Science.gov

Sample records for isolation structure determination

  1. Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.

    PubMed

    Gregersen, Jonas Lindholt; Mattle, Daniel; Fedosova, Natalya U; Nissen, Poul; Reinhard, Linda

    2016-04-01

    Na(+),K(+)-ATPase is responsible for the transport of Na(+) and K(+) across the plasma membrane in animal cells, thereby sustaining vital electrochemical gradients that energize channels and secondary transporters. The crystal structure of Na(+),K(+)-ATPase has previously been elucidated using the enzyme from native sources such as porcine kidney and shark rectal gland. Here, the isolation, crystallization and first structure determination of bovine kidney Na(+),K(+)-ATPase in a high-affinity E2-BeF3(-)-ouabain complex with bound magnesium are described. Crystals belonging to the orthorhombic space group C2221 with one molecule in the asymmetric unit exhibited anisotropic diffraction to a resolution of 3.7 Å with full completeness to a resolution of 4.2 Å. The structure was determined by molecular replacement, revealing unbiased electron-density features for bound BeF3(-), ouabain and Mg(2+) ions. PMID:27050261

  2. Isolation and structure determination of a lignan from the bark of Salix alba.

    PubMed

    Du, Qizhen; Jerz, Gerold; Shen, Lianqing; Xiu, Lili; Winterhalter, Peter

    2007-05-01

    A lignan, sisymbrifolin (1) found in the fruits of Solanum sisymbriflolium has been isolated from the bark extract of Salix alba (Salicaceae). Its structure was elucidated by its direct spectrum data of ESI-MS and one- and two-dimensional NMR spectroscopy for the first time.

  3. Isolation and structure determination of blepharismin, a conjugation initiating gamone in the ciliate blepharisma.

    PubMed

    Kubota, T; Tokoroyama, T; Tsukuda, Y; Koyama, H; Miyake, A

    1973-01-26

    One of the gamones (gamone II) which are effective for the induction of conjugation in Blepharisma intermedium has been isolated in a crystalline form and designated as blepharismin. From the result of chemical and spectroscopic investigations, in which x-ray crystallographic analysis was used as a definitive tool, blepharismin has been found to have the structure of calcium 3-(2'-formylamino-5'-hydroxybenzoyl)lactate.

  4. Structural determination of the polysaccharide isolated from biofilms produced by a clinical strain of Klebsiella pneumoniae.

    PubMed

    Cescutti, Paola; De Benedetto, Gianluigi; Rizzo, Roberto

    2016-07-22

    Klebsiella pneumoniae are Gram negative opportunistic pathogens producing capsular (K) polysaccharides. Seventy-seven different K antigens have been described and they are the basis for K serotyping. Capsular polysaccharides are important virulence factors and have a relevant role for the structure of biofilm communities. Nevertheless, little information is available on the polysaccharides produced in biofilm matrices by Klebsiella spp. In the present study, a clinical isolate of Klebsiella pneumoniae was grown both on cellulose membranes deposited on agar plates, where it formed an adherent biofilm, and in liquid medium, where it formed floating biofilms (flocs). Extraction and purification of the polysaccharide fraction showed that only one main carbohydrate polymer was present in both adherent biofilms and flocs. Composition and linkage analysis, Smith degradation followed by ESI-MS, 1D and 2D NMR spectroscopy revealed that the polysaccharide belong to the type K24 and has the following structure. PMID:27182661

  5. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.

    PubMed

    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

  6. 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

  7. 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

  8. 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

  9. Isolation and primary structure determination of a metallothionein from Paracentrotus lividus (Echinodermata, Echinoidea).

    PubMed

    Scudiero, R; Capasso, C; Del Vecchio-Blanco, F; Savino, G; Capasso, A; Parente, A; Parisi, E

    1995-06-01

    A low-molecular-mass zinc-binding protein was purified from the eggs of the sea urchin Paracentrotus lividus using procedures that included gel-permeation and anion-exchange chromatography followed by HPLC. The primary structure of this protein was derived from the sequences of peptide fragments obtained by digestion with trypsin and thermolysin. The reconstructed sequence showed the presence of 20 cysteinyl residues, thus resembling that of a metallothionein. The Paracentrotus protein was most similar to the metallothionein of Strongylocentrotus purpuratus, another member of the order of Echinoida, living along the coast of the Pacific Ocean. However, the presence of non-conservative amino acid substitution, together with a deletion of two residues in the Strongylocentrotus metallothionein, make the similarity scores of the two sea urchin proteins lower than that of metallothioneins from vertebrates of the same order. In addition, the present data show that sea urchin metallothioneins display no homology with metallothioneins of any other species. PMID:7599993

  10. 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

    2015-05-01

    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. PMID:26006715

  11. Isolation and structure determination of the unstable 13 2, 17 3-Cyclopheophorbide a enol from recent sediments

    NASA Astrophysics Data System (ADS)

    Ocampo, Rubén; Sachs, Julian P.; Repeta, Daniel J.

    1999-11-01

    We observed that the unstable 13 2, 17 3-cyclopheophorbide a enol is one of the most abundant pigments in recent sediments (Black Sea, Mediterranean Sea, Peru margin) and here we report its isolation and structure determination (high-performance liquid chromatography, ultraviolet-visible spectrometry, mass spectrometry, and nuclear magnetic resonance). This enol has been considered as the precusor of sedimentary chlorins and porphyrins bearing either a seven + five- or a seven-membered ring system. Analysis of sediment trap samples collected from the Peru Upwelling area revealed relatively high concentrations of 13 2, 17 3-cyclopheophorbide a enol in trap samples containing high concentrations of metabolically derived carotenoid transformation products. The abundance of 13 2, 17 3-cyclopheophorbide a enol in sediment trap samples and recent sediments suggests that formation of an exocyclic seven-membered ring is a major diagenetic pathway for chlorophylls. Biologically mediated transformations of chlorophylls can therefore yield products not included in the classical Triebs degradation scheme for cyclic tetrapyrroles.

  12. MM 55266 and MM 55268, glycopeptide antibiotics produced by a new strain of Amycolatopsis. Isolation, purification and structure determination.

    PubMed

    Box, S J; Coates, N J; Davis, C J; Gilpin, M L; Houge-Frydrych, C S; Milner, P H

    1991-08-01

    Two novel glycopeptide antibiotics MM 55266 and MM 55268 containing fatty acid acyl functions, and of molecular formula C86H89N8O35Cl5 and C87H91N8O35Cl5, respectively, have been isolated and identified from a complex produced by Amycolatopsis sp. NCIB 40089. Fermentation conditions for their production, and methods for their isolation are described. Structures have been deduced by use of COSY and NOE NMR techniques and supported by chemical degradation studies. Both glycopeptides possessed good antibacterial activity against Gram-positive organisms. PMID:1917694

  13. Isolation and structure determination of obyanamide, a novel cytotoxic cyclic depsipeptide from the marine cyanobacterium Lyngbya confervoides.

    PubMed

    Williams, Philip G; Yoshida, Wesley Y; Moore, Richard E; Paul, Valerie J

    2002-01-01

    Obyanamide (1) was isolated from a variety of the marine cyanobacterium Lyngbya confervoides collected in Saipan, Commonwealth of the Northern Mariana Islands. Gross structure elucidation of this novel cyclic depsipeptide relied on extensive application of 2D NMR techniques. The absolute stereochemistry was deduced by chiral chromatography of the hydrolysis products and comparison with authentic and synthetic standards. Obyanamide (1) was cytotoxic against KB cells with an IC(50) of 0.58 microg/mL.

  14. Determination by NMR spectroscopy of the structure and conformational features of the enterobacterial common antigen isolated from Escherichia coli.

    PubMed

    Bruix, M; Jiménez-Barbero, J; Cronet, P

    1995-08-25

    Complete 1H and 13C spectrum of a polysaccharide isolated from Escherichia coli, which is the major component of the enterobacterial common antigen, has been analyzed through two-dimensional nuclear magnetic resonance spectroscopy. In addition, distance constraints from NOESY and ROESY experiments have been combined with molecular dynamic simulations to determine its major conformation in water solution. Data resulting from both free dynamic simulations and restrained dynamic simulations have been compared with experimental data and discussed.

  15. Bioactive Metabolites Produced by Pseudonocardia endophytica VUK-10 from Mangrove Sediments: Isolation, Chemical Structure Determination and Bioactivity.

    PubMed

    Mangamuri, Usha Kiranmayi; Vijayalakshmi, Muvva; Poda, Sudhakar; Manavathi, Bramanandam; Bhujangarao, Ch; Venkateswarlu, Y

    2015-05-01

    Chemical investigation of the actinobacterial isolate Pseudonocardia endophytica VUK-10 has led to the segregation of two known bioactive compounds, namely 4-(2-acetamidoethyl) phenyl acetate and 4-((1, 4-dioxooctahydropyrrolo [1, 2-a] pyrazin-3-yl) methyl) phenyl acetate. The strain was isolated from a sediment sample of the Nizampatnam mangrove ecosystem, south coastal Andhra Pradesh, India. The chemical structure of the active compounds was established on the basis of spectroscopic analysis, including (1)H NMR and (13)C NMR spectroscopies, FTIR, and EIMS. The antimicrobial and cytotoxic activities of the bioactive compounds produced by the strain were tested against opportunistic and pathogenic bacteria and fungi and on MDA-MB-231, OAW, HeLa, and MCF-7 cell lines. The compounds exhibited antimicrobial activities against gram-positive and gram-negative bacteria and fungi and also showed potent cytotoxic activity against MDA-MB-231, OAW, HeLa, and MCF-7 cell lines. This is the first example for this class of bioactive compounds isolated from Pseudonocardia of mangrove origin. PMID:25418482

  16. Bioactive Metabolites Produced by Pseudonocardia endophytica VUK-10 from Mangrove Sediments: Isolation, Chemical Structure Determination and Bioactivity.

    PubMed

    Mangamuri, Usha Kiranmayi; Vijayalakshmi, Muvva; Poda, Sudhakar; Manavathi, Bramanandam; Bhujangarao, Ch; Venkateswarlu, Y

    2015-05-01

    Chemical investigation of the actinobacterial isolate Pseudonocardia endophytica VUK-10 has led to the segregation of two known bioactive compounds, namely 4-(2-acetamidoethyl) phenyl acetate and 4-((1, 4-dioxooctahydropyrrolo [1, 2-a] pyrazin-3-yl) methyl) phenyl acetate. The strain was isolated from a sediment sample of the Nizampatnam mangrove ecosystem, south coastal Andhra Pradesh, India. The chemical structure of the active compounds was established on the basis of spectroscopic analysis, including (1)H NMR and (13)C NMR spectroscopies, FTIR, and EIMS. The antimicrobial and cytotoxic activities of the bioactive compounds produced by the strain were tested against opportunistic and pathogenic bacteria and fungi and on MDA-MB-231, OAW, HeLa, and MCF-7 cell lines. The compounds exhibited antimicrobial activities against gram-positive and gram-negative bacteria and fungi and also showed potent cytotoxic activity against MDA-MB-231, OAW, HeLa, and MCF-7 cell lines. This is the first example for this class of bioactive compounds isolated from Pseudonocardia of mangrove origin.

  17. 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

  18. 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. PMID:26599487

  19. Isolation and structural determination of three peptides from the insect Locusta migratoria. Identification of a deoxyhexose-linked peptide.

    PubMed

    Nakakura, N; Hietter, H; Van Dorsselaer, A; Luu, B

    1992-02-15

    We have isolated three novel peptides from the aqueous extract of the pars intercerebralis of male and female adults of the insect Locusta migratoria. After extensive HPLC purification, the peptides were characterised by automated Edman degradation and electrospray mass spectrometry: one is a 35-residue peptide (3752.3 +/- 1.1 Da) containing six cysteines involved in three intramolecular disulfide bridges, the second is a 36-residue peptide (3919.2 +/- 0.9 Da), also cross-linked by three intramolecular disulfide bridges. This second peptide is post-translationally modified by a single fucose moiety, which was identified by gas chromatography coupled to mass spectrometry. These two peptides show a strong sequence similarity. Additionally, they were also found in larger amounts in the fat body of Locusta; this finding raises the question of their exact site of synthesis. The third peptide (5776.3 +/- 0.9 Da), a 54-residue peptide cross-linked by six intramolecular disulfide bridges, is structurally related to the two other peptides, but to a lesser extent. Mass spectrometry has shown that all the cysteines within these three peptides are involved in intramolecular disulfide bridges; however, the location of these bridges is not yet established and is currently being investigated. A computer search of sequence data banks did not reveal any significant similarity of these three peptides with other known proteins. PMID:1740125

  20. 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.

  1. A novel human erythrocyte glycosylphosphatidylinositol (GPI)-anchored glycoprotein ACA. Isolation, purification, primary structure determination, and molecular parameters of its lipid structure.

    PubMed

    Becker Kojić, Zorica A; Terness, Peter

    2002-10-25

    A method has been elaborated to isolate and purify up to homogeneity a novel membrane glycoprotein containing a glycosyl-phosphatidylinositol (GPI) anchor by means of salting out with ammonium sulfate (40-80% saturation), followed by preparative SDS-PAGE, chromatography and acetone precipitation. The preparation obtained was homogeneous upon electrophoresis in the presence of 0.1% SDS after reduction with 2-mercaptoethanol. It is protein-soluble at its isoelectrical point (pH 5.5) with molecular mass of 65,000 daltons. The isolated protein is linked to the membrane via glycosyl-phosphatidylinositol susceptible to cleavage by purified phospholipase C. The hydrophobic portion of the glycolipid membrane anchor of the protein was radiolabeled with the photoactivated reagent 3-(trifluoromethyl)-3-(m-[(125)I]iodophenyl)diazirine and hydrolyzed with glycosyl-phosphatidylinositol-specific phospholipase C, followed by enzymatic deacetylation of the remaining lipid. Thin-layer chromatography showed that the generated radiolabeled fragment migrates with the same mobility as that of variant surface glycoprotein (VSG), obtained in the same manner. In this study we describe a novel erythrocyte membrane GPI-linked protein with the structural feature of an anchor that, in contrast to other GPI-linked erythrocyte proteins, has a non-acetylated inositol ring and diacylglycerol rather than alkyl-acyl glycerol as a lipid tail of the anchor.

  2. Determining the invariant structure elements of the HIV-1 variable V3 loops: insight into the HIV-MN and HIV-Haiti isolates.

    PubMed

    Andrianov, Alexander M

    2008-10-01

    The computer approaches that combined the 3D protein structure modeling with the mathematical statistics methods were used to compute the NMR-based 3D structures of the HIV-1 gp120 V3 loop for the HIV-MN and HIV-Haiti isolates in water as well as to compare their conformational characteristics with the purpose of determining the structure elements common for the two virus modifications. As a result, the variability of the amino acid sequence was found to stimulate the considerable structural rearrangements of the V3 loop. However, despite this fact, one functionally crucial stretch of V3 and a greater portion of its residues were shown to preserve the conformations in the viral strains of interest. To reveal the structural motifs and individual amino acids giving rise to the close conformations in the HIV-MN and HIV-Haiti V3 loops regardless of the sequence and environment variability, the simulated structures were collated with those deciphered previously in terms of NMR data in a water/trifluoroethanol mixed solvent. The structure elements and single residues of V3 residing in its biologically significant sites and keeping the conformations in all of the cases at question are considered to be the promising targets for anti-AIDS drugs studies. In this context, the structurally inflexible motifs of V3 presenting the weak units in the virus protection system may be utilized as the most convenient landing-places for molecular docking of the V3 loop and ligand structures followed by selecting chemical compounds suitable as a basis for the design of safe and effective antiviral agents. PMID:18597546

  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. 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.

  6. Active isolation of vibrations with adaptive structures

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    Vibration transmission in structures is controlled by means of a technique which employs distributed arrays of piezoelectric transducers bonded to the supporting structure. Distributed PVDF piezoelectric strips are employed as error sensors, and a two-channel feedforward adaptive LMS algorithm is used for minimizing error signals and thereby controlling the structure. A harmonic force input excites a thick plate, and a receiving plate is configured with three pairs of piezoelectric actuators. Modal analyses are performed to determine the resonant frequencies of the system, and a scanning laser vibrometer is used to study the shape of the response of the receiving plate during excitation with and without the control algorithm. Efficient active isolation of the vibrations is achieved with modal suppression, and good control is noted in the on-resonance cases in which increased numbers of PVDF sensors and piezoelectric actuators are employed.

  7. Membrane structure in isolated and intact myelins.

    PubMed Central

    Inouye, H; Karthigasan, J; Kirschner, D A

    1989-01-01

    The biochemical composition of myelin and the topology of its constituent lipids and proteins are typically studied using membranes that have been isolated from whole, intact tissue using procedures involving hypotonic shock and sucrose density gradient centrifugation. To what extent, however, are the structure and intermembrane interactions of isolated myelin similar to those of intact myelin? We have previously reported that intact and isolated myelins do not always show identical myelin periods, indicating a difference in membrane-membrane interactions. The present study addresses the possibility that this is due to altered membrane structure. Because x-ray scattering from isolated myelin sometimes consists of overlapping Bragg reflections or is continuous, we developed nonlinear least squares procedures for analyzing the total intensity distribution after film scaling, background subtraction, and Lorentz correction. We calculated electron density profiles of isolated myelin for comparison with membrane profiles from intact myelin. The change in the width of the extracellular space and the relative invariance of the cytoplasmic space as a function of pH and ionic strength that we previously found for intact nerve was largely paralleled by isolated myelin. There were two exceptions: isolated CNS myelin was resistant to swelling under all conditions, and isolated PNS myelin in hypotonic saline showed indefinite swelling at the extracellular apposition. However, electron density profiles of isolated myelins, calculated to 30 A resolution, did not show any major change in structure compared with intact myelin that could account for the differences in interactions. PMID:2752082

  8. 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.

  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. 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.

  11. Isolation and Structure Elucidation of Pentahydroxyscirpene, a Trichothecene Fusarium Mycotoxin

    PubMed Central

    2013-01-01

    Pentahydroxyscirpene, a novel trichothecene-type compound, was isolated from Fusarium-inoculated rice. The structure of pentahydroxyscirpene was elucidated by 1D and 2D NMR spectroscopy and X-ray single-crystal diffraction. The conformation in solution was determined by NOESY experiments supported by quantum chemical calculations. In vitro toxicity tests showed that pentahydroxyscirpene inhibits protein synthesis as do other trichothecenes. PMID:24367932

  12. Crystal structure determination of Efavirenz

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Needle-shaped single crystals of the title compound, C14H9ClF3NO2, 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.

  13. Determinants and Polynomial Root Structure

    ERIC Educational Resources Information Center

    De Pillis, L. G.

    2005-01-01

    A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. Structural determinants of GAD antigenicity.

    PubMed

    Arafat, Yasir; Fenalti, Gustavo; Whisstock, James C; Mackay, Ian R; Garcia de la Banda, Maria; Rowley, Merrill J; Buckle, Ashley M

    2009-12-01

    Our aim was to ascertain structural determinants of autoantigenicity based on the model of the diabetes autoantigen glutamic acid decarboxylase 65 kDa isoform (GAD65) in comparison with that of the non-autoantigenic isoform GAD67. This difference exists despite the two isoforms having the same fold and high sequence identity. Autoantibodies to GAD65 precede the development of type 1 diabetes and are clinical markers of this and certain neural autoimmune diseases. To date, epitope mapping has been based on particular amino acid differences between the two isoforms, and there is no explanation as to why autoantibodies that react with GAD65 only infrequently cross-react with GAD67. To characterize each isoform of the enzyme and gain insights into their contrasting autoantigenic properties, we have used the recently determined crystal structures of GAD65 and GAD67 to compare their structure, hydrophobicity, electrostatics, flexibility and physiochemical properties. The results revealed striking differences which appear almost exclusively at the C-terminal domain of the isoforms. Whereas GAD65 displayed a highly charged and flexible C-terminal domain containing numerous patches of high electrostatic and solvation energies, these characteristics were absent in the GAD67 molecule. Additionally, analysis indicated potential N-terminal and PLP domain binding sites surrounding the C-terminal domain of GAD65, a major region of autoantigenic activity, but not of GAD67. These features agree with good accuracy with published epitope-mapping data. Our analysis suggests that the high flexibility and charge of GAD65 in the C-terminal domain is coupled with the mobility of its catalytic loop, a property that is absolutely required for its enzymatic function. Thus, the structural features that distinguish GAD65 from GAD67 as a B cell autoantigen are related to functional requirements for its enzymatic mechanism. This could well apply to the various other enzyme autoantigens and, if

  19. 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.

  20. 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.

  1. 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

  2. Purification and primary structure determination of human lysosomal dipeptidase.

    PubMed

    Dolenc, Iztok; Mihelic, Marko

    2003-02-01

    The lysosomal metallopeptidase is an enzyme that acts preferentially on dipeptides with unsubstituted N- and C-termini. Its activity is highest in slightly acidic pH. Here we describe the isolation and characterization of lysosomal dipeptidase from human kidney. The isolated enzyme has the amino-terminal sequence DVAKAIINLAVY and is a homodimer with a molecular mass of 100 kDa. So far no amino acid sequence has been determined for this metallopeptidase. The complete primary structure as deduced from the nucleotide sequence revealed that the isolated dipeptidase is similar to blood plasma glutamate carboxypeptidase.

  3. Structure determination of transient transcription complexes.

    PubMed

    Cramer, Patrick

    2016-08-15

    The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects. PMID:27528766

  4. 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

    2016-10-01

    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.

  5. Structural confirmation of novel oligosaccharides isolated from sugar beet molasses.

    PubMed

    Abe, Tatsuya; Kikuchi, Hiroto; Aritsuka, Tsutomu; Takata, Yusuke; Fukushi, Eri; Fukushi, Yukiharu; Kawabata, Jun; Ueno, Keiji; Onodera, Shuichi; Shiomi, Norio

    2016-07-01

    Eleven oligosaccharides were isolated from sugar beet molasses using carbon-Celite column chromatography and HPLC. The constituent sugars and linkage positions were determined using methylation analysis, MALDI-TOF-MS, and NMR measurements. The configurations of isolated oligosaccharides were confirmed based on detailed NMR analysis. Based on our results, three of the 11 oligosaccharides were novel. PMID:26920296

  6. Wire rope isolators for vibration isolation of equipment and structures - A review

    NASA Astrophysics Data System (ADS)

    Balaji, P. S.; Rahman, M. E.; Moussa, Leblouba; Lau, H. H.

    2015-04-01

    Vibrations and shocks are studied using various techniques and analyzed to predict their detrimental effect on the equipment and structures. In cases, where the effects of vibration become unacceptable, it may cause structural damage and affect the operation of the equipment. Hence, adding a discrete system to isolate the vibration from source becomes necessary. The Wire Rope Isolator (WRI) can be used to effectively isolate the system from disturbing vibrations. The WRI is a type of passive isolator that exhibits nonlinear behavior. It consists of stranded wire rope held between two metal retainer bars and the metal wire rope is made up of individual wire strands that are in frictional contact with each other, hence, it is a kind of friction-type isolator. This paper compiles the research work on wire rope isolators. This paper presents the research work under two categories, namely monotonic and cyclic loading behaviors of WRI. The review also discusses the different terminologies associated with vibration isolation system and highlights the comparison between various isolation systems.

  7. 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

  8. 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

  9. Structural determinants of hospital closure.

    PubMed

    Longo, D R; Chase, G A

    1984-05-01

    In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.

  10. 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

  11. Mitochondrial Structure and Function Are Disrupted by Standard Isolation Methods

    PubMed Central

    Picard, Martin; Taivassalo, Tanja; Ritchie, Darmyn; Wright, Kathryn J.; Thomas, Melissa M.; Romestaing, Caroline; Hepple, Russell T.

    2011-01-01

    Mitochondria regulate critical components of cellular function via ATP production, reactive oxygen species production, Ca2+ handling and apoptotic signaling. Two classical methods exist to study mitochondrial function of skeletal muscles: isolated mitochondria and permeabilized myofibers. Whereas mitochondrial isolation removes a portion of the mitochondria from their cellular environment, myofiber permeabilization preserves mitochondrial morphology and functional interactions with other intracellular components. Despite this, isolated mitochondria remain the most commonly used method to infer in vivo mitochondrial function. In this study, we directly compared measures of several key aspects of mitochondrial function in both isolated mitochondria and permeabilized myofibers of rat gastrocnemius muscle. Here we show that mitochondrial isolation i) induced fragmented organelle morphology; ii) dramatically sensitized the permeability transition pore sensitivity to a Ca2+ challenge; iii) differentially altered mitochondrial respiration depending upon the respiratory conditions; and iv) dramatically increased H2O2 production. These alterations are qualitatively similar to the changes in mitochondrial structure and function observed in vivo after cellular stress-induced mitochondrial fragmentation, but are generally of much greater magnitude. Furthermore, mitochondrial isolation markedly altered electron transport chain protein stoichiometry. Collectively, our results demonstrate that isolated mitochondria possess functional characteristics that differ fundamentally from those of intact mitochondria in permeabilized myofibers. Our work and that of others underscores the importance of studying mitochondrial function in tissue preparations where mitochondrial structure is preserved and all mitochondria are represented. PMID:21512578

  12. Surface structure determines dynamic wetting

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    Dynamic wetting, the spontaneous spreading process after droplet contacts a solid surface, is important in various engineering processes, such as in printing, coating, and lubrication. In the recent years, experiments and numerical simulations have greatly progressed the understanding in the dynamic wetting particularly on ``flat'' substrates. To gain further insight into the governing physics of the dynamic wetting, we perform droplet-wetting experiments on microstructured surfaces, just a few micrometers in size, with complementary numerical simulations, and investigate the dependence of the spreading rate on the microstructure geometries and fluid properties. We reveal that the influence of microstructures 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. The systematic study is also of practical importance since structures and roughness are omnipresent and their influence on spreading rate would give us additional degrees of freedom to control the dynamic wetting. This work was financially supported in part by, the Japan Society for the Promotion of Science (J.W., J.C., and J.S) and Swedish Governmental Agency for Innovation Systems (M.D.-Q. and G.A.).

  13. 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

  14. Isolation and structure elucidation of a new antifungal and antibacterial antibiotic produced by Streptomyces sp. 201.

    PubMed

    Bordoloi, G N; Kumari, B; Guha, A; Bordoloi, M; Yadav, R N; Roy, M K; Bora, T C

    2001-08-01

    An antibacterial and antifungal antibiotic was isolated from the culture filtrate of Streptomyces sp. 201, and its structure was determined as 2-methyl-heptyl isonicotinate by extensive use of NMR spectroscopy. The compound exhibited marked antimicrobial activity against Bacillus subtilis, Shigella sp., Klebsiella sp., E. coli, Proteus mirabilis, and the pathogenic fungi, Fusarium moniliforme, F. semitectum, F. oxysporum, F. solani and Rhizoctonia solani.

  15. 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.

  16. Isolation, structural assignment, and total synthesis of barmumycin.

    PubMed

    Lorente, Adriana; Pla, Daniel; Cañedo, Librada M; Albericio, Fernando; Alvarez, Mercedes

    2010-12-17

    Barmumycin was isolated from an extract of the marine actinomycete Streptomyces sp. BOSC-022A and found to be cytotoxic against various human tumor cell lines. On the basis of preliminary one- and two-dimensional (1)H and (13)C NMR spectra, the natural compound was initially assigned the structure of macrolactone-type compound 1, which was later prepared by two different routes. However, major spectroscopic differences between isolated barmumycin and 1 led to revision of the proposed structure as E-16. On the basis of the synthesis of this new compound, and subsequent spectroscopic comparison of it to an authentic sample of barmumycin, the structure of the natural compound was indeed confirmed as that of E-16.

  17. RNA Secondary Structure Determination by NMR.

    PubMed

    Chen, Jonathan L; Bellaousov, Stanislav; Turner, Douglas H

    2016-01-01

    Dynamic programming methods for predicting RNA secondary structure often use thermodynamics and experimental restraints and/or constraints to limit folding space. Chemical mapping results typically restrain certain nucleotides not to be in AU or GC pairs. Two-dimensional nuclear magnetic resonance (NMR) spectra can reveal the order of AU, GC, and GU pairs in double helixes. This chapter describes a program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS), that constrains possible secondary structures on the basis of the NMR determined order and 5'-3' direction of AU, GC, and GU pairs in helixes. NAPSS-CS minimally requires input of the order of base pairs as determined from nuclear Overhauser effect spectroscopy (NOESY) of imino protons. The program deduces the 5'-3' direction of the base pairs if certain chemical shifts are also input. Secondary structures predicted by the program provide assignments of input chemical shifts to particular nucleotides in the sequence, thus facilitating an important step for determination of the three dimensional structure by NMR. The method is particularly useful for revealing pseudoknots and an example is provided. The method may also allow determination of secondary structures when a sequence folds into two structures that exchange slowly. PMID:27665599

  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. Distributed structure determination at the JCSG

    SciTech Connect

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

    2011-04-01

    The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures. 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.

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

    PubMed

    Coura, Fernanda Morcatti; 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

  2. 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

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

    PubMed

    Coura, Fernanda Morcatti; 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.

  4. 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

  5. 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.

  6. 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.…

  7. 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.

  8. Crystal structure determination of anti-DNA Fab A52.

    PubMed

    Stanfield, Robyn L; Eilat, Dan

    2014-08-01

    A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

  9. 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

  10. Accurate SHAPE-directed RNA structure determination

    PubMed Central

    Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.

    2009-01-01

    Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441

  11. 76 FR 31611 - Biennial Determination of the Waste Isolation Pilot Plant's Compliance with Applicable Federal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-01

    .... SUMMARY: Based on documentation submitted by the U.S. Department of Energy (DOE) for the Waste Isolation... AGENCY Biennial Determination of the Waste Isolation Pilot Plant's Compliance with Applicable Federal.... The Secretary of Energy was notified of the determination via a letter from EPA Administrator Lisa...

  12. 78 FR 34380 - Biennial Determination of the Waste Isolation Pilot Plant's Compliance With Applicable Federal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-07

    .... SUMMARY: Based on documentation submitted by the U.S. Department of Energy (DOE) for the Waste Isolation... AGENCY Biennial Determination of the Waste Isolation Pilot Plant's Compliance With Applicable Federal.... The Secretary of Energy was notified of the determination via a letter from EPA Acting...

  13. 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.

  14. Structure of mutant human oncogene protein determined

    SciTech Connect

    Baum, R.

    1989-01-16

    The protein encoded by a mutant human oncogene differs only slightly in structure from the native protein that initiates normal cell division, a finding that may complicate efforts to develop inhibitors of the mutant protein. Previously, the x-ray structure of the protein encoded by the normal c-Ha-ras gene, a protein believed to signal cells to start or stop dividing through its interaction with guanosine triphosphate (GTP), was reported. The structure of the protein encoded by a transforming c-Ha-ras oncogene, in which a valine codon replaces the normal glycine codon at position 12 in the gene, has now been determined. The differences in the structures of the mutant and normal proteins are located primarily in a loop that interacts with the /beta/-phosphate of a bound guanosine diphosphate (GDP) molecule.

  15. Structural features determining thermal adaptation of esterases.

    PubMed

    Kovacic, Filip; Mandrysch, Agathe; Poojari, Chetan; Strodel, Birgit; Jaeger, Karl-Erich

    2016-02-01

    The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.

  16. Oligosaccharides in goat milk: structure, health effects and isolation.

    PubMed

    Kiskini, A; Difilippo, E

    2013-11-03

    Oligosaccharides have been widely recognized for their prebiotic and anti-infective properties. Among the different types of mammalian milk, the one of humans is the richest source of naturally derived oligosaccharides. However, their use as a basis for functional foods is hampered, due to their structural complexity, which in turn makes their re-synthesis extremely difficult. Thus, oligosaccharides from other sources have to be used. In this sense, goat milk constitutes a very appealing candidate, as it contains the highest amount of oligosaccharides among domestic animals, while goat milk oligosaccharides show significant similarities to human milk oligosaccharides from a structural point of view. Studies on goat milk oligosaccharides are scant, and more data is required in order to provide solid clinical evidence of their beneficial effects on humans. The aim of this review is to collect and present the main research findings on goat milk oligosaccharides structure, health effects and isolation.

  17. Optical investigation of functional structures in isolated perfused pig heart

    NASA Astrophysics Data System (ADS)

    Rauh, Robert; Boehnert, Markus; Mahlke, Christine; Kessler, Manfred D.

    2000-11-01

    Light scattering in tissue of mammals and humans is affected by subcellular structures. Since these structures correlate well with the status of cells and tissue, light scattering seems to be ideal for monitoring of functional tissue state. By use of EMPHO SSK Oxyscan we investigated functional parameters in a novel kind of isolated perfused pig heart model. In this perfusion model we use organs obtained by the local slaughterhouse that are reanimated at our institute by application of a heart-lung machine. By creating 3D-images of tissue scattering we found an interesting relation between anatomical structures of myocardium and the 3D-images. Additionally, we detected coherence between backscattered light intensity and functional tissue status. Furthermore, we got a sight into the redox state of cytochrome aa3, b and c by creating difference spectra. We believe that this new kind of tissue imaging method will give us the opportunity to get new insights into myocardial function.

  18. Crystal structure of methane oxidation enzyme determined

    SciTech Connect

    Baum, R.

    1994-01-10

    A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.

  19. Amino acid sequence of a protease inhibitor isolated from Sarcophaga bullata determined by mass spectrometry.

    PubMed

    Papayannopoulos, I A; Biemann, K

    1992-02-01

    The amino acid sequence of a protease inhibitor isolated from the hemolymph of Sarcophaga bullata larvae was determined by tandem mass spectrometry. Homology considerations with respect to other protease inhibitors with known primary structures assisted in the choice of the procedure followed in the sequence determination and in the alignment of the various peptides obtained from specific chemical cleavage at cysteines and enzyme digests of the S. bullata protease inhibitor. The resulting sequence of 57 residues is as follows: Val Asp Lys Ser Ala Cys Leu Gln Pro Lys Glu Val Gly Pro Cys Arg Lys Ser Asp Phe Val Phe Phe Tyr Asn Ala Asp Thr Lys Ala Cys Glu Glu Phe Leu Tyr Gly Gly Cys Arg Gly Asn Asp Asn Arg Phe Asn Thr Lys Glu Glu Cys Glu Lys Leu Cys Leu.

  20. Isolation of extracellular vesicles: Determining the correct approach (Review).

    PubMed

    Szatanek, Rafal; Baran, Jarek; Siedlar, Maciej; Baj-Krzyworzeka, Monika

    2015-07-01

    The discovery of extracellular vesicles (EVs) has revised the interpretation of intercellular communication. It is now well established that EVs play a significant role in coagulation, inflammation, cancer and stem cell renewal and expansion. Their release presents an intriguing, transporting/trafficking network of biologically active molecules, which are able to reach and modulate the function/behavior of the target cells in a variety of ways. Moreover, the presence of EVs in various body fluids points to their potential for use as biomarkers and prognostic indicators in the surveillance/monitoring of a variety of diseases. Although vast knowledge on the subject of EVs has accumulated over the years, there are still fundamental issues associated with the correct approach for their isolation. This review comprises the knowledge on EV isolation techniques that are currently available. The aim of this reveiw was to make both experienced researchers and newcomers to the field aware that different types of EVs require unique isolation approaches. The realization of this 'uniqueness' is the first step in the right direction for the complete assessment of EVs. PMID:25902369

  1. Isolation of extracellular vesicles: Determining the correct approach (Review).

    PubMed

    Szatanek, Rafal; Baran, Jarek; Siedlar, Maciej; Baj-Krzyworzeka, Monika

    2015-07-01

    The discovery of extracellular vesicles (EVs) has revised the interpretation of intercellular communication. It is now well established that EVs play a significant role in coagulation, inflammation, cancer and stem cell renewal and expansion. Their release presents an intriguing, transporting/trafficking network of biologically active molecules, which are able to reach and modulate the function/behavior of the target cells in a variety of ways. Moreover, the presence of EVs in various body fluids points to their potential for use as biomarkers and prognostic indicators in the surveillance/monitoring of a variety of diseases. Although vast knowledge on the subject of EVs has accumulated over the years, there are still fundamental issues associated with the correct approach for their isolation. This review comprises the knowledge on EV isolation techniques that are currently available. The aim of this reveiw was to make both experienced researchers and newcomers to the field aware that different types of EVs require unique isolation approaches. The realization of this 'uniqueness' is the first step in the right direction for the complete assessment of EVs.

  2. Membrane protein structure determination - the next generation.

    PubMed

    Moraes, Isabel; Evans, Gwyndaf; Sanchez-Weatherby, Juan; Newstead, Simon; Stewart, Patrick D Shaw

    2014-01-01

    The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.

  3. Structure and synthesis of a unique isonitrile lipid isolated from the marine mollusk Actinocyclus papillatus.

    PubMed

    Manzo, Emiliano; Carbone, Marianna; Mollo, Ernesto; Irace, Carlo; Di Pascale, Antonio; Li, Yan; Ciavatta, Maria Letizia; Cimino, Guido; Guo, Yue-Wei; Gavagnin, Margherita

    2011-04-15

    The first chemical study of an Actinocyclidae nudibranch, Actinocyclus papillatus, resulted in the isolation of (-)-actisonitrile (1), a lipid based on a 1,3-propanediol ether skeleton. The structure was established by spectroscopic methods, whereas the absolute configuration of the chiral center was determined by comparing the optical properties of natural actisonitrile with those of (+)- and (-)-synthetic enantiomers, opportunely prepared. Both (-)- and (+)-actisonitrile were tested in preliminary in vitro cytotoxicity bioassays on tumor and nontumor mammalian cells. PMID:21405058

  4. Isolation and structural elucidation of a new cyclohexenone compound from Lasiodiplodia theobromae.

    PubMed

    Kitaoka, Naoki; Nabeta, Kensuke; Matsuura, Hideyuki

    2009-08-01

    A new cyclohexenone compound was isolated as a mixture of enantiomers from a culture filtrate of Lasiodiplodia theobromae. The relative structure was determined to be 4,5-dihydroxy-3-methyl-cyclohex-2-enone on the basis of MS, (1)H-NMR, and (13)C-NMR spectroscopic analyses, including 2D-NMR experiments. Resolution of the enantiomers was conducted by a coupling reaction with (S)-MTPA-Cl followed by HPLC separation. PMID:19661717

  5. Isolation and structural analysis of ajugose from Vigna mungo L.

    PubMed

    Kotiguda, Girigowda; Peterbauer, Thomas; Mulimani, Veerappa H

    2006-09-01

    The hexasaccharide ajugose, alpha-D-galactopyranosyl-(1-->6)-alpha-D-galactopyranosyl-(1-->6)-O-alpha-D-galactopyranosyl-(1-->6)-alpha-D-galactopyranosyl-(1-->6)-alpha-D-glucopyranosyl-(1<-->2)-beta-D-fructofuranoside, generally uncommon in legumes, was detected in the seeds of Vigna mungo L. by TLC and paper chromatography. Ajugose was then isolated by silica gel chromatography and its structure was established by acid and enzymatic hydrolysis, fast atom bombardment mass spectrometry and both one- and two-dimensional 1H and 13C NMR techniques.

  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. [Isolation and determination of silver-resistant bacteria plasmids].

    PubMed

    Li, Junmin; Jin, Zexin

    2006-02-01

    Through the enrichment of the active mud obtained from three chemical plants and the domestication with different concentration Ag+ solution, thirty bacteria strains with silver (Ag+)-resistance were isolated, among which, the highest Ag+ -resistant concentration was 80 mg x ml(-1). The plasmids in these bacteria were extracted, with the detection rate of 76.67%. The elimination rate of the plasmid in HAg4 bacteria was 98.75% by 40 mmol x L(-1) sodium benzoate, and 77.78% by 350 microg x ml(-1) acridine orange. It was suggested that the Ag+ -resistance of bacteria was highly correlated with their plasmids.

  8. 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.

  9. 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.

  10. Intraspecific variability of Bipolaris sorokiniana isolates determined by random-amplified polymorphic DNA (RAPD).

    PubMed

    de Oliveira, Andréia M R; Matsumura, Aida T S; Prestes, Ariano M; Van Der Sand, Sueli T

    2002-01-01

    Isolates of Bipolaris sorokiniana were analyzed by random-amplified polymorphic DNA (RAPD) techniques to determine the amount of intraspecific genetic variability and to study host-pathogen interactions. Ten isolates originated from different regions of Brazil were examined. Plants of the wheat cultivars BR8, BH1146 (original host) and IAC-5 Maringá, classified as resistant, moderately resistant or susceptible to B. sorokiniana, respectively, were inoculated with these 10 isolates. Twenty-seven isolates were recovered from these cultivars and were analyzed by RAPD assay and compared to the RAPD of the original 10 isolates. According to the RAPD profiles there was a high level of genetic variability among the isolates. We detected 69 polymorphic fragments, ranging from 1.6 to 0.54 kb, in the original 10 isolates; 57 fragments with sizes between 1.98 and 0.38 kb from the isolates recovered from BH1146; 47 polymorphic bands, ranging from 1.96-0.54 kb, were detected in the isolates from BR8 and 32 fragments between 1.98 and 0.42 kb in isolates were recovered from IAC-5 Maringá. The number of polymorphic fragments varied, even for the same isolate, when the isolates were recovered from different cultivar hosts.

  11. 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

  12. 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

    2016-01-01

    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.

  13. 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

    2016-01-01

    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. PMID:26673855

  14. A procedure for the isolation and determination of deoxyribose derivatives

    PubMed Central

    Pestell, R. Q. W.; Woodland, H. R.

    1972-01-01

    A method of determining deoxyribose derivatives in biological material is described. It has high sensitivity, and is particularly useful in that it can be applied to a large range of tissues for which the other available assays are unsuitable. This is because the method is applicable to complex mixtures of nucleotides in which such substances as ribonucleotides are present in very large excess over deoxyribonucleotides, and it is not necessary to equilibrate the nucleotide-precursor pool with radioactive phosphate. The method has mainly been developed with the object of determining deoxyribonucleoside triphosphates, but it can be used to assay ribonucleoside triphosphates, as well as the mono- and diphosphates of both types of nucleoside. The procedure used involves three basic techniques: (1) periodate oxidation and methylamine-induced cleavage of the sugar ring to destroy 2′- and 3′-unsubstituted ribonucleosides; (2) column chromatography to separate the deoxyribonucleotides from each other and from other substances, such as the products of the periodate oxidation; (3) fluorimetric determination of deoxyribose after labilization of the pyrimidine–glycosidic bond by bromination of the heterocyclic ring. Each of these three procedures can be used independently, in conjunction with other analytical procedures. PMID:4342491

  15. Exploiting Microbeams for Membrane Protein Structure Determination.

    PubMed

    Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L

    2016-01-01

    A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238

  16. 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

  17. 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

  18. Urovirulence determinants in Escherichia coli isolates causing first-episode and recurrent cystitis in women.

    PubMed

    Stapleton, A; Moseley, S; Stamm, W E

    1991-04-01

    To assess the prevalence of urovirulence determinants among Escherichia coli isolates from women with acute uncomplicated cystitis, 121 isolates from 87 women with first-episode or recurrent cystitis and 156 fecal isolates from 52 women without recent urinary tract infection were tested using DNA probes for P fimbriae, hemolysin, aerobactin, and diffuse adhesin and for expression of hemolysin and P and F adhesins. P fimbrial genotype (P = .002), hemolysin phenotype (P = .007), and the diffuse adhesin determinant (P = .03), but not aerobactin, were found more frequently in E. coli from women with acute cystitis, and expression of the F adhesin (41%) was more common than the P adhesin (24%; P = .001). E. coli isolates that caused cystitis in women using diaphragms had fewer virulence determinants than those from nonusers (P = .04), suggesting that diaphragm use may allow infection with less virulent E. coli.

  19. 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. PMID:16330169

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

    PubMed

    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 {(1)H}-(15)N 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

  1. 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

  2. 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

  3. 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.

  4. Meroparamycin production by newly isolated Streptomyces sp. strain MAR01: taxonomy, fermentation, purification and structural elucidation.

    PubMed

    El-Naggar, Moustafa Y; El-Assar, Samy A; Abdul-Gawad, Sahar M

    2006-08-01

    Twelve actinomycete strains were isolated from Egyptian soil. The isolated actinomycete strains were then screened with regard to their potential to generate antibiotics. The most potent of the producer strains was selected and identified. The cultural and physiological characteristics of the strain identified the strain as a member of the genus Streptomyces. The nucleotide sequence of the 16S rRNA gene (1.5 kb) of the most potent strain evidenced a 99% similarity with Streptomyces spp. and S. aureofaciens 16S rRNA genes, and the isolated strain was ultimately identified as Streptomyces sp. MAR01. The extraction of the fermentation broth of this strain resulted in the isolation of one major compound, which was active in vitro against gram-positive, gram-negative representatives and Candida albicans. The chemical structure of this bioactive compound was elucidated based on the spectroscopic data obtained from the application of MS, IR, UV, 1H NMR, 13C NMR, and elemental analysis techniques. Via comparison to the reference data in the relevant literature and in the database search, this antibiotic, which had a molecular formula of C19H29NO2 and a molecular weight of 303.44, was determined to differ from those produced by this genus as well as the available known antibiotics. Therefore, this antibiotic was designated Meroparamycin. PMID:16953179

  5. Structure of turbulent wedges created by isolated surface roughness

    NASA Astrophysics Data System (ADS)

    Kuester, Matthew S.; White, Edward B.

    2016-04-01

    Isolated surface roughness in a laminar boundary layer can create a wedge of turbulence that spreads laterally into the surrounding laminar flow. Some recent studies have identified high- and low-speed streaks along the exterior of turbulent wedges. In this experiment, developing turbulent wedges are measured to observe the creation of these streaks. Naphthalene shear stress surface visualization and hotwire measurements are utilized to investigate the details of turbulent wedges created by cylinders in a laminar flat-plate boundary layer. Both the surface visualization and the hotwire measurements show high- and low-speed streaks in the wake of the cylinder that devolve into a turbulent wedge. The turbulent wedge spreading is associated with the emergence of these high- and low-speed streaks along the outside of the wedge. As the wedge evolves in the streamwise direction, these streaks persist inside of the core of the wedge, while new, lower amplitude streaks form along the outside of the wedge. Adding asymmetry to the cylinder moved the virtual origin closer to the roughness and increased the vortex shedding frequency, while adding small-scale roughness features did not strongly affect turbulent wedge development. Intermittency calculations additionally show the origin of the turbulent core inside of the wedge. The structure and spacing of the high-speed streaks along the extremities of the turbulent wedge give insight into the spreading angle of the turbulent wedge.

  6. 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.

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

    PubMed

    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

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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.

  10. Nonlinear dynamic analysis of multi-base seismically isolated structures with uplift potential I: formulation

    NASA Astrophysics Data System (ADS)

    Tsopelas, Panos C.; Roussis, Panayiotis C.; Constantinou, Michael C.

    2009-09-01

    The complexity of modern seismically isolated structures requires the analysis of the structural system and the isolation system in its entirety and the ability to capture potential discontinuous phenomena such as isolator uplift and their effects on the superstructures and the isolation hardware. In this paper, an analytical model is developed and a computational algorithm is formulated to analyze complex seismically isolated superstructures even when undergoing highly-nonlinear phenomena such as uplift. The computational model has the capability of modeling various types of isolation devices with strong nonlinearities, analyzing multiple superstructures (up to five separate superstructures) on multiple bases (up to five bases), and capturing the effects of lateral loads on bearing axial forces, including bearing uplift. The model developed herein has been utilized to form the software platform 3D-BASIS-ME-MB, which provides the practicing engineering community with a versatile tool for analysis and design of complex structures with modern isolation systems.

  11. Microcin determinants are associated with B2 phylogroup of human fecal Escherichia coli isolates.

    PubMed

    Micenková, Lenka; Bosák, Juraj; Štaudová, Barbora; Kohoutová, Darina; Čejková, Darina; Woznicová, Vladana; Vrba, Martin; Ševčíková, Alena; Bureš, Jan; Šmajs, David

    2016-06-01

    Escherichia coli strains are classified into four main phylogenetic groups (A, B1, B2, and D) and strains of these phylogroups differ in a number of characteristics. This study tested whether human fecal E. coli isolates belonging to different phylogroups differ in prevalence of bacteriocinogenic isolates and prevalence of individual bacteriocinogenic determinants. A set of 1283 fecal E. coli isolates from patients with different diseases was tested for the presence of DNA regions allowing classification into E. coli phylogroups and for the ability to produce bacteriocins (23 colicins and 7 microcins). Of the isolates tested, the most common was phylogroup B2 (38.3%) followed by phylogroups A (28.3%), D (26.3%) and B1 (7.2%). Altogether, 695 bacteriocin producers were identified representing 54.2% of all tested isolates. The highest prevalence of bacteriocin producers was found in group B2 (60.3%) and the lowest in group B1 (44.6%). Determinants encoding colicins E1, Ia, and microcin mV were most common in phylogroup A, determinants encoding microcins mM and mH47 were most common in phylogroup B2, and determinant encoding mB17 was most common in phylogroup D. The highest prevalence of bacteriocinogeny was found in phylogroup B2, suggesting that bacteriocinogeny and especially the synthesis of microcins was associated with virulent and resident E. coli strains.

  12. Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates.

    PubMed

    Kong, P; Rubio, L; Polek, M; Falk, B W

    2000-10-01

    The Closterovirus, Citrus tristeza virus (CTV) is an aphid-borne RNA virus that is the causal agent of important worldwide economic losses in citrus. Biological and molecular variation has been observed for many CTV isolates. In this work we detected and analyzed sequence variants (haplotypes) within individual CTV isolates. We studied the population structure of five California CTV isolates by single strand conformation polymorphism (SSCP) analysis of four CTV genomic regions. Also, we estimated the genetic diversity within and between isolates by analysis of haplotype nucleotide sequences. Most CTV isolates were composed of a population of genetically related variants (haplotypes), one being predominant. However in one case, we found a high nucleotide divergence between haplotypes of the same isolate. Comparison of these haplotypes with those from other isolates suggests that some CTV isolates could have arisen as result of a mixed infection of two divergent isolates. PMID:11129629

  13. Zebrafish cardiac muscle thick filaments: isolation technique and three-dimensional structure.

    PubMed

    González-Solá, Maryví; Al-Khayat, Hind A; Behra, Martine; Kensler, Robert W

    2014-04-15

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes.

  14. Zebrafish Cardiac Muscle Thick Filaments: Isolation Technique and Three-Dimensional Structure

    PubMed Central

    González-Solá, Maryví; AL-Khayat, Hind A.; Behra, Martine; Kensler, Robert W.

    2014-01-01

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes. PMID:24739166

  15. 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.

  16. 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

  17. Molecular Analysis of Antibiotic Resistance Determinants and Plasmids in Malaysian Isolates of Multidrug Resistant Klebsiella pneumoniae

    PubMed Central

    Al-Marzooq, Farah; Mohd Yusof, Mohd Yasim; Tay, Sun Tee

    2015-01-01

    Infections caused by multidrug resistant Klebsiella pneumoniae have been increasingly reported in many parts of the world. A total of 93 Malaysian multidrug resistant K. pneumoniae isolated from patients attending to University of Malaya Medical Center, Kuala Lumpur, Malaysia from 2010-2012 were investigated for antibiotic resistance determinants including extended-spectrum beta-lactamases (ESBLs), aminoglycoside and trimethoprim/sulfamethoxazole resistance genes and plasmid replicons. CTX-M-15 (91.3%) was the predominant ESBL gene detected in this study. aacC2 gene (67.7%) was the most common gene detected in aminoglycoside-resistant isolates. Trimethoprim/sulfamethoxazole resistance (90.3%) was attributed to the presence of sul1 (53.8%) and dfrA (59.1%) genes in the isolates. Multiple plasmid replicons (1-4) were detected in 95.7% of the isolates. FIIK was the dominant replicon detected together with 13 other types of plasmid replicons. Conjugative plasmids (1-3 plasmids of ~3-100 kb) were obtained from 27 of 43 K. pneumoniae isolates. An ESBL gene (either CTX-M-15, CTX-M-3 or SHV-12) was detected from each transconjugant. Co-detection with at least one of other antibiotic resistance determinants [sul1, dfrA, aacC2, aac(6ˊ)-Ib, aac(6ˊ)-Ib-cr and qnrB] was noted in most conjugative plasmids. The transconjugants were resistant to multiple antibiotics including β-lactams, gentamicin and cotrimoxazole, but not ciprofloxacin. This is the first study describing the characterization of plasmids circulating in Malaysian multidrug resistant K. pneumoniae isolates. The results of this study suggest the diffusion of highly diverse plasmids with multiple antibiotic resistance determinants among the Malaysian isolates. Effective infection control measures and antibiotic stewardship programs should be adopted to limit the spread of the multidrug resistant bacteria in healthcare settings. PMID:26203651

  18. Distribution and transferability of tetracycline resistance determinants in Escherichia coli isolated from meat and meat products.

    PubMed

    Koo, Hyon-Ji; Woo, Gun-Jo

    2011-02-28

    Escherichia coli is used to assess the hygienic quality of food products and the dissemination of antimicrobial resistance. In particular, tetracycline-resistant E. coli can be chosen as an indicator of antibiotic resistant bacteria because it has a high frequency of occurrence. The purpose of this study was to investigate the distribution and transfer of tetracycline resistance determinants in meatborne E. coli. A total of 121 tetracycline-resistant E. coli isolates were collected from meat and meat products (raw meat, fish, and processed foods) from 2004 to 2006 in Korea. Among these isolates, tet(A) (52.4%) was the most frequent tetracycline resistance determinant, followed by tet(B) (41.3%), whereas tet(C) (1.7%) and tet(D) (0.8%) were less frequently identified. Two isolates (1.6%) contained two tet genes simultaneously, tet(A) and tet(B). Minimal inhibitory concentrations (MICs) to tetracycline family antibiotics, such as tetracycline, minocycline, doxycycline, oxytetracycline, and chlortetracycline were higher for isolates carrying the tet(B) gene compared to isolates carrying tet(A) (P<0.0001). Conjugation experiments were performed by the broth mating method; 119 isolates (98.3%) containing at least one of the tet genes were shown to transfer tetracycline resistance to recipient E. coli J53. Also, we observed high diversity of tetracycline-resistant E. coli isolates in meat and meat products in Korea by using XbaI pulsed-field gel electrophoresis (PFGE) typing. This study suggests that the high prevalence of tetracycline-resistant E. coli in meat may be due to the high transferability of tet determinants. PMID:21324543

  19. Molecular Analysis of Antibiotic Resistance Determinants and Plasmids in Malaysian Isolates of Multidrug Resistant Klebsiella pneumoniae.

    PubMed

    Al-Marzooq, Farah; Mohd Yusof, Mohd Yasim; Tay, Sun Tee

    2015-01-01

    Infections caused by multidrug resistant Klebsiella pneumoniae have been increasingly reported in many parts of the world. A total of 93 Malaysian multidrug resistant K. pneumoniae isolated from patients attending to University of Malaya Medical Center, Kuala Lumpur, Malaysia from 2010-2012 were investigated for antibiotic resistance determinants including extended-spectrum beta-lactamases (ESBLs), aminoglycoside and trimethoprim/sulfamethoxazole resistance genes and plasmid replicons. CTX-M-15 (91.3%) was the predominant ESBL gene detected in this study. aacC2 gene (67.7%) was the most common gene detected in aminoglycoside-resistant isolates. Trimethoprim/sulfamethoxazole resistance (90.3%) was attributed to the presence of sul1 (53.8%) and dfrA (59.1%) genes in the isolates. Multiple plasmid replicons (1-4) were detected in 95.7% of the isolates. FIIK was the dominant replicon detected together with 13 other types of plasmid replicons. Conjugative plasmids (1-3 plasmids of ~3-100 kb) were obtained from 27 of 43 K. pneumoniae isolates. An ESBL gene (either CTX-M-15, CTX-M-3 or SHV-12) was detected from each transconjugant. Co-detection with at least one of other antibiotic resistance determinants [sul1, dfrA, aacC2, aac(6')-Ib, aac(6')-Ib-cr and qnrB] was noted in most conjugative plasmids. The transconjugants were resistant to multiple antibiotics including β-lactams, gentamicin and cotrimoxazole, but not ciprofloxacin. This is the first study describing the characterization of plasmids circulating in Malaysian multidrug resistant K. pneumoniae isolates. The results of this study suggest the diffusion of highly diverse plasmids with multiple antibiotic resistance determinants among the Malaysian isolates. Effective infection control measures and antibiotic stewardship programs should be adopted to limit the spread of the multidrug resistant bacteria in healthcare settings.

  20. 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.

  1. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. Isolation and primary structure of glucagon from the endocrine pancreas of Thunnus obesus.

    PubMed

    Navarro, I; Gutiérrez, J; Caixach, J; Rivera, J; Planas, J

    1991-08-01

    Glucagon has been isolated from the endocrine pancreas of a tunid, Thunnus obesus. The primary structure of the glucagon molecule was established as H S E G T F S N D Y S K Y L E T R R A Q D F V Q W L K N S. The sequence is identical to those of sculpin and flounder glucagon and glucagon II from anglerfish. It also shows high homology to the mammalian hormone (76%). The mass determined by fast-atom bombardment (3508) was consistent with the proposed structure. Immunological properties of the tuna glucagon were analyzed by radioimmunoassay, showing a high degree of cross-reactivity with the 30K antibody. PMID:1916209

  4. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    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.

  5. 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.

  6. Determining Probabilities by Examining Underlying Structure.

    ERIC Educational Resources Information Center

    Norton, Robert M.

    2001-01-01

    Discusses how dice games pose fairness issues that appeal to students and examines a structure for three games involving two dice in a way that leads directly to the theoretical probabilities for all possible outcomes. (YDS)

  7. 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

    2016-01-01

    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

  8. 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

  9. 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. PMID:27468468

  10. 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

  11. 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. PMID:17570621

  12. Semi-active control of isolated and damaged structures using online damage detection

    NASA Astrophysics Data System (ADS)

    Amini, Fereidoun; Mohajeri, Seyed Ahmad; Javanbakht, Majd

    2015-10-01

    The idea of using semi-active or active control devices within a base isolation system has been developed recently, since applying this system to building structures has some shortcomings such as the creation of large displacements at the base level and the system's lack of adaptability to different seismic excitations. In this study, an integrated structural health monitoring and semi-active control scheme is proposed to enhance the seismic behavior of damaged isolated structures. The nonlinear behavior of an isolated structure is limited to the isolator level and the superstructure is assumed to remain linear. Then, using an online damage detection algorithm based on identified system Markov parameters and a semi-active fuzzy controller, the damage in the base isolator is mitigated and the seismic response of the structure is reduced. In addition, a magnetorheological damper is utilized as a well-studied semi-active actuator in the control system. The effectiveness of the proposed control system is evaluated through the numerical study of a six-degrees-of-freedom model of base-isolated buildings excited by various near-fault and far-field earthquake records. The results of the simulation show that the integrated algorithm is substantially effective in improving the dynamic behavior of isolated structures and reducing the damage in the isolator.

  13. 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.

  14. Luminescence from electroformed metal-isolator-metal-structures

    NASA Astrophysics Data System (ADS)

    Bischoff, Manfred

    The electroluminescence from metal-isolator-metal diodes is measured with a photon counter. From the time dependance of the electron temperature and density it appears that the electrons are not heated in the conduction band of the separating isolator or in vaccuum between the electrodes but in a highly degenerated semiconductor. The experimental results show that the grid temperature of the semiconductor filament material in case of a voltage pulse adds up to 1,500 K. The temperature of the hot electrons drops from 3,000 to 2,000 K. The charge carrier density and the recombination rate also increase.

  15. 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.

  16. Photochemical determination of different DNA structures.

    PubMed

    Xu, Yan; Tashiro, Ryu; Sugiyama, Hiroshi

    2007-01-01

    The various conformations of DNA are thought to have important biological roles. Investigation of the local DNA conformational changes associated with biological events is therefore essential to an understanding of the functions of DNA. We have reported the photoreactivities of 5-halouracil in the five characteristic local DNA structures: the A, B and Z forms, protein-induced DNA kinks and the G-quadruplex form. These studies demonstrate the detailed relationships between the local DNA structures and the photochemical products of photoinduced hydrogen abstraction by the resulting uracil-5-yl radicals, and show that this photochemical method can be used to detect DNA structures. Here, we describe in detail procedures that have been developed in our laboratory for probing DNA conformations by product analysis of photoirradiated 5-halouracil-containing DNA. The protocol includes the preparation of 5-halouracil-containing DNA and the characterization of the photoproducts, and it can be completed in 2 weeks.

  17. 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.

  18. 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.

  19. 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.

  20. 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…

  1. Vascular structure determines pulmonary blood flow distribution.

    PubMed

    Hlastala, M P; Glenny, R W

    1999-10-01

    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.

  2. Determining Factor Structure in a Multidimensional Inventory.

    ERIC Educational Resources Information Center

    Deeter, Thomas E.; Gill, Diane L.

    A two-step procedure is described and used to revise a multidimensional inventory in its developmental stages. First, the latent factors influencing the observed variables on the inventory are determined and justified using the following five methods: Kaiser's criterion, root staring, examination of difference values, examination of root mean…

  3. 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.

  4. 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

  5. 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. PMID:1861610

  6. 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. PMID:26847667

  7. 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.

  8. 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.

  9. 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.

  10. Structural determinants of proton blockage in aquaporins.

    PubMed

    Chakrabarti, Nilmadhab; Roux, Benoît; Pomès, Régis

    2004-10-15

    Aquaporins are an important class of membrane channels selective for water and linear polyols but impermeable to ions, including protons. Recent computational studies have revealed that the relay of protons through the water-conduction pathway of aquaporin channels is opposed by a substantial free energy barrier peaking at the signature NPA motifs. Here, free-energy simulations and continuum electrostatic calculations are combined to examine the nature and the magnitude of the contribution of specific structural elements to proton blockage in the bacterial glycerol uptake facilitator, GlpF. Potential of mean-force profiles for both hop and turn steps of structural diffusion in the narrow pore are obtained for artificial variants of the GlpF channel in which coulombic interactions between the pore contents and conserved residues Asn68 and Asn203 at the NPA signature motifs, Arg206 at the selectivity filter, and the peptidic backbone of the two half-helices M3 and M7, which are arranged in head-to-head fashion around the NPA motifs, are turned off selectively. A comparison of these results with electrostatic energy profiles for the translocation of a probe cation throughout the water permeation pathway indicates that the free-energy profile for proton movement inside the narrow pore is dominated by static effects arising from the distribution of charged and polar groups of the channel, whereas dielectric effects contribute primarily to opposing the access of H+ to the pore mouths (desolvation penalty). The single most effective way to abolish the free-energy gradients opposing the movement of H+ around the NPA motif is to turn off the dipole moments of helices M3 and M7. Mutation of either of the two NPA Asn residues to Asp compensates for charge-dipole and dipole-dipole effects opposing the hop and turn steps of structural diffusion, respectively, and dramatically reduces the free energy barrier of proton translocation, suggesting that these single mutants could

  11. 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

  12. 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"…

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  14. 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

  15. Magnetic Structure Determinations at NBS/NIST

    PubMed Central

    Lynn, J. W.; Borchers, J. A.; Huang, Q.; Santoro, A.; Erwin, R. W.

    2001-01-01

    Magnetic neutron scattering plays a central role in determining and understanding the microscopic properties of a vast variety of magnetic systems, from the fundamental nature, symmetry, and dynamics of magnetically ordered materials to elucidating the magnetic characteristics essential in technological applications. From the early days of neutron scattering measurements at NBS/NIST, magnetic diffraction studies have been a central theme involving many universities, industrial and government labs from around the United States and worldwide. Such measurements have been used to determine the spatial arrangement and directions of the atomic magnetic moments, the atomic magnetization density of the individual atoms in the material, and the value of the ordered moments as a function of thermodynamic parameters such as temperature, pressure, and applied magnetic field. These types of measurements have been carried out on single crystals, powders, thin films, and artificially grown multilayers, and often the information collected can be obtained by no other experimental technique. This article presents, in an historical perspective, a few examples of work carried out at the NIST Center for Neutron Research (NCNR), and discusses the key role that the Center can expect to play in future magnetism research. PMID:27500056

  16. 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.

  17. New anthracycline antibiotics produced by interspecific recombinants of streptomycetes. III. Isolation and structure of iremycin.

    PubMed

    Ihn, W; Schlegel, B; Fleck, W F; Sedmera, P

    1980-12-01

    The structure of the anthracycline antibiotic iremycin isolated from Streptomyces violaceus subspecies iremyceticus has been elucidated as 10-(alpha-L-rhodosaminyl)-gamma-rhodomycinone (I) on the basis of spectroscopic analyses and chemical reactions. PMID:7251489

  18. 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.

  19. Isolation and structure elucidation of vicenistatin M, and importance of the vicenisamine aminosugar for exerting cytotoxicity of vicenistatin.

    PubMed

    Matsushima, Y; Nakayama, T; Fujita, M; Bhandari, R; Eguchi, T; Shindo, K; Kakinuma, K

    2001-03-01

    A new analogue of vicenistatin was isolated from the producing strain Streptomyces sp. HC-34. A characteristic of the elucidated structure involved the existence of a neutral sugar mycarose instead of an aminosugar vicenisamine of vicenistatin. The absolute stereochemistry of the new analogue (named as vicenistatin M) was determined by the synthesis of D-mycarose and of vicenistatin M itself. Biological testing of vicenistatin M suggested the importance of vicenisamine for exerting the cytotoxicity of vicenistatin. PMID:11372778

  20. 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. PMID:21872183

  1. Isolation, structure elucidation and cytotoxic evaluation of endiandrin B from the Australian rainforest plant Endiandra anthropophagorum.

    PubMed

    Davis, Rohan A; Barnes, Emma C; Longden, James; Avery, Vicky M; Healy, Peter C

    2009-02-01

    Chemical investigations of the DCM extract from the roots of Endiandra anthropophagorum resulted in the isolation of a new cyclobutane lignan endiandrin B (1), together with the known natural products, endiandrin A (2), and (-)-dihydroguaiaretic acid (3). The structure of 1 was determined by extensive spectroscopic analyses, and confirmed by single crystal X-ray crystallography. Methylation of 1 using diazomethane afforded the previously reported natural product, cinbalansan (4). All compounds were evaluated for their cytotoxicity towards human lung carcinoma cells (A549) using high-content screening. (-)-Dihydroguaiaretic acid (3) was found to be the most potent cytotoxin against the A549 lung carcinoma cell line, with an IC(50) value of 7.49 microM.

  2. 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

  3. 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.

  4. Isolation and structural elucidation of biotransformation products from acarbose.

    PubMed

    Boberg, M; Kurz, J; Ploschke, H J; Schmitt, P; Scholl, H; Schüller, M; Wünsche, C

    1990-05-01

    Following oral administration the a-glucosidase inhibitor acarbose (O-4,6-dideoxy-4-[[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl) -2-cyclohexen-1-yl]amino]-a-D-glucopyranosyl-(1----4)-O-a-D-glu copyranosyl-(1----4)-D-glucopyranose, Bay g 5421) is degraded by digestive enzymes and/or intestinal microorganism. The effect of anaerobic intestinal bacteria can be studied in an in vitro model which involves the incubation of acarbose with human or animal intestinal flora. Acarbose and nine biotransformation products can be isolated from the incubation mixture. These products were identified by nuclear magnetic resonance and mass spectrometry as so-called component 2 (loss of the terminal glucose), component 1 (loss of both glucose rings), hexose homologues of acarbose and component 2, methyl homologues of acarbose, butyric acid ester of component 2, basic disaccharide (loss of the cyclitol ring of component 2), delta-aminovaleric acid and gamma-aminobutyric acid. Following oral administration of [14C]-acarbose to healthy volunteers, 35% of the radioactivity was excreted in the form of at least 13 metabolites in the urine. Three of the metabolites were isolated by Craig countercurrent distribution and ion-pair HPLC and characterized by virtue of their nuclear magnetic resonance and mass spectra as derivatives of 4-methylpyrogallol. Two were shown to be monomethylether-monosulphates while the third was a monosulphate-monoglucuronide. The synthesis of ten reference substances and the comparison of HPLC and UV data clearly indicated that the majority of the non-isolated metabolites were also 4-methylpyrogallol derivatives. The peculiarities of the nuclear magnetic resonance and mass spectra of this type of compound are discussed.

  5. Virulence and resistance determinants of German Staphylococcus aureus ST398 isolates from nonhuman sources.

    PubMed

    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

    2011-05-01

    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.

  6. Determining building interior structures using compressive sensing

    NASA Astrophysics Data System (ADS)

    Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse

    2013-04-01

    We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.

  7. 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

  8. 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.

  9. 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. PMID:27401040

  10. 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

  11. Structure of catalase determined by MicroED.

    PubMed

    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. PMID:25303172

  12. 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

  13. Structural determinants of Tau aggregation inhibitor potency.

    PubMed

    Schafer, Kelsey N; Cisek, Katryna; Huseby, Carol J; Chang, Edward; Kuret, Jeff

    2013-11-01

    Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers.

  14. Structural Determinants of Tau Aggregation Inhibitor Potency*

    PubMed Central

    Schafer, Kelsey N.; Cisek, Katryna; Huseby, Carol J.; Chang, Edward; Kuret, Jeff

    2013-01-01

    Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers. PMID:24072703

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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. PMID:27375864

  20. 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.

  1. Structural features of a novel polysaccharide isolated from a New Zealand Maori mushroom Iliodiction cibarium.

    PubMed

    Ren, Lu; Edwards, Patrick J B; Perera, Conrad O; Hemar, Yacine

    2015-04-10

    A purified water-soluble fraction (ICP5) of a polysaccharide, isolated from a local Maori mushroom Iliodiction cibarium in New Zealand, was investigated for its structural properties. Size exclusion chromatography and dynamic light scattering showed that ICP5 had a large MW of 1.6 × 10(5) Da with a hydrodynamic diameter of 83 ± 8 nm. Particle size measurements also displayed the tendency of ICP5 to aggregate when suspended in water. The results of GC-MS, FTIR and NMR analyses allowed some characteristics of the chemical structure of ICP5 to be determined. GC-MS results showed that ICP5 contained only glucose (81.61%), galactose (12.90%) and mannose (5.49%) monomers. The characterized fragment structures of ICP5 were found to be dominantly consisting of uronic acids, which formed a backbone containing 1,4-β-D-GlcpA. A small amount of unsaturated uronic acid also appeared to be present.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. Isolation and structure of the cytotoxin lyngbyabellin B and absolute configuration of lyngbyapeptin A from the marine cyanobacterium Lyngbya majuscula.

    PubMed

    Luesch, H; Yoshida, W Y; Moore, R E; Paul, V J

    2000-10-01

    An analogue of the potent microfilament-disrupter lyngbyabellin A (1) has been isolated as a minor metabolite from the marine cyanobacterium Lyngbya majuscula collected at Apra Harbor, Guam. It possesses slightly weaker cytotoxicity than 1 and has been named lyngbyabellin B (2). Primarily NMR spectroscopy was used to determine its structure. The absolute configuration of 2 has been ascertained by chiral HPLC analysis of degradation products and by comparison with lyngbyabellin A (1). The known modified tetrapeptide lyngbyapeptin A (3) has also been found in the same extract, and its absolute stereochemistry could be determined for the first time.

  8. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    PubMed

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method.

  9. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

    PubMed

    Fromm, S A; Sachse, C

    2016-01-01

    Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. PMID:27572732

  10. Separation by thin-layer chromatography and structure elucidation of bilirubin conjugates isolated from dog bile.

    PubMed Central

    Heirwegh, K P; Fevery, J; Michiels, R; van Hees, G P; Compernolle, F

    1975-01-01

    1. A system for separation of bile pigments by t.l.c. and for their structure elucidation is presented. Separated bile pigments are characterized by t.l.c. of derived dipyrrolic azopigments. 2. At the tetrapyrrolic stage hydrolysis in strongly alkaline medium followed by t.l.c. demonstrates the presence of bilirubin-IIIalpha, -IXalpha and -XIIIalpha and allows assessment of their relative amounts. 3. Most structural information is derived from analysis of dipyrrolic azopigments. Such derivatives, obtained by treatment of separated bile pigments with diazotized ethyl anthranilate, were separated and purified by t.l.c. Micro methods showed (a) the nature of the dipyrrolic aglycone, (b) the nature of the bonds connecting aglycone to a conjugating group, (c) the ratio of vinyl/isovinyl isomers present in the aglycone and, (d) the nature of the conjugating groups (by suitable derivative formation and t.l.c. with reference to known compounds). 4. In bile of normal dogs at least 20 tetrapyrrolic, diazo-positive bile pigments could be recognized. Except for two pigments the tetrapyrrolic nucleus corresponded predominantly to bilirubin-IXalpha. All conjugated pigments had their conjugating groups connected in ester linkage to the tetrapyrrolic aglycone, Apart from bilirubin-IXalpha, monoconjugates and homogeneous and mixed diconjugates of bilirubin were demonstrated; conjugating groups of major importance were xylose, glucose and glucuronic acid. 5. Bilirubin isomer determination on native bile and isolated bile pigments, and dipyrrole-exchange assays with [14C8]bilirubin indicated (a) that the conjugates pre-exist in bile, and (b) that no significant dipyrrole exchange occurs during isolation of the pigments. PMID:1156357

  11. Isolation and X-ray structures of labile benzoic- and acetic-acidium carbocations.

    PubMed

    Lindeman, S V; Neretin, I S; Davlieva, M G; Kochi, J K

    2005-04-15

    New carbocationic salts (via O-protonation of substituted benzoic acids) are prepared for the first time by controlled hydration of the corresponding benzoylium salts and isolated in pure crystalline form. Precise X-ray structural analyses reveal the rather unexpected (electronic) structure of the carboxylic-acidium functionality. PMID:15822990

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. Isolation, Characterization, and Aggregation of a Structured Bacterial Matrix Precursor*

    PubMed Central

    Chai, Liraz; Romero, Diego; Kayatekin, Can; Akabayov, Barak; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

    2013-01-01

    Biofilms are surface-associated groups of microbial cells that are embedded in an extracellular matrix (ECM). The ECM is a network of biopolymers, mainly polysaccharides, proteins, and nucleic acids. ECM proteins serve a variety of structural roles and often form amyloid-like fibers. Despite the extensive study of the formation of amyloid fibers from their constituent subunits in humans, much less is known about the assembly of bacterial functional amyloid-like precursors into fibers. Using dynamic light scattering, atomic force microscopy, circular dichroism, and infrared spectroscopy, we show that our unique purification method of a Bacillus subtilis major matrix protein component results in stable oligomers that retain their native α-helical structure. The stability of these oligomers enabled us to control the external conditions that triggered their aggregation. In particular, we show that stretched fibers are formed on a hydrophobic surface, whereas plaque-like aggregates are formed in solution under acidic pH conditions. TasA is also shown to change conformation upon aggregation and gain some β-sheet structure. Our studies of the aggregation of a bacterial matrix protein from its subunits shed new light on assembly processes of the ECM within bacterial biofilms. PMID:23632024

  17. [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.

  18. Isolation, characterization and determination of trace organic impurities in FD&C red no. 40.

    PubMed

    Richfield-Fratz, N; Baczynskyj, W M; Miller, G C; Bailey, J E

    1989-04-21

    The unsulfonated aromatic amine 4-nitro-p-cresidine (2-methoxy-5-methyl-4-nitrobenzenamine) was identified as an impurity in the regulated color additive FD&C Red. No. 40. The compound was isolated from the water-soluble color by extraction with chloroform, followed by transfer of the free amines to acid solution and subsequent separation by reversed-phase high-performance liquid chromatography. The 4-nitro-p-cresidine was collected and then identified by gas chromatography-mass spectrometry. The levels of 4-nitro-p-cresidine as well as p-cresidine and aniline were determined in commercial batches of FD&C Red. No. 40.

  19. Molecular Screening of Enterococcus Virulence Determinants and Potential for Genetic Exchange between Food and Medical Isolates

    PubMed Central

    Eaton, Tracy J.; Gasson, Michael J.

    2001-01-01

    Enterococci are used as starter and probiotic cultures in foods, and they occur as natural food contaminants. The genus Enterococcus is of increased significance as a cause of nosocomial infections, and this trend is exacerbated by the development of antibiotic resistance. In this study, we investigated the incidence of known virulence determinants in starter, food, and medical strains of Enterococcus faecalis, E. faecium, and E. durans. PCR and gene probe strategies were used to screen enterococcal isolates from both food and medical sources. Different and distinct patterns of incidence of virulence determinants were found for the E. faecalis and E. faecium strains. Medical E. faecalis strains had more virulence determinants than did food strains, which, in turn, had more than did starter strains. All of the E. faecalis strains tested possessed multiple determinants (between 6 and 11). E. faecium strains were generally free of virulence determinants, with notable exceptions. Significantly, esp and gelE determinants were identified in E. faecium medical strains. These virulence determinants have not previously been identified in E. faecium strains and may result from regional differences or the evolution of pathogenic E. faecium. Phenotypic testing revealed the existence of apparently silent gelE and cyl genes. In E. faecalis, the trend in these silent genes mirrors that of the expressed determinants. The potential for starter strains to acquire virulence determinants by natural conjugation mechanisms was investigated. Transconjugation in which starter strains acquired additional virulence determinants from medical strains was demonstrated. In addition, multiple pheromone-encoding genes were identified in both food and starter strains, indicating their potential to acquire other sex pheromone plasmids. These results suggest that the use of Enterococcus spp. in foods requires careful safety evaluation. PMID:11282615

  20. 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. PMID:25970192

  1. 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.

  2. 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

  3. Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase .

    PubMed

    Hall, Richard S; Agarwal, Rakhi; Hitchcock, Daniel; Sauder, J Michael; Burley, Stephen K; Swaminathan, Subramanyam; Raushel, Frank 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 A resolution (Protein Data Bank entry 2PAJ ). This protein folds as a distorted (beta/alpha)(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(-1), 8.0 muM, and 1.3 x 10(5) M(-1) s(-1) (k(cat), K(m), and k(cat)/K(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 residues were used to identify 24 other genes

  4. 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.

  5. Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.

    PubMed

    Rödström, Karin E J; Lindkvist-Petersson, Karin

    2016-01-01

    Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.

  6. 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.

  7. 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

  8. Isolation of eight microsatellite markers from Moina macrocopa for assessing cryptic genetic structure in the wild.

    PubMed

    Tatsuta, Haruki; Yao, Izumi; Tanaka, Yoshinari

    2009-05-01

    We isolated eight polymorphic microsatellite loci from the zooplankton Moina macrocopa (Straus), which is sensitive to pollutants such as insecticides and heavy metals. The isolated loci were polymorphic, with three to seven alleles among 23 individuals. Expected heterozygosities ranged from 0.167 to 0.787. These loci can be used to examine cryptic genetic structure and to infer the connectivity among metapopulations. PMID:21564785

  9. 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.

  10. NMRFAM-SDF: a protein structure determination framework.

    PubMed

    Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C; Cornilescu, Gabriel; Assadi-Porter, Fariba M; Westler, William M; Eghbalnia, Hamid R; Markley, John L

    2015-08-01

    The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).

  11. Draft Genome Sequence of Neisseria gonorrhoeae Strain NG_869 with Penicillin, Tetracycline and Ciprofloxacin Resistance Determinants Isolated from Malaysia.

    PubMed

    Ang, Geik Yong; Yu, Choo Yee; Yong, Delicia Ann; Cheong, Yuet Meng; Yin, Wai-Fong; Chan, Kok-Gan

    2016-06-01

    Gonorrhea is a sexually transmitted infection caused by Neisseria gonorrhoeae and the increasing reports of multidrug-resistant gonococcal isolates are a global public health care concern. Herein, we report the genome sequence of N. gonorrhoeae strain NG_869 isolated from Malaysia which may provide insights into the drug resistance determinants in gonococcal bacteria. PMID:27570316

  12. 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)

  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. 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.

  15. 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.

  16. Isolation and structural characterization of chondroitin sulfate from bony fishes.

    PubMed

    Maccari, Francesca; Galeotti, Fabio; Volpi, Nicola

    2015-09-20

    Chondroitin sulfate (CS) was purified from the bones of common fishes, monkfish, cod, spiny dogfish, salmon and tuna, and characterized in an effort to find alternative sources and new peculiar structures of this complex biomacromolecule utilized in the pharmaceutical and nutraceutical industry. Quantitative analyses yielded a CS content ranging from 0.011% for cod up to 0.34% for monkfish. The disaccharide pattern showed the presence of nonsulfated disaccharide, monosulfated species ΔDi6s and ΔDi4s, and disulfated disaccharides in different percentages. The disulfated species ΔDi2,6dis was present in all CS extracts in a range of 1.3-10.5%. The presence of these disulfated disaccharides may be a useful marker for the marine origin of CS. The newly identified sources would certainly enable the production of CS with unique disaccharide composition and properties.

  17. Structure and Interactions of Isolated Biomolecular Building Blocks.

    NASA Astrophysics Data System (ADS)

    de Vries, Mattanjah

    2006-03-01

    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  18. Isolation and sequence determination of trichorzianines A antifungal peptides from Trichoderma harzianum.

    PubMed

    el Hajji, M; Rebuffat, S; Lecommandeur, D; Bodo, B

    1987-02-01

    Trichorzianines A, membrane active peptides of the peptaibol class, were isolated from cultures of the mould Trichoderma harzianum. Trichorzianines A were separated into pure components by HPLC on octadecyl bonded and SiO2 phases successively. Nine trichorzianines A (IIa, IIIa, IIIb, IIIc, IVb, Vb, VIa, VIb and VII) were isolated from the complex microheterogeneous mixture. Their N-terminal amino acid is acetylated, the C-terminal amino alcohol is either tryptophanol or phenylalaninol, 7 to 8 of the 19 residues are alpha-aminoisobutyric acid. Gas chromatography on a chiral phase showed isovaline to have the D-configuration and all the other optically active amino acids and amino alcohols to have the L-configuration. The amino acid sequences were determined from their positive ion FAB mass spectra which exhibited the preferential cleavage of the Aib 12-Pro 13 amide bond as a main fragmentation. The resulting fragments subsequently underwent amide bond ruptures that generated two series of abundant acylium ions which enabled direct determination of the 1-19 sequence. The relative position of the isomeric amino acids in the sequence of trichorzianine AVII was assigned from analysis of the N- and C-terminal oligopeptides yielded by its selective acidic hydrolysis. The microheterogeneity of trichorzianines A results mainly from single or multiple substitution of amino acids at the specific positions 5, 14, 16 and 19. PMID:3570662

  19. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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, ...

  1. RNA structure determination by solid-state NMR spectroscopy

    PubMed Central

    Marchanka, Alexander; Simon, Bernd; Althoff-Ospelt, Gerhard; Carlomagno, Teresa

    2015-01-01

    Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize— and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies. PMID:25960310

  2. Structure Determination of Natural Products by Mass Spectrometry.

    PubMed

    Biemann, Klaus

    2015-01-01

    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. PMID:26161970

  3. 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.

  4. 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.

  5. 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

  6. Isolation and chemical structure of aklanonic acid, an early intermediate in the biosynthesis of anthracyclines.

    PubMed

    Eckardt, K; Tresselt, D; Schumann, G; Ihn, W; Wagner, C

    1985-08-01

    The fermentation, isolation and structure elucidation of aklanonic acid are described. The compound was isolated from fermentations of Streptomyces strain ZIMET 43,717. Aklanonic acid is a yellow-orange crystalline substance, melting at 203-204 degrees C (dec), having the molecular formula C21H16O8, and possessing UV maxima at 258, 282 (sh) and 438 nm (CHCl3). In dimethyl sulfoxide or pyridine aklanonic acid is unstable and a new compound (aklanone) is formed as a conversion product. The elucidation of the structures has shown that aklanonic acid and aklanone are derivatives of 1,8-dihydroxyanthraquinone. PMID:3862658

  7. A major inducer of anticarcinogenic protective enzymes from broccoli: isolation and elucidation of structure.

    PubMed Central

    Zhang, Y; Talalay, P; Cho, C G; Posner, G H

    1992-01-01

    Consumption of vegetables, especially crucifers, reduces the risk of developing cancer. Although the mechanisms of this protection are unclear, feeding of vegetables induces enzymes of xenobiotic metabolism and thereby accelerates the metabolic disposal of xenobiotics. Induction of phase II detoxication enzymes, such as quinone reductase [NAD(P)H:(quinone-acceptor) oxidoreductase, EC 1.6.99.2] and glutathione S-transferases (EC 2.5.1.18) in rodent tissues affords protection against carcinogens and other toxic electrophiles. To determine whether enzyme induction is responsible for the protective properties of vegetables in humans requires isolation of enzyme inducers from these sources. By monitoring quinone reductase induction in cultured murine hepatoma cells as the biological assay, we have isolated and identified (-)-1-isothiocyanato-(4R)-(methylsulfinyl)butane [CH3-SO-(CH2)4-NCS, sulforaphane] as a major and very potent phase II enzyme inducer in SAGA broccoli (Brassica oleracea italica). Sulforaphane is a monofunctional inducer, like other anticarcinogenic isothiocyanates, and induces phase II enzymes selectively without the induction of aryl hydrocarbon receptor-dependent cytochromes P-450 (phase I enzymes). To elucidate the structural features responsible for the high inducer potency of sulforaphane, we synthesized racemic sulforaphane and analogues differing in the oxidation state of sulfur and the number of methylene groups: CH3-SOm-(CH2)n-NCS, where m = 0, 1, or 2 and n = 3, 4, or 5, and measured their inducer potencies in murine hepatoma cells. Sulforaphane is the most potent inducer, and the presence of oxygen on sulfur enhances potency. Sulforaphane and its sulfide and sulfone analogues induced both quinone reductase and glutathione transferase activities in several mouse tissues. The induction of detoxication enzymes by sulforaphane may be a significant component of the anticarcinogenic action of broccoli. Images PMID:1549603

  8. 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.

  9. 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

  10. Large-scale isolation of flavonolignans from Silybum marianum extract affords new minor constituents and preliminary structure-activity relationships.

    PubMed

    Sy-Cordero, Arlene; Graf, Tyler N; Nakanishi, Yuka; Wani, Mansukh C; Agarwal, Rajesh; Kroll, David J; Oberlies, Nicholas H

    2010-04-01

    The gram-scale isolation of the major flavonolignan diastereoisomers from milk thistle ( Silybum marianum) extract provided an entree into the isolation of two related analogues that are present in extremely minute quantities. The isolation and structure elucidation of these two new compounds, which we have termed isosilybin C and isosilybin D due to their structural similarities to isosilybin A and isosilybin B, respectively, afforded a preliminary analysis of structure-activity relationships toward prostate cancer growth, survival, and apoptotic endpoints.

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

    PubMed

    Pomin, Vitor H

    2015-09-01

    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.

  12. NEW STRATEGIES FOR THE ISOLATION AND ACTIVITY DETERMINATION OF NATURALLY OCCURRING TYPE-4 GLUTATHIONE PEROXIDASE

    PubMed Central

    Kernstock, Robert M.; Girotti, Albert W.

    2008-01-01

    Type 4 glutathione peroxidase (GPx4) is a widely expressed mammalian selenoenzyme known to play a vital role in cytoprotection against lipid hydroperoxide (LOOH)-mediated oxidative stress and regulation of oxidative signaling cascades. Since prokaryotes are not equipped to express mammalian selenoproteins, preparation of recombinant GPx4 via commonly used bacterial transformation is not feasible. A published procedure for isolating the enzyme from rat testis employs affinity chromatography on bromosulfophthalein-glutathione-linked agarose as the penultimate step in purification. Since this resin is no longer commercially available and preparing it in satisfactory operational form is tedious, we have developed an alternative purification approach based on sequential anion exchange, size exclusion, and cation exchange chromatography. Final preparations were found to be essentially homogeneous in GPx4 (Mr ∼20 kDa), as demonstrated by SDS-PAGE with protein staining and immunoblotting. Specific enzymatic activity was determined using a novel thin layer chromatographic approach in which the kinetics of phosphatidylcholine hydroperoxide loss or cholesterol-7α-hydroperoxide loss were monitored. A >400-fold purification of active enzyme has been attained. The relatively straightforward isolation procedure described should prove valuable for further functional studies on GPx4, e.g. how its ability to catalyze LOOH reduction compares with that of other LOOH detoxifying enzymes. PMID:18723092

  13. Isolation of flavonoids from Delonix elata and determination of its rutin content using capillary electrophoresis.

    PubMed

    Al-Taweel, Areej Mohammed; Abdel-Kader, Maged Saad; Fawzy, Ghada Ahmed; Perveen, Shagufta; Maher, Hadir Mohamed; Al-Zoman, Nourah Zoman; Al-Shehri, Mona Mohamed; Al-Johar, Haya; Al-Showiman, Hessa

    2015-09-01

    Delonix elata (L.) Gamble (Fabaceae) is an important, traditionally used plant in Saudi Arabia. It is used to relieve rheumatic pain, flatulence and the seeds are employed as purgatives. The aim of the present study was to isolate chemical constituents of the n-butanol fraction (BF) of D. elata and to find out, by capillary electrophoresis (CE), percentage of rutin present in this BF. Three quercetin glycosides and one kaempferol rutinoside were isolated from the BF of aerial parts of D. elata; namely, Quercetin 3-O-rutinoside-7-O-glucoside (1), Quercetin 3,7-diglucoside (2), Quercetin 3-O-rutinoside (RUT) (3) and Kaempferol 3-O-rutinoside (4). Rutin, an active constituent has been reported to possess good pharmacological as well as therapeutic potentials. A sensitive and rapid procedure for quantitative determination of RUT by capillary electrophoresis was developed and its content was found to be 7.349 mg/gm, relative to n-butanol fraction and 18.373 mg%, relative to the dry powder of D. elata. The method could be recommended for approval and use in the pharmaceutical and food industries. PMID:26525033

  14. Virulence determinants invA and spvC in salmonellae isolated from poultry products, wastewater, and human sources.

    PubMed

    Swamy, S C; Barnhart, H M; Lee, M D; Dreesen, D W

    1996-10-01

    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.

  15. 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.

  16. Isolation and structure elucidation of new nitrile and mustard oil glycosides from Moringa oleifera and their effect on blood pressure.

    PubMed

    Faizi, S; Siddiqui, B S; Saleem, R; Siddiqui, S; Aftab, K; Gilani, A H

    1994-09-01

    Bioassay-guided analysis of an EtOH extract of Moringa oleifera leaves showing hypotensive activity led to the isolation of two nitrile glycosides, niazirin [1] and niazirinin [2], and three mustard oil glycosides, 4-[(4'-O-acetyl-alpha-L-rhamnosyloxy)benzyl]isothiocyanate [4], niaziminin A, and niaziminin B. Glycoside 2 is a new compound. Niaziminins A and B have previously been obtained from the left extract as a mixture, while compound 4 is new from this source. Structural determination was accomplished by means of spectroscopic methods including appropriate 2D nmr experiments and chemical reactions. This is the first report of the isolation of nitriles, an isothiocyanate, and thiocarbamates from the same plant species. Isothiocyanate 4 and the thiocarbamate glycosides niaziminin A and B showed hypotensive activity while nitrile glycosides 1 and 2 were found to be inactive in this regard. PMID:7798960

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Hydramycin, a new antitumor antibiotic. Taxonomy, isolation, physico-chemical properties, structure and biological activity.

    PubMed

    Hanada, M; Kaneta, K; Nishiyama, Y; Hoshino, Y; Konishi, M; Oki, T

    1991-08-01

    A new antitumor antibiotic hydramycin was isolated from the fermentation broth of Streptomyces violaceus P950-4 (ATCC 53807). It showed potent antibacterial and cytotoxic activity and increased the survival time of mice inoculated with P388 leukemia. A new structure related to the pluramycin group antibiotics was assigned by its spectroscopic experiments. PMID:1833366

  4. On inertia nonlinearity in irregular-plan isolated structures under seismic excitations

    NASA Astrophysics Data System (ADS)

    Amin Afshar, Majid; Aghaei Pour, Sepehr

    2016-02-01

    The influence of nonlinear inertia as a function of acceleration, velocity, and displacement is investigated for an asymmetric isolated structure. Six degrees of freedom (6-DOFs) are defined to illustrate translational and rotational displacements of the superstructure and base isolation. Motion equations of such DOFs are derived using the Lagrangian formalism. Two coordinate systems of the reference are defined, one fixed on the building base (global coordinate) and the other at the torsional isolation level (local coordinate). The motion governing equations in the conventional approach is formulated on a linear form in the global coordinate system, whereas in the novel approach, the local coordinate system leads to a nonlinear form of dynamic equations. The difference between two linear and nonlinear models is appeared because of the existence of nonlinear inertia terms just in the nonlinear one. Afterwards, three particular types of isolated structures are employed with the peculiar ratio of torsional-lateral coupled frequency on symmetric frequency. Numerical analysis is applied to investigate the performance of two structural models by exerting harmonic excitations and earthquakes. The results are obtained while analyzing time history and frequency content and show that the coupling effects of nonlinear inertia lead to differences in the responses of linear and nonlinear models of such structures; also, some nonlinear phenomena such as energy transfer between modes, saturation, rigid displacement, and super-harmonic created due to geometrical (inertial) nonlinearities are studied.

  5. Improved isolation protocol to detect high molecular weight polysaccharide structures of Campylobacter jejuni.

    PubMed

    Kovács, Judit K; Felső, Péter; Emődy, Levente; Schneider, György; Kocsis, Béla

    2014-12-01

    Simple detection of high molecular weight, LPS-like structures of Campylobacter jejuni is still an unsolved problem. A phenol-free extraction method for the detection of HMW polysaccharide was developed without the need for Western blot. This method provides a reliable technique for large-scale screening and comparative characterization study of different isolates.

  6. 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.

  7. 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…

  8. Structure and non-enzymatic light emission of two luciferin precursors isolated from the luminous mushroom Panellus stipticus.

    PubMed

    Shimomura, O; Satoh, S; Kishi, Y

    1993-01-01

    The chemical structure of two luciferin precursors PS-A and PS-B, isolated from the luminous mushroom Panellus stipticus, were determined as 1-O-decanoylpanal (2) and 1-O-dodecanoylpanal (3), respectively. Both PS-A and PS-B were converted into chemiluminescent luciferins by treatment with 50 mmol/l methylamine in a pH 3.5 buffer solution containing an anionic surfactant Tergitol 4 at 25-35 degrees C. The luciferins emitted chemiluminescence in a pH 7-8 buffer solution containing a cationic surfactant in the presence of O2 and O2-.

  9. Tachyplesin, a class of antimicrobial peptide from the hemocytes of the horseshoe crab (Tachypleus tridentatus). Isolation and chemical structure.

    PubMed

    Nakamura, T; Furunaka, H; Miyata, T; Tokunaga, F; Muta, T; Iwanaga, S; Niwa, M; Takao, T; Shimonishi, Y

    1988-11-15

    A cationic peptide, designated tachyplesin, was isolated from acid extracts of horseshoe crab (Tachypleus tridentatus) hemocyte debris. It consists of 17 residues and the structure determined by Edman degradation is: (formula; see text) The carboxyl-terminal end of this peptide was identified as arginine alpha-amide, and the whole sequence including the alpha-amide was also confirmed by fast atom bombardment mass spectrometry, indicating a mass value of 2263. Tachyplesin inhibits growth of both Gram-negative and -positive bacteria at low concentrations and formed a complex with bacterial lipopolysaccharide. Tachyplesin seems likely to act as antimicrobial peptide for self-defense in the horseshoe crab against invading microorganisms.

  10. Hyaluronidase in ram semen. Quantitative determination, and isolation of multiple forms.

    PubMed Central

    Harrison, R A

    1988-01-01

    A study was made of hyaluronidase in ram semen. The end-group assay conditions used to determine activity quantitatively were chosen to ensure reliability as well as sensitivity [Gacesa, Savitsky, Dodgson & Olavesen (1981) Anal. Biochem. 118, 76-84]; they led to 1 W.H.O. Standard International Hyaluronidase Unit displaying 0.1263 EC munit (1 EC unit of activity releases 1 mumol equivalent of N-acetylglucosamine end groups/min at 37 degrees C). All the activity in the semen was shown to be sperm-derived, and intact spermatozoa were estimated to contain 1.23 EC units per 10(9) cells. In a low-ionic-strength medium, only some 20% of the hyaluronidase was extractable, although up to 80% of the activity could be extracted as the ionic strength was increased; further addition of detergent extracted the remainder. During purification of the enzyme, it was found that inclusion of poly(vinyl alcohol) in the media stabilized the activity; detergent inclusion also improved the yield, especially during early stages. As a consequence both of reliable quantitative determination and of stabilization, a number of forms of hyaluronidase could be isolated in high yield, by using anion-exchange chromatography, cation-exchange chromatography, affinity chromatography and gel filtration. The existence of all these forms was confirmed by electrophoresis and immunoblotting with the use of a monoclonal anti-(ram hyaluronidase) antibody, and their presence in very freshly prepared sperm extracts was demonstrated. The specific activity of the isolated major hyaluronidase form was 15.0 EC units/mg; this was equivalent to 119,000 W.H.O. units/mg, higher than any other previously reported values. Images Fig. 4. Fig. 5. PMID:3421926

  11. A Bayesian View on Cryo-EM Structure Determination

    PubMed Central

    Scheres, Sjors H.W.

    2012-01-01

    Three-dimensional (3D) structure determination by single-particle analysis of cryo-electron microscopy (cryo-EM) images requires many parameters to be determined from extremely noisy data. This makes the method prone to overfitting, that is, when structures describe noise rather than signal, in particular near their resolution limit where noise levels are highest. Cryo-EM structures are typically filtered using ad hoc procedures to prevent overfitting, but the tuning of arbitrary parameters may lead to subjectivity in the results. I describe a Bayesian interpretation of cryo-EM structure determination, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain. The statistical framework dictates how data and prior knowledge should be combined, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained. Application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures. PMID:22100448

  12. 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. PMID:9468630

  13. 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.

  14. Elucidation of the chemical structure and determination of the production conditions for a bioactive Maillard reaction product, [5-(5,6-dihydro-4H-pyridin-3-ylidenemethyl)furan-2-yl]methanol, isolated from a glucose-lysine heated mixture.

    PubMed

    Chen, Xiu-Min; Chen, Gang; Chen, Hongwen; Zhang, Yilin; Kitts, David D

    2015-02-18

    We previously isolated a bioactive molecule, named F3-A, from an aqueous glucose (Glc) and lysine (Lys) Maillard reaction (MR) model system. Herein, F3-A was verified as [5-(5,6-dihydro-4H-pyridin-3-ylidenemethyl)furan-2-yl]methanol (5) and was subsequently synthesized for confirmation of bioactivity. Using Taguchi and factorial designs, we determined that the conditions which best increased the yield of F3-A were at pH 6 with a sugar:amino acid ratio of 2:1 and heating time of 12 h at 100 °C. The MR mixtures containing glucose produced highest yield, compared to fructose, lactose, and sucrose. Both the F3-A recovered from Glc-Lys MR mixture and the synthesized product exhibited significant (P < 0.05), dose dependent, nitric oxide (NO) inhibitory activity in Caco-2 cells that was comparable to aminoguanidine (AG) and pyrrolidine dithiocarbamate (PDTC), respectively. Finally, an additional inhibitory effect of F3-A was determined when coincubated with AG in cytokine-induced Caco-2 cells. This bioactivity points to a potential role in preventing intestinal inflammation.

  15. 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.

  16. 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.

  17. Accelerated decolorization of structurally different azo dyes by newly isolated bacterial strains.

    PubMed

    Khalid, Azeem; Arshad, Muhammad; Crowley, David E

    2008-02-01

    Wastewater effluents from the textile and other dye-stuff industries contain significant amounts of synthetic dyes that require treatment to prevent groundwater contamination. In research aimed at biotechnology for treatment of azo dyes, this study examined 288 strains of azo-dye degrading bacteria to identify efficient strains and determine incubation times required for decolorization. Initial enrichment cultures were carried out using a mixture of four structurally different dyes (Acid Red 88, Reactive Black 5, Direct Red 81, and Disperse Orange 3) as the sole source of C and N to isolate the bacteria from soil, activated sludge, and natural asphalt. Six strains were selected for further study based on their prolific growth and ability to rapidly decolorize the dyes individually or in mixtures. Treatment times required by the most efficient strain, AS96 (Shewanella putrefaciens) were as short as 4 h for complete decolorization of 100 mg l(-1) of AR-88 and DR-81 dyes under static conditions, and 6 and 8 h, respectively, for complete decolorization of RB-5 and DO-3. To our knowledge, these bacterial strains are the most efficient azo-dye degrading bacteria that have been described and may have practical application for biological treatment of dye-polluted wastewater streams.

  18. 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. PMID:25839789

  19. Isolation, structural characterization and neurotrophic activity of a polysaccharide from Phellinus ribis.

    PubMed

    Liu, Yuhong; Liu, Chunhui; Jiang, Haiqiang; Zhou, Honglei; Li, Pingli; Wang, Fengshan

    2015-01-01

    A new polysaccharide named PRG was isolated from the fruiting bodies of Phellinus ribis by hot water extraction, ethanol precipitation, anion-exchange and gel-filtration chromatography. PRG was homogeneous, with a molecular weight of 5.16 × 10(3)Da, as determined by high-performance size-exclusion chromatography-multiangle laser light scattering analysis. Its structural characteristics were investigated and elucidated by methylation analysis, partial acid hydrolysis, gas-liquid chromatography mass spectrometry, Fourier transform infrared and nuclear magnetic resonance spectroscopy. Based on obtained data, PRG was found to be a β-d-glucan containing a (1 → 3)-linked backbone, with a branch of two (1 → 6)-linked and one terminal glucoses substituting at the C-6 position every three residues, along the main chain. PRG exhibited neurotrophic activity, which significantly promoted the neurite outgrowth of the nerve growth factor-stimulated PC12 cells, suggesting that it might be a potential candidate for the treatment of neurodegenerative diseases.

  20. Amitorines A and B, Nitrogenous Diterpene Metabolites of Theonella swinhoei: Isolation, Structure Elucidation, and Asymmetric Synthesis.

    PubMed

    Ota, Koichiro; Hamamoto, Yukiko; Eda, Wakiko; Tamura, Kenta; Sawada, Akiyoshi; Hoshino, Ayako; Mitome, Hidemichi; Kamaike, Kazuo; Miyaoka, Hiroaki

    2016-04-22

    Two new nitrogenous prenylbisabolanes never before found in Lithistid sponges have been isolated from Theonella swinhoei. These new diterpenes, named amitorine A (1) and amitorine B (2), containing a prenylbisabolane skeleton have been characterized by spectroscopic analyses, and the relative and absolute configurations of 1 and 2 were determined by asymmetric synthesis of both diastereomers via the common bicyclic lactone 6 intermediate.

  1. Amitorines A and B, Nitrogenous Diterpene Metabolites of Theonella swinhoei: Isolation, Structure Elucidation, and Asymmetric Synthesis.

    PubMed

    Ota, Koichiro; Hamamoto, Yukiko; Eda, Wakiko; Tamura, Kenta; Sawada, Akiyoshi; Hoshino, Ayako; Mitome, Hidemichi; Kamaike, Kazuo; Miyaoka, Hiroaki

    2016-04-22

    Two new nitrogenous prenylbisabolanes never before found in Lithistid sponges have been isolated from Theonella swinhoei. These new diterpenes, named amitorine A (1) and amitorine B (2), containing a prenylbisabolane skeleton have been characterized by spectroscopic analyses, and the relative and absolute configurations of 1 and 2 were determined by asymmetric synthesis of both diastereomers via the common bicyclic lactone 6 intermediate. PMID:27007992

  2. 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

  3. 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.

  4. 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. PMID:22653729

  5. Structural and functional interactions between extraradical mycelia of ectomycorrhizal Pisolithus isolates.

    PubMed

    Wu, Bingyun; Maruyama, Haruka; Teramoto, Munemasa; Hogetsu, Taizo

    2012-06-01

    Extraradical mycelia from different ectomycorrhizal (ECM) roots coexist and interact under the forest floor. We investigated structural connections of conspecific mycelia and translocation of carbon and phosphorus between the same or different genets. Paired ECM Pinus thunbergii seedlings colonized by the same or different Pisolithus isolates were grown side by side in a rhizobox as their mycelia contacted each other. (14)CO(2) or (33)P-phosphoric acid was fed to leaves or a spot on the mycelium in one of the paired seedlings. Time-course distributions of (14)C and (33)P were visualized using a digital autoradiographic technique with imaging plates. Hyphal connections were observed between mycelia of the same Pisolithus isolate near the contact site, but hyphae did not connect between different isolates. (14)C and (33)P were translocated between mycelia of the same isolate. In (33)P-fed mycelia, accumulation of (33)P from the feeding spot toward the host ECM roots was observed. No (14)C and (33)P translocation occurred between mycelia of different isolates. These results provide direct evidence that contact and hyphal connection between mycelia of the same ECM isolate can cause nutrient translocation. The ecological significance of contact between extraradical mycelia is discussed.

  6. [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.

  7. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins.

    PubMed

    Brookes, David H; Head-Gordon, Teresa

    2016-04-01

    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.

  8. High-throughput determination of RNA structure by proximity ligation.

    PubMed

    Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

    2015-09-01

    We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures. PMID:26237516

  9. 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

  10. Sympatric species distribution, genetic diversity and population structure of Haemonchus isolates from domestic ruminants in Pakistan.

    PubMed

    Hussain, Tanveer; Periasamy, Kathiravan; Nadeem, Asif; Babar, Masroor Ellahi; Pichler, Rudolf; Diallo, Adama

    2014-12-15

    Haemonchus species are major gastro-intestinal parasites affecting ruminants across the world. The present study aimed to assess the sympatric species distribution, genetic diversity, population structure and frequency of β-tubulin isotype 1 alleles associated with benzimidazole resistance. Internal transcribed spacer 2 (ITS2) sequences revealed three sympatric species of Haemonchus, H. contortus, H. placei and H. longistipes with 12 distinct genotypes circulating among ruminant hosts in Pakistan. High genetic variability was observed in Pakistani Haemonchus isolates at nicotine amide dehydrogenase subunit 4 (ND4) and cytochrome oxidase subunit 1 (COI) gene loci. Intra-population diversity parameters were higher in H. contortus isolates than H. placei. Phylogenetic analysis of ND4 and COI sequences did not reveal clustering of haplotypes originating from a particular host indicating high rate of gene flow among Haemonchus parasites infecting sheep, goat and cattle in Pakistan. ND4 and COI haplotypes from Pakistan were compared to sequences of Haemonchus isolates from 11 countries to elucidate the population structure. Multidimensional scaling (MDS) plot of pairwise FST derived from 531 ND4 haplotypes revealed clustering together of H. contortus from Pakistan, China, Malaysia and Italy while the isolates from Yemen and United States were found to be genetically distinct. With respect to H. placei, isolates from Pakistan were found to be genetically differentiated from isolates of other countries. The tests for selective neutrality revealed negative D statistics and did not reveal significant deviations in Pakistani Haemonchus populations while significant deviation (P < 0.05) was observed in Brazilian and Chinese H. contortus populations. Median Joining (MJ) network of ND4 haplotypes revealed Yemenese H. contortus being closer to H. placei cluster. β-tubulin isotype 1 genotyping revealed 7.86% frequency of Y allele associated with benzimidazole resistance at F200Y

  11. Sympatric species distribution, genetic diversity and population structure of Haemonchus isolates from domestic ruminants in Pakistan.

    PubMed

    Hussain, Tanveer; Periasamy, Kathiravan; Nadeem, Asif; Babar, Masroor Ellahi; Pichler, Rudolf; Diallo, Adama

    2014-12-15

    Haemonchus species are major gastro-intestinal parasites affecting ruminants across the world. The present study aimed to assess the sympatric species distribution, genetic diversity, population structure and frequency of β-tubulin isotype 1 alleles associated with benzimidazole resistance. Internal transcribed spacer 2 (ITS2) sequences revealed three sympatric species of Haemonchus, H. contortus, H. placei and H. longistipes with 12 distinct genotypes circulating among ruminant hosts in Pakistan. High genetic variability was observed in Pakistani Haemonchus isolates at nicotine amide dehydrogenase subunit 4 (ND4) and cytochrome oxidase subunit 1 (COI) gene loci. Intra-population diversity parameters were higher in H. contortus isolates than H. placei. Phylogenetic analysis of ND4 and COI sequences did not reveal clustering of haplotypes originating from a particular host indicating high rate of gene flow among Haemonchus parasites infecting sheep, goat and cattle in Pakistan. ND4 and COI haplotypes from Pakistan were compared to sequences of Haemonchus isolates from 11 countries to elucidate the population structure. Multidimensional scaling (MDS) plot of pairwise FST derived from 531 ND4 haplotypes revealed clustering together of H. contortus from Pakistan, China, Malaysia and Italy while the isolates from Yemen and United States were found to be genetically distinct. With respect to H. placei, isolates from Pakistan were found to be genetically differentiated from isolates of other countries. The tests for selective neutrality revealed negative D statistics and did not reveal significant deviations in Pakistani Haemonchus populations while significant deviation (P < 0.05) was observed in Brazilian and Chinese H. contortus populations. Median Joining (MJ) network of ND4 haplotypes revealed Yemenese H. contortus being closer to H. placei cluster. β-tubulin isotype 1 genotyping revealed 7.86% frequency of Y allele associated with benzimidazole resistance at F200Y

  12. 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.

  13. Rhizomes of Eremostachys laciniata: Isolation and Structure Elucidation of Chemical Constituents and a Clinical Trial on Inflammatory Diseases

    PubMed Central

    Delazar, Abbas; Sarker, Satyajit D.; Nahar, Lutfun; Jalali, Shahriar Barzegar; Modaresi, Masoud; Hamedeyazdan, Sanaz; Babaei, Hossein; Javadzadeh, Yousef; Asnaashari, Solmaz; Bamdad Moghadam, Sadeighe

    2013-01-01

    Purpose: The purpose of this study was the isolation and structure elucidation of chemical compounds from the rhizomes of Eremostachys laciniata (L) Bunge (EL), an Iranian traditional medicinal herb with a thick root and pale purple or white flowers as well as the clinical studies on the therapeutic efficacy and safety of topical application of the EL extract in the management of some inflammatory conditions, e.g., arthritis, rheumatoid arthritis and septic arthritis (Riter’s syndrome). Methods: The structures of the isolated compounds were elucidated unequivocally on the basis of one and two dimensional NMR, UV and HR-FABMS spectroscopic data analyses. A single-blinded randomized clinical trial was carried out with the extract of the rhizomes of E. laciniata (EL) to determine the efficacy and safety of the traditional uses of EL compared to that of piroxicam in treatment of inflammatory diseases, e.g., osteoarthritis, rheumatoid arthritis and Reiter’s syndrome. Results: Eleven iridoid glycosides, two phenylethanoids and two phytosterols were isolated and identified for the first time from the rhizomes of EL. After 14 days of treatment with the EL and piroxicam ointments, all groups showed significant improvements compared to the control groups. EL (5%) ointment induced better initial therapeutic response than piroxicam (5%) onitment. Conclusion: This clinical trial established that EL was suitable for topical applications as a safe and effective complementary therapy for inflammatory diseases. PMID:24312865

  14. 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.)

  15. 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…

  16. 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)

  17. 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.

  18. 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.

  19. 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.

  20. Determination of discriminating dose and evaluation of amitraz resistance status in different field isolates of Rhipicephalus (Boophilus) microplus in India.

    PubMed

    Kumar, Sachin; Sharma, Anil Kumar; Ray, D D; Ghosh, Srikant

    2014-07-01

    Field tick isolates of Rhipicephalus (Boophilus) microplus were collected from eleven districts located in the northern and eastern states of India to access the resistance status to "Amitraz". Adult immersion test was optimized using laboratory reared acaricide susceptible IVRI-I line and minimum effective concentration was determined as 487.7 ppm with 95 % confidence interval of 455.8-521.8. The discriminating concentration was determined as 975.4 ppm and was tested on female ticks collected by two stage stratified sampling from organized dairy farms and villages. Based on three variables, viz.,mortality, egg masses and reproductive index, the resistance level was categorized.Resistance to amitraz was detected at level I in 3 isolates (RF = 1.56-5.0), at level II in 6 isolates (RF = 9.3-23.3) and at level III in 1 isolate (RF = 27.3) whereas one isolate was found susceptible. The highest resistance was found in the SKR isolate (RF = 27.3) and minimal resistance was detected in the N-24P isolate (RF = 1.56). These experimental data will help in designing tick control strategy which is suffering from acaricide failure and to overcome development of resistance in ticks. PMID:24659517

  1. Comparison of lipopolysaccharide structures of Bordetella pertussis clinical isolates from pre- and post-vaccine era.

    PubMed

    Albitar-Nehme, Sami; Basheer, Soorej M; Njamkepo, Elisabeth; Brisson, Jean-Robert; Guiso, Nicole; Caroff, Martine

    2013-08-30

    Endotoxins are lipopolysaccharides (LPS), and major constituents of the outer membrane of Gram-negative bacteria. Bordetella pertussis LPS were the only major antigens, of this agent of whooping-cough, that were not yet analyzed on isolates from the pre- and post-vaccination era. We compared here the LPS structures of four clinical isolates with that of the vaccine strain BP 1414. All physico-chemical analyses, including SDS-PAGE, TLC, and different MALDI mass spectrometry approaches were convergent. They helped demonstrating that, on the contrary to some other B. pertussis major antigens, no modification occurred in the dodecasaccharide core structure, as well as in the whole LPS molecules. These results are rendering these major antigens good potential vaccine components. Molecular modeling of this conserved LPS structure also confirmed the conclusions of previous experiments leading to the production of anti-LPS monoclonal antibodies and defining the main epitopes of these major antigens.

  2. 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

  3. The isolation, identification and determination of dehydrotumulosic acid in Poria cocos.

    PubMed

    Song, Zonghua; Bi, Kaishun; Luo, Xu; Chan, Kelvin

    2002-05-01

    Poria cocos (Fuling), a popular Chinese medicinal (CM) herb of fungal origin, has been included in many combinations with other CM herbs for its traditionally claimed activities of inducing diuresis, excreting dampness, invigorating the spleen and tranquilizing the mind and its modern pharmacological use of modulating the immune system of the body. Dehydrotumulosic acid, one of the effective constituents of Fuling, was isolated from the chloroform-soluble material of ethanol extract of the fungus. After further purification by a high-performance liquid chromatographic method on a C18 column, the purified constituent was identified using modern analytical techniques, such as UV, 13C-NMR and EI-MS. A reversed-phase high-performance liquid chromatographic method has been developed for the determination of dehydrotumulosic acid in Poria cocos. The determination can be accomplished in less than 50 min using methanol-acetonitrile-2% glacial acetic acid as the mobile phase at a flow rate of 1.0 mL/min, with a UV detector setting at 242 nm and testosterone propionate used as an internal standard. This assay for dehydrotumulosic acid is simple, rapid and with good reproducibility. PMID:12036119

  4. 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

  5. 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.

  6. Advanced Structural Determination of Diterpene Esters Using Molecular Modeling and NMR Spectroscopy.

    PubMed

    Nothias-Scaglia, Louis-Félix; Gallard, Jean-François; Dumontet, Vincent; Roussi, Fanny; Costa, Jean; Iorga, Bogdan I; Paolini, Julien; Litaudon, Marc

    2015-10-23

    Three new jatrophane esters (1-3) were isolated from Euphorbia amygdaloides ssp. semiperfoliata, including an unprecedented macrocyclic jatrophane ester bearing a hemiketal substructure, named jatrohemiketal (3). The chemical structures of compounds 1-3 and their relative configurations were determined by spectroscopic analysis. The absolute configuration of compound 3 was determined unambiguously through an original strategy combining NMR spectroscopy and molecular modeling. Conformational search calculations were performed for the four possible diastereomers 3a-3d differing in their C-6 and C-9 stereocenters, and the lowest energy conformer was used as input structure for geometry optimization. The prediction of NMR parameters ((1)H and (13)C chemical shifts and (1)H-(1)H coupling constants) by density functional theory (DFT) calculations allowed identifying the most plausible diastereomer. Finally, the stereostructure of 3 was solved by comparison of the structural features obtained by molecular modeling for 3a-3d with NMR-derived data (the values of dihedral angles deduced from the vicinal proton-proton coupling constants ((3)JHH) and interproton distances determined by ROESY). The methodology described herein provides an efficient way to solve or confirm structural elucidation of new macrocyclic diterpene esters, in particular when no crystal structure is available.

  7. 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

  8. 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

  9. 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.

  10. Analysis of population structure among Korean and Japanese Legionella pneumophila isolates using hsp60 sequences.

    PubMed

    Park, Chan Geun; Kim, Byoung Jun; Kim, Hee-Youn; Yun, Yeo-Jun; Ko, Kwan Soo; Miyamoto, Hiroshi; Kim, Bum-Joon; Kook, Yoon-Hoh

    2012-08-01

    The population structure of Korean (150 strains) and Japanese (92 strains) Legionella pneumophila isolates along with 18 reference strains were investigated using hsp60 sequence (1647 bp) analysis. Twelve clonal subgroups (hsP-I to hsP-X and hsF-I and hsF-II) were designated on the hsp60 tree, inferred from representative sequences using the neighbor-joining method. Some of the isolates showed unique subgroups depending on the source of isolates, including hsP-I, hsF-I, and hsF-II from cooling tower water, and subgroups hsP-VIII and hsP-X from circulating hot water bath. These subgroups may be useful for epidemiological studies to chase or specify sources of infection in Korea and Japan. PMID:22672106

  11. 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.

  12. Occurrence of aminoglycoside phosphotransferase subclass I and II structural genes among Enterobacteriaceae spp. isolated from meat samples.

    PubMed

    Jayaratne, A H; Collins-Thompson, D L; Trevors, J T

    1990-08-01

    3'-Aminoglycoside phosphotransferase [APH(3')] enzymes are a group responsible for resistance to the antibiotics kanamycin (Km) and neomycin (Nm) in bacteria. Escherichia coli ECT24, originally isolated from a meat sample, harboured an 83-kb conjugative R-plasmid (pRPJ24) that carries transferable resistance to Km and Nm. Plasmid pRPJ24 was transferred by conjugation to Enterobacter cloacae 94R, which was used as the source of plasmid DNA in development of a probe for the Km-resistance determinant. Random cloning of BamHI and HindIII double-digest restriction fragments of pRPJ24 in the pUC18 vector plasmid produced clones resistant to both Nm and Km carrying a 1.9-kb DNA insert. Southern hybridization of pRPJ24 cloned chimeric plasmid DNA (pKPJ94) showed homology with the APH(3')II gene from transposon Tn5. A PstI digest of pKPJ94 produced a 920-bp fragment which hybridized with the APH(3')II structural gene, and was used as a DNA probe for the APH(3')II subclass gene. A 980-bp BamHI fragment from plasmid pGH54 carrying the APH(3')I gene from transposon Tn903 was used as a subclass I probe. Total DNA from 206 randomly screened Km-resistant Enterobacteriaceae isolates from raw ground beef and chicken meat samples were examined for the occurrence of APH(3') subclass I and II using non-radioactively-labelled DNA probes. Thirty-six percent and 60% of the isolates examined carried subclass I and II resistances, respectively, in the isolates from chicken meat samples. The corresponding values for bacterial strains from raw ground beef samples were 51% and 72%, respectively. Four percent of the resistant bacterial isolates from chicken samples did not display homology to either probe.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Characterization of structures in biofilms formed by a Pseudomonas fluorescens isolated from soil

    PubMed Central

    2009-01-01

    Background Microbial biofilms represent an incompletely understood, but fundamental mode of bacterial growth. These sessile communities typically consist of stratified, morphologically-distinct layers of extracellular material, where numerous metabolic processes occur simultaneously in close proximity. Limited reports on environmental isolates have revealed highly ordered, three-dimensional organization of the extracellular matrix, which may hold important implications for biofilm physiology in vivo. Results A Pseudomonas spp. isolated from a natural soil environment produced flocculent, nonmucoidal biofilms in vitro with unique structural features. These mature biofilms were made up of numerous viable bacteria, even after extended culture, and contained up to 50% of proteins and accumulated 3% (by dry weight) calcium, suggesting an important role for the divalent metal in biofilm formation. Ultrastructurally, the mature biofilms contained structural motifs consisting of dense, fibrillary clusters, nanofibers, and ordered, honeycomb-like chambers enveloped in thin sheets. Conclusion Mature biofilms contained living bacteria and were structurally, chemically, and physiologically heterogeneous. The principal architectural elements observed by electron microscopy may represent useful morphological clues for identifying bacterial biofilms in vivo. The complexity and reproducibility of the structural motifs observed in bacterial biofilms appear to be the result of organized assembly, suggesting that this environmental isolate may possess ecological advantages in its natural habitat. PMID:19460161

  14. 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

  15. An analytical approach for detecting isolated periodic solution branches in weakly nonlinear structures

    NASA Astrophysics Data System (ADS)

    Hill, T. L.; Neild, S. A.; Cammarano, A.

    2016-09-01

    This paper considers isolated responses in nonlinear systems; both in terms of isolas in the forced responses, and isolated backbone curves (i.e. the unforced, undamped responses). As isolated responses are disconnected from other response branches, reliably predicting their existence poses a significant challenge. Firstly, it is shown that breaking the symmetry of a two-mass nonlinear oscillator can lead to the breaking of a bifurcation on the backbone curves, generating an isolated backbone. It is then shown how an energy-based, analytical method may be used to compute the points at which the forced responses cross the backbone curves at resonance, and how this may be used as a tool for finding isolas in the forced responses. This is firstly demonstrated for a symmetric system, where an isola envelops the secondary backbone curves, which emerge from a bifurcation. Next, an asymmetric configuration of the system is considered and it is shown how isolas may envelop a primary backbone curve, i.e. one that is connected directly to the zero-amplitude solution, as well as the isolated backbone curve. This is achieved by using the energy-based method to determine the relationship between the external forcing amplitude and the positions of the crossing points of the forced response. Along with predicting the existence of the isolas, this technique also reveals the nature of the responses, thus simplifying the process of finding isolas using numerical continuation.

  16. 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.

  17. Observation and Structure Determination of an Oxide Quasicrystal Approximant.

    PubMed

    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

    2016-08-26

    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 3^{2}.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 TiO_{3} clusters, leading to a fundamental edge length of the tiling 6.7 Å. PMID:27610863

  18. Direct structure determination by atomic-resolution incoherent STEM imaging

    SciTech Connect

    Nellist, P.D.; Xin, Y.; Pennycook, S.J.

    1997-11-01

    Use of a large, annular dark-field (ADF) detector in a scanning transmission electron microscope is shown to give images that can allow direct structure determination, being a convolution between the illuminating probe intensity and an object function localized at the atomic column positions. The ADF image is also shown to resolve crystal spacings more than twice smaller than the phase contrast point resolution limit of the microscope used, with sub-angstrom structural information being retrieved. ADF image of several semiconductor materials are studied.

  19. 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.

  20. Isolation, properties, and structural features of divalent cation ionophores derived from beef heart mitochondria.

    PubMed

    Blondin, G A

    1975-12-30

    The notion of small molecular weight ion carriers in biological systems is herein documented by a description of the isolation and ionophoretic properties of a family of oxyoctadecadienoate congeners derived from beef-heart mitochondria. Although certain members of this family of compounds have been shown to possess unique ionophoretic properties, one should not lose sight of the fact that the compounds that we have described represented only a portion of the total picture. Other chemically unrelated, yet structurally unknown species have been isolated from beef-heart mitochondria, and compounds similar in both chromatographic and spectroscopic properties to the oxyoctadecadienoate family, as well as other unique structures, have been isolated in our laboratory from sarcoplasmic reticulum and chloroplasts. The important points to be derived from these findings are that there is an apparent abundance of natural ionophores and we should no longer concern should address ourselves to the more relevant task of digging them out and ourselves with the question "are there ionophores in biological systems?" but describing their chemical and physical properties. In view of the apparent abundance of natural ionophores, this is an enormous task, especially when one considers that it only represents half of the problem. The isolation and description of the ionophoroprotein or channel-forming complexes share equally in the overall significance and level of understanding attributable to this area of inquiry and it would appear that many fruitful collaborative ventures are, or should be, on the horizon.

  1. 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

  2. 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

  3. Team assembly mechanisms determine collaboration network structure and team performance.

    PubMed

    Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Amaral, Luís A Nunes

    2005-04-29

    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.

  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. Examination of adhesive determinants in three species of Lactobacillus isolated from chicken.

    PubMed

    Gusils, C; Cuozzo, S; Sesma, F; González, S

    2002-01-01

    The microbial adhesion process includes passive forces; electrostatic interactions; hydrophobic, steric forces; lipoteichoic acids; and specific structures, such as external appendages (lectins) and (or) extracellular polymers. In a previous work, we showed that Lactobacillus animalis, L. fermentum, and L. fermentum ssp. cellobiosus had lectinlike proteic structures on their surfaces and high hydrophobicity values on the cell surface of L. fermentum ssp. cellobiosus. Here, we examined the presence of the bacterial forces or structures that could be involved in the interaction between bacteria and epithelial cells. Lactobacillus animalis and L. fermentum possessed a net negative surface charge, whereas L. fermentum ssp. cellobiosus showed similar affinity to both cationic and anionic exchange resins, aggregated in the presence of ammonium sulfate, and had high affinity (75.4%) to a hydrophobic matrix. Only L. animalis was shown to have ribitol teichoic acids in the cell wall. The amount of polysaccharides from cell walls varied between different strains, with L. fermentum ssp. cellobiosus having the highest concentration. Lectin extracts obtained from lactobacilli did not possess sugar residues, thereby demonstrating the proteic nature of the superficial surface structures of three strains. The lactic acid bacteria studied here showed different surface determinants, which could be involved in the interactions between these lactobacilli and intestinal epithelial cells. PMID:11888161

  6. Susceptibility of whey protein isolate to oxidation and changes in physicochemical, structural, and digestibility characteristics.

    PubMed

    Feng, Xianchao; Li, Chenyi; Ullah, Niamat; Cao, Jiqianrui; Lan, Yongli; Ge, Wupeng; Hackman, Robert M; Li, Zhixi; Chen, Lin

    2015-11-01

    Oxidation is an important factor for denaturing of whey protein isolate (WPI) during food processing. We studied the effects of chemical oxidation on physicochemical and structural changes along with in vitro digestibility of WPI in this work. Evaluation of physicochemical changes showed that carbonyl level and dityrosine content increased, whereas total and free thiol group levels decreased for oxidized WPI samples. For the structural changes, protein aggregation was measured by surface hydrophobicity, turbidity, and particle diameter, which was increased for oxidized WPI samples. The increase of the secondary structure β-sheets and antiparallel β-sheet also supported the aggregation of oxidized WPI. A direct quantitative relationship between physicochemical and structural changes and protein digestibility indicated that oxidation-related damage restricts the susceptibility of WPI to proteases. In conclusion, WPI had high susceptibility to oxidative stress, and both physicochemical and structural changes caused by severe oxidative stress could decrease the rate of in vitro digestibility of WPI.

  7. Low-resolution molecular structures of isolated functional units from arthropodan and molluscan hemocyanin.

    PubMed Central

    Grossmann, J G; Ali, S A; Abbasi, A; Zaidi, Z H; Stoeva, S; Voelter, W; Hasnain, S S

    2000-01-01

    Synchrotron x-ray scattering measurements were performed on dilute solutions of the purified hemocyanin subunit (Bsin1) from scorpion (Buthus sindicus) and the N-terminal functional unit (Rta) from a marine snail (Rapana thomasiana). The model-independent approach based on spherical harmonics was applied to calculate the molecular envelopes directly from the scattering profiles. Their molecular shapes in solution could be restored at 2-nm resolution. We show that these units represent stable, globular building blocks of the two hemocyanin families and emphasize their conformational differences on a subunit level. Because no crystallographic or electron microscopy data are available for isolated functional units, this study provides for the first time structural information for isolated, monomeric functional subunits from both hemocyanin families. This has been made possible through the use of low protein concentrations (< or = 1 mg/ml). The observed structural differences may offer advantages in building very different overall molecular architectures of hemocyanin by the two phyla. PMID:10653810

  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. 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. PMID:26691463

  11. Determination of lytic enzyme activities of indigenous Trichoderma isolates from Pakistan

    PubMed Central

    Asad, Saeed Ahmad; Tabassum, Ayesha; Hameed, Abdul; Hassan, Fayyaz ul; Afzal, Aftab; Khan, Sabaz Ali; Ahmed, Rafiq; Shahzad, Muhammad

    2015-01-01

    Abstract 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. PMID:26691463

  12. 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.

  13. Combinations of Macrolide Resistance Determinants in Field Isolates of Mannheimia haemolytica and Pasteurella multocida▿

    PubMed Central

    Desmolaize, Benoit; Rose, Simon; Wilhelm, Cornelia; Warrass, Ralf; Douthwaite, Stephen

    2011-01-01

    Respiratory tract infections in cattle are commonly associated with the bacterial pathogens Mannheimia haemolytica and Pasteurella multocida. These infections can generally be successfully treated in the field with one of several groups of antibiotics, including macrolides. A few recent isolates of these species exhibit resistance to veterinary macrolides with phenotypes that fall into three distinct classes. The first class has type I macrolide, lincosamide, and streptogramin B antibiotic resistance and, consistent with this, the 23S rRNA nucleotide A2058 is monomethylated by the enzyme product of the erm(42) gene. The second class shows no lincosamide resistance and lacks erm(42) and concomitant 23S rRNA methylation. Sequencing of the genome of a representative strain from this class, P. multocida 3361, revealed macrolide efflux and phosphotransferase genes [respectively termed msr(E) and mph(E)] that are arranged in tandem and presumably expressed from the same promoter. The third class exhibits the most marked drug phenotype, with high resistance to all of the macrolides tested, and possesses all three resistance determinants. The combinations of erm(42), msr(E), and mph(E) are chromosomally encoded and intermingled with other exogenous genes, many of which appear to have been transferred from other members of the Pasteurellaceae. The presence of some of the exogenous genes explains recent reports of resistance to additional drug classes. We have expressed recombinant versions of the erm(42), msr(E), and mph(E) genes within an isogenic Escherichia coli background to assess their individually contributions to resistance. Our findings indicate what types of compounds might have driven the selection for these resistance determinants. PMID:21709086

  14. 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. PMID:26595290

  15. 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.

  16. Isolation and Structure of Cancer Cell Growth Inhibitory Tetracyclic Triterpenoids from the Zimbabwean Monadenium lugardae.

    PubMed

    Pettit, George R; Ye, Qinghua; Herald, Delbert L; Knight, John C; Hogan, Fiona; Melody, Noeleen; Mukku, Venugopal J R V; Doubek, Dennis L; Chapuis, Jean-Charles

    2016-06-24

    The Zimbabwean medicinal plant Monadenium lugardae was evaluated as a potential source of new anticancer constituents. Four new tetracyclic triterpene (1-4) were isolated, accompanied by four previously known triterpenes (5-8). Against a panel of human tumor cell lines, lugardstatins 1 (1) and 2 (2) had good cancer cell growth inhibitory activity. All of the triterpene structures (1-8) were established by 1D and 2D NMR spectrometric and HR mass spectrometric analysis. PMID:27214528

  17. Isolation and structure elucidation of azoricasterol, a new sterol of the deepwater sponge Macandrewia azorica

    NASA Astrophysics Data System (ADS)

    Gross, Harald; Reitner, Joachim; König, Gabriele M.

    2004-09-01

    Chemical investigation of the deepwater sponge Macandrewia azorica, collected from the flanks of the Gettysburg and Ormonde Sea Mount, North Atlantic, from a depth of 600 m, has led to the isolation of a new sterol with an unusual side chain (1), along with S-methylergothioneine (2). The structures of compounds 1 and 2 were established by employing spectroscopic techniques (NMR, MS, UV, IR and polarimetry). This is the first report of metabolites of a sponge belonging to the genus Macandrewia.

  18. Isolation and structural elucidation of chondrosterins F-H from the marine fungus Chondrostereum sp.

    PubMed

    Li, Hou-Jin; Chen, Ting; Xie, Ying-Lu; Chen, Wen-Dan; Zhu, Xiao-Feng; Lan, Wen-Jian

    2013-02-01

    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.

  19. Isolation and structure elucidation of phenolic antioxidants from Tamarind (Tamarindus indica L.) seeds and pericarp.

    PubMed

    Sudjaroen, Y; Haubner, R; Würtele, G; Hull, W E; Erben, G; Spiegelhalder, B; Changbumrung, S; Bartsch, H; Owen, R W

    2005-11-01

    Although it is already known that Tamarind (Tamarindus indica L.) seeds contain phenolic substances, the individual components of the seeds have not been fully identified and quantitated, and in the case of Tamarind pericarp not reported. Therefore, major polyphenolic compounds were extracted using organic solvents and the metabolites were isolated by semi-preparative high performance liquid chromatography. Their structures were elucidated by liquid chromatography-electrospray-ionisation-mass spectrometry (LC-ESI-MS), nano-electrospray-ionisation mass spectrometry (ESI-MS), and where possible by gas chromatography-mass spectrometry (GC-MS) and 1H and 13C NMR. Quantitative analysis of polyphenolic compounds in Tamarind seeds and pericarp was conducted by analytical high performance liquid chromatography (HPLC), calculated against standard curves of authentic compounds. The yields of total phenolic compounds after Soxhlet extraction with methanol were 6.54 and 2.82 g/kg (dry weight) in the seeds and pericarp respectively. The profile (%) of polyphenolics in Tamarind pericarp was dominated by proanthcyanidins (73.4) in various forms (+)-catechin (2.0), procyanidin B2 (8.2), (-)-epicatechin (9.4), procyanidin trimer (11.3), procyanidin tetramer (22.2), procyanidin pentamer (11.6), procyanidin hexamer (12.8) along with taxifolin (7.4), apigenin (2.0), eriodictyol (6.9), luteolin (5.0) and naringenin (1.4) of total phenols, respectively. The content of Tamarind seeds comprised only procyanidins, represented (%) mainly by oligomeric procyanidin tetramer (30.2), procyanidin hexamer (23.8), procyanidin trimer (18.1), procyanidin pentamer (17.6) with lower amounts of procyanidin B2 (5.5) and (-)-epicatechin (4.8). Extraction of Tamarind pericarp and seeds using acetone:methanol:acetic acid gave only procyanidin oligomers, but in much higher yield and variety. The antioxidant capacities of the Soxhlet methanolic extracts were determined, and indicates that Tamarind may be an

  20. 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.

  1. 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.

  2. 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.

  3. Optimal isotope labelling for NMR protein structure determinations.

    PubMed

    Kainosho, Masatsune; Torizawa, Takuya; Iwashita, Yuki; Terauchi, Tsutomu; Mei Ono, Akira; Güntert, Peter

    2006-03-01

    Nuclear-magnetic-resonance spectroscopy can determine the three-dimensional structure of proteins in solution. However, its potential has been limited by the difficulty of interpreting NMR spectra in the presence of broadened and overlapping resonance lines and low signal-to-noise ratios. Here we present stereo-array isotope labelling (SAIL), a technique that can overcome many of these problems by applying a complete stereospecific and regiospecific pattern of stable isotopes that is optimal with regard to the quality and information content of the resulting NMR spectra. SAIL uses exclusively chemically and enzymatically synthesized amino acids for cell-free protein expression. We demonstrate for the 17-kDa protein calmodulin and the 41-kDa maltodextrin-binding protein that SAIL offers sharpened lines, spectral simplification without loss of information, and the ability to rapidly collect the structural restraints required to solve a high-quality solution structure for proteins twice as large as commonly solved by NMR. It thus makes a large class of proteins newly accessible to detailed solution structure determination.

  4. 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 conflict in social groups in general and group behavior in extreme, isolated environments in particular. Recent advances in the analysis of social networks and intracultural variation have improved the methods and have shifted the theoretical questions. The research is motivated by three classes of questions: (1) What are the characteristics of the social relations among individuals working and living together in extreme and isolated environments?; (2) What do individuals understand about their group, how does that understanding develop, and how is it socially distributed?; and (3) What is the relationship between that understanding and the functioning of the social group? Answers to these questions are important if we are to advance our knowledge of how individuals and groups adapt to extreme environments. Second, although Antarctic winter-over candidates may be evaluated as qualified on the basis of individual characteristics, they may fail to adapt because of certain characteristics of the social group. Consequently, the ability of winter

  5. 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.

  6. 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.

  7. 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.

  8. 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. PMID:26164553

  9. 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.

  10. 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.

  11. 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

    2015-09-01

    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.

  12. 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.

  13. Isolation and structure of the principal products of preproglucagon processing, including an amidated glucagon-like peptide.

    PubMed

    Andrews, P C; Hawke, D H; Lee, T D; Legesse, K; Noe, B D; Shively, J E

    1986-06-25

    The principal products derived from in vivo processing of anglerfish preproglucagon II were isolated and their structures determined. The structures were confirmed by a combination of automated Edman degradation, amino acid analysis, and fast atom bombardment mass spectrometry. The peptide corresponding to anglerfish preproglucagon II-(22-49) (numbering from the amino terminus of preproglucagon) was isolated intact and defines the site of signal cleavage to be between Gln-21 and Met-22. Glucagon from the anglerfish preproglucagon gene II was found to correspond to preproglucagon II-(52-80) (numbering from the amino terminus). Three forms of a glucagon-like peptide derived from preproglucagon II were also isolated. The structure of the longest form was consistent with the sequence of preproglucagon II-(89-122) deduced from the cDNA, His-Ala-Asp-Gly-Thr-Tyr-Thr-Ser-Asp-Val-Ser-Ser-Tyr-Leu-Gln-Asp-Gln-Ala- Ala-Lys-Asp-Phe-Val-Ser-Trp-Leu-Lys-Ala-Gly-Arg-Gly-Arg-Arg-Glu. The carboxyl-terminal portion deduced from the cDNA remains intact in this form. A second form, preproglucagon II-(89-119) appears to result from proteolytic processing of the major form at the two adjacent arginine residues occurring at the carboxyl terminus. This second form has a glycine residue at its carboxyl terminus and is processed to the third form (preproglucagon II-(89-118)) which contains a carboxyl-terminal arginineamide. Radiolabeling studies in primary tissue culture support the observation that glucagon (preproglucagon II-(52-80], preproglucagon II-(89-122), and preproglucagon II-(89-119) are products of proglucagon processing in vivo. PMID:3755132

  14. Protein Folding Determinants: Structural Features Determining Alternative Disulfide Pairing in α- and χ/λ-Conotoxins†, ‡

    PubMed Central

    Kang, Tse Siang; Radić, Zoran; Talley, Todd T.; Jois, Seetharama D. S.; Taylor, Palmer; Kini, R. Manjunatha

    2016-01-01

    α-Conotoxins isolated from Conus venoms contain 11–19 residues and preferentially fold into the globular conformation that possesses a specific disulfide pairing pattern (C1–3, C2–4). We and others isolated a new family of χ-conotoxins (also called λ conotoxins) with the conserved cysteine framework of α-conotoxins but with alternative disulfide pairing (C1–4, C2–3) resulting in the ribbon conformation. In both families, disulfide pairing and hence folding are important for their biological potency. By comparing the structural differences, we identified potential structural determinants responsible for the folding tendencies of these conotoxins. We examined the role of conserved proline in the first intercysteine loop and the conserved C-terminal amide on folding patterns of synthetic analogues of ImI conotoxin by comparing the isoforms with the regiospecifically synthesized conformers. Deamidation at the C-terminus and substitution of proline in the first intercysteine loop switch the folding pattern from the globular form of α-conotoxins to the ribbon form of χ/λ-conotoxins. The findings are corroborated by reciprocal folding of CMrVIA χ/λ-conotoxins. Substitution of Lys-6 from the first intercysteine loop of CMrVIA conotoxin with proline, as well as the inclusion of an amidated C-terminal shifted the folding preference of CMrVIA conotoxin from its native ribbon conformation toward the globular conformation. Binding assays of ImI conotoxin analogues with Aplysia and Bulinus acetylcholine binding protein indicate that both these substitutions and their consequent conformational change substantially impact the binding affinity of ImI conotoxin. These results strongly indicate that the first intercysteine loop proline and C-terminal amidation act as conformational switches in α- and χ/λ-conotoxins. PMID:17315952

  15. Glycolonitrile oligomerization: structure of isolated oxazolines, potential heterocycles on the early earth

    NASA Technical Reports Server (NTRS)

    Arrhenius, G.; Baldridge, K. K.; Richards-Gross, S.; Siegel, J. S.; Bada, J. L. (Principal Investigator)

    1997-01-01

    A study of glycolonitrile polymerization has led to the isolation and characterization of two 2,5-dihydro-4-aminooxazoles, 4 and 5. Previous reports have misassigned these structures as s-triazines or pyrimidines. X-ray diffraction analysis of crystals of 4 and an acetylated oxazole derivative of 5 (6) confirm the proposed structures. Ab initio computations are used to assess the relative thermodynamic stability of three trimer isomers (an s-triazine, an aminohydroxypyrimidine, and an aminooxazoline), and the results indicate that 4 is a novel kinetic product. Mechanistic considerations rationalize kinetic oxazole formation over the more customary triazine or pyrimidine trimers.

  16. Isolation and structural characterization of a mainly ligand-based dimetallic radical.

    PubMed

    Li, Shuyu; Wang, Xingyong; Zhang, Zaichao; Zhao, Yue; Wang, Xinping

    2015-12-14

    A radical cation of ruthenium was isolated and structurally characterized. The EPR spectrum and theoretical calculations indicate that the spin density mainly resides on ligands. The X-ray structure shows that the change in metal-metal bond lengths is negligible upon one-electron oxidation. sp(3) C-H bond activation was observed during the reaction of the parent molecule with the trityl cation, which possibly occurs via an oxidative EC mechanism: a thermodynamically favorable electron-transfer to give the radical cation intermediate, followed by the hydrogen atom abstraction to afford a cationic tetramethylfulvene complex with formation of a metal-carbon bond.

  17. Roles of soil-structure interaction and damping in base-isolated structures built on numerous soil layers overlying a half-space

    NASA Astrophysics Data System (ADS)

    Tsai, C. S.; Hsueh, C. I.; Su, H. C.

    2016-06-01

    This study examines the roles of soil-structure interaction (SSI), higher modes, and damping in a base-isolated structure built on multiple layers of soil overlying a half space. Closed-form solutions for the entire system, including a superstructure, seismic isolator, and numerous soil layers overlying a half-space, were obtained. The formulations obtained in this study simply in terms of well-known frequencies and mechanical impedance ratios can explicitly interpret the dynamic behavior of a base-isolated structure interacting with multiple soil layers overlying a half-space. The key factors influencing the performance of the isolation system are the damping ratio of the isolator and the ratio of the natural frequency of the fixed-base structure to that of the isolated structure by assuming that the superstructure moves as a rigid body. This study reveals that higher damping in the base isolator is unfavorable to higher mode responses that usually dominate the responses of the superstructure and that the damping mechanism plays an important role in transmitting energy in addition to absorbing energy. It is also concluded that it is possible to design a soft soil layer as an isolation system for isolating vibration energy.

  18. Nonlinear dynamic analysis of multi-base seismically isolated structures with uplift potential II: verification examples

    NASA Astrophysics Data System (ADS)

    Roussis, Panayiotis C.; Tsopelas, Panos C.; Constantinou, Michael C.

    2010-03-01

    The work presented in this paper serves as numerical verification of the analytical model developed in the companion paper for nonlinear dynamic analysis of multi-base seismically isolated structures. To this end, two numerical examples have been analyzed using the computational algorithm incorporated into program 3D-BASIS-ME-MB, developed on the basis of the newly-formulated analytical model. The first example concerns a seven-story model structure that was tested on the earthquake simulator at the University at Buffalo and was also used as a verification example for program SAP2000. The second example concerns a two-tower, multi-story structure with a split-level seismic-isolation system. For purposes of verification, key results produced by 3D-BASIS-ME-MB are compared to experimental results, or results obtained from other structural/finite element programs. In both examples, the analyzed structure is excited under conditions of bearing uplift, thus yielding a case of much interest in verifying the capabilities of the developed analysis tool.

  19. Determinants of femoral geometry and structure during adolescent growth.

    PubMed

    van der Meulen, M C; Ashford, M W; Kiratli, B J; Bachrach, L K; Carter, D R

    1996-01-01

    Our goal was to understand developmental determinants of femoral structure during growth and sexual maturation by relating femoral measurements to gender and developmental factors (age, pubertal stage, height, and body mass). The bone mineral content of the femur was measured by dual energy x-ray absorptiometry in 101 healthy Caucasian adolescents and young adults, 9-26 years of age. After some simplifying assumptions had been made, cross-sectional geometric properties of the femoral midshaft were estimated. Two geometry-based structural indicators, the section modulus and whole bone strength index, were calculated to assess the structural characteristics of the femur. Femoral strength, as described by these structural indicators, increased dramatically from childhood through young adulthood. Regressions were performed between these femoral measurements and the developmental factors. Our data show that of age, pubertal stage, body mass, and height, body mass is the strongest predictor of femoral cross-sectional properties, and the correlation of body mass with femoral cross-sectional structure is independent of gender. A model including all four developmental factors and gender did not substantially increase the accuracy of predictions compared with the model with body mass alone. In light of previous research, we hypothesize that body mass is an indicator of in vivo loading and that this in vivo loading influences the cross-sectional growth of the long bones.

  20. 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.

  1. Contribution of spoligotyping to the characterization of the population structure of Mycobacterium tuberculosis isolates in Portugal.

    PubMed

    David, Suzana; Ribeiro, Diana Raposo; Antunes, Abílio; Portugal, Clara; Sancho, Luísa; de Sousa, José Germano

    2007-09-01

    Tuberculosis is a major health problem in Portugal. To begin characterizing the population structure of Mycobacterium tuberculosis, spoligotyping was used for the systematic typing, through consecutive sampling, of patient isolates from the Amadora-Sintra area of Greater Lisbon. Distribution amongst major spoligotype families, including the Latin American Mediterranean (LAM), T, Haarlem and Beijing, was compared to that of the international spoligotype database SpolDB4 and to the European countries of traditional Portuguese immigration represented in SpolDB4. Spoligotypes from 665 isolates were analyzed and 97 shared international types (SITs) identified. In SpolDB4 Portugal is represented by part of the spoligotypes from this study explaining the reduced number of unidentified patterns. The importance of the LAM family, and especially of LAM1 and LAM9 sub-families that alone represented 38% of all the isolates in this study as compared to 8% relative to the European sub group, led us to believe that at least in this respect the population structure was closer to that of Africa and South America than to Europe. Spoligotypes characteristic of Portugal or Portuguese related settings were identified. These included SIT244 a T1 sub-family predominant in Portugal and Bangladesh, SIT64 a LAM 6 sub-family common to Portugal and Brazil, and SIT1106 a LAM 9 sub-family. These studies were the first in Portugal stressing the importance of monitoring the population structure of M. tuberculosis isolates, an important step towards gaining an understanding of tuberculosis and the dynamics of this disease.

  2. Structural characterization of heparan sulfate proteoglycan subclasses isolated from bovine aortic endothelial cell cultures

    SciTech Connect

    Kinsella, M.G.; Wight, T.N.

    1988-03-22

    Labeled heparan sulfate proteoglycans (HSPG) were isolated from wounded and confluent cultures of bovine aortic endothelial cells by nondegradative extraction with 4 M guanidine hydrochloride and detergent. HSPG were separated from more highly charged chondroitin or dermatan sulfate proteoglycans by ion-exchange chromatography, and subclasses of different hydrodynamic size were isolated by gel filtration. Three major subclasses of HSPG were characterized structurally with respect to the presence and relative size of protein core, the presence and amount of nonsulfated oligosaccharide, and size and structure of heparan sulfate (HS) chains. The largest (600-800-kDa) HSPG subclass (I), isolated from cell layers and media of confluent cultures, bears 38-kDa HS chains on an apparently heterogeneous class of relatively large glycoprotein cores. HSPG II (150-200 kDa), isolated from cell layer or media, has 22-kDa HS chains and smaller core glycoproteins (less than 50 kDa). HSPG III, the subclass of smallest hydrodynamic size, has 13-kDa HS chains and a glycopeptide core of less than 15 kDa. All subclasses bear varying proportions of non-sulfated oligosaccharides of similar sizes. Comparisons of HS chain structure indicated that the different subclasses have similar proportions (49-55%) of N-sulfate, with both O-sulfate and highly N-sulfated blocks of disaccharide distributed similarly along HS chains. In addition, HS chains from subclasses II and III contain sequences that are insensitive to periodate oxidation or heparitinase digestion, suggesting that they contain increased proportions of iduronate.

  3. New complete structure of Hafnia alvei clinical isolate strain PCM 2670 semi-rough lipopolysaccharide.

    PubMed

    Bobko, Ewelina; Tyras, Michal; Jachymek, Wojciech

    2013-06-01

    Hafnia alvei strain PCM 2670 is a clinical isolate from a patient with chronic reproductive tract infection. The novel structure of the semi-rough lipopolysaccharide was established with the use of NMR spectroscopy and mass spectrometry as well as immunochemical techniques. According to the mass spectrometry data, heptose in the oligosaccharide is partially substituted by glycine. H. alvei PCM 2670 core structure encompasses the common core of H. alvei which is modified with two additional galactose units. [structure: see text]. The 6-substituted galactose is the O-antigen repeating unit substitution residue. The repeating unit consists of five monosaccharide residues and has the following structure: →2)-β-Galp-(1→6)-α-Glcp-(1→6)-αGlcpNAc3OAc-(1→4)-α-GalpA-(1→3)-β-GlcpNAc6OAc-(1→6)-core. PMID:23643833

  4. Vibration control of platform structures with magnetorheological elastomer isolators based on an improved SAVS law

    NASA Astrophysics Data System (ADS)

    Xu, Zhao-Dong; Suo, Si; Lu, Yong

    2016-06-01

    This paper presents a study on the vibration control of platform structures with magnetorheological elastomer (MRE) isolators. Firstly, a novel MRE isolator design is put forward based on the mechanical properties of MREs, and subsequently a single-degree-of-freedom (SDOF) dynamic model and a multiple-degree-of-freedom (MDOF) dynamic model for platform systems incorporating such isolators are developed. In order to overcome the shortcomings of the conventional on–off control law, an improved semi-active variable stiffness (SAVS) control law is proposed. The proposed SAVS scheme makes full use of the continuously variable stiffness of MREs, and it takes into account the influence of the sampling interval such that the field-dependent restoring force is made to do negative work during the whole sampling interval as far as possible. The results of numerical simulations demonstrate that the improved SAVS control law can achieve better vibration-control effectiveness than the on–off control law. The comparative results are discussed through examining the mechanisms of these two control laws in light of the power spectral density and the energy input. For an MDOF platform a simplified approach is proposed to combine the local response signals with an equivalent SDOF representation to generate the control parameters for individual isolators, and the effectiveness of such a scheme is also verified through numerical simulation.

  5. 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

  6. Tackling the crystallographic structure determination of the COP9 signalosome.

    PubMed

    Bunker, Richard D

    2016-03-01

    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

  7. 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

  8. 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.

  9. 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

  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. PMID:26325598

  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. 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.

  13. The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

    PubMed

    Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

    2016-01-01

    Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change.

  14. Qualitative Fault Isolation of Hybrid Systems: A Structural Model Decomposition-Based Approach

    NASA Technical Reports Server (NTRS)

    Bregon, Anibal; Daigle, Matthew; Roychoudhury, Indranil

    2016-01-01

    Quick and robust fault diagnosis is critical to ensuring safe operation of complex engineering systems. A large number of techniques are available to provide fault diagnosis in systems with continuous dynamics. However, many systems in aerospace and industrial environments are best represented as hybrid systems that consist of discrete behavioral modes, each with its own continuous dynamics. These hybrid dynamics make the on-line fault diagnosis task computationally more complex due to the large number of possible system modes and the existence of autonomous mode transitions. This paper presents a qualitative fault isolation framework for hybrid systems based on structural model decomposition. The fault isolation is performed by analyzing the qualitative information of the residual deviations. However, in hybrid systems this process becomes complex due to possible existence of observation delays, which can cause observed deviations to be inconsistent with the expected deviations for the current mode in the system. The great advantage of structural model decomposition is that (i) it allows to design residuals that respond to only a subset of the faults, and (ii) every time a mode change occurs, only a subset of the residuals will need to be reconfigured, thus reducing the complexity of the reasoning process for isolation purposes. To demonstrate and test the validity of our approach, we use an electric circuit simulation as the case study.

  15. Tuning upconversion through a sensitizer/activator-isolated NaYF4 core/shell structure

    NASA Astrophysics Data System (ADS)

    Ye, Shuai; Chen, Guanying; Shao, Wei; Qu, Junle; Prasad, Paras N.

    2015-02-01

    The ability to tune the emission color of upconversion nanoparticles (UCNPs) will greatly enhance the scope of their applications, ranging from infrared solar cells to volumetric multiplexed bioimaging. Conventional methods to tune upconversion are to vary the type and/or the concentration of doped rare-earth ions in these nanoparticle formulations. Here, we introduce a different approach to vary the emission colors of the frequently used sensitizer/activator pairs of Yb3+/RE3+ (RE = Ho, Er, Tm) via utilization of a sensitizer/activator-isolated NaYF4 core-shell structure. We show that the typical green, yellow, and blue luminescent colors from Yb3+/Ho3+-, Yb3+/Er3+-, and Yb3+/Tm3+-co-doped NaYF4 UCNPs can be converted into the quasi-white, green, and pink blue, when corresponding core-shell structures of NaYF4:Yb3+ @NaYF4:Ho3+, NaYF4:Yb3+ @NaYF4:Er3+ and NaYF4:Yb3+ @NaYF4:Tm3+ are built. Time-resolved spectra indicate that decay lifetimes of the emission bands from the sensitizer/activator-isolated core-shell structure significantly vary from that of the sensitizer/activator-codoped NaYF4 UCNPs, verifying the strain-induced modulation of emission channels in the core-shell structure. These sensitizer-activator-isolated core-shell UCNPs have implications for a range of biophotonic or photonic applications.The ability to tune the emission color of upconversion nanoparticles (UCNPs) will greatly enhance the scope of their applications, ranging from infrared solar cells to volumetric multiplexed bioimaging. Conventional methods to tune upconversion are to vary the type and/or the concentration of doped rare-earth ions in these nanoparticle formulations. Here, we introduce a different approach to vary the emission colors of the frequently used sensitizer/activator pairs of Yb3+/RE3+ (RE = Ho, Er, Tm) via utilization of a sensitizer/activator-isolated NaYF4 core-shell structure. We show that the typical green, yellow, and blue luminescent colors from Yb3+/Ho3+-, Yb3+/Er

  16. Structure Determination of a Membrane Protein in Proteoliposomes

    PubMed Central

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

    2012-01-01

    An NMR method for determining the three-dimensional structures of membrane proteins in proteoliposomes is demonstrated by determining the structure of MerFt, the 60-residue helix–loop–helix integral membrane core of the 81-residue mercury transporter MerF. The method merges elements of oriented sample (OS) solid-state NMR and magic angle spinning (MAS) solid-state NMR techniques to measure orientation restraints relative to a single external axis (the bilayer normal) from individual residues in a uniformly 13C/15N labeled protein in unoriented liquid crystalline phospholipid bilayers. The method relies on the fast (>105 Hz) rotational diffusion of membrane proteins in bilayers to average the static chemical shift anisotropy and heteronuclear dipole–dipole coupling powder patterns to axially symmetric powder patterns with reduced frequency spans. The frequency associated with the parallel edge of such motionally averaged powder patterns is exactly the same as that measured from the single line resonance in the spectrum of a stationary sample that is macroscopically aligned parallel to the direction of the applied magnetic field. All data are collected on unoriented samples undergoing MAS. Averaging of the homonuclear 13C/13C dipolar couplings, by MAS of the sample, enables the use of uniformly 13C/15N labeled proteins, which provides enhanced sensitivity through direct 13C detection as well as the use of multidimensional MAS solid-state NMR methods for resolving and assigning resonances. The unique feature of this method is the measurement of orientation restraints that enable the protein structure and orientation to be determined in unoriented proteoliposomes. PMID:22217388

  17. 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.

  18. 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.

  19. Prevalence of plasmid-mediated quinolone resistance determinants in Citrobacter freundii isolates from Anhui province, PR China.

    PubMed

    Shao, Yibo; Xiong, Zizhong; Li, Xu; Hu, Lifen; Shen, Jilu; Li, Tao; Hu, Fupin; Chen, Shudan

    2011-12-01

    This study was conducted to detect and analyse the presence of plasmid-mediated quinolone resistance (PMQR) determinants [qnr, aac(6')-Ib-cr and qepA] among Citrobacter freundii isolates from patients in Anhui province, PR China. During 2009-2010, 31 C. freundii strains were collected from various hospital units and patient specimens. Using PCR, qnr genes were detected in eight isolates, but aac(6')-Ib-cr and qepA genes were not found. The genes qnrA1, qnrB1, qnrB2, qnrB4, qnrB10 and qnrB24 were present in 6.5, 3.2, 6.5, 3.2, 3.2 and 3.2% of C. freundii isolates, respectively. A new subgene of qnrB variant (qnrB24) was found and identified for what we believe to be the first time. PFGE after XbaI digestion of genomic DNA indicated that qnr-positive strains were not clonally related. Conjugation experiments were conducted to determine whether the qnr-carrying plasmids were self-transferable, and plasmids of transconjugants were extracted and analysed. The qnr genes were transferred from three clinical isolates to their transconjugants. Two qnrA1 genes transferred quinolone resistance with a plasmid of ~11 kb, whilst the size of the plasmid carrying the qnrB4 gene was ~64 kb. The susceptibility of positive isolates and transconjugants was tested using an agar dilution method according to Clinical and Laboratory Standards Institute guidelines, and the MICs of ciprofloxacin and levofloxacin were determined using Etest strips. Most isolates with qnr genes were resistant to fluoroquinolones and other antimicrobial agents. The MICs of transconjugants showed reduced susceptibility to fluoroquinolones.

  20. Analysis of Drug Resistance Determinants in Klebsiella pneumoniae Isolates from a Tertiary-Care Hospital in Beijing, China

    PubMed Central

    Wang, Qi; Woo, Patrick C. Y.; Tan, Lin; Jing, Hua; Gao, George F.; Liu, Cui Hua

    2012-01-01

    Background The rates of multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) isolates among Enterobacteriaceae isolates, particularly Klebsiella pneumoniae, have risen substantially worldwide. Methodology/Principal Findings To better understand the molecular mechanisms of drug resistance in K. pneumoniae, we analyzed the drug resistance determinants for K. pneumoniae isolates collected from the 306 Hospital, a tertiary-care hospital in Beijing, China, for the period of September 1, 2010-October 31, 2011. Drug susceptibility testing, PCR amplification and sequencing of the drug resistance determinants were performed. Conjugation experiments were conducted to examine the natural ability of drug resistance to disseminate among Enterobacteriaceae strains using a sodium azide-resistant Escherichia coli J53 strain as a recipient. Among the 223 consecutive non-repetitive K. pneumoniae isolates included in this study, 101 (45.3%) were extended-spectrum beta-lactamases (ESBLs) positive. The rates of MDR, XDR, and PDR isolates were 61.4% (n = 137), 22.0% (n = 49), and 1.8% (n = 4), respectively. Among the tested drug resistance-associated genes, the following ones were detected at relatively high rates blaCTX-M-10 (80, 35.9%), aacC2 (73, 32.7%), dhfr (62, 27.8%), qnrS (58, 26.0%), aacA4 (57, 25.6%), aadA1 (56, 25.1%). Results from conjugation experiments indicate that many of the drug resistance genes were transmissible. Conclusions/Significance Our data give a “snapshot” of the complex genetic background responsible for drug resistance in K. pneumoniae in China and demonstrate that a high degree of awareness and monitoring of those drug resistance determinants are urgently needed in order to better control the emergence and transmission of drug-resistant K. pneumoniae isolates in hospital settings. PMID:22860106

  1. The determinants of health: structure, context and agency.

    PubMed

    Williams, Gareth H

    2003-01-01

    The concept of social structure is one of the main building blocks of the social sciences, but it lacks any precise technical definition within general sociological theory. This paper reviews the way in which the concept has been deployed within medical sociology, arguing that in recent times it has been used primarily as a frame for the sociological interpretation of health inequalities and their social determinants. It goes on to examine the contribution that medical sociologists have made to the debate over health inequalities, giving particular attention to contributions to Sociology of Health and Illness. These have often provided a focus for discussions outside or critical of the mainstream debates that have been driven primarily by epidemiologists. The paper reviews some of the main points of criticism of epidemiological approaches, focusing in particular on the methodological constraints that limit the capacity of epidemiologists to develop more theoretically satisfactory accounts of the inter-relationships of social structure, context and agency in their impact on health and well being. Some recent examples from the Journal of more theoretically innovative and analytically fine-grained approaches to understanding the impact of social structure on health are then explored. The paper concludes with an argument for a more historically-informed analysis of the relationships between social structure and health, using the knowledgeable narratives of people in places as a window onto those relationships. PMID:14498934

  2. Mathematical aspects of protein structure determination with NMR orientational restraints.

    PubMed

    Quine, J R; Cross, Timothy A; Chapman, Michael S; Bertram, Richard

    2004-11-01

    The field of structural biology is becoming increasingly important as new technological developments facilitate the collection of data on the atomic structures of proteins and nucleic acids. The solid-state NMR method is a relatively new biophysical technique that holds particular promise for determining the structures of peptides and proteins that are located within the cell membrane. This method provides information on the orientation of the peptide planes relative to an external magnetic field. In this article, we discuss some of the mathematical methods and tools that are useful in deriving the atomic structure from these orientational data. We first discuss how the data are viewed as tensors, and how these tensors can be used to construct an initial atomic model, assuming ideal stereochemistry. We then discuss methods for refining the models using global optimization, with stereochemistry constraints treated as penalty functions. These two processes, initial model building followed by refinement, are the two crucial steps between data collection and the final atomic model.

  3. 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.

  4. 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.

  5. Population genetic structure of Theileria parva field isolates from indigenous cattle populations of Uganda.

    PubMed

    Muwanika, Vincent; Kabi, Fredrick; Masembe, Charles

    2016-03-01

    Theileria parva causes East Coast Fever (ECF) a protozoan infection which manifests as a non-symptomatic syndrome among endemically stable indigenous cattle populations. Knowledge of the current genetic diversity and population structure of T. parva is critical for predicting pathogen evolutionary trends to inform development of effective control strategies. In this study the population genetic structure of 78 field isolates of T. parva from indigenous cattle (Ankole, n=41 and East African shorthorn Zebu (EASZ), n=37) sampled from the different agro ecological zones (AEZs) of Uganda was investigated. A total of eight mini- and micro-satellite markers encompassing the four chromosomes of T. parva were used to genotype the study field isolates. The genetic diversity of the surveyed T. parva populations was observed to range from 0.643±0.55 to 0.663±0.41 among the Central and Western AEZs respectively. The overall Wright's F index showed significant genetic variation between the surveyed T. parva populations based on the different AEZs and indigenous cattle breeds (FST=0.133, p<0.01) and (FST=0.101, p<0.01) respectively. Significant pairwise population genetic differentiations (p<0.05) were observed with FST values ranging from 0.048 to 0.173 between the eastern and northern, eastern and western populations respectively. The principal component analysis (PCA) showed a high level of genetic and geographic sub-structuring among populations. Linkage disequilibrium was observed when populations from all the study AEZs were treated as a single population and when analysed separately. On the overall, the significant genetic diversity and geographic sub-structuring exhibited among the study T. parva isolates has critical implications for ECF control. PMID:26613662

  6. Tuning upconversion through a sensitizer/activator-isolated NaYF₄ core/shell structure.

    PubMed

    Ye, Shuai; Chen, Guanying; Shao, Wei; Qu, Junle; Prasad, Paras N

    2015-03-01

    The ability to tune the emission color of upconversion nanoparticles (UCNPs) will greatly enhance the scope of their applications, ranging from infrared solar cells to volumetric multiplexed bioimaging. Conventional methods to tune upconversion are to vary the type and/or the concentration of doped rare-earth ions in these nanoparticle formulations. Here, we introduce a different approach to vary the emission colors of the frequently used sensitizer/activator pairs of Yb(3+)/RE(3+) (RE = Ho, Er, Tm) via utilization of a sensitizer/activator-isolated NaYF4 core-shell structure. We show that the typical green, yellow, and blue luminescent colors from Yb(3+)/Ho(3+)-, Yb(3+)/Er(3+)-, and Yb(3+)/Tm(3+)-co-doped NaYF4 UCNPs can be converted into the quasi-white, green, and pink blue, when corresponding core-shell structures of NaYF4:Yb(3+) @NaYF4:Ho(3+), NaYF4:Yb(3+) @NaYF4:Er(3+) and NaYF4:Yb(3+) @NaYF4:Tm(3+) are built. Time-resolved spectra indicate that decay lifetimes of the emission bands from the sensitizer/activator-isolated core-shell structure significantly vary from that of the sensitizer/activator-codoped NaYF4 UCNPs, verifying the strain-induced modulation of emission channels in the core-shell structure. These sensitizer-activator-isolated core-shell UCNPs have implications for a range of biophotonic or photonic applications.

  7. Isolation, structure elucidation and DFT study on two novel oligosaccharides from yak milk

    NASA Astrophysics Data System (ADS)

    Singh, Meenakshi; Kumar, Alok; Srivastava, Gaurav; Deepak, Desh; Singh, M. P. V. V.

    2016-08-01

    Two novel oligosaccharides were isolated from yak milk. The milk was processed by the method of Kobata and Ginsberg involving deproteination, centrifugation and lyophilization followed by gel filtrate chromatography acetylation and silica gel column chromatography of derivatized oligosaccharides while their homogeneity was confirmed by HPLC. The structures of these isolated oligosaccharides were elucidated by chemical transformation, chemical degradation, 1H, 13C NMR, 2D NMR (COSY, TOCSY and HSQC) and mass spectrometry. The geometry of compound A (Bosiose) and B (Bovisose) have been optimized at B3LYP method and 6-311 + G(d,p) basis set. The difference between the energies of A and B is 1.269 a.u. or 796.309 kcal/mol.

  8. Isolation and structure of whiskey polyphenols produced by oxidation of oak wood ellagitannins.

    PubMed

    Fujieda, Miho; Tanaka, Takashi; Suwa, Yoshihide; Koshimizu, Seiichi; Kouno, Isao

    2008-08-27

    Three new phenolic compounds named whiskey tannins A and B and carboxyl ellagic acid were isolated from commercial Japanese whiskey, along with gallic acid, ellagic acid, brevifolin carboxylic acid, three galloyl glucoses, a galloyl ester of phenolic glucoside, 2,3-(S)-hexahydroxydiphenoylglucose, and castacrenin B. Whiskey tannins A and B were oxidation products of a major oak wood ellagitannin, castalagin, in which the pyrogallol ring at the glucose C-1 position of castalagin was oxidized to a cyclopentenone moiety. These tannins originated from ellagitannins contained in the oak wood used for barrel production; however, the original oak wood ellagitannins were not detected in the whiskey. To examine whether the whiskey tannins were produced during the charring process of barrel production, pyrolysis products of castalagin were investigated. Dehydrocastalagin and a new phenolcarboxylic acid trislactone having an isocoumarin structure were isolated, along with castacrenin F and ellagic acid. However, whiskey tannins were not detected in the products.

  9. Isolation and structure of whiskey polyphenols produced by oxidation of oak wood ellagitannins.

    PubMed

    Fujieda, Miho; Tanaka, Takashi; Suwa, Yoshihide; Koshimizu, Seiichi; Kouno, Isao

    2008-08-27

    Three new phenolic compounds named whiskey tannins A and B and carboxyl ellagic acid were isolated from commercial Japanese whiskey, along with gallic acid, ellagic acid, brevifolin carboxylic acid, three galloyl glucoses, a galloyl ester of phenolic glucoside, 2,3-(S)-hexahydroxydiphenoylglucose, and castacrenin B. Whiskey tannins A and B were oxidation products of a major oak wood ellagitannin, castalagin, in which the pyrogallol ring at the glucose C-1 position of castalagin was oxidized to a cyclopentenone moiety. These tannins originated from ellagitannins contained in the oak wood used for barrel production; however, the original oak wood ellagitannins were not detected in the whiskey. To examine whether the whiskey tannins were produced during the charring process of barrel production, pyrolysis products of castalagin were investigated. Dehydrocastalagin and a new phenolcarboxylic acid trislactone having an isocoumarin structure were isolated, along with castacrenin F and ellagic acid. However, whiskey tannins were not detected in the products. PMID:18672883

  10. Vibration isolation and reduction by spring-stiffness control based on theory of variable structure systems

    SciTech Connect

    Yamaguchi, H.; Shioya, S.; Oda, M.

    1995-12-31

    By controlling spring stiffness, vibration reduction and isolation for the mass-spring system are achieved in this paper. The control algorithm of the spring stiffness is based on the variable structure systems (VSS) theory. The stiffness-controllable spring is achieved by using two straight bars that are hinged to the mass in a line perpendicular to the direction of mass motion and are applied axial force. Since the axial force causes restoring force equivalent to the spring, the stiffness is controlled by the axial force. In the numerical simulations and experiments, the settling time of the impulse response and the displacement transmissibility are investigated. The results show that the proposed method is effective in suppressing shock motion and isolating vibration transmitted from the floor.

  11. 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

  12. Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism.

    PubMed

    Thompson, F L; Hoste, B; Vandemeulebroecke, K; Swings, J

    2001-12-01

    The genomic diversity among 506 strains of the family Vibrionaceae was analysed using Fluorescent Amplified Fragments Length Polymorphisms (FAFLP). Isolates were from different sources (e.g. fish, mollusc, shrimp, rotifers, artemia, and their culture water) in different countries, mainly from the aquacultural environment. Clustering of the FAFLP band patterns resulted in 69 clusters. A majority of the actually known species of the family Vibrionaceae formed separate clusters. Certain species e.g. V. alginolyticus, V. cholerae, V. cincinnatiensis, V. diabolicus, V. diazotrophicus, V. harveyi, V. logei, V. natriegens, V. nereis, V. splendidus and V. tubiashii were found to be ubiquitous, whereas V. halioticoli, V. ichthyoenteri, V. pectenicida and V. wodanis appear to be exclusively associated with a particular host or geographical region. Three main categories of isolates could be distinguished: (1) isolates with genomes related (i.e. with > or =45% FAFLP pattern similarity) to one of the known type strains; (2) isolates clustering (> or =45% pattern similarity) with more than one type strain; (3) isolates with genomes unrelated (<45% pattern similarity) to any of the type strains. The latter group consisted of 236 isolates distributed in 31 clusters indicating that many culturable taxa of the Vibrionaceae remain as yet to be described.

  13. Prevalence of Virulence-Related Determinants in Clinical Isolates of Staphylococcus epidermidis

    PubMed Central

    Najar Peerayeh, Shahin; Jazayeri Moghadas, Ali; Behmanesh, Mehrdad

    2016-01-01

    Background Staphylococcus epidermidis, a member of the human flora, is recognized as an opportunistic pathogen and cause of nosocomial infections. Staphylococcus epidermidis surface components are able to establish bacteria on the host surface, and cause infection. Objectives The frequency of icaA, IS256, aap, fbe and bhp in clinical isolates of S. epidermidis were investigated in this study. Materials and Methods Fifty-nine S. epidermidis isolates were collected from blood (50), wound (1), urine (4) and tracheal (4) samples (Tehran, Iran). Staphylococcus epidermidis isolates were identified with conventional bacteriological tests. Virulence-associated genes were detected by specific polymerase chain reactions (PCRs). Results Of the 59 S. epidermidis, fbe was found in 89.8%, while aap and bhp were observed in 64.4% and 15.3% of the samples, respectively. Coexistence of aap and fbe was found in 32 isolates, while coexistence of bhp and fbe was observed in five isolates. Two isolates were negative for the investigated genes. Conclusions Prevalence of fbe and aap was significantly different from similar studies, yet frequency of bhp was in accordance with other studies. Prevalence of icaA and IS256 was not significantly different from some studies while a significant difference was observed when results were compared with some other studies. PMID:27800129

  14. Primate retroviruses: immunological cross-reactivity between major structural proteins of new and old world primate virus isolates.

    PubMed Central

    Devare, S G; Arthur, L O; Fine, D L; Stephenson, J R

    1978-01-01

    The major 35,000-molecular-weight internal antigen (p35) of the squirrel monkey retrovirus (SMRV) was isolated and partially characterized. Immunological analysis of SMRV p35 led to the demonstration of antigenic determinants common to SMRV and the Mason-Pfizer monkey virus (MPMV). A broadly reactive competition immunoassay was developed utilizing antiserum to MPMV to precipitate 125I-labeled SMRV p35. Although the major structural proteins of MPMV and SMRV competed with equal efficiency in this assay, type B and type C oncornavirus proteins lacked detectable reactivity. Antibodies reactive with the major structural proteins of both MPMV and SMRV were observed in sera of several normal rhesus monkeys with known prior exposure to MPMV-infected animals. These findings demonstrate the ability of sera from naturally immunized primates to recognize broadly reactive interspecies antigenic determinants shared by the major structural proteins of type D oncornaviruses, and they suggest possible horizontal transmission of MPMV among rhesus monkeys. Although sera from a number of squirrel monkeys contained antibody to SMRV p35, the possibility that this latter reactivity was due to endogenous virus activation rather than horizontal transmission cannot be ruled out. PMID:76686

  15. Disrupted topological organization of structural and functional brain connectomes in clinically isolated syndrome and multiple sclerosis

    PubMed Central

    Shu, Ni; Duan, Yunyun; Xia, Mingrui; Schoonheim, Menno M.; Huang, Jing; Ren, Zhuoqiong; Sun, Zheng; Ye, Jing; Dong, Huiqing; Shi, Fu-Dong; Barkhof, Frederik; Li, Kuncheng; Liu, Yaou

    2016-01-01

    The brain connectome of multiple sclerosis (MS) has been investigated by several previous studies; however, it is still unknown how the network changes in clinically isolated syndrome (CIS), the earliest stage of MS, and how network alterations on a functional level relate to the structural level in MS disease. Here, we investigated the topological alterations of both the structural and functional connectomes in 41 CIS and 32 MS patients, compared to 35 healthy controls, by combining diffusion tensor imaging and resting-state functional MRI with graph analysis approaches. We found that the structural connectome showed a deviation from the optimal pattern as early as the CIS stage, while the functional connectome only showed local changes in MS patients, not in CIS. When comparing two patient groups, the changes appear more severe in MS. Importantly, the disruptions of structural and functional connectomes in patients occurred in the same direction and locally correlated in sensorimotor component. Finally, the extent of structural network changes was correlated with several clinical variables in MS patients. Together, the results suggested early disruption of the structural brain connectome in CIS patients and provided a new perspective for investigating the relationship of the structural and functional alterations in MS. PMID:27403924

  16. 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.

  17. Biological evaluation and determination of the absolute configuration of chloromonilicin, a strong antimicrobial metabolite isolated from Alternaria sonchi.

    PubMed

    Cimmino, Alessio; Pescitelli, Gennaro; Berestetskiy, Alexander; Dalinova, Anna; Krivorotov, Denis; Tuzi, Angela; Evidente, Antonio

    2016-01-01

    Chloromonilicin was isolated for the first time from Alternaria sonchi, a mycoherbicide proposed for the control of the noxious weed Sonchus arvensis. The already known alternethanoxins A and B and the three recently isolated phytotoxic polycyclic ethanones named alternethanoxins C-E were also isolated from the same source. Chloromonilicin was identified by spectroscopic data (essentially one-dimensional NMR, 2-dimensional NMR and high-resolution ESI-MS) and its structure was confirmed by single X-ray analysis, which also allowed the assignment of the absolute configuration. This latter was independently confirmed by electronic CD calculations. When chloromonilicin was tested for its antimicrobial activity, it was active at concentrations 0.5-1 μg per disc against four bacterial species and a yeast fungus. The compound inhibited conidial germination of four plant pathogens at concentration of 1-10 μg ml(-1). No phytotoxic activity of this antibiotic by leaf-disc puncture bioassay was detected.

  18. Full-length sequence analysis of hepatitis E virus isolates: showing potential determinants of virus genotype and identity.

    PubMed

    Yang, Dong; Jiang, Mei; Jin, Min; Qiu, Zhigang; Cui, Weihong; Shen, Zhiqiang; Li, Bo; Gong, Lianfeng; Chen, Zhaoli; Wang, Xinwei; Li, Jun-Wen

    2013-12-01

    The complete genome sequence of a genotype 4 strain of hepatitis E virus (CH-YT-HEV02) from a patient (in Yantai, China) has been determined. Phylogenetic analysis showed that CH-YT-HEV02 belongs to genotype 4, subtype 4a. However, the phylogenetic analysis indicated that it was most closely related to JKO-CHiSai98C (AB197673) strain, sharing only 91.6% sequence identity with it. Judging from the phylogenetic tree based on the full-length nucleotide sequences of all 70 genotype 4 HEV isolates retrieved from GenBank up to May, 2013, the CH-YT-HEV02 isolates could serve as a Yantai-indigenous strain. A broader comparison with other genotype isolates revealed that there are a few conserved amino acids in the HVR region of different HEV genotypes, and two amino acid motifs in ORF2 and ORF3 might serve as signatures of genotype diversity of HEV.

  19. Isolation of Fungi and Bacteria Associated with the Guts of Tropical Wood-Feeding Coleoptera and Determination of Their Lignocellulolytic Activities

    PubMed Central

    Rojas-Jiménez, Keilor; Hernández, Myriam

    2015-01-01

    The guts of beetle larvae constitute a complex system where relationships among fungi, bacteria, and the insect host occur. In this study, we collected larvae of five families of wood-feeding Coleoptera in tropical forests of Costa Rica, isolated fungi and bacteria from their intestinal tracts, and determined the presence of five different pathways for lignocellulolytic activity. The fungal isolates were assigned to three phyla, 16 orders, 24 families, and 40 genera; Trichoderma was the most abundant genus, detected in all insect families and at all sites. The bacterial isolates were assigned to five phyla, 13 orders, 22 families, and 35 genera; Bacillus, Serratia, and Pseudomonas were the dominant genera, present in all the Coleopteran families. Positive results for activities related to degradation of wood components were determined in 65% and 48% of the fungal and bacterial genera, respectively. Our results showed that both the fungal and bacterial populations were highly diverse in terms of number of species and their phylogenetic composition, although the structure of the microbial communities varied with insect host family and the surrounding environment. The recurrent identification of some lignocellulolytic-positive inhabitants suggests that particular microbial groups play important roles in providing nutritional needs for the Coleopteran host. PMID:26379709

  20. Isolation of Fungi and Bacteria Associated with the Guts of Tropical Wood-Feeding Coleoptera and Determination of Their Lignocellulolytic Activities.

    PubMed

    Rojas-Jiménez, Keilor; Hernández, Myriam

    2015-01-01

    The guts of beetle larvae constitute a complex system where relationships among fungi, bacteria, and the insect host occur. In this study, we collected larvae of five families of wood-feeding Coleoptera in tropical forests of Costa Rica, isolated fungi and bacteria from their intestinal tracts, and determined the presence of five different pathways for lignocellulolytic activity. The fungal isolates were assigned to three phyla, 16 orders, 24 families, and 40 genera; Trichoderma was the most abundant genus, detected in all insect families and at all sites. The bacterial isolates were assigned to five phyla, 13 orders, 22 families, and 35 genera; Bacillus, Serratia, and Pseudomonas were the dominant genera, present in all the Coleopteran families. Positive results for activities related to degradation of wood components were determined in 65% and 48% of the fungal and bacterial genera, respectively. Our results showed that both the fungal and bacterial populations were highly diverse in terms of number of species and their phylogenetic composition, although the structure of the microbial communities varied with insect host family and the surrounding environment. The recurrent identification of some lignocellulolytic-positive inhabitants suggests that particular microbial groups play important roles in providing nutritional needs for the Coleopteran host.

  1. Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions.

    PubMed

    Stamm, A; Bernhard, D; Gerhards, M

    2016-06-01

    In this paper we present the first investigations on an isolated linear depsipetide CyCO-Gly-Lac-NH-PhOMe (cyclohexylcarbonyl-glycine-lactate-2-anisidine abbreviated as MOC) in a molecular beam experiment. Depsipeptides are a special subclass of peptides which contain at least one ester bond replacing a peptide bond. This leads to a different folding behavior and a different biological activity compared to a "normal" peptide. In order to analyze the folding of an isolated depsipeptide on a molecular level a variety of combined IR/UV methods including IR/IR/UV experiments are applied to MOC. Three different isomers are identified in combination with DFT calculations using the hybrid functional B3LYP-D3 with a TZVP basis set. The most stable structure shows a tweezer-like arrangement between the aromatic chromophore and the aliphatic cyclohexyl ring. A characteristic feature of this structure is that it is stabilized by dispersion interactions resulting from CH/π interactions. If dispersion is not taken into account this structural arrangement is no longer a minimum on the potential energy surface indicating the importance of dispersion interactions.

  2. Dissipativity analysis of the base isolated benchmark structure with magnetorheological fluid dampers

    NASA Astrophysics Data System (ADS)

    Erkus, Baris; Johnson, Erik A.

    2011-10-01

    This paper investigates the dissipativity and performance characteristics of the semiactive control of the base isolated benchmark structure with magnetorheological (MR) fluid dampers. Previously, the authors introduced the concepts of dissipativity and dissipativity indices in the semiactive control of structures with smart dampers and studied the dissipativity characteristics of simple structures with idealized dampers. To investigate the effects of semiactive controller dissipativity characteristics on the overall performance of the base isolated benchmark building, a clipped optimal control strategy with a linear quadratic Gaussian (LQG) controller and a 20 ton MR fluid damper model is used. A cumulative index is proposed for quantifying the overall dissipativity of a control system with multiple control devices. Two control designs with different dissipativity and performance characteristics are considered as the primary controller in clipped optimal control. Numerical simulations reveal that the dissipativity indices can be classified into two groups that exhibit distinct patterns. It is shown that the dissipativity indices identify primary controllers that are more suitable for application with MR dampers and provide useful information in the semiactive design process that complements other performance indices. The computational efficiency of the proposed dissipativity indices is verified by comparing computation times.

  3. Coupled structural joint inversion and Euler deconvolution of isolated gravity and magnetic anomalies

    NASA Astrophysics Data System (ADS)

    Fregoso, E.; Gallardo, L. A.; García-Abdeslem, J.

    2013-05-01

    The cross-gradient joint inversion is nowadays applied to a diversity of combinations of geophysical data in the search for structurally similar models that facilitate the interpretation of the subsurface characteristics. In line with these results, the cross-gradients joint inversion of gravity and magnetic data, in particular, has succeeded on finding commonly collocated density and magnetization structures. However, the inherent lack of depth resolution in the inversion of potential data still yields density and magnetization models with ambiguities at depth. In our work, we propose that the use of conceptually different interpretation strategies may help to resolve this difficulty and we performed some experiments incorporating the more conventional Euler deconvolution strategy in the joint inversion scheme. In this study we present a methodology to jointly invert potential field data incorporating Euler deconvolution for both magnetic and density sources characterized by the upper part of isolated tridimensional causative bodies. This information feeds, as a priori constraint, the cross-gradient joint 3D inversion methodology. Using synthetic and field data we demonstrate that the coupling of both methodologies generally produce more realistic density and magnetization models than when cross-gradient joint inversion is applied alone. Even though our experiments are performed on isolated anomalies, we suggest that the methodology may be suitable to regions described by sedimentary basins, faults, irregular sills, etc., in order to improve representative models of the true structures.

  4. Simple surface structure determination from Fourier transforms of angle-resolved photoemission extended fine structure

    SciTech Connect

    Zheng, Y. |; Shirley, D.A.

    1995-02-01

    The authors show by Fourier analyses of experimental data, with no further treatment, that the positions of all the strong peaks in Fourier transforms of angle-resolved photoemission extended fine structure (ARPEFS) from adsorbed surfaces can be explicitly predicted from a trial structure with an accuracy of about {+-} 0.3 {angstrom} based on a single-scattering cluster model together with the concept of a strong backscattering cone, and without any additional analysis. This characteristic of ARPEFS Fourier transforms can be developed as a simple method for determining the structures of adsorbed surfaces to an accuracy of about {+-} 0.1 {angstrom}.

  5. New methods of structure refinement for macromolecular structure determination by NMR

    PubMed Central

    Clore, G. Marius; Gronenborn, Angela M.

    1998-01-01

    Recent advances in multidimensional NMR methodology have permitted solution structures of proteins in excess of 250 residues to be solved. In this paper, we discuss several methods of structure refinement that promise to increase the accuracy of macromolecular structures determined by NMR. These methods include the use of a conformational database potential and direct refinement against three-bond coupling constants, secondary 13C shifts, 1H shifts, T1/T2 ratios, and residual dipolar couplings. The latter two measurements provide long range restraints that are not accessible by other solution NMR parameters. PMID:9600889

  6. Structures of Large RNAs and RNA-Protein Complexes: Toward Structure Determination of Riboswitches.

    PubMed

    Grigg, Jason C; Ke, Ailong

    2015-01-01

    Riboswitches are widespread and important regulatory elements. They are typically present in the mRNA of the gene under their regulation, where they form complex three-dimensional structures that can bind an effector and regulate either transcription or translation of the mRNA. Structural biology has been essential to our understanding of their ligand recognition and conformational switching mechanisms, but riboswitch determination presents several important complications. Overcoming these challenges requires a synergistic approach using rational design of the constructs and supporting methods to biochemically validate the designs and resulting structures. PMID:26068743

  7. Rapid Enzyme Immunoassay for Determination of Toxigenicity among Clinical Isolates of Corynebacteria

    PubMed Central

    Engler, Kathryn H.; Efstratiou, Androulla

    2000-01-01

    A rapid enzyme immunoassay (EIA) was developed for the phenotypic detection of diphtheria toxin among clinical isolates of corynebacteria. The assay uses equine polyclonal antitoxin as the capture antibody and an alkaline phosphatase-labeled monoclonal antibody, specific for fragment A of the toxin molecule, as the detecting antibody. The assay is rapid, sensitive, and specific: a final result is available within 3 h of colony selection, and the limits of detection are 0.1 ng of pure diphtheria toxin/ml. Toxigenicity could be detected with isolates grown on a diverse range of culture media, including selective agars. Toxin detection using the EIA was compared to that with the Elek test and PCR detection of fragment A of the diphtheria toxin (tox) gene, using 245 isolates of corynebacteria. The results for the EIA were in complete concordance with those of the Elek test: 87 toxigenic and 158 nontoxigenic isolates. Ten of the phenotypically nontoxigenic strains were found to contain fragment A of the tox gene but did not express the toxin protein. These isolates were found to be nontoxigenic in the Vero cell tissue culture cytotoxicity assay and were therefore nontoxigenic for diagnostic purposes. The EIA is a simple rapid phenotypic test which provides a definitive result on toxigenicity within one working day. PMID:10747112

  8. Population size and time since island isolation determine genetic diversity loss in insular frog populations.

    PubMed

    Wang, Supen; Zhu, Wei; Gao, Xu; Li, Xianping; Yan, Shaofei; Liu, Xuan; Yang, Ji; Gao, Zengxiang; Li, Yiming

    2014-02-01

    Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used nine microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square-root-transformed) and population size (log-transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations.

  9. Dorrigocins: novel antifungal antibiotics that change the morphology of ras-transformed NIH/3T3 cells to that of normal cells. II. Isolation and elucidation of structures.

    PubMed

    Hochlowski, J E; Whittern, D N; Hill, P; McAlpine, J B

    1994-08-01

    Two novel antifungal antibiotics, named dorrigocin A and B have been isolated from the fermentation broth and mycelium of Streptomyces platensis subsp. rosaceus. These closely related compounds were separated from one another by countercurrent chromatography on an Ito coil planet centrifuge. The structures of the dorrigocins were determined by NMR and IR spectroscopy and mass spectrometry. Each is a putative propionate-acetate derived straight chain fatty acid terminating in cycloheximide. The dorrigocins differ from one another only in their oxidation pattern.

  10. Molecular structure and transferability of Tn1546-like elements in Enterococcus faecium isolates from clinical, sewage, and surface water samples in Iran.

    PubMed

    Talebi, M; Pourshafie, M R; Katouli, M; Möllby, R

    2008-03-01

    The molecular structure and transferability of Tn1546 in 143 vancomycin-resistant Enterococcus faecium (VREF) isolates obtained from patients (n = 49), surface water (n = 28), and urban and hospital sewage (n = 66) in Tehran, Iran, were investigated. Molecular characterization of Tn1546 elements in vanA VREF was performed using a combination of restriction fragment length polymorphism analysis and DNA sequencing of the internal PCR fragments of vanA transposons. Long-PCR amplification showed that the molecular size of Tn1546 elements varied from 10.8 to 12.8 kb. The molecular analysis of Tn1546 showed that 45 isolates (31.5%) harbored a deletion/mutation upstream from nucleotide 170. No horizontal transfer of Tn1546 was observed following filter-mating conjugation with these isolates. Nevertheless, the rates of transferability for other isolates were 10(-5) to 10(-6) per donor. Insertion sequences IS1216V and IS1542 were present in 103 (72%) and 138 (96.5%) of the isolates, respectively. The molecular analysis of Tn1546 elements resulted in three genomic organizations. The genomic organization lineage 1 was dominated by the isolates from clinical samples (3.4%), lineage 2 was dominated mostly by sewage isolates (24.5%), and lineage 3 contained isolates obtained from all sources (72.1%). The genetic diversity determined using pulsed-field gel electrophoresis (PFGE) revealed a single E. faecium clone, designated 44, which was common to the samples obtained from clinical specimens and hospital and municipal sewage. Furthermore, the results suggest that lineage 3 Tn1546 was highly disseminated among our enterococcal isolates in different PFGE patterns. PMID:18192406

  11. {sup 13}C-NMR study on the structure of isolated Sc{sub 2}@C{sub 84} metallofullerene

    SciTech Connect

    Yamamoto, Etsuji; Tansho, Masataka; Tomiyama, Tetsuo; Shinohara, Hisanori; Kawahara, Hironori; Kobayashi, Yuji

    1996-03-06

    Here we report the first {sup 13}C-NMR results on the metallofullerene, Sc{sub 2}@C{sub 84}, which determines an isomer cage structure for the metallofullerene. The Sc{sub 2}@C{sub 84} fullerene was separated and isolated from the various hollow fullerenes (C{sub 60}-C{sub 110}) and other scandium metallofullerenes by the multistage high-performance liquid chromatography (HPLC) method by using two complementary types of HPLC columns. The purity of Sc{sub 2}@C{sub 84} relative to other fullerenes was more than 99.9%. {sup 13}C-NMR measurements were made using a 600 MHz NMR (JEOL JNM-A600) at room temperature in CS{sub 2} solvent. 30 refs., 3 figs.

  12. Isolation, structural elucidation, and biological evaluation of a 5-hydroxymethyl-2-furfural derivative, asfural, from enzyme-treated asparagus extract.

    PubMed

    Ito, Tomohiro; Sato, Atsuya; Ono, Tomoko; Goto, Kazunori; Maeda, Takahiro; Takanari, Jun; Nishioka, Hiroshi; Komatsu, Kenichi; Matsuura, Hideyuki

    2013-09-25

    A novel 5-hydroxymethyl-2-furfural (HMF; 1) derivative, which is named asfural (compound 2), was isolated from enzyme-treated asparagus extract (ETAS) along with HMF (1) as a heat shock protein 70 (HSP70) inducible compound. The structure of compound 2 was elucidated on the basis of its spectroscopic data from HREIMS and NMR, whereas the absolute configuration was determined using chiral HPLC analysis, compared to two synthesized compounds, (S)- and (R)-asfural. As a result, compound 2 derived from ETAS was assigned as (S)-(2-formylfuran-5-yl)methyl 5-oxopyrrolidine-2-carboxylate. When compound 2, synthesized (S)- and (R)-asfural, and HMF (1) were evaluated in terms of HSP70 mRNA expression-enhancing activity in HL-60 cells, compound 2 and (S)-asfural significantly increased the expression level in a concentration-dependent manner. HMF (1) also showed significant activity at 0.25 mg/mL.

  13. The molecular structure and lubricating activity of lubricin isolated from bovine and human synovial fluids.

    PubMed Central

    Swann, D A; Silver, F H; Slayter, H S; Stafford, W; Shore, E

    1985-01-01

    Lubricin was isolated from bovine ankle, metacarpophalangeal and knee and human knee synovial fluids. The lubricins isolated from the bovine joint fluids had the same amino acid and carbohydrate compositions, but differences were observed in the relative molecular masses. The Mr values of bovine metacarpophalangeal and ankle lubricin determined by light-scattering measurements were about 200 000, whereas values of 132 000 and 143 000 were obtained for the bovine knee lubricin. The human knee lubricin had a similar carbohydrate composition to bovine knee lubricin except for the higher glucosamine content, and the amino acid composition differed slightly. The human sample had a lower glutamic acid content and a leucine/isoleucine ratio of 2:1 compared with 1:1 in the bovine. The Mr value of the human knee lubricin (166 000) was also lower than that of the bovine metacarpophalangeal and ankle samples. The Mr value of the bovine knee lubricin determined by sedimentation-equilibrium measurements was 171 000. The length measurements determined by electron microscopy and also the sedimentation measurements showed considerable polydispersity and indicate that the degree of extension of lubricin molecules can vary. Friction measurements showed that the human knee synovial-fluid lubricin had equivalent lubricating ability in a test system in vitro to that observed for lubricin isolated from normal bovine synovial fluids. The lubricating ability of lubricin was concentration-dependent, and each lubricin sample was able to act as a lubricant in vitro in an equivalent manner to whole synovial fluid at concentrations that are thought to occur in vivo. PMID:3977823

  14. Isolation, structural elucidation, and neuroprotective effects of iridoids from Valeriana jatamansi.

    PubMed

    Xu, Jing; Li, Yushan; Guo, Yuanqiang; Guo, Ping; Yamakuni, Tohru; Ohizumi, Yasushi

    2012-01-01

    Two new iridoids, jatadoids A (1) and B (2), and two known compounds (3 and 4) were isolated from Valeriana jatamansi. Their structures were elucidated on the basis of extensive spectroscopic analyses (IR, ESI-MS, HR-ESI-MS, 1D and 2D NMR). Compound 1 possessed an isovaleroxy group at the C-3 position that has previously been unreported in the class of iridoids. Four compounds were evaluated and compounds 1 and 3 showed moderate neuroprotective effects against MPP+-induced neuronal cell death in human dopaminergic neuroblastoma SH-SY5Y cells.

  15. Structural investigation of a heteropolysaccharide isolated from the green fruits of Capsicum annuum.

    PubMed

    Mondal, Subhas; Das, Debsankar; Maiti, Debabrata; Roy, Sadhan K; Islam, Syed S

    2009-06-12

    A water-soluble polysaccharide isolated from the hot water extract of the green fruits of Capsicum annuum was found to consist of 3-O-acyl-L-rhamnose, D-methyl galacturonate, 6-O-methyl-D-galactose in a molar proportion of nearly 1:2:1. Structural investigation of the polysaccharide was carried out using total hydrolysis, methylation analysis, periodate oxidation followed by GLC-MS, and NMR experiments. On the basis of the above-mentioned experiments it is concluded that the following repeating unit is present in the polysaccharide.

  16. Strain field reconstruction in shallow trench isolation structures by CBED and LACBED

    NASA Astrophysics Data System (ADS)

    Spessot, A.; Frabboni, S.; Balboni, R.; Armigliato, A.

    2006-12-01

    Using a combination of the CBED and the LACBED techniques in the transmission electron microscopy (TEM), we have investigated the strain field in the silicon active region of a shallow trench isolation structure, underlying a TiSi 2 layer. Starting from the analysis of the deformation in a sample, thinned for TEM analysis, we have reconstructed the displacement field, simulating the split HOLZ lines visible in the experimental CBED patterns. From the comparison between the experimental LACBED patterns, taken in a suitable sample orientation to evidence the stressors distribution in the polycrystalline silicide layer, and the corresponding dynamically simulated ones, we have reproduced the strain field in the unthinned, bulk sample.

  17. Aurantimycins, new depsipeptide antibiotics from Streptomyces aurantiacus IMET 43917. Production, isolation, structure elucidation, and biological activity.

    PubMed

    Gräfe, U; Schlegel, R; Ritzau, M; Ihn, W; Dornberger, K; Stengel, C; Fleck, W F; Gutsche, W; Härtl, A; Paulus, E F

    1995-02-01

    Aurantimycins A (1), B (2) and C (3) were isolated from the mycelium of Streptomyces aurantiacus JA 4570 as new representatives of the azinothricin group of hexadepsipeptide antibiotics. Their structures were settled by X-ray diffraction analysis of crystalline aurantimycin A (1), high field homo- and heteronuclear 2D NMR experiments, high-resolution mass spectrometry and amino acid analysis. Aurantimycins are characterized by a new side chain containing fourteen carbon atoms. They display strong activity against Gram-positive bacteria and cytotoxic effects against L-929 mouse fibroblast cells.

  18. Use of the VNTR typing technique to determine the origin of Mycobacterium tuberculosis strains isolated from Filipino patients in Korea.

    PubMed

    Lee, Jihye; Tupasi, Thelma E; Park, Young Kil

    2014-05-01

    With increasing international interchange of personnel, international monitoring is necessary to decrease tuberculosis incidence in the world. This study aims to develop a new tool to determine origin of Mycobacterium tuberculosis strains isolated from Filipino patients living in Korea. Thirty-two variable number tandem repeat (VNTR) loci were used for discrimination of 50 Filipino M. tuberculosis strains isolated in the Philippines, 317 Korean strains isolated in Korea, and 8 Filipino strains isolated in Korea. We found that the VNTR loci 0580, 0960, 2531, 2687, 2996, 0802, 2461, 2163a, 4052, 0424, 1955, 2074, 2347, 2401, 3171, 3690, 2372, 3232, and 4156 had different mode among copy numbers or exclusively distinct copy number in VNTR typing between Filipino and Korean M. tuberculosis strains. When these differences of the VNTR loci were applied to 8 Filipino M. tuberculosis strains isolated in Korea, 6 of them revealed Filipino type while 2 of them had Korean type. Using the differences of mode or repeated number of VNTR loci were very useful in distinguishing the Filipino strain from Korean strain.

  19. Comparative Proteomic Analysis of Human Liver Tissue and Isolated Hepatocytes with a Focus on Proteins Determining Drug Exposure.

    PubMed

    Vildhede, Anna; Wiśniewski, Jacek R; Norén, Agneta; Karlgren, Maria; Artursson, Per

    2015-08-01

    Freshly isolated human hepatocytes are considered the gold standard for in vitro studies of liver functions, including drug transport, metabolism, and toxicity. For accurate predictions of the in vivo outcome, the isolated hepatocytes should reflect the phenotype of their in vivo counterpart, i.e., hepatocytes in human liver tissue. Here, we quantified and compared the membrane proteomes of freshly isolated hepatocytes and human liver tissue using a label-free shotgun proteomics approach. A total of 5144 unique proteins were identified, spanning over 6 orders of magnitude in abundance. There was a good global correlation in protein abundance. However, the expression of many plasma membrane proteins was lower in the isolated hepatocytes than in the liver tissue. This included transport proteins that determine hepatocyte exposure to many drugs and endogenous compounds. Pathway analysis of the differentially expressed proteins confirmed that hepatocytes are exposed to oxidative stress during isolation and suggested that plasma membrane proteins were degraded via the protein ubiquitination pathway. Finally, using pitavastatin as an example, we show how protein quantifications can improve in vitro predictions of in vivo liver clearance. We tentatively conclude that our data set will be a useful resource for improved hepatocyte predictions of the in vivo outcome.

  20. Structural isomerization of synephrine influences its uptake and ensuing glutathione depletion in rat-isolated cardiomyocytes.

    PubMed

    Rossato, Luciana Grazziotin; Costa, Vera Marisa; de Pinho, Paula Guedes; Carvalho, Félix; de Lourdes Bastos, Maria; Remião, Fernando

    2011-08-01

    Synephrine is a natural compound, frequently added to ephedra-free dietary supplements for weight-loss, due to its effects as a nonspecific adrenergic agonist. Though only p-synephrine has been documented in plants, the presence of m-synephrine has also been reported in weight-loss products. The use of synephrine in dietary supplements was accompanied by reports of adverse effects, especially at the cardiovascular level. It is well known that the imbalance in cardiac glutathione levels can increase the risk of cardiomyopathy. The present work aimed to study the role of organic cation-mediated transport of m- and p-synephrine and the possibility that p- and m-synephrine induce intracellular changes in glutathione levels in calcium-tolerant freshly isolated cardiomyocytes from adult rat. After a 3 h incubation with 1 mM p- or m-synephrine, the intracellular content of synephrine was measured by gas chromatography/ion trap-mass spectrometry (GC/IT-MS); cell viability and intracellular glutathione levels were also determined. To evaluate the potential protective effects of antioxidants against the adverse effects elicited by m-synephrine, cells were pre-incubated for 30 min with Tiron (100 μM) or N-acetyl-cysteine (NAC) (1 mM). To assess the influence of α(1)-adrenoceptors activation in glutathione depletion, a study with prazosin (100 nM) was also performed. The results obtained provide evidence that organic cation transporters OCT3 and OCT1 play a major role in m- and p-synephrine-mediated transport into the cardiomyocytes. The importance of these transporters seems similar for both isomers, although p-synephrine enters more into the cardiomyocytes. Furthermore, only m-synephrine induced intracellular total glutathione (GSHt) and reduced glutathione (GSH) depletion. NAC and Tiron were able to counteract the m-synephrine-induced GSH and GSHt decrease. On the other hand, the incubation with prazosin was not able to change m-synephrine-induced glutathione

  1. Isolation and structure elucidation of phenolic antioxidants from Tamarind (Tamarindus indica L.) seeds and pericarp.

    PubMed

    Sudjaroen, Y; Haubner, R; Würtele, G; Hull, W E; Erben, G; Spiegelhalder, B; Changbumrung, S; Bartsch, H; Owen, R W

    2005-11-01

    Although it is already known that Tamarind (Tamarindus indica L.) seeds contain phenolic substances, the individual components of the seeds have not been fully identified and quantitated, and in the case of Tamarind pericarp not reported. Therefore, major polyphenolic compounds were extracted using organic solvents and the metabolites were isolated by semi-preparative high performance liquid chromatography. Their structures were elucidated by liquid chromatography-electrospray-ionisation-mass spectrometry (LC-ESI-MS), nano-electrospray-ionisation mass spectrometry (ESI-MS), and where possible by gas chromatography-mass spectrometry (GC-MS) and 1H and 13C NMR. Quantitative analysis of polyphenolic compounds in Tamarind seeds and pericarp was conducted by analytical high performance liquid chromatography (HPLC), calculated against standard curves of authentic compounds. The yields of total phenolic compounds after Soxhlet extraction with methanol were 6.54 and 2.82 g/kg (dry weight) in the seeds and pericarp respectively. The profile (%) of polyphenolics in Tamarind pericarp was dominated by proanthcyanidins (73.4) in various forms (+)-catechin (2.0), procyanidin B2 (8.2), (-)-epicatechin (9.4), procyanidin trimer (11.3), procyanidin tetramer (22.2), procyanidin pentamer (11.6), procyanidin hexamer (12.8) along with taxifolin (7.4), apigenin (2.0), eriodictyol (6.9), luteolin (5.0) and naringenin (1.4) of total phenols, respectively. The content of Tamarind seeds comprised only procyanidins, represented (%) mainly by oligomeric procyanidin tetramer (30.2), procyanidin hexamer (23.8), procyanidin trimer (18.1), procyanidin pentamer (17.6) with lower amounts of procyanidin B2 (5.5) and (-)-epicatechin (4.8). Extraction of Tamarind pericarp and seeds using acetone:methanol:acetic acid gave only procyanidin oligomers, but in much higher yield and variety. The antioxidant capacities of the Soxhlet methanolic extracts were determined, and indicates that Tamarind may be an

  2. On the molecular structure of the amylopectin fraction isolated from "high-amylose" ae maize starches.

    PubMed

    Peymanpour, Ghazal; Marcone, Massimo; Ragaee, Sanaa; Tetlow, Ian; Lane, Christopher C; Seetharaman, Koushik; Bertoft, Eric

    2016-10-01

    The amylopectin fractions from starch of a series of amylose-extender (ae) maize samples (HYLON(®) V, VII and VIII starches) were isolated and analysed for their molecular composition and structure. The fractions from all samples contained both a high and a low molecular weight fraction (HMF and LMF), of which LMF increased with the amylose content of the starch and appeared to have substantially more of long chains than HMF. A normal amylose-containing maize starch (NMS), which served as a reference sample, contained very little LMF, which suggested that LMF was the inherent result of the effect of the loss of starch branching enzyme IIb activity in the ae mutants. Clusters were isolated from the amylopectin fractions using Bacillus amyloliquefaciens α-amylase, which effectively hydrolyses long internal chain segments between clusters. During the hydrolysis process, clearly more of small dextrins were released from the ae starches in comparison to NMS. It appeared that some of these small dextrins did not precipitate in methanol together with the majority of the clusters. Nevertheless, isolated clusters from the HYLON starch samples were smaller than in NMS and the clusters possessed a lower density of branches with longer chains. The composition of small, branched building blocks was also clearly different: HYLON starch samples possessed much more of single-branched blocks and less multiple-branched blocks than NMS. PMID:27296443

  3. Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments.

    PubMed

    Penone, Caterina; Weinstein, Ben G; Graham, Catherine H; Brooks, Thomas M; Rondinini, Carlo; Hedges, S Blair; Davidson, Ana D; Costa, Gabriel C

    2016-08-31

    The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale. PMID:27559061

  4. beta-Lactam resistance phenotype determination in Escherichia coli isolates from University Malaya Medical Centre.

    PubMed

    Wong, Jeanne Sze Lyn; Mohd Azri, Zainal Abidin; Subramaniam, Geetha; Ho, Siaw Eng; Palasubramaniam, Selvi; Navaratnam, Parasakthi

    2003-12-01

    beta-Lactamases have been identified as the major cause of antimicrobial resistance to beta-lactam antibiotics in Escherichia coli. The activities of ampicillin-sulbactam and amoxicillin-clavulanate as well as a range of beta-lactam antibiotics were studied with 87 clinical E. coli isolates from patients of the University Malaya Medical Center using the disc diffusion technique. Susceptible, intermediate and resistant categories were established based on the diameter of zones of inhibition set by the National Committee for Clinical Laboratory Standards (NCCLS). The isolates were then classified into 6 phenotypes according to the criteria stated in the methodology: S (susceptible to all beta-lactams); TL (resistant to aminopenicillins; amoxicillin-clavulanate susceptible and susceptible or intermediate to ampicillin-sulbactam); TI (resistant to aminopenicillins and ampicillin-sulbactam; susceptible to amoxicilin-clavulanate); TH-IRT (resistant to aminopenicillins; intermediate or resistant to amoxicillin-clavulanate; resistant to ampicillin-sulbactam); ESBL (resistant to aminopenicillins and oxyimino cephalosporins; positive results with the double-disc diffusion test); and CP (resistant to aminopenicillins, beta-lactam-beta-lactamase inhibitor combinations, oxyimino cephalosporins and cephamycins). Results showed that the TL phenotype was the commonest (40.2% of the isolates) followed by S (31%), TH-IRT (16.1%), ESBL and CP (3.4% each) and TI (2.3%). One isolate showed both ESBL and CP phenotypes while two isolates were classified as inconclusive. Representatives from each phenotype were further analysed for the presence of beta-lactamases which revealed a predominance of TEM and SHV enzyme producers. PCR-SSCP analysis of the SHV gene from all the ESBL and CP isolates revealed the predominance of SHV 5-type enzyme which was concurrent with our previous studies.

  5. Nanoscale structural features determined by AFM for single virus particles.

    PubMed

    Chen, Shu-wen W; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-11-21

    In this work, we propose "single-image analysis", as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis. PMID:24056758

  6. Clinical islet isolation and transplantation outcomes with deceased cardiac death donors are similar to neurological determination of death donors.

    PubMed

    Andres, Axel; Kin, Tatsuya; O'Gorman, Doug; Livingstone, Scott; Bigam, David; Kneteman, Norman; Senior, Peter; Shapiro, A M James

    2016-01-01

    In islet transplantation, deceased cardiac death (DCD) donation has been identified as a potential extended source. There are currently no studies comparing outcomes between these categories, and our goal was to compare islet isolation success rates and transplantation outcomes between DCD and neurological determination of death (NDD) donors. Islet isolations from 15 DCD and 418 NDD were performed in our centre between September 2008 and September 2014. Donor variables, islet yields, metabolic function of isolated isled and insulin requirements at 1-month post-transplant were compared. Compared to NDD, pancreata from DCD were more often procured locally and donors required less vasopressive support (P < 0.001 and P = 0.023, respectively), but the other variables were similar between groups. Pre- and postpurification islet yields were similar between NDD and DCD (576 vs. 608 × 10(3) islet equivalent, P = 0.628 and 386 vs. 379, P = 0.881, respectively). The metabolic function was similar between NDD and DCD, as well as the mean decrease in insulin requirement at 1-month post-transplantation (NDD: 64.82%; DCD: 60.17% reduction, P = 0.517). These results support the broader use of DCD pancreata for islet isolation. A much larger DCD islet experience will be required to truly determine noninferiority of both short- and long-term outcomes.

  7. Isolation, Identification, and Sequencing of a Goose-Derived Newcastle Disease Virus and Determination of Its Pathogenicity.

    PubMed

    Chen, Xiao-Qing; Li, Zi-Bing; Hu, Gui-Xue; Gu, Song-Zhi; Zhang, Shuang; Ying, Ying; Gao, Feng-Shan

    2015-06-01

    In August 2010, geese in the Meihekou area of Jilin province in China were found to be infected by a pathogen that caused a disease similar to Newcastle disease. To determine the causative agent of the infections, a virus was isolated from liver tissues of infected geese, followed by a pathogenicity determination. The isolated virus was named NDV/White Goose/China/Jilin(Meihekou)/MHK-1/2010. Specific primers were designed to amplify the whole genome of the MHK-1 virus, followed by sequencing and splicing of the entire genome. Sequencing and phylogenetic analysis of MHK-1 showed that the isolate was a virulent strain of Newcastle disease virus. The MHK-1 genome is 15,192 nucleotides long, and it belongs to the class II branch of Newcastle disease viruses, as evidenced by the amino acid sequence (112R-R-Q-K-R-F117) of the F protein. The hemagglutinin titer was 1:128 to 1:512. The chicken embryo mean death time, the intracerebral pathogenicity index, and the median lethal dose of chicken embryos of MHK-1 were 43 hr, 1.63, and 10(9)/ml, respectively, which revealed that the newly isolated MHK-1 strain is strongly pathogenic to geese. PMID:26473673

  8. Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates.

    PubMed

    Schuster, Brian M; Tyzik, Anna L; Donner, Rachel A; Striplin, Megan J; Almagro-Moreno, Salvador; Jones, Stephen H; Cooper, Vaughn S; Whistler, Cheryl A

    2011-11-01

    Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic population, with clones recurring in both years. Certain isolates were closely related to toxigenic O1 strains, yet no virulence genes were detected. Multiple statistical tests revealed evidence of recombination among strains that contributed to allelic diversity equally as mutation. This relatively isolated population discovered on the northern limit of detection for V. cholerae can serve as a model of natural population dynamics that augments predictive models for disease emergence.

  9. Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus

    NASA Astrophysics Data System (ADS)

    Knolhoff, Ann M.; Zheng, Jie; McFarland, Melinda A.; Luo, Yan; Callahan, John H.; Brown, Eric W.; Croley, Timothy R.

    2015-08-01

    The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to exhibit antimicrobial activity against a number of pathogens, such as E. coli, Salmonella, and methicillin-resistant Staphylococcus aureus (MRSA). The responsible antimicrobial compounds were isolated from these Paenibacillus strains and a combination of low and high resolution mass spectrometry with multiple-stage tandem mass spectrometry was used for identification. A group of closely related cyclic lipopeptides was identified, differing primarily by fatty acid chain length and one of two possible amino acid substitutions. Variation in the fatty acid length resulted in mass differences of 14 Da and yielded groups of related MSn spectra. Despite the inherent complexity of MS/MS spectra of cyclic compounds, straightforward analysis of these spectra was accomplished by determining differences in complementary product ion series between compounds that differ in molecular weight by 14 Da. The primary peptide sequence assignment was confirmed through genome mining; the combination of these analytical tools represents a workflow that can be used for the identification of complex antibiotics. The compounds also share amino acid sequence similarity to a previously identified broad-spectrum antibiotic isolated from Paenibacillus. The presence of such a wide distribution of related compounds produced by the same organism represents a novel class of broad-spectrum antibiotic compounds.

  10. Population Structure, Pathogenicity, and Mating Type Distribution of Magnaporthe oryzae Isolates from East Africa.

    PubMed

    Onaga, Geoffrey; Wydra, Kerstin; Koopmann, Birger; Séré, Yakouba; von Tiedemann, Andreas

    2015-08-01

    Rice blast, caused by Magnaporthe oryzae, is one of the emergent threats to rice production in East Africa (EA), where little is known about the population genetics and pathogenicity of this pathogen. We investigated the genetic diversity and mating type (MAT) distribution of 88 isolates of M. oryzae from EA and representative isolates from West Africa (WA) and the Philippines (Asia) using amplified fragment length polymorphism markers and mating-type-specific primer sets. In addition, the aggressiveness of each isolate was evaluated by inoculating on the susceptible Oryza sativa indica 'Co39', scoring the disease severity and calculating the disease progress. Hierarchical analysis of molecular variance revealed a low level of genetic differentiation at two levels (FST 0.12 and FCT 0.11). No evidence of population structure was found among the 65 isolates from EA, and gene flow among EA populations was high. Moreover, pairwise population differentiation (GST) in EA populations ranged from 0.03 to 0.04, suggesting that >96% of genetic variation is derived from within populations. However, the populations from Asia and WA were moderately differentiated from EA ones. The spatial analysis of principal coordinates and STRUCTURE revealed overlapping between individual M. oryzae isolates from EA, with limited distinctness according to the geographic origin. All the populations were clonal, given the positive and significant index of association (IA) and standardized index of association (rd), which indicates a significant (P<0.001) departure from panmixia (IA and rd=0). Both MAT1-1 and MAT1-2 were detected. However, MAT1-1 was more prevalent than MAT1-2. Pathogenicity analysis revealed variability in aggressiveness, suggesting a potential existence of different races. Our data suggest that either M. oryzae populations from EA could be distributed as a single genetic population or gene flow is exerting a significant influence, effectively swamping the action of selection

  11. Structural characterization of amphiphilic siderophores produced by a soda lake isolate, Halomonas sp. SL01, reveals cysteine-, phenylalanine- and proline-containing head groups.

    PubMed

    Figueroa, Luis O'mar Serrano; Schwarz, Benjamin; Richards, Abigail M

    2015-11-01

    Soap Lake, located in Washington State, is a naturally occurring saline and alkaline lake. Several organisms inhabiting this lake have been identified as producers of siderophores that are unique in structure. Bacterial isolates, enriched from Soap Lake sediment and water samples, were screened for siderophore production using both the chrome azurol S (CAS) agar plate and liquid methods. Bacterial isolate Halomonas sp. SL01 was found to produce relatively high concentrations of siderophores in liquid medium (up to 40 µM). Siderophores from the isolate were separated from the culture supernatant using solid phase extraction and purified by high-performance liquid chromatography (HPLC). Siderophore structure was determined using LC/MS/MS (liquid chromatography/mass spectrometry/mass spectrometry) and fatty acid methyl ester (FAME) GC. Two distinct new families of amphiphilic siderophores were produced by isolate SL01. All siderophores ranged in size from 989 to 1096 atomic mass units and consisted of a conserved peptidic head group (per family), which coordinates iron, coupled to fatty acid moieties. The fatty acyl moieties were C10-C14 in length and some with hydroxyl substitutions at the third α position. These siderophores resembled amphiphilic aquachelin siderophores produced by Halomonas aquamarina strain DS40M3, a marine bacterium as well as siderophores from isolate Halomonas sp. SL28 that was found to produce amphiphilic siderophores. Bacteria thriving under saline and alkaline conditions are capable of producing unique siderophores resembling those produced by microbes inhabiting marine environments.

  12. Structural characterization of amphiphilic siderophores produced by a soda lake isolate, Halomonas sp. SL01, reveals cysteine-, phenylalanine- and proline-containing head groups.

    PubMed

    Figueroa, Luis O'mar Serrano; Schwarz, Benjamin; Richards, Abigail M

    2015-11-01

    Soap Lake, located in Washington State, is a naturally occurring saline and alkaline lake. Several organisms inhabiting this lake have been identified as producers of siderophores that are unique in structure. Bacterial isolates, enriched from Soap Lake sediment and water samples, were screened for siderophore production using both the chrome azurol S (CAS) agar plate and liquid methods. Bacterial isolate Halomonas sp. SL01 was found to produce relatively high concentrations of siderophores in liquid medium (up to 40 µM). Siderophores from the isolate were separated from the culture supernatant using solid phase extraction and purified by high-performance liquid chromatography (HPLC). Siderophore structure was determined using LC/MS/MS (liquid chromatography/mass spectrometry/mass spectrometry) and fatty acid methyl ester (FAME) GC. Two distinct new families of amphiphilic siderophores were produced by isolate SL01. All siderophores ranged in size from 989 to 1096 atomic mass units and consisted of a conserved peptidic head group (per family), which coordinates iron, coupled to fatty acid moieties. The fatty acyl moieties were C10-C14 in length and some with hydroxyl substitutions at the third α position. These siderophores resembled amphiphilic aquachelin siderophores produced by Halomonas aquamarina strain DS40M3, a marine bacterium as well as siderophores from isolate Halomonas sp. SL28 that was found to produce amphiphilic siderophores. Bacteria thriving under saline and alkaline conditions are capable of producing unique siderophores resembling those produced by microbes inhabiting marine environments. PMID:26439615

  13. Plasmid-mediated QnrS2 determinant in an Aeromonas caviae isolate recovered from a patient with diarrhoea.

    PubMed

    Arias, A; Seral, C; Navarro, F; Miró, E; Coll, P; Castillo, F J

    2010-07-01

    A qnrS2 gene was identified in an Aeromonas caviae isolate (MICs of ciprofloxacin, norfloxacin and ofloxacin >32 mg/L) from a stool sample collected from a patient with gastroenteritis. The analysis of the gyrA and parC genes revealed amino acid substitutions Ser83-Ile and Ser80-Thr, respectively. In addition, five out of 41 nalidixic acid-resistant Aeromonas isolates studied (26 identified as Aeromonas veronii bv sobria and 15 identified as A. caviae) showed ciprofloxacin resistance. The identification of plasmid-mediated qnr genes outside of the Enterobacteriaceae underlines a possible diffusion of these resistance determinants among Gram-negative rods. This emphasizes the importance of monitoring the emergence of these determinants as well as their dissemination among the Aeromonadaceae.

  14. Mollusc communities in Bulgarian fens: predictive power of the environment, vegetation, and spatial structure in an isolated habitat

    NASA Astrophysics Data System (ADS)

    Horsák, Michal; Hájek, Michal; Hájková, Petra; Cameron, Robert; Cernohorsky, Nicole; Apostolova, Iva

    2011-08-01

    Mollusc communities of previously unexplored Bulgarian fens were studied in order to determine and generalise the patterns of species richness and composition along the mineral richness gradient. The aim was also to compare predictive values of the environment, vegetation and spatial structure. Altogether, 44 mollusc species were recorded at 40 treeless fen sites. Species richness varied from 0 to 18 species per site, and it was positively associated with the mineral gradient and negatively with altitude. However, the best predictor was obtained using plant species composition. All explanatory variables had higher effect on land snails than on the entire mollusc assemblage (including aquatic species). Species richness and abundance were significantly and positively correlated with the species composition turnover; the communities were highly nested, with poor sites having subsets of the fauna found in the richest. The main direction of mollusc species turnover was highly associated with that observed for vegetation, and the main gradient of plant species composition was able to explain nearly 20% of total variation in mollusc data. We found that spatial structure explained by far the highest proportion of independent variation, which reflected the high level of geographical isolation of Bulgarian fens and regional differences independent of any environmental variation. Our results demonstrate (1) the general role of mineral richness gradient for structuring mollusc communities in fens, (2) the pivotal indicator role of plant species composition in predicting species composition of mollusc communities, despite being trophically independent and (3) the effect of isolation and origins of the habitat on species composition: most species have wide geographical distributions within the habitat type, and geographical patterns within Bulgaria may have a stochastic element.

  15. Mollusc communities in Bulgarian fens: predictive power of the environment, vegetation, and spatial structure in an isolated habitat.

    PubMed

    Horsák, Michal; Hájek, Michal; Hájková, Petra; Cameron, Robert; Cernohorsky, Nicole; Apostolova, Iva

    2011-08-01

    Mollusc communities of previously unexplored Bulgarian fens were studied in order to determine and generalise the patterns of species richness and composition along the mineral richness gradient. The aim was also to compare predictive values of the environment, vegetation and spatial structure. Altogether, 44 mollusc species were recorded at 40 treeless fen sites. Species richness varied from 0 to 18 species per site, and it was positively associated with the mineral gradient and negatively with altitude. However, the best predictor was obtained using plant species composition. All explanatory variables had higher effect on land snails than on the entire mollusc assemblage (including aquatic species). Species richness and abundance were significantly and positively correlated with the species composition turnover; the communities were highly nested, with poor sites having subsets of the fauna found in the richest. The main direction of mollusc species turnover was highly associated with that observed for vegetation, and the main gradient of plant species composition was able to explain nearly 20% of total variation in mollusc data. We found that spatial structure explained by far the highest proportion of independent variation, which reflected the high level of geographical isolation of Bulgarian fens and regional differences independent of any environmental variation. Our results demonstrate (1) the general role of mineral richness gradient for structuring mollusc communities in fens, (2) the pivotal indicator role of plant species composition in predicting species composition of mollusc communities, despite being trophically independent and (3) the effect of isolation and origins of the habitat on species composition: most species have wide geographical distributions within the habitat type, and geographical patterns within Bulgaria may have a stochastic element.

  16. Determination of internal transcribed spacer regions (ITS) in Trichomonas vaginalis isolates and differentiation among Trichomonas species.

    PubMed

    Ibáñez-Escribano, Alexandra; Nogal-Ruiz, Juan José; Arán, Vicente J; Escario, José Antonio; Gómez-Barrio, Alicia; Alderete, J F

    2014-04-01

    The nucleotide sequence of the 5.8S rRNA gene and the flanked internal transcribed spacer (ITS) regions of six Trichomonas vaginalis isolates with different metronidazole sensitivity and geographic origin were genotyped. A multiple sequence alignment was performed with different sequences of other isolates available at the GenBank/EMBL/DDBJ databases, which revealed 5 different sequence patterns. Although a stable mutation in position 66 of the ITS1 (C66T) was observed in 26% (9/34) of the T. vaginalis sequences analyzed, there was 99.7% ITS nucleotide sequence identity among isolates for this sequence. The nucleotide sequence variation among other species of the genus Trichomonas ranged from 3.4% to 9.1%. Surprisingly, the % identity between T. vaginalis and Pentatrichomonas hominis was ~83%. There was >40% divergence in the ITS sequence between T. vaginalis and Tritrichomonas spp., including Tritrichomonas augusta, Tritrichomonas muris, and Tritrichomonas nonconforma and with Tetratrichomonas prowazeki. Dendrograms grouped the trichomonadid sequences in robust clades according to their genera. The absence of nucleotide divergence in the hypervariable ITS regions between T. vaginalis isolates suggests the early divergence of the parasite. Importantly, these data show this ITS1-5.8S rRNA-ITS2 region suitable for inter-species differentiation.

  17. Carbapenem Susceptibility Patterns for Clinical Isolates of Mycobacterium abscessus Determined by the Etest Method▿

    PubMed Central

    Chihara, Shingo; Smith, Geremy; Petti, Cathy A.

    2010-01-01

    Mycobacterium abscessus is resistant to multiple antibiotics, creating treatment challenges. Carbapenems are tested to increase therapeutic alternatives. We performed in vitro susceptibility testing by Etest of four carbapenems for M. abscessus isolates. Imipenem demonstrated the most in vitro activity, and testing of other carbapenems provided no additional value. PMID:20018813

  18. Determination of internal transcribed spacer regions (ITS) in Trichomonas vaginalis isolates and differentiation among Trichomonas species.

    PubMed

    Ibáñez-Escribano, Alexandra; Nogal-Ruiz, Juan José; Arán, Vicente J; Escario, José Antonio; Gómez-Barrio, Alicia; Alderete, J F

    2014-04-01

    The nucleotide sequence of the 5.8S rRNA gene and the flanked internal transcribed spacer (ITS) regions of six Trichomonas vaginalis isolates with different metronidazole sensitivity and geographic origin were genotyped. A multiple sequence alignment was performed with different sequences of other isolates available at the GenBank/EMBL/DDBJ databases, which revealed 5 different sequence patterns. Although a stable mutation in position 66 of the ITS1 (C66T) was observed in 26% (9/34) of the T. vaginalis sequences analyzed, there was 99.7% ITS nucleotide sequence identity among isolates for this sequence. The nucleotide sequence variation among other species of the genus Trichomonas ranged from 3.4% to 9.1%. Surprisingly, the % identity between T. vaginalis and Pentatrichomonas hominis was ~83%. There was >40% divergence in the ITS sequence between T. vaginalis and Tritrichomonas spp., including Tritrichomonas augusta, Tritrichomonas muris, and Tritrichomonas nonconforma and with Tetratrichomonas prowazeki. Dendrograms grouped the trichomonadid sequences in robust clades according to their genera. The absence of nucleotide divergence in the hypervariable ITS regions between T. vaginalis isolates suggests the early divergence of the parasite. Importantly, these data show this ITS1-5.8S rRNA-ITS2 region suitable for inter-species differentiation. PMID:24412628

  19. Structure determination of trans-cinnamaldehyde by broadband microwave spectroscopy.

    PubMed

    Zinn, Sabrina; Betz, Thomas; Medcraft, Chris; Schnell, Melanie

    2015-06-28

    The rotational spectrum of trans-cinnamaldehyde ((E)-3-phenyl-2-propenal, C9H8O) was recorded by chirped-pulse Fourier transform microwave spectroscopy in the frequency range of 2-8.5 GHz. The odourant molecule is the essential component of cinnamon oil and causes the characteristic smell. The rotational signatures of two conformers were observed: s-trans-trans- and s-cis-trans-cinnamaldehyde. The rotational spectra of s-trans-trans-cinnamaldehyde and all of its (13)C-monosubstituted species in natural abundance were assigned and the corresponding carbon backbone structure was determined. The second conformer s-cis-trans-cinnamaldehyde is about 9 kJ mol(-1) higher in energy and could also be identified in the spectrum.

  20. Annular dark field transmission electron microscopy for protein structure determination.

    PubMed

    Koeck, Philip J B

    2016-02-01

    Recently annular dark field (ADF) transmission electron microscopy (TEM) has been advocated as a means of recording images of biological specimens with better signal to noise ratio (SNR) than regular bright field images. I investigate whether and how such images could be used to determine the three-dimensional structure of proteins given that an ADF aperture with a suitable pass-band can be manufactured and used in practice. I develop an approximate theory of ADF-TEM image formation for weak amplitude and phase objects and test this theory using computer simulations. I also test whether these simulated images can be used to calculate a three-dimensional model of the protein using standard software and discuss problems and possible ways to overcome these. PMID:26656466

  1. Shape determination and control for large space structures

    NASA Technical Reports Server (NTRS)

    Weeks, C. J.

    1981-01-01

    An integral operator approach is used to derive solutions to static shape determination and control problems associated with large space structures. Problem assumptions include a linear self-adjoint system model, observations and control forces at discrete points, and performance criteria for the comparison of estimates or control forms. Results are illustrated by simulations in the one dimensional case with a flexible beam model, and in the multidimensional case with a finite model of a large space antenna. Modal expansions for terms in the solution algorithms are presented, using modes from the static or associated dynamic mode. These expansions provide approximated solutions in the event that a used form analytical solution to the system boundary value problem is not available.

  2. Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity

    SciTech Connect

    Pruitt, Rory N.; Chumbler, Nicole M.; Rutherford, Stacey A.; Farrow, Melissa A.; Friedman, David B.; Spiller, Ben; Lacy, D. Borden

    2012-03-28

    The principle virulence factors in Clostridium difficile pathogenesis are TcdA and TcdB, homologous glucosyltransferases capable of inactivating small GTPases within the host cell. We present crystal structures of the TcdA glucosyltransferase domain in the presence and absence of the co-substrate UDP-glucose. Although the enzymatic core is similar to that of TcdB, the proposed GTPase-binding surface differs significantly. We show that TcdA is comparable with TcdB in its modification of Rho family substrates and that, unlike TcdB, TcdA is also capable of modifying Rap family GTPases both in vitro and in cells. The glucosyltransferase activities of both toxins are reduced in the context of the holotoxin but can be restored with autoproteolytic activation and glucosyltransferase domain release. These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell.

  3. Lipooligosaccharide Structures of Invasive and Carrier Isolates of Neisseria meningitidis Are Correlated with Pathogenicity and Carriage.

    PubMed

    John, Constance M; Phillips, Nancy J; Din, Richard; Liu, Mingfeng; Rosenqvist, Einar; Høiby, E Arne; Stein, Daniel C; Jarvis, Gary A

    2016-02-12

    The degree of phosphorylation and phosphoethanolaminylation of lipid A on neisserial lipooligosaccharide (LOS), a major cell-surface antigen, can be correlated with inflammatory potential and the ability to induce immune tolerance in vitro. On the oligosaccharide of the LOS, the presence of phosphoethanolamine and sialic acid substituents can be correlated with in vitro serum resistance. In this study, we analyzed the structure of the LOS from 40 invasive isolates and 25 isolates from carriers of Neisseria meningitidis without disease. Invasive strains were classified as groups 1-3 that caused meningitis, septicemia without meningitis, and septicemia with meningitis, respectively. Intact LOS was analyzed by high resolution matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Prominent peaks for lipid A fragment ions with three phosphates and one phosphoethanolamine were detected in all LOS analyzed. LOS from groups 2 and 3 had less abundant ions for highly phosphorylated lipid A forms and induced less TNF-α in THP-1 monocytic cells compared with LOS from group 1. Lipid A from all invasive strains was hexaacylated, whereas lipid A of 6/25 carrier strains was pentaacylated. There were fewer O-acetyl groups and more phosphoethanolamine and sialic acid substitutions on the oligosaccharide from invasive compared with carrier isolates. Bioinformatic and genomic analysis of LOS biosynthetic genes indicated significant skewing to specific alleles, dependent on the disease outcome. Our results suggest that variable LOS structures have multifaceted effects on homeostatic innate immune responses that have critical impact on the pathophysiology of meningococcal infections. PMID:26655715

  4. Lipooligosaccharide Structures of Invasive and Carrier Isolates of Neisseria meningitidis Are Correlated with Pathogenicity and Carriage.

    PubMed

    John, Constance M; Phillips, Nancy J; Din, Richard; Liu, Mingfeng; Rosenqvist, Einar; Høiby, E Arne; Stein, Daniel C; Jarvis, Gary A

    2016-02-12

    The degree of phosphorylation and phosphoethanolaminylation of lipid A on neisserial lipooligosaccharide (LOS), a major cell-surface antigen, can be correlated with inflammatory potential and the ability to induce immune tolerance in vitro. On the oligosaccharide of the LOS, the presence of phosphoethanolamine and sialic acid substituents can be correlated with in vitro serum resistance. In this study, we analyzed the structure of the LOS from 40 invasive isolates and 25 isolates from carriers of Neisseria meningitidis without disease. Invasive strains were classified as groups 1-3 that caused meningitis, septicemia without meningitis, and septicemia with meningitis, respectively. Intact LOS was analyzed by high resolution matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Prominent peaks for lipid A fragment ions with three phosphates and one phosphoethanolamine were detected in all LOS analyzed. LOS from groups 2 and 3 had less abundant ions for highly phosphorylated lipid A forms and induced less TNF-α in THP-1 monocytic cells compared with LOS from group 1. Lipid A from all invasive strains was hexaacylated, whereas lipid A of 6/25 carrier strains was pentaacylated. There were fewer O-acetyl groups and more phosphoethanolamine and sialic acid substitutions on the oligosaccharide from invasive compared with carrier isolates. Bioinformatic and genomic analysis of LOS biosynthetic genes indicated significant skewing to specific alleles, dependent on the disease outcome. Our results suggest that variable LOS structures have multifaceted effects on homeostatic innate immune responses that have critical impact on the pathophysiology of meningococcal infections.

  5. Population size and time since island isolation determine genetic diversity loss in insular frog populations.

    PubMed

    Wang, Supen; Zhu, Wei; Gao, Xu; Li, Xianping; Yan, Shaofei; Liu, Xuan; Yang, Ji; Gao, Zengxiang; Li, Yiming

    2014-02-01

    Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used nine microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square-root-transformed) and population size (log-transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations. PMID:24351057

  6. Isolate Identity Determines Plant Tolerance to Pathogen Attack in Assembled Mycorrhizal Communities

    PubMed Central

    Lewandowski, Thaddeus J.; Dunfield, Kari E.; Antunes, Pedro M.

    2013-01-01

    Arbuscular mycorrhizal fungi (AMF) are widespread soil microorganisms that associate mutualistically with plant hosts. AMF receive photosynthates from the host in return for various benefits. One of such benefits is in the form of enhanced pathogen tolerance. However, this aspect of the symbiosis has been understudied compared to effects on plant growth and its ability to acquire nutrients. While it is known that increased AMF species richness positively correlates with plant productivity, the relationship between AMF diversity and host responses to pathogen attack remains obscure. The objective of this study was to test whether AMF isolates can differentially attenuate the deleterious effects of a root pathogen on plant growth, whether the richest assemblage of AMF isolates provides the most tolerance against the pathogen, and whether AMF-induced changes to root architecture serve as a mechanism for improved plant disease tolerance. In a growth chamber study, we exposed the plant oxeye daisy (Leucanthemum vulgare) to all combinations of three AMF isolates and to the plant root pathogen Rhizoctonia solani. We found that the pathogen caused an 81% reduction in shoot and a 70% reduction in root biomass. AMF significantly reduced the highly deleterious effect of the pathogen. Mycorrhizal plants infected with the pathogen produced 91% more dry shoot biomass and 72% more dry root biomass relative to plants solely infected with R. solani. AMF isolate identity was a better predictor of AMF-mediated host tolerance to the pathogen than AMF richness. However, the enhanced tolerance response did not result from AMF-mediated changes to root architecture. Our data indicate that AMF communities can play a major role in alleviating host pathogen attack but this depends primarily on the capacity of individual AMF isolates to provide this benefit. PMID:23620744

  7. Genetic structure, reproductive biology and ecology of isolated populations of asplenium csikii (Aspleniaceae, pteridophyta)

    PubMed

    Vogel; Rumsey; Russell; Cox; Holmes; Bujnoch; Stark; Barrett; Gibby

    1999-11-01

    The potential for environmental heterogeneity to generate spatial structuring of genotypes in seed-plant populations that occupy patchy habitats has been demonstrated by several studies, but little is known about the population structure of pteridophytes occupying patchy environments. In this study we have examined the genetic structure of isolated populations of the rock fern Asplenium csikii, an ecological specialist, growing almost exclusively on perpendicular walls of natural rock outcrops. All genetic variation observed in this taxon was partitioned between localities; no allozyme variation was found within a site and each site was colonized by a single multilocus phenotype (MLP). In total, five different MLPs were recorded from the nine localities, with two MLPs present at more than one site. Previous examination of population structure and genetic diversity in another rock fern, A. ruta-muraria, showed that the genetic diversity increases through multiple colonization over time. However, we cannot find any such correlation for A. csikii. All populations are genetically uniform, despite the probably considerable age of the populations and sites. Earlier studies concluded that the ample production of wind-borne propagules would lead to multiple colonization of sites and that reproductive features, such as single-spore colonization and subsequent intragametophytic selfing, would lead to very little genetic structuring of fern populations. In contrast to this prediction, it appears that ecological specialization and the scarcity of the narrowly defined niche contribute strongly to the pronounced partitioning of genetic variability observed in populations of A. csikii.

  8. Construction and characterization of infectious hepatitis C virus chimera containing structural proteins directly from genotype 1b clinical isolates.

    PubMed

    Lu, Jie; Tao, Wanyin; Li, Rui; Xiang, Yu; Zhang, Nan; Xiang, Xiaogang; Xie, Qing; Zhong, Jin

    2013-08-15

    HCV genotype is a major determinant of clinical outcome, and GT1b HCV infection is the most difficult to treat and also the predominant genotype in East Asia and Europe. We developed 1b/JFH-1 inter-genotypic recombinants containing the structural genes (Core, E1, E2), p7 and the 1stTMD of NS2 directly from GT1b clinical isolates. Through a cloning selection strategy, we obtained 4 functional clones from 3 cases of GT1b patients' sera, which could produce infectious viruses in Huh7.5.1 cells. Sequencing analysis of recovered viruses from serial passage and reverse genetics revealed that adaptive mutations in the GT1b-originated region were enough for the enhancement of infectivity. A monoclonal antibody to E2 and original patient sera could efficiently block 3 of the viruses (26C3mt, 52B6mt and 79L9) while had little effect on 26C6mt viruses. The availability of 1b/JFH-1 chimeric viruses will be important for studies of isolate-specific neutralization and useful in evaluating antiviral therapies.

  9. Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods.

    PubMed

    Song, Yuqin; Sun, Zhihong; Guo, Chenyi; Wu, Yarong; Liu, Wenjun; Yu, Jie; Menghe, Bilige; Yang, Ruifu; Zhang, Heping

    2016-03-04

    Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2-CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1-L6, with various homologous recombination rates. Although L2-L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.

  10. Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods

    PubMed Central

    Song, Yuqin; Sun, Zhihong; Guo, Chenyi; Wu, Yarong; Liu, Wenjun; Yu, Jie; Menghe, Bilige; Yang, Ruifu; Zhang, Heping

    2016-01-01

    Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2–CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1–L6, with various homologous recombination rates. Although L2–L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation. PMID:26940047

  11. Isolation and structural elucidation of novel antimicrobial compounds from maggots of Chrysomyis megacephala Fabricius.

    PubMed

    Gao, Jiayu; Li, Wenyuan; Niu, Lanlan; Cao, Ranran; Yin, Weiping

    2015-02-01

    The excretions/secretions from the maggot of Chrysomyis megacephala Fabricius are traditionally used to treat serious infections in China. In this study, bioassay-guided fractionation led to the isolation of three novel antibacterial compounds (1-3), including important fluorinated compounds (3 and 5), together with other nine known compounds from 70% methanol extract of C. megacephala. The structures of the new compounds were elucidated by NMR spectroscopic analysis and high-resolution mass spectroscopy. The antibacterial activities of the isolated compounds were evaluated using agar disc diffusion method. New compounds 1 and 2 exhibited moderate activity against Bacillus subtilis with a minimum inhibitory concentration (MIC) of 250 μg mL(- 1). The most active compounds 3 and 5 displayed a broad spectrum of antimicrobial activity with an MIC of 125 μg mL(- 1) against G(+) and G(- ) bacteria. The structure of the above-mentioned novel compounds and their antimicrobial activities are herein reported for the first time from the natural product of insects.

  12. Protein structure determination with paramagnetic solid-state NMR spectroscopy.

    PubMed

    Sengupta, Ishita; Nadaud, Philippe S; Jaroniec, Christopher P

    2013-09-17

    Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2

  13. The Structural Determinants behind the Epigenetic Role of Histone Variants

    PubMed Central

    Cheema, Manjinder S.; Ausió, Juan

    2015-01-01

    Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism. PMID:26213973

  14. Comparison of different torsion angle approaches for NMR structure determination.

    PubMed

    Bardiaux, Benjamin; Malliavin, Thérèse E; Nilges, Michael; Mazur, Alexey K

    2006-03-01

    A new procedure for NMR structure determination, based on the Internal Coordinate Molecular Dynamics (ICMD) approach, is presented. The method finds biopolymer conformations that satisfy usual NMR-derived restraints by using high temperature dynamics in torsion angle space. A variable target function algorithm gradually increases the number of NOE-based restraints applied, with the treatment of ambiguous and floating restraints included. This soft procedure allows combining artificially high temperature with a general purpose force-field including Coulombic and Lennard-Jones non-bonded interactions, which improves the quality of the ensemble of conformations obtained in the gas-phase. The new method is compared to existing algorithms by using the structures of eight ribosomal proteins earlier obtained with state-of-the-art procedures and included into the RECOORD database [Nederveen, A., Doreleijers, J., Vranken, W., Miller, Z., Spronk, C., Nabuurs, S., Guntert, P., Livny, M., Markley, M., Nilges, M., Ulrich, E., Kaptein, R. and Bonvin, A.M. (2005) Proteins, 59, 662-672]. For the majority of tested proteins, the ICMD algorithm shows similar convergence and somewhat better quality Z scores for the phi, psi distributions. The new method is more computationally demanding although the overall load is reasonable.

  15. Isolation and structural proof of the large diamond molecule, cyclohexamantane (C26H30)

    USGS Publications Warehouse

    Dahl, J.E.P.; Moldowan, J.M.; Peakman, T.M.; Clardy, J.C.; Lobkovsky, E.; Olmstead, M.M.; May, P.W.; Davis, T.J.; Steeds, J.W.; Peters, K.E.; Pepper, A.; Ekuan, A.; Carlson, R.M.K.

    2003-01-01

    Ace of diamonds: Cyclohexamantane (C26H30), a large diamond-like molecule containing six peri-fused adamantane cages was identified in petroleum and its structure proven by X-ray crystallography (see picture), Never synthesized because of severe mechanistic difficulties, the structure of cyclohexamantane has appeared in theoretical molecular-simulation studies related to diamond; its experimentally determined properties are now discussed.

  16. Individual sarcomere length determination from isolated cardiac cells using high-resolution optical microscopy and digital image processing.

    PubMed Central

    Roos, K P; Brady, A J

    1982-01-01

    Discrete sarcomere lengths have been determined from dynamically contracting isolated cardiac cells with a high-speed, high-resolution direct optical imaging system. Calcium-tolerant cardiac cells from the rat are isolated by perfusion with collagenase and hyaluronidase. Individual sarcomere lengths can be determined by directly imaging the cell's striation pattern onto a solid-state charge-coupled device (CCD) detector interfaced with a digital computer. The precision of detection in a real light microscopic optical system is discussed in relation to the type of image detector, optical contract enhancement techniques, and digital image processing. The optical performance of the direct striation pattern image apparatus has been determined empirically with test grids under standard bright-field and Nomarski-differential interference contrast (DIC) conditions for application to real muscle imaging. Discrete striation positions of isolated cells have been detected and followed with high precision during phasic contraction-relaxation cycles down to average sarcomere lengths as short as 1.43 +/- 0.053 microns. The maximum rates of contraction and relaxation are rapid and synchronous in time course along the length of the cell. These results indicate that direct optical imaging can provide an accurate means to monitor discrete striations and sarcomere lengths along the length of Ca2+-tolerant heart cells. Images FIGURE 1 FIGURE 4 PMID:7183337

  17. Determining the structure of supersymmetry breaking with renormalization group invariants

    SciTech Connect

    Carena, Marcela; Draper, Patrick; Shah, Nausheen R.; Wagner, Carlos E. M.

    2010-10-01

    If collider experiments demonstrate that the minimal supersymmetric standard model (MSSM) is a good description of nature at the weak scale, the experimental priority will be the precise determination of superpartner masses. These masses are governed by the weak scale values of the soft supersymmetry-breaking (SUSY-breaking) parameters, which are in turn highly dependent on the SUSY-breaking scheme present at high scales. It is therefore of great interest to find patterns in the soft parameters that can distinguish different high-scale SUSY-breaking structures, identify the scale at which the breaking is communicated to the visible sector, and determine the soft breaking parameters at that scale. In this work, we demonstrate that 1-loop renormalization group invariant quantities present in the MSSM may be used to answer each of these questions. We apply our method first to generic flavor-blind models of SUSY breaking, and then we examine in detail the subset of these models described by general gauge mediation and the constrained MSSM with nonuniversal Higgs masses. As renormalization group invariance generally does not hold beyond leading-log order, we investigate the magnitude and direction of the 2-loop corrections. We find that with superpartners at the TeV scale, these 2-loop effects are either negligible, or they are of the order of optimistic experimental uncertainties and have definite signs, which allows them to be easily accounted for in the overall uncertainty.

  18. MOLECULAR DETECTION OF ANTIBIOTIC-RESISTANCE DETERMINANTS IN ESCHERICHIA COLI ISOLATED FROM THE ENDANGERED AUSTRALIAN SEA LION (NEOPHOCA CINEREA).

    PubMed

    Delport, Tiffany C; Harcourt, Robert G; Beaumont, Linda J; Webster, Koa N; Power, Michelle L

    2015-07-01

    Greater interaction between humans and wildlife populations poses significant risks of anthropogenic impact to natural ecosystems, especially in the marine environment. Understanding the spread of microorganisms at the marine interface is therefore important if we are to mitigate adverse effects on marine wildlife. We investigated the establishment of Escherichia coli in the endangered Australian sea lion (Neophoca cinerea) by comparing fecal isolation from wild and captive sea lion populations. Fecal samples were collected from wild colonies March 2009-September 2010 and from captive individuals March 2011-May 2013. Using molecular screening, we assigned a phylotype to E. coli isolates and determined the presence of integrons, mobile genetic elements that capture gene cassettes conferring resistance to antimicrobial agents common in fecal coliforms. Group B2 was the most abundant phylotype in all E. coli isolates (n = 37), with groups A, B1, and D also identified. Integrons were not observed in E. coli (n = 21) isolated from wild sea lions, but were identified in E. coli from captive animals (n = 16), from which class I integrases were detected in eight isolates. Sequencing of gene cassette arrays identified genes conferring resistance to streptomycin-spectinomycin (aadA1) and trimethoprim (dfrA17, dfrB4). Class II integrases were not detected in the E. coli isolates. The frequent detection in captive sea lions of E. coli with resistance genes commonly identified in human clinical cases suggests that conditions experienced in captivity may contribute to establishment. Identification of antibiotic resistance in the microbiota of Australian sea lions provides crucial information for disease management. Our data will inform conservation management strategies and provide a mechanism to monitor microorganism dissemination to sensitive pinniped populations. PMID:25919463

  19. MOLECULAR DETECTION OF ANTIBIOTIC-RESISTANCE DETERMINANTS IN ESCHERICHIA COLI ISOLATED FROM THE ENDANGERED AUSTRALIAN SEA LION (NEOPHOCA CINEREA).

    PubMed

    Delport, Tiffany C; Harcourt, Robert G; Beaumont, Linda J; Webster, Koa N; Power, Michelle L

    2015-07-01

    Greater interaction between humans and wildlife populations poses significant risks of anthropogenic impact to natural ecosystems, especially in the marine environment. Understanding the spread of microorganisms at the marine interface is therefore important if we are to mitigate adverse effects on marine wildlife. We investigated the establishment of Escherichia coli in the endangered Australian sea lion (Neophoca cinerea) by comparing fecal isolation from wild and captive sea lion populations. Fecal samples were collected from wild colonies March 2009-September 2010 and from captive individuals March 2011-May 2013. Using molecular screening, we assigned a phylotype to E. coli isolates and determined the presence of integrons, mobile genetic elements that capture gene cassettes conferring resistance to antimicrobial agents common in fecal coliforms. Group B2 was the most abundant phylotype in all E. coli isolates (n = 37), with groups A, B1, and D also identified. Integrons were not observed in E. coli (n = 21) isolated from wild sea lions, but were identified in E. coli from captive animals (n = 16), from which class I integrases were detected in eight isolates. Sequencing of gene cassette arrays identified genes conferring resistance to streptomycin-spectinomycin (aadA1) and trimethoprim (dfrA17, dfrB4). Class II integrases were not detected in the E. coli isolates. The frequent detection in captive sea lions of E. coli with resistance genes commonly identified in human clinical cases suggests that conditions experienced in captivity may contribute to establishment. Identification of antibiotic resistance in the microbiota of Australian sea lions provides crucial information for disease management. Our data will inform conservation management strategies and provide a mechanism to monitor microorganism dissemination to sensitive pinniped populations.

  20. Structure Determination of Novel Oxidation Products from Epicatechin: Thearubigin-Like Molecules.

    PubMed

    Uchida, Kazuhiro; Ogawa, Kazuki; Yanase, Emiko

    2016-02-26

    Following the oxidation of epicatechin (EC), three novel compounds and two known compounds were isolated. The chemical structures of these oxidation products were determined by mass spectrometry (MS) and various nuclear magnetic resonance (NMR) experiments, and the A-ring-B-ring linkage that is characteristic of catechin was found in each molecule. Three compounds showed similar ultraviolet-visible (UV-Vis) spectra to EC, whereas two compounds showed different spectral absorption in the region between 300 and 500 nm. A similar spectrum was obtained for the thearubigin fraction prepared from a black tea infusion. This result suggests that the condensation reaction between the A-ring and B-ring is more important than reaction between B-rings for thearubigin formation.

  1. Structure of the novel steroidal antibiotic squalamine determined by two-dimensional NMR spectroscopy.

    PubMed

    Wehrli, S L; Moore, K S; Roder, H; Durell, S; Zasloff, M

    1993-08-01

    Squalamine is a novel aminosterol recently isolated from the dogfish shark, Squalus acanthias. This water-soluble steroid exhibits potent antibacterial activity against both gram-negative and gram-positive bacteria. In addition, squalamine is fungicidal and induces osmotic lysis of protozoa. We report here the structural determination of squalamine, 3 beta-N-1-[N(3-[4-aminobutyl])-1,3 diaminopropane]-7 alpha,24 zeta-dihydroxy-5 alpha-cholestane 24-sulfate, which was deduced from the analysis of fast atom bombardment spectra and a series of two-dimensional nuclear magnetic resonance (NMR) spectra. Squalamine is a cationic steroid characterized by a condensation of an anionic bile salt intermediate with the polyamine, spermidine. This molecule is a potential host-defense agent in the shark, and provides insight into a new class of vertebrate antimicrobial molecules. PMID:8212087

  2. 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

    2015-09-01

    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. PMID:26244445

  3. Isolation of major components from the roots of Godmania aesculifolia and determination of their antifungal activities.

    PubMed

    Tamayo-Castillo, Giselle; Vásquez, Víctor; Ríos, María Isabel; Rodríguez, María Victoria; Solano, Godofredo; Zacchino, Susana; Gupta, Mahabir P

    2013-12-01

    From the methanol root extract of Godmania aesculifolia, a species selected in a multinational OAS program aimed at discovering antifungal compounds from Latin American plants, a new chavicol diglycoside (1), the known 3,4-dihydroxy-2-(3-methylbut-2-en-1-yl)-3,4-dihydronaphthalen-1(2H)-one (2), and lapachol (3) were isolated and characterized by 1D and 2D NMR and MS techniques. Only 3 exhibited fairly good activity against a panel of clinical isolates of Cryptococcus neoformans (MIC50 between 7.8 and 31.2 µg/mL) and moderate activities against Candida spp. and non-albicans Candida spp. PMID:24356871

  4. Experimental Determination of Structure Factors of Titanium Aluminum and Silicon

    NASA Astrophysics Data System (ADS)

    Subramanian, Swaminathan

    . The 220 structure factor of silicon has been measured, as a test case, to an accuracy < 0.1%. The temperature dependence of the coefficient of 220 absorption potential has been determined. The results indicate the Einstein phonon model (Bird and King (1990)) underestimates the coefficient of 220 absorption potential of silicon.

  5. Synthetic Efforts for Stereo Structure Determination of Cytotoxic Marine Natural Product Pericosines as Metabolites of Periconia sp. from Sea Hare

    PubMed Central

    Usami, Yoshihide; Ichikawa, Hayato; Arimoto, Masao

    2008-01-01

    Pericosines are unique C7 cyclohexenoid metabolites of Periconia byssoides OUPS-N133 fungus that was originally isolated from the sea hare, Aplysia kurodai. Pericosines show significant in vitro cytotoxicity against P388 lymphocytic leukemia cells. Pericosine A, in particular, shows the most potent activity and significant in vivo antitumor activity against P388 cells. Thus, pericosines are promising candidates for seed compounds of anticancer drugs. However, before the total syntheses of pericosines were accomplished, their stereo structures could not be determined by spectral analyses because they have multi-functionalized cyclohexenoid structures with torsional strain. In this review, synthetic efforts for pericosines in this decade are surveyed. PMID:19325758

  6. [Characterization and determination of antibiotic resistance profiles of a single clone Acinetobacter baumannii strains isolated from blood cultures].

    PubMed

    Karagöz, Alper; Baran, Irmak; Aksu, Neriman; Acar, Sümeyra; Durmaz, Rıza

    2014-10-01

    Acinetobacter baumannii which is a significant cause of nosocomial infections, increases the rate of morbidity and mortality in health care settings especially in intensive care units (ICUs). The aim of this study was to determine the antibiotic resistance profiles of A.baumannii strains isolated from blood cultures of inpatients from different ICUs, wards and hospital environment and evaluate their clonal relationships and epidemiologic features. A total of 54 A.baumannii strains (47 from the blood cultures and 7 from the hospital environment), identified between 01 January 2012-28 December 2012 at the Clinical Microbiology Laboratory of Ankara Numune Training and Research Hospital, Turkey, were included in the study. Identification of A.baumannii isolates and their antimicrobial [sulbactam-ampicillin (SAM), piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CFZ), cefoperazone-sulbactam (SCF), cefepime (CEF), imipenem (IMP), meropenem (MER), amikacin (AMK), gentamicin (GEN), netilmicin (NT), ciprofloxacin (CIP), levofloxacin (LVF), tetracycline (TET), tigecycline (TG), colistin (COL), trimethoprim-sulfamethoxazole (SXT)] susceptibility testing were performed by Vitek 2 (bioMérieux, France) system. The clonal relationship between the A.baumannii isolates was analysed by pulsed-field gel electrophoresis (PFGE). In our study colistin, tigecycline and netilmicin were found to be the most effective agents against A.baumannii isolates. All of the clinical isolates (n= 47) were found susceptible to COL, however all were resistant to SAM, PIP, TZP, CEF, IPM, CFZ, MER and CIP. While 1.85%, 14.8%, 14.8%, 16.6%, 59.2% and 22.2% of the isolates were susceptible to SCF, AMK, NT, GEN, TG and SXT, respectively; 1.85%, 1.85%, 9.2%, 16.6%, 38.8% and 27.7% of the isolates were intermediate to SCF, TET, AMK, NT, LVF and TG, respectively. Similarly, all of the environmental A.baumannii isolates (n= 7) were resistant to SAM, PIP, TZP, CFZ, CEF, IPM, MER and CIP, and all

  7. Presence of the Tet M Determinant in a Clinical Isolate of Acinetobacter baumannii

    PubMed Central

    Ribera, Anna; Ruiz, Joaquim; Vila, Jordi

    2003-01-01

    The tet(M) gene encodes a protein which is related to tetracycline ribosomal protection, one of the mechanisms of tetracycline resistance. A tet(M) gene that is 100% homologous to the tet(M) gene of Staphylococcus aureus has been found in a clinical isolate of Acinetobacter baumannii, which also carries the tet(A) gene encoding a tetracycline efflux pump. PMID:12821485

  8. Isolation of Cellulose-Degrading Bacteria and Determination of Their Cellulolytic Potential

    PubMed Central

    Gupta, Pratima; Samant, Kalpana; Sahu, Avinash

    2012-01-01

    Eight isolates of cellulose-degrading bacteria (CDB) were isolated from four different invertebrates (termite, snail, caterpillar, and bookworm) by enriching the basal culture medium with filter paper as substrate for cellulose degradation. To indicate the cellulase activity of the organisms, diameter of clear zone around the colony and hydrolytic value on cellulose Congo Red agar media were measured. CDB 8 and CDB 10 exhibited the maximum zone of clearance around the colony with diameter of 45 and 50 mm and with the hydrolytic value of 9 and 9.8, respectively. The enzyme assays for two enzymes, filter paper cellulase (FPC), and cellulase (endoglucanase), were examined by methods recommended by the International Union of Pure and Applied Chemistry (IUPAC). The extracellular cellulase activities ranged from 0.012 to 0.196 IU/mL for FPC and 0.162 to 0.400 IU/mL for endoglucanase assay. All the cultures were also further tested for their capacity to degrade filter paper by gravimetric method. The maximum filter paper degradation percentage was estimated to be 65.7 for CDB 8. Selected bacterial isolates CDB 2, 7, 8, and 10 were co-cultured with Saccharomyces cerevisiae for simultaneous saccharification and fermentation. Ethanol production was positively tested after five days of incubation with acidified potassium dichromate. PMID:22315612

  9. Structural and Functional Properties of Soy Protein Isolates Modified by Soy Soluble Polysaccharides.

    PubMed

    Xu, Yan-Teng; Liu, Ling-Ling

    2016-09-28

    Aiming to achieve the modification to soy protein isolate (SPI) by soy soluble polysaccharides (SSPS), electrically driven complex systems were first established in the environment of pH 3.0, and then reconstituted SPI particles with different SPI-SSPS ratios were obtained under freeze-drying process. Through this treatment, the structures of SPI particles were partly unfolded and adsorbed SSPS mainly via hydrophobic interactions and hydrogen bonding with larger particle sizes. The adherence of SSPS decreased the surface hydrophobicity of reconstituted SPI particles, but exerted not much influence on the emulsifying and foaming activities and increased the corresponding stabilities due to enhancing the unfolded extent of structure and improving the conformation flexibility. Reconstituted SPI-SSPS particles might rearrange and link each other due to the presence of SSPS on the air-water interface to better stabilize these systems. At SPI-SSPS ratio of 10:1, lower temperature was required to form gels with lower gel intensity and porous structure. The findings provide a further comprehension to the relationship between structures and functional properties of SPI modified by SSPS and the feasibility of applying these reconstituted particles to needed areas. PMID:27608266

  10. Impact of magnetic isolation on pointing system performance in the presence of structural flexibility

    NASA Technical Reports Server (NTRS)

    Seller, J.

    1985-01-01

    The inertial pointing stability of a gimbal pointing system (AGS) was compared with a magnetic pointing/gimbal followup system (ASPS), under certain conditions of system structural flexibility and disturbance inputs from the gimbal support structure. Separate 3 degree-of-freedom (3DOF) linear models based on NASTRAN modal flexibility data for the gimbal and support structures were generated for the ASPS configurations. Using the models inertial pointing control loops providing 6dB of gain margin and 45 deg of phase margin were defined for each configuration. The pointing loop bandwidth obtained for the ASPS is more than twice the level achieved for the AGS configuration. The AGS limit is attributed to the gimbal and support structure flexibility. As a result of the higher ASPS pointing loop bandwidth and the disturbance rejection provided by the magnetic isolation ASPS pointing performane is significantly better than that of the AGS system. The low frequency peak of the ASPS transfer function from base disturbance to payload angular motion is almost 60dB lower than AGS low frequency peak.

  11. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry.

    PubMed

    Müllner, Petra; Collins-Emerson, Julie M; Midwinter, Anne C; Carter, Philip; Spencer, Simon E F; van der Logt, Peter; Hathaway, Steve; French, Nigel P

    2010-04-01

    In New Zealand the number of campylobacteriosis notifications increased markedly between 2000 and 2007. Notably, this country's poultry supply is different than that of many developed countries as the fresh and frozen poultry available at retail are exclusively of domestic origin. To examine the possible link between human cases and poultry, a sentinel surveillance site was established to study the molecular epidemiology of Campylobacter jejuni over a 3-year period from 2005 to 2008 using multilocus sequence typing. Studies showed that 60.1 to 81.4% of retail poultry carcasses from the major suppliers were contaminated with C. jejuni. Differences were detected in the probability and level of contamination and the relative frequency of genotypes for individual poultry suppliers and humans. Some carcasses were contaminated with isolates belonging to more than one sequence type (ST), and there was evidence of both ubiquitous and supplier-associated strains, an epidemiological pattern not recognized yet in other countries. The common poultry STs were also common in human clinical cases, providing evidence that poultry is a major contributor to human infection. Both internationally rare genotypes, such as ST-3069 and ST-474, and common genotypes, such as ST-45 and ST-48, were identified in this study. The dominant human sequence type in New Zealand, ST-474, was found almost exclusively in isolates from one poultry supplier, which provided evidence that C. jejuni has a distinctive molecular epidemiology in this country. These results may be due in part to New Zealand's geographical isolation and its uniquely structured poultry industry. PMID:20154115

  12. Bordetella pertussis naturally occurring isolates with altered lipooligosaccharide structure fail to fully mature human dendritic cells.

    PubMed

    Brummelman, Jolanda; Veerman, Rosanne E; Hamstra, Hendrik Jan; Deuss, Anna J M; Schuijt, Tim J; Sloots, Arjen; Kuipers, Betsy; van Els, Cécile A C M; van der Ley, Peter; Mooi, Frits R; Han, Wanda G H; Pinelli, Elena

    2015-01-01

    Bordetella pertussis is a Gram-negative bacterium and the causative agent of whooping cough. Despite high vaccination coverage, outbreaks are being increasingly reported worldwide. Possible explanations include adaptation of this pathogen, which may interfere with recognition by the innate immune system. Here, we describe innate immune recognition and responses to different B. pertussis clinical isolates. By using HEK-Blue cells transfected with different pattern recognition receptors, we found that 3 out of 19 clinical isolates failed to activate Toll-like receptor 4 (TLR4). These findings were confirmed by using the monocytic MM6 cell line. Although incubation with high concentrations of these 3 strains resulted in significant activation of the MM6 cells, it was found to occur mainly through interaction with TLR2 and not through TLR4. When using live bacteria, these 3 strains also failed to activate TLR4 on HEK-Blue cells, and activation of MM6 cells or human monocyte-derived dendritic cells was significantly lower than activation induced by the other 16 strains. Mass spectrum analysis of the lipid A moieties from these 3 strains indicated an altered structure of this molecule. Gene sequence analysis revealed mutations in genes involved in lipid A synthesis. Findings from this study indicate that B. pertussis isolates that do not activate TLR4 occur naturally and that this phenotype may give this bacterium an advantage in tempering the innate immune response and establishing infection. Knowledge on the strategies used by this pathogen in evading the host immune response is essential for the improvement of current vaccines or for the development of new ones.

  13. Sulfated phenolic compounds from Limonium caspium: Isolation, structural elucidation, and biological evaluation

    PubMed Central

    Gadetskaya, Anastassiya V.; Tarawneh, Amer H.; Zhusupova, Galiya E.; Gemejiyeva, Nadezhda G.; Cantrell, Charles L.; Cutler, Stephen J.; Ross, Samir A.

    2016-01-01

    Three new compounds, (2S,3S)-5-methyldihydromyricetin (1), (2S,3S)-5-methyldihydromyricetin-3′-O-sulfate (2) and β-D-glucopyranoside, 3-methyl, but-3-en-1-yl 4-O-α-L-rhamnopyranosyl (3) have been isolated from the Limonium caspium, together with dihydromyricetin (4), dihydromyricetin-3′-O-sulfate (5), myricetin-3′-O-sulfate (6), 5-methylmyricetin (7), myricetin (8), myricetin-3-O-β-glucoside (9), as well as phloridzin (10), and tyramine (11). Compounds 5 and 6 were isolated for the first time as acids. This is the first report of all these compounds from this plant. Their structures were established by extensive NMR studies (1H NMR, 13C NMR, DEPT, 1H–1H COSY, HSQC, HMBC) as well as HRESIMS. All isolated compounds were evaluated for their antibacterial, antifungal, antimalarial and antileishmanial activities. Compounds 7, 8 and 9 exhibited good antifungal activity against Candida glabrata with IC50 values of 6.79, 15.37 and 8.53 μg/mL, respectively. Compound 8 displayed significant antimalarial activity against resistant and sensitive strains of Plasmodium falciparum with IC50 values of 1.82 and 1.51 μg/mL, respectively. Compounds 1, 4, 6, 8 and 9 showed excellent activity against Trypanosoma brucei with IC50 values of 6.93, 9.65, 8.52, 7.67 and 6.31 μg/mL, respectively. To date, this is the first report on the phytochemical and biological activity of secondary metabolites from L. caspium. PMID:26025854

  14. SS316 structure fabricated by selective laser melting and integrated with strain isolated optical fiber high temperature sensor

    NASA Astrophysics Data System (ADS)

    Mathew, Jinesh; Havermann, Dirk; Polyzos, Dimitrios; MacPherson, William N.; Hand, Duncan P.; Maier, Robert R. J.

    2015-09-01

    Smart metal having integrated high temperature sensing capability is reported. The SS316 structure is made by additive layer manufacturing via selective laser melting (SLM). Sensor component is embedded in to the structure during the SLM build process. The strain isolated in-fiber Fabry-Perot cavity sensor measures temperature up to 1100 °C inside the metal.

  15. A facile method to determine the absolute structure of achiral molecules: supramolecular-tilt structures.

    PubMed

    Tejedor, Rosa María; Uriel, Santiago; Graus, Sara; Sierra, Teresa; Serrano, José Luis; Claramunt, Rosa M; López, Concepción; Pérez-Torralba, Marta; Alkorta, Ibon; Elguero, José

    2013-05-01

    Achiral compounds 4-methoxy-4-(p-methoxyphenyl)cyclohexanoneethylene ketal (2), 4-hydroxy-4-(p-methoxy phenyl)cyclohexanoneethylene ketal (3), and 3,5-dimethyl-4-nitropyrazole (4) crystallized in chiral structures and the samples showed an enantiomeric excess. We have determined the absolute structures of these compounds by using X-ray diffraction with copper radiation at low temperatures. Moreover, we have also established the prevalent absolute structures in these samples, by comparing their calculated and solid-state vibrational circular dichroism (VCD) spectra. The consistency of this method was confirmed by using (R,R)-2,8-diiodo-4,10-dimethyl-6 H,12H-5,11-methano-dibenzo[b,f][1,5]diazocine, Tröger's base, (R,R)-1, as a chiral compound of known absolute configuration.

  16. Structural determination of Bi-doped magnetite multifunctional nanoparticles for contrast imaging.

    PubMed

    Laguna-Marco, M A; Piquer, C; Roca, A G; Boada, R; Andrés-Vergés, M; Veintemillas-Verdaguer, S; Serna, C J; Iadecola, A; Chaboy, J

    2014-09-14

    To determine with precision how Bi atoms are distributed in Bi-doped iron oxide nanoparticles their structural characterization has been carried out by X-ray absorption spectroscopy (XAS) recorded at the K edge of Fe and at the L3 edge of Bi. The inorganic nanoparticles are nominally hybrid structures integrating an iron oxide core and a bismuth oxide shell. Fe K-edge XAS indicates the formation of a structurally ordered, non-stoichiometric magnetite (Fe3-δO4) phase for all the nanoparticles. The XAS spectra show that, in the samples synthesized by precipitation in aqueous media and laser pyrolysis, the Bi atoms neither enter into the iron oxide spinel lattice nor form any other mixed Bi-Fe oxides. No modification of the local structure around the Fe atoms induced by the Bi atoms is observed at the Fe K edge. In addition, contrary to expectations, our results indicate that the Bi atoms do not form a well-defined Bi oxide structure. The XAS study at the Bi L3 edge indicates that the environment around Bi atoms is highly disordered and only a first oxygen coordination shell is observed. Indefinite [BiO6-x(OH)x] units (isolated or aggregated forming tiny amorphous clusters) bonded through hydroxyl bridges to the nanoparticle, rather than a well defined Bi2O3 shell, surround the nanoparticle. On the other hand, the XAS study indicates that, in the samples synthesized by thermal decomposition, the Bi atoms are embedded in a longer range ordered structure showing the first and second neighbors.

  17. Picosecond laser structuring of thin film platinum layers covered with tantalum pentoxide isolation

    SciTech Connect

    Heise, Gerhard; Huber, Heinz; Trappendreher, Daniel; Ilchmann, Florian; Weiss, Robin S.; Wolf, Bernhard

    2012-07-01

    A thin film layer system consisting of platinum (Pt) as conductive layer on a glass substrate and tantalum pentoxide as isolating layer on top of the platinum is attractive for designing biocompatible conductor paths and contact pads for bio sensor chips. For the flexible and rapid patterning of the conductive and the isolating layers, both, the complete removal and the selective ablation of the individual thin films were investigated using ultra-short laser pulses with about 10 ps pulse duration and 1064 nm wavelength at low laser fluences. A platinum film covered with tantalum pentoxide shows a significantly lower ablation threshold than a single Pt film on glass alone when illuminated from the front side. Furthermore, we explored that the tantalum pentoxide film can be removed by glass side illumination from the Pt film, without affecting the Pt film and leaving the Pt film on the glass substrate intact. Those ablation phenomena occur at laser fluences of about 0.2 J/cm{sup 2}, far below the evaporation limit of platinum. We present a detailed ablation threshold value examination for the structuring of these layer systems by front side and glass side irradiation for different film thicknesses. Furthermore, we discuss the possible underlying physical mechanisms of these ablation phenomena.

  18. Isolated starches from yams (Dioscorea sp) grown at the Venezuelan Amazons: structure and functional properties.

    PubMed

    Pérez, Elevina; Rolland-Sabaté, Agnès; Dufour, Dominique; Guzmán, Romel; Tapia, María; Raymundez, Marìa; Ricci, Julien; Guilois, Sophie; Pontoire, Bruno; Reynes, Max; Gibert, Olivier

    2013-10-15

    This work aimed to characterize the molecular structure and functional properties of starches isolated from wild Dioscorea yams grown at the Amazons, using conventional and up-to-date methodologies. Among the high purity starches isolated (≥99%), the chain lengths were similar, whereas variations in gelatinization profile were observed. Starches have shown varied-shaped granules with monomodal distribution, and B-type crystallinity. Variations in amylose contents found by three analyses were hypothesized being related to intermediate material. Linear chain lengths were similar, and their amylopectins showed a dense, spherical conformation and similar molecular characteristics. The average molar mass and the radius of gyration of the chromatograms of the yam amylopectin, M¯W and R¯G were ranging between 174×10(6) g mol(-1) and 237×10(6) g mol(-1), and 201 nm and 233 nm, respectively. The white yams starches were more sensible to enzymes than the other two. All starches have shown a wide range of functional and nutritional properties.

  19. Isolated catalyst sites on amorphous supports: A systematic algorithm for understanding heterogeneities in structure and reactivity

    NASA Astrophysics Data System (ADS)

    Goldsmith, Bryan R.; Sanderson, Evan D.; Bean, Daniel; Peters, Baron

    2013-05-01

    Methods for modeling catalytic sites on amorphous supports lag far behind methods for modeling catalytic sites on metal surfaces, zeolites, and other crystalline materials. One typical strategy for amorphous supports uses cluster models with arbitrarily chosen constraints to model the rigid amorphous support, but these constraints arbitrarily influence catalyst site activity. An alternative strategy is to use no constraints, but this results in catalytic sites with unrealistic flexibility. We present a systematic ab initio method to model isolated active sites on insulating amorphous supports using small cluster models. A sequential quadratic programming framework helps us relate chemical properties, such as the activation energy, to active site structure. The algorithm is first illustrated on an empirical valence bond model energy landscape. We then use the algorithm to model an off-pathway kinetic trap in olefin metathesis by isolated Mo sites on amorphous SiO2. The cluster models were terminated with basis set deficient fluorine atoms to mimic the properties of an extended silica framework. We also discuss limitations of the current algorithm formulation and future directions for improvement.

  20. Isolation, structure and expression of mammalian genes for histidyl-tRNA synthetase.

    PubMed Central

    Tsui, F W; Siminovitch, L

    1987-01-01

    A full length cDNA clone that codes for human histidyl-tRNA synthetase (HRS) and cDNA clones that span the full length transcript of hamster HRS have been isolated. The full length human HRS cDNA was expressed after transfection into Cos 1 cells and a CHO ts mutant defective in the gene for HRS. The complete nucleotide sequence of the hamster and human gene were obtained and extensive homologies were observed in three regions on comparing these sequences between themselves and with the sequence of HRS derived from yeast. These results provide unequivocal evidence that we have indeed cloned the hamster and human gene for HRS. Three overlapping phage recombinants containing the complete hamster chromosomal gene for HRS have also been isolated. The genomic HRS is divided into 13 exons. The precise locations of each of the 5' and 3' exon-intron boundaries were defined by sequencing the appropriate regions of the cloned genomic DNA and aligning them with the sequence of HRS cDNAs. These studies provide the basis for future structural and functional analysis of the gene for HRS. In particular, it will be of interest to examine if different exons of HRS correlate to different domains of the HRS polypeptide. Images PMID:3554142

  1. Bioassay-Guided Isolation and Structural Modification of the Anti-TB Resorcinols from Ardisia gigantifolia.

    PubMed

    Guan, Yi-Fu; Song, Xun; Qiu, Ming-Hua; Luo, Shi-Hong; Wang, Bao-Jie; Van Hung, Nguyen; Cuong, Nguyen M; Soejarto, Djaja Doel; Fong, Harry H S; Franzblau, Scott G; Li, Sheng-Hong; He, Zhen-Dan; Zhang, Hong-Jie

    2016-08-01

    Tuberculosis (TB) is a highly contagious disease mainly caused by Mycobacterium tuberculosis H37 RV . Antitubercular (anti-TB) bioassay-guided isolation of the CHCl3 extract of the leaves and stems of the medicinal plant Ardisia gigantifolia led to the isolation of two anti-TB 5-alkylresorcinols, 5-(8Z-heptadecenyl) resorcinol (1) and 5-(8Z-pentadecenyl) resorcinol (2). We further synthesized 15 derivatives based on these two natural products. These compounds (natural and synthetic) were evaluated for their anti-TB activity against Mycobacterium tuberculosis H37 RV . Resorcinols 1 and 2 exhibited anti-TB activity with MIC values at 34.4 and 79.2 μm in MABA assay, respectively, and 91.7 and 168.3 μm in LORA assay, respectively. Among these derivatives, compound 8 was found to show improved anti-TB activity than its synthetic precursor (2) with MIC values at 42.0 μm in MABA assay and 100.2 μm in LORA assay. The active compounds should be regarded as new hits for further study as a novel class of anti-TB agents. The distinct structure-activity correlations of the parent compound were elucidated based on these derivatives.

  2. [Isolation and structural elucidation of secondary metabolites from marine Streptomyces sp. SCSIO 1934].

    PubMed

    Niu, Siwen; Li, Sumei; Tian, Xinpeng; Hu, Tao; Ju, Jianhua; Ynag, Xiaohong; Zhang, Si; Zhang, Changsheng

    2011-07-01

    Marine Actinobacteria are emerging as new resources for bioactive natural products with promise in novel drug discovery. In recent years, the richness and diversity of marine Actinobacteria from the South China Sea and their ability in producing bioactive products have been investigated. The objective of this work is to isolate and identify bioactive secondary metabolites from a marine actinobacterium SCSIO 1934 derived from sediments of South China Sea. The strain was identified as a Streptomyces spieces by analyzing its 16S rDNA sequence. Streptomyces sp. SCSIO 1934 was fermented under optimized conditions and seven bioactive secondary metabolites were isolated and purified by chromatographic methods including colum chromatography over silica gel and Sephadex LH-20. Their structures were elucidated as 17-O-demethylgeldanamycin (1), lebstatin (2), 17-O-demethyllebstatin (3), nigericin (4), nigericin sodium salt (5), abierixin (6), respectively, by detailed NMR spectroscopic data (1H, 13C, COSY, HSQC and HMBC). This work provided a new marine actinobacterium Streptomyces sp. SCSIO 1934, capable of producing diverse bioactive natural products.

  3. Species-specific PCR for the Diagnosis and Determination of Antibiotic Susceptibilities of Brucella Strains Isolated from Tehran, Iran

    PubMed Central

    Irajian, Gholam Reza; Masjedian Jazi, Faramarz; Mirnejad, Reza; Piranfar, Vahhab; Zahraei salehi, Taghi; Amir Mozafari, Noor; Ghaznavi-rad, Ehsanollah; Khormali, Mahmoud

    2016-01-01

    Background: Brucellosis is an endemic zoonotic disease in the Middle East. This study intended to design a uniplex PCR assay for the detection and differentiation of Brucella at the species level and determining the antibiotic susceptibility pattern of Brucella in Iran. Methods: Sixty-eight Brucella specimens (38 animal and 30 human specimens) were analyzed using PCR (using one pair of primers). Antibiotic susceptibility patterns were evaluated and compared using the E-Test and disk diffusion susceptibility test. Tigecycline susceptibility pattern was compared with other antibiotics. Results: Thirty six isolates of B. melitensis, 2 isolates of B. abortus and 1 isolate of B. suis from the 38 animal specimens, 24 isolates of B. melitensis and 6 isolates of B. abortus from the 30 human specimens were differentiated. The MIC50 values of doxycycline for human and animal specimens were 125 and 10 μg/ml, respectively, tigecycline 0.064 μg/ml for human specimens and 0.125μg/ml for animal specimens, and trimethoprim/ sulfamethoxazole and ciprofloxacin 0.065 and 0.125μg/ml, respectively, for both human and animal specimens. The highest MIC50 value of streptomycin in the human specimens was 0.5μg/ml and 1μg/ml for the animal specimens. The greatest resistance shown was to tetracycline and gentamicin, respectively. Conclusion: Uniplex PCR for the detection and differentiation of Brucella at the strain level is faster and less expensive than multiplex PCR, and the antibiotics doxycycline, rifampin, trimethoprim-sulfamethoxazole, ciprofloxacin, and ofloxacin are the most effective antibiotics for treating brucellosis. Resistance to tigecycline is increasing, and we recommend that it be used in a combination regimen. PMID:27799972

  4. High Prevalence of Biocide Resistance Determinants in Staphylococcus aureus Isolates from Three African Countries.

    PubMed

    Conceição, Teresa; Coelho, Céline; de Lencastre, Hermínia; Aires-de-Sousa, Marta

    2016-01-01

    We assessed the prevalence of six biocide resistance genes among 82 methicillin-resistant Staphylococcus aureus (MRSA) and 219 methicillin-susceptible S. aureus (MSSA) isolates from three African countries; the prevalence was very high for sepA (95.3%), mepA (89.4%), and norA (86.4%), intermediate for lmrS (60.8%) and qacAB (40.5%), and low for smr (3.7%). A significant association between biocide resistance genes and antibiotic resistance was observed, and a new cutoff MIC of ≥1 mg/liter for chlorhexidine nonsusceptibility was defined. PMID:26552979

  5. Determining cleanup levels in bioremediation: Quantitative structure activity relationship techniques

    SciTech Connect

    Arulgnanendran, V.R.J.; Nirmalakhandan, N.

    1995-12-31

    An important feature in the process of planning and initiating bioremediation is the quantification of the toxicity of either an individual chemical or a group of chemicals when multiple chemicals are involved. A laboratory protocol was developed to test the toxicity of single chemicals and mixtures of organic chemicals in a soil medium. Portions of these chemicals are used as a training set to develop Quantitative Structure Activity Relationship (QSAR) models. These predictive models are tested using the chemicals in the testing set, i.e., the remaining chemicals. Moreover mixtures with 10 contaminants in each mixture are tested experimentally to determine joint toxicity for mixtures of chemicals. Using the concepts of Toxic Units, Additivity Index, and Mixture Toxicity Index, the laboratory results are tested for additive, synergistic, or antagonistic effects of the contaminants. These concepts are further validated on mixtures containing eight chemicals that are tested in the laboratory. In addition to the use of the predictive models in evaluating cleanup levels for hazardous waste locations, they are useful to predict microbial toxicity in soils of new chemicals from a congeneric group acting by the same mode of toxicity. These models are applicable when the contaminants act singly or jointly in a mixture.

  6. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

    Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

  7. Molecular structure of an apolipoprotein determined at 2. 5- angstrom resolution

    SciTech Connect

    Breiter, D.R.; Benning, M.M.; Wesenberg, G.; Holden, H.M.; Rayment, I. ); Kanost, M.R.; Law, J.H.; Wells, M.A. )

    1991-01-22

    The three-dimensional structure of an apolipoprotein isolated from the African migratory locust Locusta migratoria has been determined by X-ray analysis to a resolution of 2.5 {angstrom}. The overall molecular architecture of this protein consists of five long {alpha}-helices connected by short loops. As predicted from amino acid sequence analyses, these helices are distinctly amphiphilic with the hydrophobic residues pointing in toward the interior of the protein and the hydrophilic side chains facing outward. The molecule falls into the general category of up-and-down {alpha}-helical bundles as previously observed, for example, in cytochrome c{prime}. Although the structure shows the presence of five long amphiphilic {alpha}-helices, the {alpha}-helical moment and hydrophobicity of the entire molecule fall into the range found for normal globular proteins. Thus, in order for the amphiphilic helices to play a role in the binding of the protein to a lipid surface, there must be a structural reorganization of the protein which exposes the hydrophobic interior to the lipid surface. The three dimensional motif of this apolipoprotein is compatible with a model in which the molecule binds to the lipid surface via a relatively nonpolar end and then spreads on the surface in such a way as to cause the hydrophobic side chains of the helices to come in contact with the lipid surface, the charged and polar residues to remain in contact with water, and the overall helical motif of the protein to be maintained.

  8. Pathogenic Vibrio parahaemolyticus isolated from biofouling on commercial vessels and harbor structures.

    PubMed

    Revilla-Castellanos, Valeria J; Guerrero, Abraham; Gomez-Gil, Bruno; Navarro-Barrón, Erick; Lizárraga-Partida, Marcial L

    2015-01-01

    Ballast water is a significant vector of microbial dissemination; however, biofouling on commercial vessel hulls has been poorly studied with regard to pathogenic bacteria transport. Biofouling on three commercial vessels and seven port structures in Ensenada, Baja California, Mexico, was examined by qPCR to identify and quantify Vibrio parahaemolyticus, a worldwide recognized food-borne human pathogen. Pathogenic variants (trh+, tdh+) of V. parahaemolyticus were detected in biofouling homogenates samples from several docks in Ensenada and on the hulls of ships with Japanese and South Korean homeports, but not in reference sampling stations. A total of 26 tdh+ V. parahaemolyticus colonies and 1 ORF8+/O3:K6 strain were also isolated from enriched biofouling homogenate samples confirming the qPCR analysis. Our results suggest that biofouling is an important reservoir of pathogenic vibrios. Thus, ship biofouling might be an overlooked vector with regard to the dissemination of pathogens, primarily pathogenic V. parahaemolyticus.

  9. [Isolation and structure identification of chemical constituents from the skin of Bufo bufo gargarizans].

    PubMed

    Dai, Li-Ping; Gao, Hui-Min; Wang, Zhi-Min; Wang, Wei-Hao

    2007-08-01

    The skin of Bufo bufo gargarizans, originated from Bufo bufo gargarizans Cantor (Bufonidae), is widely used in traditional Chinese medicine for the treatment of hepatoma, lung cancer and etc. The preparation of the aqueous components has significant therapeutic effect against the digestive tract cancer. The water-soluble chemical constituents in the skin of Bufo bufo gargarizans were then investigated to make clear the active compounds. Six compounds were isolated and purified by recrystallization and column chromatography on silica gel and ODS, their structures were elucidated as 4-amido-3-hydroxymethyl-cyclooctylamidezotetra-alpha-furanone (I), bufogargarizanine C (II), bufothionine (III), dehydrobufotenine hydrobromide (IV), suberic acid (V) and succinic acid (VI) on the basis of physicochemical properties and spectral data (UV, IR, 1H NMR, 13C NMR and MS). Of the above compounds, compounds I and II are new compounds and named bufogargarizanine B and C, respectively. PMID:17944235

  10. Structural analysis and antioxidant activities of polysaccharide isolated from Jinqian mushroom.

    PubMed

    Liu, Yong; Du, Yi-Qun; Wang, Jun-Hui; Zha, Xue-Qiang; Zhang, Jian-Bo

    2014-03-01

    Jinqian mushroom is a precious edible mushroom with delicious taste and high nutritional value. In this paper, a polysaccharide fraction JQPs was isolated and purified from the fruiting body of Jinqian mushroom. The chemical structure, chain conformation and antioxidant activities of JQPs were investigated. The results indicated that JQPs was mainly composed of glucose with trace amounts of xylose. The backbone of JQPs consisted of β-(1 → 3)-D-glucan with β-(1 → 6)-glucosyl side chain. The chain conformation analysis showed that JQPs was a triple helical polysaccharide. The antioxidant activity tests in vitro revealed that JQPs exhibited high DPPH radical and ABTS radical scavenging activities, moderate superoxide radical and hydroxyl radical scavenging activities, low reducing power and Fe(2+) chelating activities. The results suggested that JQPs could be used as a potential natural antioxidant.

  11. Isolation and Structure Elucidation of GM4-Type Gangliosides from the Okinawan Starfish Protoreaster nodosus

    PubMed Central

    Pan, Ke; Tanaka, Chiaki; Inagaki, Masanori; Higuchi, Ryuichi; Miyamoto, Tomofumi

    2012-01-01

    Three new ganglioside molecular species, termed PNG-1, PNG-2A, and PNG-2B were isolated from pyloric caeca of the starfish Protoreaster nodosus. Their structures were elucidated using a combination of spectroscopic and chemical methods, and characterized as 1-O-[8-O-methyl-N-acetyl-α-neuraminosyl-(2→3)-β-galactopyranosyl]-ceramide for PNG-1, 1-O-[β-galactofuranosyl-(1→3)-α-galactopyranosyl-(1→4)-8-O-methyl-N-acetyl-α-neuraminosyl-(2→3)-β-galactopyranosyl]-ceramide for PNG-2A, and 1-O-[β-galactofuranosyl-(1→3)-α-galactopyranosyl-(1→9)-N-acetyl-α-neuraminosyl-(2→3)-β-galactopyranosyl]-ceramide for PNG-2B. PNG-2A and PNG-2B represent the first GM4 elongation products in nature. PMID:23203271

  12. High-yield isolation and subcellular proteomic characterization of nuclear and subnuclear structures from trypanosomes.

    PubMed

    DeGrasse, Jeffrey A; Chait, Brian T; Field, Mark C; Rout, Michael P

    2008-01-01

    The vast evolutionary distance between the Opisthokonta (animals and yeast) and the excavata (a major group of protists, including Giardia and Trypanosoma) presents a significant challenge to in silico functional genomics and ortholog identification. Subcellular proteomic identification of the constituents of highly enriched organelles can alleviate this problem by both providing localization evidence and yielding a manageably sized proteome for detailed in silico functional assignment. We describe a method for the high-yield isolation of nuclei from the kinetoplastid Trypanosoma brucei. We also describe the subsequent purification of subnuclear compartments, including the nuclear envelope and nucleolus. Finally, using several proteomic strategies, we survey the proteome of a subcellular structure or organelle, using the nuclear pore complex as an example.

  13. Isolation and structural characterization of a new tadalafil analog (chloropropanoylpretadalafil) found in a dietary supplement.

    PubMed

    Kern, Sara E; Lorenz, Lisa M; Lanzarotta, Adam; Nickum, Elisa A; Litzau, Jonathan J

    2016-09-01

    A screen for known PDE-5 inhibitors in a dietary supplement product marketed for "enhanced sexual performance" detected a compound that structurally resembled chloropretadalafil, a known analog of tadalafil. The compound was isolated from the supplement matrix using high performance liquid chromatography with ultraviolet detection (HPLC-UV) and a fraction collector, and was further characterized using gas chromatography with Fourier Transform infrared detection and mass spectral detection (GC/FT-IR/MS), as well as high resolution mass spectrometry (HRMS). The analog had an accurate mass of m/z 441.1216 (error is 0.8706ppm) for the protonated species [M+H](+), corresponding to a molecular formula of C23H22ClN2O5. HRAM and GC/FT-IR/MS mass spectral fragmentation data suggested that the modification is a chloropropanoyl moiety extending from the nitrogen on the piperidine ring of chloropretadalafil. The proposed new analog has been named chloropropanoylpretadalafil. PMID:27337189

  14. Isolation and structure elucidation of linolipins C and D, complex oxylipins from flax leaves.

    PubMed

    Chechetkin, Ivan R; Blufard, Alexander S; Khairutdinov, Bulat I; Mukhitova, Fakhima K; Gorina, Svetlana S; Yarin, Andrey Y; Antsygina, Larisa L; Grechkin, Alexander N

    2013-12-01

    Two complex oxylipins (linolipins C and D) were isolated from the leaves of flax plants inoculated with phytopathogenic bacteria Pectobacterium atrosepticum. Their structures were elucidated based on UV, MS and NMR spectroscopic data. Both oxylipins were identified as digalactosyldiacylglycerol (DGDG) molecular species. Linolipin C contains one residue of divinyl ether (ω5Z)-etherolenic acid and one α-linolenate residue at sn-1 and sn-2 positions, respectively. Linolipin D possesses two (ω5Z)-etherolenic acid residues at both sn-1 and sn-2 positions. The rapid formation (2-30min) of linolipins C and D alongside with linolipins A and B occurred in the flax leaves upon their damage by freezing-thawing.

  15. Structural and Immunological Activity Characterization of a Polysaccharide Isolated from Meretrix meretrix Linnaeus

    PubMed Central

    Li, Li; Li, Heng; Qian, Jianying; He, Yongfeng; Zheng, Jialin; Lu, Zhenming; Xu, Zhenghong; Shi, Jinsong

    2015-01-01

    Polysaccharides from marine clams perform various biological activities, whereas information on structure is scarce. Here, a water-soluble polysaccharide MMPX-B2 was isolated from Meretrix meretrix Linnaeus. The proposed structure was deduced through characterization and its immunological activity was investigated. MMPX-B2 consisted of d-glucose and d-galctose residues at a molar ratio of 3.51:1.00. The average molecular weight of MMPX-B2 was 510 kDa. This polysaccharide possessed a main chain of (1→4)-linked-α-d-glucopyranosyl residues, partially substituted at the C-6 position by a few terminal β-d-galactose residues or branched chains consisting of (1→3)-linked β-d-galactose residues. Preliminary immunological tests in vitro showed that MMPX-B2 could stimulate the murine macrophages to release various cytokines, and the structure-activity relationship was then established. The present study demonstrated the potential immunological activity of MMPX-B2, and provided references for studying the active ingredients in M. meretrix. PMID:26729136

  16. Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms

    PubMed Central

    Balasco, Nicole; Esposito, Luciana; Simone, Alfonso De; Vitagliano, Luigi

    2013-01-01

    It has been recently discovered that the connection of secondary structure elements (ββ-unit, βα- and αβ-units) in proteins follows quite stringent principles regarding the chirality and the orientation of the structural units (Koga et al., Nature 2012;491:222–227). By exploiting these rules, a number of protein scaffolds endowed with a remarkable thermal stability have been designed (Koga et al., Nature 2012;491:222–227). By using structural databases of proteins isolated from either mesophilic or thermophilic organisms, we here investigate the influence of supersecondary associations on the thermal stability of natural proteins. Our results suggest that β-hairpins of proteins from thermophilic organisms are very frequently characterized by shortenings of the loops. Interestingly, this shortening leads to states that display a very strong preference for the most common connectivity of the strands observed in native protein hairpins. The abundance of selective states in these proteins suggests that they may achieve a high stability by adopting a strategy aimed to reduce the possible conformations of the unfolded ensemble. In this scenario, our data indicate that the shortening is effective if it increases the adherence to these rules. We also show that this mechanism may operate in the stabilization of well-known protein folds (thioredoxin and RNase A). These findings suggest that future investigations aimed at defining mechanism of protein stabilization should also consider these effects. PMID:23661276

  17. Structure of constituents isolated from the flower buds of Cananga odorata and their inhibitory effects on aldose reductase.

    PubMed

    Matsumoto, Takahiro; Nakamura, Seikou; Fujimoto, Katsuyoshi; Ohta, Tomoe; Ogawa, Keiko; Yoshikawa, Masayuki; Matsuda, Hisashi

    2014-10-01

    Three new terpenoid derivatives, canangaterpenes IV-VI, were isolated from the flower buds of Cananga odorata, cultivated in Thailand, together with eight known flavonoids. The chemical structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. The inhibitory effects of the isolated compounds on aldose reductase were also investigated. Several terpenoid derivatives and flavonoids were shown to inhibit aldose reductase. PMID:24816646

  18. Structural Information Inference from Lanthanoid Complexing Systems: Photoluminescence Studies on Isolated Ions

    NASA Astrophysics Data System (ADS)

    Greisch, Jean Francois; Harding, Michael E.; Chmela, Jiri; Klopper, Willem M.; Schooss, Detlef; Kappes, Manfred M.

    2016-06-01

    The application of lanthanoid complexes ranges from photovoltaics and light-emitting diodes to quantum memories and biological assays. Rationalization of their design requires a thorough understanding of intramolecular processes such as energy transfer, charge transfer, and non-radiative decay involving their subunits. Characterization of the excited states of such complexes considerably benefits from mass spectrometric methods since the associated optical transitions and processes are strongly affected by stoichiometry, symmetry, and overall charge state. We report herein spectroscopic measurements on ensembles of ions trapped in the gas phase and soft-landed in neon matrices. Their interpretation is considerably facilitated by direct comparison with computations. The combination of energy- and time-resolved measurements on isolated species with density functional as well as ligand-field and Franck-Condon computations enables us to infer structural as well as dynamical information about the species studied. The approach is first illustrated for sets of model lanthanoid complexes whose structure and electronic properties are systematically varied via the substitution of one component (lanthanoid or alkali,alkali-earth ion): (i) systematic dependence of ligand-centered phosphorescence on the lanthanoid(III) promotion energy and its impact on sensitization, and (ii) structural changes induced by the substitution of alkali or alkali-earth ions in relation with structures inferred using ion mobility spectroscopy. The temperature dependence of sensitization is briefly discussed. The focus is then shifted to measurements involving europium complexes with doxycycline an antibiotic of the tetracycline family. Besides discussing the complexes' structural and electronic features, we report on their use to monitor enzymatic processes involving hydrogen peroxide or biologically relevant molecules such as adenosine triphosphate (ATP).

  19. Bioactive heterocyclic alkaloids with diterpene structure isolated from traditional Chinese medicines.

    PubMed

    Xu, Tengfei; Liu, Shu; Meng, Lulu; Pi, Zifeng; Song, Fengrui; Liu, Zhiqiang

    2016-07-15

    The diterpenoid alkaloids as one type of heterocyclic alkaloids have been found in many traditional herbal medicines, such as genus Consolida, Aconitum, and Delphinium (Ranunculaceae). Pharmacological researches have indicated that many diterpenoid alkaloids are the main bioactive components which have analgesic, anti-inflammatory, anti-microbial, anti-tumor, cardiotonic, and anti-arrhythmic activities. Studies focused on the determination, quantitation and pharmacological properties of these alkaloids have dramatically increased during the past few years. Up to now, newly discovered diterpenoid alkaloids with important biological activities have been isolated and synthesized. Considering their significant role and diffusely used in many disease treatments, we summarized the information of their analysis methods, bioactivity, metabolism and biotransformation in vivo as well as the pharmacological mechanisms. Based on above review, the further researches are suggested.

  20. Autosomal STR analyses in native Amazonian tribes suggest a population structure driven by isolation by distance.

    PubMed

    Dos Santos, Sidney E B; Ribeiro-Rodrigues, Elzemar M; Ribeiro-Dos-Santos, Andrea K C; Hutz, Mara H; Tovo-Rodrigues, Luciana; Salzano, Francisco M; Callegari-Jacques, Sidia M

    2009-02-01

    Eleven short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, TH01, and TPOX) were investigated in 232 individuals from 6 Amazonian native tribes (Tiriyó, Waiãpi, Zoé, Urubu-Kaapor, Awa-Guajá, and Parakanã). We added the new data to a database that included five previously typed native populations from the same area (Wai Wai, Gavião, Zoró, Suruí, and Xavante). The results presented here concern this new data set, which accounts for 526 individuals in total. We tested whether major geographic or linguistic barriers to gene flow exist among such human groups and tried to find a possible anthropological or ethnological explanation for such patterns. We measured the average heterozygosity (H) and the number of alleles (N(A) ) and found that both are lower than values observed in populations of different ethnic backgrounds, such as European or African descendants. Despite such a result, we found high between-population variation; lower H and/or N(A) values were obtained from four isolated tribes that came into contact with external nonnative populations in recent times (1921-1989). By applying analysis of molecular variance, generalized hierarchical modeling, and the Structure Bayesian analysis, we were not able to detect any significant geographic or linguistic barrier to gene flow. Geographic autocorrelation analysis suggests that the genetic structure of native Amazonian tribes is better explained by isolation by distance because the level of genetic similarity decreases according to linear geographic distance, reaching null or negative values at a scale of 300 km.

  1. NMR Structure of Francisella tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins.

    PubMed

    Zook, James; Mo, Gina; Sisco, Nicholas J; Craciunescu, Felicia M; Hansen, Debra T; Baravati, Bobby; Cherry, Brian R; Sykes, Kathryn; Wachter, Rebekka; Van Horn, Wade D; Fromme, Petra

    2015-06-01

    Tularemia is a potentially fatal bacterial infection caused by Francisella tularensis, and is endemic to North America and many parts of northern Europe and Asia. The outer membrane lipoprotein, Flpp3, has been identified as a virulence determinant as well as a potential subunit template for vaccine development. Here we present the first structure for the soluble domain of Flpp3 from the highly infectious Type A SCHU S4 strain, derived through high-resolution solution nuclear magnetic resonance (NMR) spectroscopy; the first structure of a lipoprotein from the genus Francisella. The Flpp3 structure demonstrates a globular protein with an electrostatically polarized surface containing an internal cavity-a putative binding site based on the structurally homologous Bet v1 protein family of allergens. NMR-based relaxation studies suggest loop regions that potentially modulate access to the internal cavity. The Flpp3 structure may add to the understanding of F. tularensis virulence and contribute to the development of effective vaccines.

  2. Extensively Drug-Resistant Pseudomonas aeruginosa Isolates Containing blaVIM-2 and Elements of Salmonella Genomic Island 2: a New Genetic Resistance Determinant in Northeast Ohio

    PubMed Central

    Perez, Federico; Hujer, Andrea M.; Marshall, Steven H.; Ray, Amy J.; Rather, Philip N.; Suwantarat, Nuntra; Dumford, Donald; O'Shea, Patrick; Domitrovic, T. Nicholas J.; Salata, Robert A.; Chavda, Kalyan D.; Chen, Liang; Kreiswirth, Barry N.; Vila, Alejandro J.; Haussler, Susanne; Jacobs, Michael R.

    2014-01-01

    Carbapenems are a mainstay of treatment for infections caused by Pseudomonas aeruginosa. Carbapenem resistance mediated by metallo-β-lactamases (MBLs) remains uncommon in the United States, despite the worldwide emergence of this group of enzymes. Between March 2012 and May 2013, we detected MBL-producing P. aeruginosa in a university-affiliated health care system in northeast Ohio. We examined the clinical characteristics and outcomes of patients, defined the resistance determinants and structure of the genetic element harboring the blaMBL gene through genome sequencing, and typed MBL-producing P. aeruginosa isolates using pulsed-field gel electrophoresis (PFGE), repetitive sequence-based PCR (rep-PCR), and multilocus sequence typing (MLST). Seven patients were affected that were hospitalized at three community hospitals, a long-term-care facility, and a tertiary care center; one of the patients died as a result of infection. Isolates belonged to sequence type 233 (ST233) and were extensively drug resistant (XDR), including resistance to all fluoroquinolones, aminoglycosides, and β-lactams; two isolates were nonsusceptible to colistin. The blaMBL gene was identified as blaVIM-2 contained within a class 1 integron (In559), similar to the cassette array previously detected in isolates from Norway, Russia, Taiwan, and Chicago, IL. Genomic sequencing and assembly revealed that In559 was part of a novel 35-kb region that also included a Tn501-like transposon and Salmonella genomic island 2 (SGI2)-homologous sequences. This analysis of XDR strains producing VIM-2 from northeast Ohio revealed a novel recombination event between Salmonella and P. aeruginosa, heralding a new antibiotic resistance threat in this region's health care system. PMID:25070102

  3. Characterization and structure of the polysaccharide produced by Pseudomonas fluorescens strain TF7 isolated from an arid region of Algeria.

    PubMed

    Taguett, Farida; Boisset, Claire; Heyraud, Alain; Buon, Laurine; Kaci, Yahia

    2015-05-01

    Many bacteria possess a natural ability to synthesize and excrete exopolysaccharides which are widely varied in structure and function. These bacteria have the ability to solubilize inorganic phosphorus, which is important to promote growth and increase crop yields. The objective of this study is to select an adaptive strain to the constraints of erratic rainfall and large temperature variations and to determine the possible synergistic effects of its EPS and organic acid on tricalcium phosphate (TCP) solubilization. The strain TF7 isolated from an arid region of Algeria was characterized on the basis of its morphological and physiological traits. Polysaccharide production and the phosphate-solubilizing activity of the strain were evaluated using sucrose and tricalcium phosphate. This EPS was studied by sugar analysis as well as proton NMR spectra. The 16S rRNA gene sequence of this strain shared a similarity of more than 96% with Pseudomonas fluorescens. The maximum polysaccharide productivity was estimated at 4.5g·L(-1) after 5 days. The analyzed sugar was comprised of fructose, glucose, and mannose in a ratio of 4:1:0.6. NMR spectra indicated that the polysaccharide produced by the strain was levan with β-(2→6)-linked fructose units in accordance with the generally accepted structure. The strain TF7 solubilizes phosphate and forms a clear halo around the colony. The phosphate-solubilizing index is 2.33.

  4. A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics.

    PubMed

    Melnikova, Daria N; Mineev, Konstantin S; Finkina, Ekaterina I; Arseniev, Alexander S; Ovchinnikova, Tatiana V

    2016-01-01

    A novel lipid transfer protein, designated as Ag-LTP, was isolated from aerial parts of the dill Anethum graveolens L. Structural, antimicrobial, and lipid binding properties of the protein were studied. Complete amino acid sequence of Ag-LTP was determined. The protein has molecular mass of 9524.4 Da, consists of 93 amino acid residues including eight cysteines forming four disulfide bonds. The recombinant Ag-LTP was overexpressed in Escherichia coli and purified. NMR investigation shows that the Ag-LTP spatial structure contains four α-helices, forming the internal hydrophobic cavity, and a long C-terminal tail. The measured volume of the Ag-LTP hydrophobic cavity is equal to ~800 A(3), which is much larger than those of other plant LTP1s. Ag-LTP has weak antifungal activity and unpronounced lipid binding specificity but effectively binds plant hormone jasmonic acid. Our results afford further molecular insight into biological functions of LTP in plants. PMID:26680443

  5. A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics.

    PubMed

    Melnikova, Daria N; Mineev, Konstantin S; Finkina, Ekaterina I; Arseniev, Alexander S; Ovchinnikova, Tatiana V

    2016-01-01

    A novel lipid transfer protein, designated as Ag-LTP, was isolated from aerial parts of the dill Anethum graveolens L. Structural, antimicrobial, and lipid binding properties of the protein were studied. Complete amino acid sequence of Ag-LTP was determined. The protein has molecular mass of 9524.4 Da, consists of 93 amino acid residues including eight cysteines forming four disulfide bonds. The recombinant Ag-LTP was overexpressed in Escherichia coli and purified. NMR investigation shows that the Ag-LTP spatial structure contains four α-helices, forming the internal hydrophobic cavity, and a long C-terminal tail. The measured volume of the Ag-LTP hydrophobic cavity is equal to ~800 A(3), which is much larger than those of other plant LTP1s. Ag-LTP has weak antifungal activity and unpronounced lipid binding specificity but effectively binds plant hormone jasmonic acid. Our results afford further molecular insight into biological functions of LTP in plants.

  6. Decoupling structural and environmental determinants of sap velocity

    NASA Astrophysics Data System (ADS)

    Caylor, K. K.; Dragoni, D.

    2007-12-01

    Characterization of transpiration based on the water use of individual tress has the advantage of preserving vital information on the plant-environment functional links and flux partitioning between species and landscape areas. Whole-tree transpiration has been estimated by means of sap velocity probes, which offer the dual advantages of practicality and repeatability. However, the assumptions underlying the technique require careful verification in order to determine total sap flow from point-based estimates of sap velocity. Our work presents a novel theoretical framework for the study of individual tree sap flow that incorporates both spatial and temporal variability in sap velocities. The instantaneous sap velocity at any point in the radial profile of xylem tissue is defined as the product of two components: (1) a time-invariant sap velocity distribution linked to the species- specific anatomical and structural properties of the conducting xylem, and (2) a time-varying term linked to the dynamics of the atmospheric water demand and available soil moisture. The separation of structural and temporal variation in sap velocity observations provides a direct mechanism for investigating how sap flow is governed by variation in environmental conditions as well as a means for comparing characteristic rates of plant water use among individuals of varying size. Most critically, this approach allows for a consistent and physically meaningful method for extrapolating point observations of sap velocity across the entire depth of conducting xylem. Experimental evidence supports our theoretical framework in the case of a population of sugar maples in a mixed deciduous forest, where observations were taken from a wide range of tree sizes, under varying soil water availability and atmospheric transpiration demand. We have also applied our approach to a small homogeneous sample of dwarf apple trees in a managed orchard, with favorable results. While these results require further

  7. Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India.

    PubMed

    Akiba, Masato; Sekizuka, Tsuyoshi; Yamashita, Akifumi; Kuroda, Makoto; Fujii, Yuki; Murata, Misato; Lee, Ken-Ichi; Joshua, Derrick Ian; Balakrishna, Keshava; Bairy, Indira; Subramanian, Kaushik; Krishnan, Padma; Munuswamy, Natesan; Sinha, Ravindra K; Iwata, Taketoshi; Kusumoto, Masahiro; Guruge, Keerthi S

    2016-05-01

    To determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446 E. coli isolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%) E. coli isolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. The blaNDM gene was detected in 14/21 carbapenem-resistant E. coli isolates: blaNDM-1 in 2 isolates, blaNDM-5 in 7 isolates, and blaNDM-7 in 5 isolates. The blaCTX-M gene was detected in 112 isolates (66.3%): blaCTX-M-15 in 108 isolates and blaCTX-M-55 in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of the blaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India. PMID:26953207

  8. Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India

    PubMed Central

    Sekizuka, Tsuyoshi; Yamashita, Akifumi; Kuroda, Makoto; Fujii, Yuki; Murata, Misato; Lee, Ken-ichi; Joshua, Derrick Ian; Balakrishna, Keshava; Bairy, Indira; Subramanian, Kaushik; Krishnan, Padma; Munuswamy, Natesan; Sinha, Ravindra K.; Iwata, Taketoshi; Kusumoto, Masahiro; Guruge, Keerthi S.

    2016-01-01

    To determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446 E. coli isolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%) E. coli isolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. The blaNDM gene was detected in 14/21 carbapenem-resistant E. coli isolates: blaNDM-1 in 2 isolates, blaNDM-5 in 7 isolates, and blaNDM-7 in 5 isolates. The blaCTX-M gene was detected in 112 isolates (66.3%): blaCTX-M-15 in 108 isolates and blaCTX-M-55 in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of the blaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India. PMID:26953207

  9. Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India.

    PubMed

    Akiba, Masato; Sekizuka, Tsuyoshi; Yamashita, Akifumi; Kuroda, Makoto; Fujii, Yuki; Murata, Misato; Lee, Ken-Ichi; Joshua, Derrick Ian; Balakrishna, Keshava; Bairy, Indira; Subramanian, Kaushik; Krishnan, Padma; Munuswamy, Natesan; Sinha, Ravindra K; Iwata, Taketoshi; Kusumoto, Masahiro; Guruge, Keerthi S

    2016-05-01

    To determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446 E. coli isolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%) E. coli isolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. The blaNDM gene was detected in 14/21 carbapenem-resistant E. coli isolates: blaNDM-1 in 2 isolates, blaNDM-5 in 7 isolates, and blaNDM-7 in 5 isolates. The blaCTX-M gene was detected in 112 isolates (66.3%): blaCTX-M-15 in 108 isolates and blaCTX-M-55 in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of the blaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India.

  10. Isolation and gas-chromatographic determinations of saturated and polycyclic aromatic hydrocarbons in mussels

    SciTech Connect

    Bulter, A.C.; Sibbald, R.R.

    1986-10-01

    The method here presented is intended for application in the analysis of trace quantities of petroleum hydrocarbons in oil-polluted mussels. It is a technique incorporating saponification, pentane extraction and silica gel cleanup, and represents a modification and ad hoc synthesis of other procedures. Recovery efficiencies of the method are 80% or greater for C/sub 15/ to C/sub 38/ n-alkanes, and vary between 0% for naphthalene and 84% for pyrene. Isolation and quantification of the polycyclic aromatic hydrocarbon (PAH) fraction are of importance in environmental monitoring; some compounds in this group are either known or suspected to be carcinogenic agents. Concomitant analysis for the saturated hydrocarbons fraction can provide essential clues to the petrogenic or pyrolytic origin of the PAHs.

  11. Isolation and gas-chromatographic determination of saturated and polycyclic aromatic hydrocarbons in mussels

    SciTech Connect

    Butler, A.C.; Sibbald, R.R.

    1986-10-01

    The method here presented is intended for application in the analysis of trace quantities of petroleum hydrocarbons in oil-polluted mussels. It is a technique incorporating saponification, pentane extraction and silica gel cleanup, and represents a modification and ad hoc synthesis of other procedures. Recovery efficiencies of the method are 80% or greater for C/sub 15/ to C/sub 38/ n-alkanes, and vary between 0% for naphthalene and 84% for pyrene. Isolation and quantification of the polycyclic aromatic hydrocarbon (PAH) fraction are of importance in environmental monitoring; some compounds in this group are either known or suspected to be carcinogenic agents. Concomitant analysis for the saturated hydrocarbons fraction can provide essential clues to the petrogenic or pyrolytic origin of the PAHs.

  12. Non-histone chromosomal proteins. Their isolation and role in determining specificity of transcription in vitro.

    PubMed

    Blüthmann, H; Mrozek, S; Gierer, A

    1975-10-15

    We describe a method for fractionation of chromatin components by selective dissociation with salt in buffers containing 5 M urea in combination with cromatography on hydroxyapatite at 4 degrees C. This results in two histone and four non-histone fractions which are recovered in high yield and with minimal proteolytic contamination. Template capacity measurements of the isolated chromatins and pre-saturation competition hybridization experiments support the idea that a group of non-histone proteins activate the transcription of specific DNA sequences which were not transcribed from purified DNA to the same extent. In reconstitution experiments a non-histone protein fraction, NH4, prepared from lymphocyte chromatin by hydroxyapatite chromatography is shown to cause transcription in vitro of lymphocyte-specific RNA sequences. A subfraction with a molecular weight of 30 000 comprising 40% of the NH4 fraction protein is characteristic for this tissue and not found in liver chromatin.

  13. Isolation and determination of ginsenosides in American ginseng leaves and root extracts by LC-MS.

    PubMed

    Ligor, T; Ludwiczuk, A; Wolski, T; Buszewski, B

    2005-12-01

    Ginseng saponins (ginsenosides) were extracted from the root and leaves of locally cultivated American ginseng (Panax quinquefolium L.). For the isolation of compounds from plant samples three different extraction methods were utilized: accelerated solvent extraction, the ultrasound-assisted solvent extraction and mechanical shaking assisted solvent extraction. The separation of compounds was achieved with a water-acetonitrile gradient system using a C18 reversed-phase column. Target compounds were identified in MS(2) and MS(3) experiments. The relative distribution of these ginsenosides in each root and leaf extract was established. The limit of detection of the method was less than 30 ng/ml. Recovery of ginseng saponins in spiked samples exceeded 80%, while the relative standard deviation ranged from 7.1 to 9.1%. The total concentrations of ginsenosides were 41 and 13 mg/g in root and leaves.

  14. Epidemic population structure of extraintestinal pathogenic Escherichia coli determined by single nucleotide polymorphism pyrosequencing.

    PubMed

    Fernández-Romero, Natalia; Romero-Gómez, María Pilar; Gómez-Gil, María Rosa; Mingorance, Jesús

    2011-10-01

    We have developed an MLST-based scheme for typing Escherichia coli isolates using pyrosequencing of single nucleotide polymorphic positions (SNP). The SNP sequences are converted into allelic patterns and analyzed using the same approach used for MLST analyses. We have tested the method in two unselected collections of clinical isolates of E. coli obtained from blood and urine cultures. The two collections had a similar structure, 25% of the profiles (representing 68% of the isolates) were common to both, and 62% of the profiles (nearly 20% of the isolates) were unique. The four major profiles accounted for 44% of the isolates, and among these the most frequent one was related to the pandemic ST131 clone. The method is easy to implement and might be useful for typing large microbial collections. PMID:21723423

  15. Genomic Variability of Haemophilus influenzae Isolated from Mexican Children Determined by Using Enterobacterial Repetitive Intergenic Consensus Sequences and PCR

    PubMed Central

    Gomez-De-Leon, Patricia; Santos, Jose I.; Caballero, Javier; Gomez, Demostenes; Espinosa, Luz E.; Moreno, Isabel; Piñero, Daniel; Cravioto, Alejandro

    2000-01-01

    Genomic fingerprints from 92 capsulated and noncapsulated strains of Haemophilus influenzae from Mexican children with different diseases and healthy carriers were generated by PCR using the enterobacterial repetitive intergenic consensus (ERIC) sequences. A cluster analysis by the unweighted pair-group method with arithmetic averages based on the overall similarity as estimated from the characteristics of the genomic fingerprints, was conducted to group the strains. A total of 69 fingerprint patterns were detected in the H. influenzae strains. Isolates from patients with different diseases were represented by a variety of patterns, which clustered into two major groups. Of the 37 strains isolated from cases of meningitis, 24 shared patterns and were clustered into five groups within a similarity level of 1.0. One fragment of 1.25 kb was common to all meningitis strains. H. influenzae strains from healthy carriers presented fingerprint patterns different from those found in strains from sick children. Isolates from healthy individuals were more variable and were distributed differently from those from patients. The results show that ERIC-PCR provides a powerful tool for the determination of the distinctive pathogenicity potentials of H. influenzae strains and encourage its use for molecular epidemiology investigations. PMID:10878033

  16. Structural characterization of lignin isolated from coconut (Cocos nucifera) coir fibers.

    PubMed

    Rencoret, Jorge; Ralph, John; Marques, Gisela; Gutiérrez, Ana; Martínez, Ángel T; del Río, José C

    2013-03-13

    The structure of the isolated milled "wood" lignin from coconut coir has been characterized using different analytical methods, including Py-GC/MS, 2D NMR, DFRC, and thioacidolysis. The analyses demonstrated that it is a p-hydroxyphenyl-guaiacyl-syringyl (H-G-S) lignin, with a predominance of G units (S/G ratio 0.23) and considerable amounts of associated p-hydroxybenzoates. Two-dimensional NMR indicated that the main substructures present in this lignin include β-O-4' alkyl aryl ethers followed by phenylcoumarans and resinols. Two-dimensional NMR spectra also indicated that coir lignin is partially acylated at the γ-carbon of the side chain with p-hydroxybenzoates and acetates. DFRC analysis showed that acetates preferentially acylate the γ-OH in S rather than in G units. Despite coir lignin's being highly enriched in G-units, thioacidolysis indicated that β-β' resinol structures are mostly derived from sinapyl alcohol. Finally, we find evidence that the flavone tricin is incorporated into the coconut coir lignin, as has been recently noted for various grasses.

  17. Conceptual structure of the 1996 performance assessment for the Waste Isolation Pilot Plant

    SciTech Connect

    HELTON,JON CRAIG; ANDERSON,D. RICHARD; BASABILVAZO,G.; JOW,HONG-NIAN; MARIETTA,MELVIN G.

    2000-05-18

    The conceptual structure of the 1996 performance assessment (PA) for the Waste Isolation Pilot Plant (WIPP) is described. This structure involves three basic entities (EN1, EN2, EN3): (1) EN1, a probabilistic characterization of the likelihood of different futures occurring at the WIPP site over the next 10,000 yr, (2) EN2, a procedure for estimating the radionuclide releases to the accessible environment associated with each of the possible futures that could occur at the WIPP site over the next 10,000 yr, and (3) EN3, a probabilistic characterization of the uncertainty in the parameters used in the definition of EN1 and EN2. In the formal development of the 1996 WIPP PA, EN1 is characterized by a probability space (S{sub st}, P{sub st}, p{sub st}) for stochastic (i.e., aleatory) uncertainly; EN2 is characterized by a function {line_integral} that corresponds to the models and associated computer programs used to estimate radionuclide releases; and EN3 is characterized by a probability space (S{sub su}, P{sub su}, p{sub su}) for subjective (i.e., epistemic) uncertainty. A high-level overview of the 1996 WIPP PA and references to additional sources of information are given in the context of (S{sub st}, P{sub st}, p{sub st}), {line_integral} and (S{sub su}, P{sub su}, p{sub su}).

  18. Isolation and structural characterization of a polysaccharide LRP4-A from Lycium ruthenicum Murr.

    PubMed

    Lv, Xiaopeng; Wang, Chengjian; Cheng, Yang; Huang, Linjuan; Wang, Zhongfu

    2013-01-10

    A complex polysaccharide, termed LRP4-A, was isolated from the fruit of Lycium ruthenicum Murr. and its structure was characterized. The crude polysaccharide LRP was obtained from the fruit of L. ruthenicum Murr. using hot water extraction followed by ethanol precipitation. The water-soluble polysaccharide LRP4-A was purified from LRP by anion-exchange chromatography and gel filtration chromatography. Its molecular weight was 1.05×10(5) Da. Monosaccharide composition analysis revealed that LRP4-A mainly consisted of rhamnose, arabinose, glucose, and galactose in the molar ratio of 1:7.6:0.5:8.6, with a trace of xylose. Structure of the polysaccharide LRP4-A was characterized using a series of analytical techniques, including methylation analysis, partial acid hydrolysis, IR, NMR, and ESI-MS. LRP4-A was identified to be a highly branching polysaccharide with a backbone of β-(1→6)-linked galactose partially substituted at O-3 position. The branches were composed of (1→3)-linked-Gal, (1→3)-linked-Ara, (1→5)-linked-Ara, and (1→2,4)-linked-Rha. Arabinose, galactose, and glucose were located at the termini of the branches.

  19. Determination of antimicrobial and heavy metal resistance profiles of some bacteria isolated from aquatic amphibian and reptile species.

    PubMed

    Hacioglu, Nurcihan; Tosunoglu, Murat

    2014-01-01

    The aim of the present study was to determine the level of antibiotic resistance patterns and distribution of heavy metal resistance of bacterial isolates from aquatic animals (Lissotriton vulgaris, Pelophylax ridibundus, Emys orbicularis, Mauremys rivulata, and Natrix natrix) in Turkey (Kavak Delta). A total of 153 bacteria have been successfully isolated from cloaca and oral samples of the aquatic amphibians and reptilians which were found, namely, Aeromonas sp. (n = 29), Plesiomonas sp. (n = 7), Vibrio sp. (n = 12), Citrobacter sp. (n = 12), Enterobacter sp. (n = 11), Escherichia sp. (n = 22), Klebsiella sp. (n = 22), Edwardsiella sp. (n = 6), Hafnia sp. (n = 1), Proteus sp. (n = 19), Providencia sp. (n = 8), and Pseudomonas sp. (n = 4). In terms of antibiotic and heavy metal susceptibility testing, each isolate was tested against 12 antibiotics and 4 metals. There was a high incidence of resistance to cefoxitin (46.40 %), ampicillin (44.44 %), erythromycin (35.29 %), and a low incidence of resistance to gentamicin (6.53 %), kanamycin (8.49 %), chloramphenicol (9.15 %), and cefotaxime (10.45 %). The multiple antibiotic resistance index of each bacterial species indicated that bacteria from raised amphibians and reptiles have been exposed to tested antibiotics, with results ranging from 0 to 0.58. Most isolates showed tolerance to different concentrations of heavy metals, and minimal inhibition concentrations ranged from100 to >3,200 μg/mL. According to these results, a significant occurrence of bacteria in the internal organs of reptiles and amphibians, with a high incidence of resistance against antibiotics and heavy metals, may risk aquatic animals and the public health. These data appoint the importance of epidemiological surveillance and microbiological monitoring and reinforce the need to implement environment protection programs for amphibian and reptile species. PMID:23959346

  20. Determination of antimicrobial and heavy metal resistance profiles of some bacteria isolated from aquatic amphibian and reptile species.

    PubMed

    Hacioglu, Nurcihan; Tosunoglu, Murat

    2014-01-01

    The aim of the present study was to determine the level of antibiotic resistance patterns and distribution of heavy metal resistance of bacterial isolates from aquatic animals (Lissotriton vulgaris, Pelophylax ridibundus, Emys orbicularis, Mauremys rivulata, and Natrix natrix) in Turkey (Kavak Delta). A total of 153 bacteria have been successfully isolated from cloaca and oral samples of the aquatic amphibians and reptilians which were found, namely, Aeromonas sp. (n = 29), Plesiomonas sp. (n = 7), Vibrio sp. (n = 12), Citrobacter sp. (n = 12), Enterobacter sp. (n = 11), Escherichia sp. (n = 22), Klebsiella sp. (n = 22), Edwardsiella sp. (n = 6), Hafnia sp. (n = 1), Proteus sp. (n = 19), Providencia sp. (n = 8), and Pseudomonas sp. (n = 4). In terms of antibiotic and heavy metal susceptibility testing, each isolate was tested against 12 antibiotics and 4 metals. There was a high incidence of resistance to cefoxitin (46.40 %), ampicillin (44.44 %), erythromycin (35.29 %), and a low incidence of resistance to gentamicin (6.53 %), kanamycin (8.49 %), chloramphenicol (9.15 %), and cefotaxime (10.45 %). The multiple antibiotic resistance index of each bacterial species indicated that bacteria from raised amphibians and reptiles have been exposed to tested antibiotics, with results ranging from 0 to 0.58. Most isolates showed tolerance to different concentrations of heavy metals, and minimal inhibition concentrations ranged from100 to >3,200 μg/mL. According to these results, a significant occurrence of bacteria in the internal organs of reptiles and amphibians, with a high incidence of resistance against antibiotics and heavy metals, may risk aquatic animals and the public health. These data appoint the importance of epidemiological surveillance and microbiological monitoring and reinforce the need to implement environment protection programs for amphibian and reptile species.