedures for analysis of bilirubin-protein conjugates, are then discussed. Since, in view of the lability and pronounced heterogeneity of bile pigments, it is important to assess the composition and nature of chromatographically isolated pigments, the review is concluded by a brief evaluation of various structural tests.

  18. Structural and energetic determinants of proton transfer in bacteriorhodopsin

    SciTech Connect

    Bondar, A.N.; Smith, Jeremy C; Fischer, S.

    2006-05-01

    In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.

  19. Shallow lunar structure determined from the passive seismic experiment

    NASA Technical Reports Server (NTRS)

    Nakamura, Y.; Dorman, J.; Duennebier, F.; Lammlein, D.; Latham, G.

    1975-01-01

    Data relevant to the shallow structure of the moon obtained at the Apollo seismic stations are compared with previously published results of the active seismic experiments. It is concluded that the lunar surface is covered by a layer of low seismic velocity which appears to be equivalent to the lunar regolith defined previously by geological observations. This layer is underlain by a zone of distinctly higher seismic velocity at all of the Apollo landing sites. The regolith thicknesses at the Apollo 11, 12, and 15 sites are estimated from the shear-wave resonance to be 4.4, 3.7, and 4.4 m, respectively. These thicknesses and those determined at the other Apollo sites by the active seismic experiments appear to be correlated with the age determinations and the abundances of extralunar components at the sites.

  20. Methods for isolation, purification and structural elucidation of bioactive secondary metabolites from marine invertebrates.

    PubMed

    Ebada, Sherif S; Edrada, Ru Angelie; Lin, Wenhan; Proksch, Peter

    2008-01-01

    In the past few decades, marine natural products bioprospecting has yielded a considerable number of drug candidates. Two marine natural products have recently been admitted as new drugs: Prialt (also known as ziconotide) as a potent analgesic for severe chronic pain and Yondelis (known also as trabectedin or E-743) as antitumor agent for the treatment of advanced soft tissue sarcoma. In this protocol, methods for bioactivity-guided isolation, purification and identification of secondary metabolites from marine invertebrates such as sponges, tunicates, soft corals and crinoids are discussed. To achieve this goal, solvent extraction of usually freeze-dried sample of marine organisms is performed. Next, the extract obtained is fractionated by liquid-liquid partitioning followed by various chromatographic separation techniques including thin layer chromatography, vacuum liquid chromatography, column chromatography (CC) and preparative high-performance reversed-phase liquid chromatography. Isolation of bioactive secondary metabolites is usually monitored by bioactivity assays, e.g., antioxidant (2,2-diphenyl-1-picryl hydrazyl) and cytotoxicity (microculture tetrazolium) activities that ultimately yield the active principles. Special care should be taken when performing isolation procedures adapted to the physical and chemical characteristics of the compounds isolated, particularly their lipo- or hydrophilic characters. Examples of isolation of compounds of different polarities from extracts of various marine invertebrates will be presented in this protocol. Structure elucidation is achieved using recent spectroscopic techniques, especially 2D NMR and mass spectrometry analysis.

  1. Xanthones, biflavanones and triterpenes from Pentadesma grandifolia (Clusiaceae): structural determination and bioactivity.

    PubMed

    Djoufack, Grace Leontine Nwabouloun; Valant-Vetschera, Karin M; Schinnerl, Johann; Brecker, Lothar; Lorbeer, Eberhard; Robien, Wolfgang

    2010-07-01

    Stem bark, roots, leaves and fruits of Pentadesma grandifolia Baker f. (Clusiaceae) have been analyzed for the presence of xanthones, biflavonoids and triterpenoids. Isolated and identified structures include the xanthones cowagarcinone B (1) and alpha-mangostin (2), further the two biflavanones 3,8"-binaringenin (3) and the corresponding 3,6"-binaringenin (4), which is here reported as natural constituent for the first time. Structures were determined by NMR and mass spectrometry, as well as by 13C-NMR CSEARCH and SPECINFO database systems. The triterpenes lupeol (5), beta-amyrin (6) and betulin (7) were also encountered. Compounds 2 - 4 exhibited antifungal activity against Cladosporium sphaerospermum. Results are discussed in context to organ-specific accumulation and to other bioactivities that may relate to the ethnomedicinal uses of this species.

  2. Toward structure determination using membrane-protein nanocrystals and microcrystals

    PubMed Central

    Hunter, Mark S.; Fromme, Petra

    2012-01-01

    Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (~ 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [Chapman H.N., et al. Femtosecond X-ray protein nanocrystallography, Nature 470 (2011) 73–81]. Many additional techniques still need to be developed to explore the

  3. Active pneumatic vibration isolation system using negative stiffness structures for a vehicle seat

    NASA Astrophysics Data System (ADS)

    Danh, Le Thanh; Ahn, Kyoung Kwan

    2014-02-01

    In this paper, an active pneumatic vibration isolation system using negative stiffness structures (NSS) for a vehicle seat in low excitation frequencies is proposed, which is named as an active system with NSS. Here, the negative stiffness structures (NSS) are used to minimize the vibratory attraction of a vehicle seat. Owing to the time-varying and nonlinear behavior of the proposed system, it is not easy to build an accurate dynamic for model-based controller design. Thus, an adaptive intelligent backstepping controller (AIBC) is designed to manage the system operation for high-isolation effectiveness. In addition, an auxiliary control effort is also introduced to eliminate the effect of the unpredictable perturbations. Moreover, a radial basis function neural network (RBFNN) model is utilized to estimate the optimal gain of the auxiliary control effort. Final control input and the adaptive law for updating coefficients of the approximate series can be obtained step by step using a suitable Lyapunov function. Afterward, the isolation performance of the proposed system is assessed experimentally. In addition, the effectiveness of the designed controller for the proposed system is also compared with that of the traditional backstepping controller (BC). The experimental results show that the isolation effectiveness of the proposed system is better than that of the active system without NSS. Furthermore, the undesirable chattering phenomenon in control effort is quite reduced by the estimation mechanism. Finally, some concluding remarks are given at the end of the paper.

  4. Membrane proteins in four acts: function precedes structure determination.

    PubMed

    Cramer, W A; Zakharov, S D; Saif Hasan, S; Zhang, H; Baniulis, D; Zhalnina, M V; Soriano, G M; Sharma, O; Rochet, J C; Ryan, C; Whitelegge, J; Kurisu, G; Yamashita, E

    2011-12-01

    Studies on four membrane protein systems, which combine information derived from crystal structures and biophysical studies have emphasized, as a precursor to crystallization, demonstration of functional activity. These assays have relied on sensitive spectrophotometric, electrophysiological, and microbiological assays of activity to select purification procedures that lead to functional complexes and with greater likelihood to successful crystallization: (I), Hetero-oligomeric proteins involved in electron transport/proton translocation. (1) Crystal structures of the eight subunit hetero-oligomeric trans-membrane dimeric cytochrome b(6)f complex were obtained from cyanobacteria using a protocol that allowed an analysis of the structure and function of internal lipids at specific intra-membrane, intra-protein sites. Proteolysis and monomerization that inactivated the complex and prevented crystallization was minimized through the use of filamentous cyanobacterial strains that seem to have a different set of membrane-active proteases. (2) An NADPH-quinone oxido-reductase isolated from cyanobacteria contains an expanded set of 17 monotopic and polytopic hetero-subunits. (II) β-Barrel outer membrane proteins (OMPs). High resolution structures of the vitamin B(12) binding protein, BtuB, solved in meso and in surfo, provide the best example of the differences in such structures that were anticipated in the first application of the lipid cubic phase to membrane proteins [1]. A structure of the complex of BtuB with the colicin E3 and E2 receptor binding domain established a "fishing pole" model for outer membrane receptor function in cellular import of nuclease colicins. (III) A modified faster purification procedure contributed to significantly improved resolution (1.83Å) of the universal porin, OmpF, the first membrane protein for which meaningful 3D crystals have been obtained [2]. A crystal structure of the N-terminal translocation domain of colicin E3 complexed to

  5. Structural determinants of tobacco vein mottling virus protease substrate specificity

    SciTech Connect

    Sun, Ping; Austin, Brian P.; Tozer, Jozsef; Waugh, David

    2010-10-28

    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-{angstrom} resolution. As observed in several crystal structures of TEV protease, the C-terminus ({approx}20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by {approx}10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1{prime} position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters k{sub cat} and K{sub m} for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.

  6. Structural determinants of tobacco vein mottling virus protease substrate specificity.

    PubMed

    Sun, Ping; Austin, Brian P; Tözsér, József; Waugh, David S

    2010-11-01

    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-Å resolution. As observed in several crystal structures of TEV protease, the C-terminus (∼20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by ∼10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1' position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters k(cat) and K(m) for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.

  7. Structural determinants of tobacco vein mottling virus protease substrate specificity

    PubMed Central

    Sun, Ping; Austin, Brian P; Tözsér, József; Waugh, David S

    2010-01-01

    Tobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac-RETVRFQSD) at 1.7-Å resolution. As observed in several crystal structures of TEV protease, the C-terminus (∼20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by ∼10-fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1′ position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters kcat and Km for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease. PMID:20862670

  8. Multilevel NLTE radiative transfer in isolated atmospheric structures: implementation of the MALI-technique.

    NASA Astrophysics Data System (ADS)

    Heinzel, P.

    1995-07-01

    We have developed and extensively tested a new multilevel NLTE transfer code for isolated solar atmospheric structures (loops, prominences, spicules etc.). The code is based on the MALI approach of Rybicki & Hummer (1991, 1992) to multilevel accelerated lambda iterations. It is demonstrated that this method is fully capable of treating a difficult problem of NLTE hydrogen excitation and ionization equilibrium, provided that we linearize the preconditioned statistical equilibrium equations with respect to atomic level populations and the electron density. With this generalization of the original MALI approach, the numerical code is robust and stable. As compared to the standard linearization method of Auer & Mihalas (1969), the new MALI code designed for 1D slabs is more than one order of magnitude faster and its accuracy is quite satisfactory. We discuss several details of our implementation of the MALI technique to isolated, externally irradiated, 1D structures and finally draw some future prospects.

  9. Determination of the most closely related bacillus isolates to Bacillus anthracis by multilocus sequence typing.

    PubMed Central

    Kim, Kijeong; Cheon, Eunhee; Wheeler, Katherine E.; Youn, Youngchul; Leighton, Terrance J.; Park, Chulmin; Kim, Wonyong; Chung, Sang-In

    2005-01-01

    There have been many efforts to develop Bacillus anthracis detection assays, but the problem of false-positive results has often been encountered. Therefore, to validate an assay for B. anthracis detection, it is critical to examine its specificity with the most closely related Bacillus isolates that are available. To define the most closely related Bacillus isolates to B. anthracis in our Bacillus collections, we analyzed by multilocus sequence typing (MLST) the phylogeny of 77 closely related Bacillus isolates selected from 264 Bacillus isolates. The selection includes all the Bacillus isolates that have been shown in our previous studies to produce false-positive results by some anthrax-detection assays. The MLST phylogenetic analyses revealed that 27 of the non-B. anthracis isolates clustered within the B. anthracis clade, and four of them (three sequence types, STs) had the highest degree of genetic relatedness with B. anthracis, 18 (11 STs) had the second highest, and five (five STs) had the third highest. We anticipate that the inclusion of the 19 ST isolates when analyzing B. anthracis detection assays will prove to be useful for screening for their specificity to detect B. anthracis. PMID:16197725

  10. Antibiotic resistance determinants and genetic analysis of Salmonella enterica isolated from food in Morocco.

    PubMed

    Murgia, Manuela; Bouchrif, Brahim; Timinouni, Mohammed; Al-Qahtani, Ahmed; Al-Ahdal, Mohammed N; Cappuccinelli, Pietro; Rubino, Salvatore; Paglietti, Bianca

    2015-12-23

    Antimicrobial-resistant non-typhoidal Salmonella (NTS) are an important cause of infection in Africa, but there is a lack of information on their molecular mechanisms of resistance and epidemiology. This study contributes to fill this gap through the characterization by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), plasmid profiling and analysis of antibiotic-resistance determinants of 94 Salmonella enterica strains isolated from food in Morocco. PFGE revealed considerable heterogeneity among the strains, showing 32 pulsotypes. MLST of strains representative of the different serovars evidenced 13 sequence types (STs), three of which were newly identified (ST1694, ST1768 and ST1818) and nine not previously reported in Morocco. Thirty-four strains harbored from one to four plasmids, of IncI1 group in S. Mbandaka, IncFIIA in S. Typhimurium, IncL/M in S. Hadar and S. Blockley. For the first time in Morocco an intact Salmonella Genomic Island 1 (SGI1) carrying the resistance genes aadA2, floR, tetG, blaPSE-1 and sul1 was detected in S. Typhimurium DT104. In serovar Hadar resistance to ampicillin, tetracycline and streptomycin was associated to blaTEM-1, tetA and strA genes respectively, whereas one mutation in gyrA (Asp87Asn) and one in parC (Thr54Ser) genes conferred resistance to nalidixic acid. These findings improve the information on foodborne Salmonella in Morocco, evidencing the presence of MDR strains potentially dangerous to humans, and provide useful data for future studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Virulence and plasmidic resistance determinants of Escherichia coli isolated from municipal and hospital wastewater treatment plants.

    PubMed

    Calhau, Vera; Mendes, Catarina; Pena, Angelina; Mendonça, Nuno; Da Silva, Gabriela Jorge

    2015-06-01

    Escherichia coli is simultaneously an indicator of water contamination and a human pathogen. This study aimed to characterize the virulence and resistance of E. coli from municipal and hospital wastewater treatment plants (WWTPs) in central Portugal. From a total of 193 isolates showing reduced susceptibility to cefotaxime and/or nalidixic acid, 20 E. coli with genetically distinct fingerprint profiles were selected and characterized. Resistance to antimicrobials was determined using the disc diffusion method. Extended spectrum β-lactamase and plasmid-mediated quinolone resistance genes, phylogroups, pathogenicity islands (PAIs) and virulence genes were screened by polymerase chain reaction (PCR). CTX-M producers were typed by multilocus sequence typing. Resistance to beta-lactams was associated with the presence of bla(TEM), bla(SHV), bla(CTX-M-15) and bla(CTX-M-32). Plasmid-mediated quinolone resistance was associated with qnrA, qnrS and aac(6')-Ib-cr. Aminoglycoside resistance and multidrug-resistant phenotypes were also detected. PAI IV(536), PAI II(CFT073), PAI II(536) and PAI I(CFT073), and uropathogenic genes iutA, papAH and sfa/foc were detected. With regard to the clinical ST131 clone, it carried bla(CTX-M-15), blaTEM-type, qnrS and aac(6')-lb-cr; IncF and IncP plasmids, and virulence factors PAI IV(536), PAI I(CFT073), PAI II(CFT073), iutA, sfa/foc and papAH were identified in the effluent of a hospital plant. WWTPs contribute to the dissemination of virulent and resistant bacteria in water ecosystems, constituting an environmental and public health risk.

  12. Structural assignment of a heteropolysaccharide isolated from the gum of Cochlospermum religiosum (Katira gum).

    PubMed

    Ojha, Arnab K; Maiti, Debabrata; Chandra, Krishnendu; Mondal, Subhas; Das Sadhan K Roy, Debsankar; Ghosh, Kaushik; Islam, Syed S

    2008-05-19

    A heteropolysaccharide isolated from the gum (Katira) of Cochlospermum religiosum was found to consist of D-galactose, D-galacturonic acid and L-rhamnose in a molar ratio 2:1:3. Structural assignment of the polysaccharide was carried out using total acid hydrolysis, methylation analysis, periodate oxidation, Smith degradation and NMR studies (1H, 13C, DQF-COSY, TOCSY, NOESY, HMBC and HSQC) and the repeating unit of the polysaccharide was established as [Formula: see text].

  13. Isolation and Structural Elucidation of Chondrosterins F–H from the Marine Fungus Chondrostereum sp

    PubMed Central

    Li, Hou-Jin; Chen, Ting; Xie, Ying-Lu; Chen, Wen-Dan; Zhu, Xiao-Feng; Lan, Wen-Jian

    2013-01-01

    The marine fungus Chondrostereum sp. was collected from a soft coral of the species Sarcophyton tortuosum from the South China Sea. Three new compounds, chondrosterins F–H (1, 4 and 5), together with three known compounds, incarnal (2), arthrosporone (3), and (2E)-decene-4,6,8-triyn-1-ol (6), were isolated. Their structures were elucidated primarily based on NMR and MS data. Incarnal (2) exhibited potent cytotoxic activity against various cancer cell lines. PMID:23434797

  14. Isolation and structure elucidation of a new prenylcoumarin from Murraya paniculata var. omphalocarpa (Rutaceae).

    PubMed

    Kinoshita, Takeshi; Shimada, Motoko

    2002-01-01

    A new C-8 prenylated 5,7-dimethoxycoumarin named omphamurrayin was isolated from the leaves of Murraya paniculata var. omphalocarpa, and its structure was established as 5,7-dimethoxy-8-(1-oxo-2-senecioyl-3-methyl-3-butenyl)-2H-1-benzopyran-2-one on the basis of the spectroscopic evidence. The taxonomic status of M. paniculata var. omphalocarpa is briefly discussed, along with its synonymity to M. paniculata from the chemosystematic viewpoint.

  15. Global search algorithms in surface structure determination using photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Duncan, D. A.; Choi, J. I. J.; Woodruff, D. P.

    2012-02-01

    Three different algorithms to effect global searches of the variable-parameter hyperspace are compared for application to the determination of surface structure using the technique of scanned-energy mode photoelectron diffraction (PhD). Specifically, a new method not previously used in any surface science methods, the swarm-intelligence-based particle swarm optimisation (PSO) method, is presented and its results compared with implementations of fast simulated annealing (FSA) and a genetic algorithm (GA). These three techniques have been applied to experimental data from three adsorption structures that had previously been solved by standard trial-and-error methods, namely H2O on TiO2(110), SO2 on Ni(111) and CN on Cu(111). The performance of the three algorithms is compared to the results of a purely random sampling of the structural parameter hyperspace. For all three adsorbate systems, the PSO out-performs the other techniques as a fitting routine, although for two of the three systems studied the advantage relative to the GA and random sampling approaches is modest. The implementation of FSA failed to achieve acceptable fits in these tests.

  16. Waveguide sensor with metamaterial structure for determination of dielectric properties

    NASA Astrophysics Data System (ADS)

    Steigmann, R.; Savin, A.; Isteníková, K.; Faktorová, D.; Fabo, P.

    2017-08-01

    Microwave sensor (MWS) compared with classical sensor, offers many advantage such as rapid and nondestructive measurement. At microwave (MW) frequencies, dielectric properties of materials depend on frequency, moisture content, bulk density and temperature. MW waveguide sensors can measure properties of materials based on MW interaction with matter, and provide information about dielectric properties of investigated dielectric material, characterized with complex permittivity. The paper presents a new approach for determination of the dielectric properties of dielectric material by embedding a metamaterial (MM) structure over the aperture of waveguide sensor in order to increase the sensing properties of classical waveguide sensor. The optimal design of MM structure for waveguide sensor tuning in MW X-band is obtained. In this new approach the MM function in two ways: like a tool for increasing the sensibility of classical waveguide sensor and the tool sensitive to the dielectric properties of investigated material through the adjusted resonance frequency of designed MM units. The numerical simulation of 2D MM structure properties and experimental results for dielectric properties of dielectric materials are carried out.

  17. Structural unit of the erythrocyte cytoskeleton. Isolation and electron microscopic examination.

    PubMed

    Matsuzaki, F; Sutoh, K; Ikai, A

    1985-11-01

    We isolated a protein complex containing major cytoskeletal components from the Triton shell of bovine erythrocytes. This protein complex, which we called the 26-S complex, consisted of three major components, spectrin, band-4.1 protein and actin, and one minor component, band-4.9 protein. The molar ratio of spectrin heterodimer:band 4.1:actin was determined by sodium dodecyl sulfate (SDS) gel electrophoresis to be about 1:2:2, approximately the same as that for the Triton shell. By electron microscopic examinations of rotary-shadowed specimens, it was revealed that the 26-S complex had a "spider-like" morphology with a central core and several spectrin heterodimers radiating from it. The number of spectrin arms in the complex was not constant but was in the range between 3 and 6. The complexes with five spectrin heterodimers were the most numerous. The results showed that the 26-S complex contained on the average five spectrin heterodimers, ten band-4.1 polypeptides and ten actin monomers. As judged from the formation of oligomeric 26-S complexes through spectrin arms, the central core of the complex presumably contains band 4.1 and actin. Supporting this conclusion, the central core acted as a nucleus for actin polymerization when the 26-S complex was mixed with G-actin under an actin-polymerizing condition. The 26-S complex could form large aggregates under a certain condition that spectrin was promoted to associate from dimer to tetramer. We conclude that the 26-S complex is the structural unit of the erythrocyte cytoskeleton.

  18. FTIR spectra and conformational structure of deutero-β-alanine isolated in argon matrices

    NASA Astrophysics Data System (ADS)

    Stepanian, Stepan G.; Ivanov, Alexander Yu; Adamowicz, Ludwik

    2016-02-01

    Low temperature FTIR spectra of β-alanine-d3 isolated in argon matrices are used to determine the conformational composition of this compound. UV irradiation of the matrix samples is found to change the relative populations of the β-alanine-d3 conformers. The populations of conformers I and II with an Nsbnd D⋯O intramolecular H-bond decrease after the UV irradiation while the populations of conformer V with an N⋯Dsbnd O H-bond and conformer IV which has no intramolecular H-bonds increase. This behavior of the β-alanine-d3 conformers are used to separate the bands of the different conformers. The analysis of the experimental FTIR spectra is based on the calculated harmonic B3LYP/6-311++G(df,pd) frequencies and on the MP2/aug-cc-pVDZ frequencies calculated with a method that includes anharmonic effects. Polynomial scaling of the calculated frequencies is used to achieve better agreement with the experimental data. The observation of the wide band of the OD stretching vibration at 2201 cm-1 is a direct evidence of the presence of the β-alanine-d3 conformer V in the Ar matrix. In total ten bands of conformer V are detected. The influence of the matrix environment on the structures and the IR spectra of the β-alanine and β-alanine-d3 conformers is investigated. This involves performing calculations of the β-alanine conformers embedded in argon clusters containing from 163 to 166 argon atoms using the M06-2X and B3LYP(GD3BJ) density-functional methods. Good agreement between the calculated and the experimental matrix splitting is demonstrated.

  19. Determining Subsurface Structure From Microtremors Using a Passive Circular Array

    NASA Astrophysics Data System (ADS)

    Folger, D. S.; Doser, D. I.; Velasco, A. A.

    2005-12-01

    The amount of damage to a structure during an earthquake is related to the ground motion at that site. Therefore, it is important to study seismic waves that propagate through specific soil types to understand site response. However, active seismic surveys are susceptible to noise interference and are limited due to spatial need while boreholes are costly. We develop a method using a passive array to study Rayleigh waves from microtremors, waves originating from building appliances, cars, pedestrians walking, etc. By using everyday noises as the source, site-specific analysis can be done in urban areas without worrying about noise interference or disturbing the public with explosions or other loud active sources. The array is comprised of short period Texans, self contained geophones, which record continuously for 24 hours. Our technique differs slightly from traditional SPAC (SPatial Auto-Correlation) methods used in passive arrays. We first cross correlate time windows between two receivers then stack the correlations to determine a phase delay. Performing the correlation at different frequencies will create a dispersion curve that can be inverted for shear velocity. This approach is similar to the two-station phase delay method used in regional tomography studies at much longer periods. Stacking removes off-azimuth energy, so we do not need to assume a source direction. Preliminary results from a previous passive array survey conducted near El Paso, Texas show 1-D velocity models can be created by cross-correlating noise at various frequencies. We will conduct another survey in alluvium sands at Rio Bosque Park east of El Paso. We will validate the results with active seismic refraction and surface wave survey results as well as other geophysical techniques to determine if a passive array using microtremors is an accurate method of determining subsurface structure.

  20. Structural degradation of Thar lignite using MW1 fungal isolate: optimization studies

    USGS Publications Warehouse

    Haider, Rizwan; Ghauri, Muhammad A.; Jones, Elizabeth J.; Orem, William H.; SanFilipo, John R.

    2015-01-01

    Biological degradation of low-rank coals, particularly degradation mediated by fungi, can play an important role in helping us to utilize neglected lignite resources for both fuel and non-fuel applications. Fungal degradation of low-rank coals has already been investigated for the extraction of soil-conditioning agents and the substrates, which could be subjected to subsequent processing for the generation of alternative fuel options, like methane. However, to achieve an efficient degradation process, the fungal isolates must originate from an appropriate coal environment and the degradation process must be optimized. With this in mind, a representative sample from the Thar coalfield (the largest lignite resource of Pakistan) was treated with a fungal strain, MW1, which was previously isolated from a drilled core coal sample. The treatment caused the liberation of organic fractions from the structural matrix of coal. Fungal degradation was optimized, and it showed significant release of organics, with 0.1% glucose concentration and 1% coal loading ratio after an incubation time of 7 days. Analytical investigations revealed the release of complex organic moieties, pertaining to polyaromatic hydrocarbons, and it also helped in predicting structural units present within structure of coal. Such isolates, with enhanced degradation capabilities, can definitely help in exploiting the chemical-feedstock-status of coal.

  1. Structure activity characterization of Bordetella petrii lipid A, from environment to human isolates.

    PubMed

    Basheer, Soorej M; Bouchez, Valerie; Novikov, Alexey; Augusto, Luis A; Guiso, Nicole; Caroff, Martine

    2016-01-01

    Bordetella petrii, a facultative anaerobic species, is the only known member of the Bordetella genus with environmental origin. However it was also recently isolated from humans. The structures of the B. petrii lipid A moieties of the endotoxins were characterized here for the first time for an environmental strain and compared to that of human isolates. Characterization was achieved using chemical analyses, gas chromatography-mass spectrometry, and Matrix Assisted Laser Desorption Ionisation mass spectrometry. The analyses revealed that the different lipid A structures contain a common bisphosphorylated β-(1→6)-linked d-glucosamine disaccharide with hydroxytetradecanoic acid in amide as well at the C-3' in ester linkages. Similar to Bordetella pertussis and Bordetella bronchiseptica lipids A, the hydroxytetradecanoic acid at the C-2' position was substituted by tetradecanoic acid. Unlike B. pertussis, the hydroxytetradecanoic acid at the C-2 position was substituted with either 12:0 or 14:0 and/or their 2-OH forms. Depending on the environmental or human origin the structures differed in the length and degree of fatty acid acylation and impacted the IL-6 and TNF-α inflammatory responses tested. In one isolate we showed the presence at the C-3 position of the short-chain 10:0(3-OH), which according to our previous analyses is more characteristic of the human pathogens in the genus like B. pertussis and Bordetella parapertussis.

  2. Summary of presentation for research on social structure, agreement, and conflict in groups in extreme and isolated environments

    NASA Technical Reports Server (NTRS)

    1990-01-01

    Despite a vast amount of research, little is known concerning the effect of group structure, and individuals' understanding of that structure, on conflict in Antarctic groups. The overall objective of the research discussed is to determine the interrelationships of group structure, social cognition, and group function and conflict in isolated and extreme environments. In the two decades following WWII, a large body of research focused on the physiological, psychological, and social psychological factors affecting the functioning of individuals and groups in a variety of extreme and isolated environments in both the Arctic and Antarctic. There are two primary reasons for further research of this type. First, Antarctic polar stations are considered to be natural laboratories for the social and behavioral sciences and provide an opportunity to address certain theoretical and empirical questions concerned with agreement and con