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Sample records for bacterial derived single

  1. A mixture of bacterial mechanical lysates is more efficient than single strain lysate and of bacterial-derived soluble products for the induction of an activating phenotype in human dendritic cells.

    Science.gov (United States)

    Morandi, Barbara; Agazzi, Alessia; D'Agostino, Antonella; Antonini, Francesca; Costa, Gregorio; Sabatini, Federica; Ferlazzo, Guido; Melioli, Giovanni

    2011-07-01

    Dendritic cells (DCs), following an optimal maturation, are able to drive an efficient immune-response. For this, both co-stimulatory molecules (CD80 and CD86), activation molecules (CD83) and peptide presenting molecules (HLA) are over-expressed. The in vitro treatment of immature DC with fragments of bacterial strains, obtained by using a mechanical lysis as well as with bacterial-derived molecules (such as lipopolysaccharide and protido-glycan), induced the maturation of DCs and the secretion of a panel of cytokines and chemokines. Of note, ex vivo treated circulating DCs and plasmacytoid DCs were also activated by these bacterial bodies. However, while the particulate fraction of single bacterial strains or soluble bacterial-derived molecules induced a sub-optimal maturation (as evaluated by the expression of an activating phenotype on DCs and the amount of cytokine secretion), the addition of the mixture of the particulate fractions of the different bacterial strains was able to mediate an optimal maturation. These results were also confirmed by using the secretion of both cytokines and chemokines as markers of DC activation. All these findings suggest that the particulate fraction of bacterial lysate mixtures, because of their ability to interact with different surface structures, might be exploited not only as an immunogen, but also as an adjuvant treatment to boost an immune-response to poorly "antigenic" proteins, such as cancer antigens or allergens.

  2. Immunotoxicity of nucleic acid reduced BioProtein - a bacterial derived single cell protein - in Wistar rats

    DEFF Research Database (Denmark)

    Mølck, Anne-marie; Poulsen, Morten; Christensen, Hanne Risager;

    2002-01-01

    BioProtein is a single cell protein produced by a mixed methanotrophic and heterotrophic bacteria culture using natural gas as energy source, which has been approved for animal feed. BioProtein contains a large amount of nucleic acids making the product less suitable for human consumption...... the same tendency, although, not statistically significant (P = 0.09). The subsets of cells identified as neutrophils and eosinophils were increased and lymphocytes decreased. The histopathological examination revealed histiocytosis and accumulation of foamy macrophages in the mesenteric lymph nodes...

  3. Comparative pharmacokinetics of single-dose administration of mammalian and bacterially-derived recombinant human granulocyte-macrophage colony-stimulating factor.

    Science.gov (United States)

    Hovgaard, D; Mortensen, B T; Schifter, S; Nissen, N I

    1993-01-01

    Pharmacokinetics of recombinant human non-glycosylated bacterially-synthesized (E. coli) granulocyte-macrophage colony-stimulating factor (GM-CSF) were studied following single intravenous (i.v.) and subcutaneous (s.c.) bolus injection, and compared to equivalent doses of glycosylated mammalian-derived CHO-GM-CSF. Each route of administration gave a different GM-CSF concentration-time profile. The highest peak serum concentrations (Cmax) were observed following i.v. bolus injection. After i.v. administration, a two-phase decline in concentration was noted for both types of GM-CSF with a significantly shorter t1/2 alpha of 7.8 minutes for the E. coli GM-CSF versus 20.0 min for the CHO-GM-CSF, while no significant difference was observed for the terminal phase. Following s.c. administration of equivalent doses, a higher peak serum concentration was observed in the E. coli-treated patients and, again, a faster elimination where pretreatment serum levels were reached after 16-20 h, versus more than 48 h after administration of CHO-GM-CSF. Although the non-glycosylated E. coli GM-CSF thus seems to undergo a faster elimination that the glycosylated CHO-GM-CSF no significant difference could be demonstrated in the in vivo effect of corresponding doses of the two compounds with respect to stimulation of granulopoiesis--with reservation for small patient numbers and a large individual variations in response.

  4. Bacterial Nanocellulose as a Microbiological Derived Nanomaterial

    Directory of Open Access Journals (Sweden)

    Stanisławska A.

    2016-12-01

    Full Text Available Bacterial nanocellulose (BNC is a nanofibrilar polymer produced by strains such as Gluconacetobacter xylinus, one of the best bacterial species which given the highest efficiency in cellulose production. Bacterial cellulose is a biomaterial having unique properties such as: chemical purity, good mechanical strength, high flexibility, high absorbency, possibility of forming any shape and size and many others. Such a large number of advantages contributes to the widespread use of the BNC in food technology, paper, electronic industry, but also the architecture in use. However, the greatest hopes are using the BNC in medicine. This text contains information about bacterial nanocellulose, its specific mechanical and biological properties and current applications.

  5. Probing bacterial adhesion at the single-cell level

    DEFF Research Database (Denmark)

    Zeng, Guanghong; Müller, Torsten; Meyer, Rikke Louise

    . Staphylococci adhere stronger on fresh glass than on hydrophilic glass, while the weaker adhesion by P. fluorescens was similar on both types of glass. These results confirmed the importance of surface hydrophobicity in bacterial adhesion. This study has demonstrated that single-cell force spectroscopy allows...... be considered. We have developed a simple and versatile method to make single-cell bacterial probes for measuring single cell adhesion by force spectroscopy using atomic force microscopy (AFM). A single-cell probe was readily made by picking up a bacterial cell from a glass surface by approaching a tipless AFM...... on the adhesion force, we explored the bond formation and adhesive strength of four different bacterial strains towards three abiotic substrates with variable hydrophobicity and surface roughness. The adhesion force and final rupture length were dependent on bacterial strains, surfaces properties, and time...

  6. Inhibition of Bacterial RNase P RNA by Phenothiazine Derivatives

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    Shiying Wu

    2016-09-01

    Full Text Available There is a need to identify novel scaffolds and targets to develop new antibiotics. Methylene blue is a phenothiazine derivative, and it has been shown to possess anti-malarial and anti-trypanosomal activities. Here, we show that different phenothiazine derivatives and pyronine G inhibited the activities of three structurally different bacterial RNase P RNAs (RPRs, including that from Mycobacterium tuberculosis, with Ki values in the lower μM range. Interestingly, three antipsychotic phenothiazines (chlorpromazine, thioridazine, and trifluoperazine, which are known to have antibacterial activities, also inhibited the activity of bacterial RPRs, albeit with higher Ki values than methylene blue. Phenothiazines also affected lead(II-induced cleavage of bacterial RPR and inhibited yeast tRNAPhe, indicating binding of these drugs to functionally important regions. Collectively, our findings provide the first experimental data showing that long, noncoding RNAs could be targeted by different phenothiazine derivatives.

  7. Bacterial proteins pinpoint a single eukaryotic root.

    Science.gov (United States)

    Derelle, Romain; Torruella, Guifré; Klimeš, Vladimír; Brinkmann, Henner; Kim, Eunsoo; Vlček, Čestmír; Lang, B Franz; Eliáš, Marek

    2015-02-17

    The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between "Unikonta" and "Bikonta," with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.

  8. Bioassays for evaluation of medical products derived from bacterial toxins.

    Science.gov (United States)

    Sesardic, Thea

    2012-06-01

    Bioassays play central role in evaluation of biological products and those derived from bacterial toxins often rely exclusively on in vivo models for assurance of safety and potency. This chapter reviews existing regulatory approved methods designed to provide information on potency and safety of complex biological medicines with an insight into strategies considered for alternative procedures.

  9. Catabolism of host-derived compounds during extracellular bacterial infections.

    Science.gov (United States)

    Meadows, Jamie A; Wargo, Matthew J

    2014-02-01

    Efficient catabolism of host-derived compounds is essential for bacterial survival and virulence. While these links in intracellular bacteria are well studied, such studies in extracellular bacteria lag behind, mostly for technical reasons. The field has identified important metabolic pathways, but the mechanisms by which they impact infection and in particular, establishing the importance of a compound's catabolism versus alternate metabolic roles has been difficult. In this review we will examine evidence for catabolism during extracellular bacterial infections in animals and known or potential roles in virulence. In the process, we point out key gaps in the field that will require new or newly adapted techniques.

  10. 21 CFR 184.1150 - Bacterially-derived protease enzyme preparation.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Bacterially-derived protease enzyme preparation... RECOGNIZED AS SAFE Listing of Specific Substances Affirmed as GRAS § 184.1150 Bacterially-derived protease enzyme preparation. (a) Bacterially-derived protease enzyme preparation is obtained from the...

  11. Micro-magnet arrays for specific single bacterial cell positioning

    Energy Technology Data Exchange (ETDEWEB)

    Pivetal, Jérémy, E-mail: jeremy.piv@netcmail.com [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Royet, David [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Ciuta, Georgeta [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Frenea-Robin, Marie [Université de Lyon, Université Lyon 1, CNRS UMR 5005, Laboratoire Ampère, F-69622 Villeurbanne (France); Haddour, Naoufel [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Dempsey, Nora M. [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Dumas-Bouchiat, Frédéric [Univ Limoges, CNRS, SPCTS UMR 7513, 12 Rue Atlantis, F-87068 Limoges (France); Simonet, Pascal [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France)

    2015-04-15

    In various contexts such as pathogen detection or analysis of microbial diversity where cellular heterogeneity must be taken into account, there is a growing need for tools and methods that enable microbiologists to analyze bacterial cells individually. One of the main challenges in the development of new platforms for single cell studies is to perform precise cell positioning, but the ability to specifically target cells is also important in many applications. In this work, we report the development of new strategies to selectively trap single bacterial cells upon large arrays, based on the use of micro-magnets. Escherichia coli bacteria were used to demonstrate magnetically driven bacterial cell organization. In order to provide a flexible approach adaptable to several applications in the field of microbiology, cells were magnetically and specifically labeled using two different strategies, namely immunomagnetic labeling and magnetic in situ hybridization. Results show that centimeter-sized arrays of targeted, isolated bacteria can be successfully created upon the surface of a flat magnetically patterned hard magnetic film. Efforts are now being directed towards the integration of a detection tool to provide a complete micro-system device for a variety of microbiological applications. - Highlights: 1.We report a new approach to selectively micropattern bacterial cells individually upon micro-magnet arrays. 2.Permanent micro-magnets of a size approaching that of bacteria could be fabricated using a Thermo-Magnetic Patterning process. 3.Bacterial cells were labeled using two different magnetic labeling strategies providing flexible approach adaptable to several applications in the field of microbiology.

  12. Micro-magnet arrays for specific single bacterial cell positioning

    Science.gov (United States)

    Pivetal, Jérémy; Royet, David; Ciuta, Georgeta; Frenea-Robin, Marie; Haddour, Naoufel; Dempsey, Nora M.; Dumas-Bouchiat, Frédéric; Simonet, Pascal

    2015-04-01

    In various contexts such as pathogen detection or analysis of microbial diversity where cellular heterogeneity must be taken into account, there is a growing need for tools and methods that enable microbiologists to analyze bacterial cells individually. One of the main challenges in the development of new platforms for single cell studies is to perform precise cell positioning, but the ability to specifically target cells is also important in many applications. In this work, we report the development of new strategies to selectively trap single bacterial cells upon large arrays, based on the use of micro-magnets. Escherichia coli bacteria were used to demonstrate magnetically driven bacterial cell organization. In order to provide a flexible approach adaptable to several applications in the field of microbiology, cells were magnetically and specifically labeled using two different strategies, namely immunomagnetic labeling and magnetic in situ hybridization. Results show that centimeter-sized arrays of targeted, isolated bacteria can be successfully created upon the surface of a flat magnetically patterned hard magnetic film. Efforts are now being directed towards the integration of a detection tool to provide a complete micro-system device for a variety of microbiological applications.

  13. High resolution imaging of surface patterns of single bacterial cells

    Energy Technology Data Exchange (ETDEWEB)

    Greif, Dominik; Wesner, Daniel [Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld (Germany); Regtmeier, Jan, E-mail: jan.regtmeier@physik.uni-bielefeld.de [Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld (Germany); Anselmetti, Dario [Experimental Biophysics and Applied Nanoscience, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld (Germany)

    2010-09-15

    We systematically studied the origin of surface patterns observed on single Sinorhizobium meliloti bacterial cells by comparing the complementary techniques atomic force microscopy (AFM) and scanning electron microscopy (SEM). Conditions ranged from living bacteria in liquid to fixed bacteria in high vacuum. Stepwise, we applied different sample modifications (fixation, drying, metal coating, etc.) and characterized the observed surface patterns. A detailed analysis revealed that the surface structure with wrinkled protrusions in SEM images were not generated de novo but most likely evolved from similar and naturally present structures on the surface of living bacteria. The influence of osmotic stress to the surface structure of living cells was evaluated and also the contribution of exopolysaccharide and lipopolysaccharide (LPS) by imaging two mutant strains of the bacterium under native conditions. AFM images of living bacteria in culture medium exhibited surface structures of the size of single proteins emphasizing the usefulness of AFM for high resolution cell imaging.

  14. OPTIMAL DESIGN OF SINGLE PHASE TRANSFORMER USING BACTERIAL FORAGING ALGORITHM

    Directory of Open Access Journals (Sweden)

    S.SUBRAMANIAN,

    2011-04-01

    Full Text Available The aim of the transformer design is to obtain the dimensions of all the parts of the transformer based on the given specification, using available materials economically in order to achieve lower cost,reduced size and better operating performance. In this paper, the task of finding optimal design of single phase transformer has been formulated as nonlinear programming problem, so as to meet thespecification with the minimum cost and improve the efficiency. Four independent variables and two constraints are taken to meet the requirement of the design. The method utilizes Bacterial ForagingAlgorithm (BFA to provide optimum design of single phase transformer. The validity of the proposed method has been tested on a sample transformer and the simulation results obtained are compared with conventional method and Particle Swarm Optimization (PSO technique. The simulation results reveal that the proposed scheme determines the optimal variables of transformer along with the performance parameters efficiently.

  15. Single Molecule Conductance of Oligothiophene Derivatives

    Science.gov (United States)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  16. A simple technique based on a single optical trap for the determination of bacterial swimming pattern.

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    Ignacio A Martínez

    Full Text Available Bacterial motility is associated to a wide range of biological processes and it plays a key role in the virulence of many pathogens. Here we describe a method to distinguish the dynamic properties of bacteria by analyzing the statistical functions derived from the trajectories of a bacterium trapped by a single optical beam. The approach is based on the model of the rotation of a solid optically trapped sphere. The technique is easily implemented in a biological laboratory, since with only a small number of optical and electronic components a simple biological microscope can be converted into the required analyzer. To illustrate the functionality of this method, we probed several Salmonella enterica serovar Typhimurium mutants that differed from the wild-type with respect to their swimming patterns. In a further application, the motility dynamics of the S. Typhimurium cheV mutant were characterized.

  17. Probing living bacterial adhesion by single cell force spectroscopy using atomic force microscopy

    DEFF Research Database (Denmark)

    Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.;

    of the mechanisms of bacterial attachment. An alternative way to study the adhesion of single bacterial cells is to measure the adhesion between immobilized bacterial cells and coated AFM cantilevers. This strategy was used to investigate the adhesive properties of novel high density poly(ethylene glycol) (PEG......) coatings on titanium. We investigate the ability of a high density poly(L-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG) coating to resist bacterial adhesion and biofilm formation from three clinically relevant bacteria: Pseudomonas aeruginosa, Staphylococcus aureus and Staphylococcus epidermis. The high...

  18. Plasmonic imaging of protein interactions with single bacterial cells.

    Science.gov (United States)

    Syal, Karan; Wang, Wei; Shan, Xiaonan; Wang, Shaopeng; Chen, Hong-Yuan; Tao, Nongjian

    2015-01-15

    Quantifying the interactions of bacteria with external ligands is fundamental to the understanding of pathogenesis, antibiotic resistance, immune evasion, and mechanism of antimicrobial action. Due to inherent cell-to-cell heterogeneity in a microbial population, each bacterium interacts differently with its environment. This large variability is washed out in bulk assays, and there is a need of techniques that can quantify interactions of bacteria with ligands at the single bacterium level. In this work, we present a label-free and real-time plasmonic imaging technique to measure the binding kinetics of ligand interactions with single bacteria, and perform statistical analysis of the heterogeneity. Using the technique, we have studied interactions of antibodies with single Escherichia coli O157:H7 cells and demonstrated a capability of determining the binding kinetic constants of single live bacteria with ligands, and quantify heterogeneity in a microbial population.

  19. Simultaneous Microcystis Algicidal and Microcystin Degrading Capability by a Single Acinetobacter Bacterial Strain.

    Science.gov (United States)

    Li, Hong; Ai, Hainan; Kang, Li; Sun, Xingfu; He, Qiang

    2016-11-01

    Measures for removal of toxic harmful algal blooms often cause lysis of algal cells and release of microcystins (MCs). In this study, Acinetobacter sp. CMDB-2 that exhibits distinct algal lysing activity and MCs degradation capability was isolated. The physiological response and morphological characteristics of toxin-producing Microcystis aeruginosa, the dynamics of intra- and extracellular MC-LR concentration were studied in an algal/bacterial cocultured system. The results demonstrated that Acinetobacter sp. CMDB-2 caused thorough decomposition of algal cells and impairment of photosynthesis within 24 h. Enhanced algal lysis and MC-LR release appeared with increasing bacterial density from 1 × 10(3) to 1 × 10(7) cells/mL; however, the MC-LR was reduced by nearly 94% within 14 h irrespective of bacterial density. Measurement of extracellular and intracellular MC-LR revealed that the toxin was decreased by 92% in bacterial cell incubated systems relative to control and bacterial cell-free filtrate systems. The results confirmed that the bacterial metabolite caused 92% lysis of Microcystis aeruginosa cells, whereas the bacterial cells were responsible for approximately 91% reduction of MC-LR. The joint efforts of the bacterium and its metabolite accomplished the sustainable removal of algae and MC-LR. This is the first report of a single bacterial strain that achieves these dual actions.

  20. Predominance of single bacterial cells in composting bioaerosols

    Science.gov (United States)

    Galès, Amandine; Bru-Adan, Valérie; Godon, Jean-Jacques; Delabre, Karine; Catala, Philippe; Ponthieux, Arnaud; Chevallier, Michel; Birot, Emmanuel; Steyer, Jean-Philippe; Wéry, Nathalie

    2015-04-01

    Bioaerosols emitted from composting plants have become an issue because of their potential harmful impact on public or workers' health. Accurate knowledge of the particle-size distribution in bioaerosols emitted from open-air composting facilities during operational activity is a requirement for improved modeling of air dispersal. In order to investigate the aerodynamic diameter of bacteria in composting bioaerosols this study used an Electrical Low Pressure Impactor for sampling and quantitative real-time PCR for quantification. Quantitative PCR results show that the size of bacteria peaked between 0.95 μm and 2.4 μm and that the geometric mean diameter of the bacteria was 1.3 μm. In addition, total microbial cells were counted by flow cytometry and revealed that these qPCR results corresponded to single whole bacteria. Finally, the enumeration of cultivable thermophilic microorganisms allowed us to set the upper size limit for fragments at an aerodynamic diameter of ∼0.3 μm. Particle-size distributions of microbial groups previously used to monitor composting bioaerosols were also investigated. In collected the bioaerosols, the aerodynamic diameter of the actinomycetes Saccharopolyspora rectivirgula-and-relatives and also of the fungus Aspergillus fumigatus, appeared to be consistent with a majority of individual cells. Together, this study provides the first culture-independent data on particle-size distribution of composting bioaerosols and reveals that airborne single bacteria were emitted predominantly from open-air composting facilities.

  1. Photodynamic antimicrobial chemotherapy using zinc phthalocyanine derivatives in treatment of bacterial skin infection

    Science.gov (United States)

    Chen, Zhuo; Zhang, Yaxin; Wang, Dong; Li, Linsen; Zhou, Shanyong; Huang, Joy H.; Chen, Jincan; Hu, Ping; Huang, Mingdong

    2016-01-01

    Photodynamic antimicrobial chemotherapy (PACT) is an effective method for killing bacterial cells in view of the increasing problem of multiantibiotic resistance. We herein reported the PACT effect on bacteria involved in skin infections using a zinc phthalocyanine derivative, pentalysine β-carbonylphthalocyanine zinc (ZnPc-Lys). Compared with its anionic ZnPc counterpart, ZnPc-Lys showed an enhanced antibacterial efficacy in vitro and in an animal model of localized infection. Meanwhile, ZnPc-Lys was observed to significantly reduce the wound skin blood flow during wound healing, indicating an anti-inflammation activity. This study provides new insight on the mechanisms of PACT in bacterial skin infection.

  2. Self-assembling bacterial pores as components of nanobiosensors for the detection of single peptide molecules

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Nano-sized bacterial pores were inserted into a lipid membrane as a nanobiosensor for the detection of single peptide molecules. Due to the intrinsic properties of single-channel conductance, the transit of individual molecules through the pore can be studied. The analysis of both the blockage current and duration is able to provide specific structural information and allows the detection of specific peptides in bulk mixtures.

  3. Bacterial replication, transcription and translation : mechanistic insights from single-molecule biochemical studies

    NARCIS (Netherlands)

    Robinson, Andrew; van Oijen, Antoine M.

    2013-01-01

    Decades of research have resulted in a remarkably detailed understanding of the molecular mechanisms of bacterial DNA replication, transcription and translation. Our understanding of the kinetics and physical mechanisms that drive these processes forward has been expanded by the ability of single-mo

  4. Excretion of purine base derivatives after intake of bacterial protein meal in pigs

    DEFF Research Database (Denmark)

    Hellwing, Anne Louise Frydendahl; Tauson, Anne-Helene; Skrede, A.

    2007-01-01

    Bacterial protein meal has a high content ofprotein but also of RNA and DNA. Sixteen barrows were allocated to four diets containing increasing levels of bacterial protein meal (BPM), from weaning to 80 kg live weight, to evaluate whether the RNA and DNA contents of BPM influenced the retention...... of nitrogen. It was hypothesised that an increased intake of RNA and DNA would lead to an increased urinary excretion of purine base derivatives and increased plasma concentrations. Retention of nitrogen was unaffected by dietary content of BPM (P=0.08) and the urinary excretion of purine base derivatives...... increased with increasing dietary content of BPM. No differences in fasting plasma concentration of uric acid, xanthine and hypoxanthine were observed. It can therefore be concluded that increasing levels of dietary BPM maintained protein accretion and led to changes in excretion of purine detrivatices...

  5. Bacterial origin of a mitochondrial outer membrane protein translocase: new perspectives from comparative single channel electrophysiology.

    Science.gov (United States)

    Harsman, Anke; Niemann, Moritz; Pusnik, Mascha; Schmidt, Oliver; Burmann, Björn M; Hiller, Sebastian; Meisinger, Chris; Schneider, André; Wagner, Richard

    2012-09-07

    Mitochondria are of bacterial ancestry and have to import most of their proteins from the cytosol. This process is mediated by Tom40, an essential protein that forms the protein-translocating pore in the outer mitochondrial membrane. Tom40 is conserved in virtually all eukaryotes, but its evolutionary origin is unclear because bacterial orthologues have not been identified so far. Recently, it was shown that the parasitic protozoon Trypanosoma brucei lacks a conventional Tom40 and instead employs the archaic translocase of the outer mitochondrial membrane (ATOM), a protein that shows similarities to both eukaryotic Tom40 and bacterial protein translocases of the Omp85 family. Here we present electrophysiological single channel data showing that ATOM forms a hydrophilic pore of large conductance and high open probability. Moreover, ATOM channels exhibit a preference for the passage of cationic molecules consistent with the idea that it may translocate unfolded proteins targeted by positively charged N-terminal presequences. This is further supported by the fact that the addition of a presequence peptide induces transient pore closure. An in-depth comparison of these single channel properties with those of other protein translocases reveals that ATOM closely resembles bacterial-type protein export channels rather than eukaryotic Tom40. Our results support the idea that ATOM represents an evolutionary intermediate between a bacterial Omp85-like protein export machinery and the conventional Tom40 that is found in mitochondria of other eukaryotes.

  6. Recombinant production of bacterial toxins and their derivatives in the methylotrophic yeast Pichia pastoris

    Directory of Open Access Journals (Sweden)

    Gurkan Cemal

    2005-12-01

    Full Text Available Abstract The methylotrophic yeast Pichia pastoris is a popular heterologous expression host for the recombinant production of a variety of prokaryotic and eukaryotic proteins. The rapid emergence of P. pastoris as a robust heterologous expression host was facilitated by the ease with which it can be manipulated and propagated, which is comparable to that of Escherichia coli and Saccharomyces cerevisiae. P. pastoris offers further advantages such as the tightly-regulated alcohol oxidase promoter that is particularly suitable for heterologous expression of foreign genes. While recombinant production of bacterial toxins and their derivatives is highly desirable, attempts at their heterologous expression using the traditional E. coli expression system can be problematic due to the formation of inclusion bodies that often severely limit the final yields of biologically active products. However, recent literature now suggests that P. pastoris may be an attractive alternative host for the heterologous production of bacterial toxins, such as those from the genera Bacillus, Clostridium, and Corynebacterium, as well as their more complex derivatives. Here, we review the recombinant production of bacterial toxins and their derivatives in P. pastoris with special emphasis on their potential clinical applications. Considering that de novo design and construction of synthetic toxin genes have often been necessary to achieve optimal heterologous expression in P. pastoris, we also present general guidelines to this end based on our experience with the P. pastoris expression of the Bacillus thuringiensis Cyt2Aa1 toxin.

  7. Nanoscale Electric Permittivity of Single Bacterial Cells at Gigahertz Frequencies by Scanning Microwave Microscopy.

    Science.gov (United States)

    Biagi, Maria Chiara; Fabregas, Rene; Gramse, Georg; Van Der Hofstadt, Marc; Juárez, Antonio; Kienberger, Ferry; Fumagalli, Laura; Gomila, Gabriel

    2016-01-26

    We quantified the electric permittivity of single bacterial cells at microwave frequencies and nanoscale spatial resolution by means of near-field scanning microwave microscopy. To this end, calibrated complex admittance images have been obtained at ∼19 GHz and analyzed with a methodology that removes the nonlocal topographic cross-talk contributions and thus provides quantifiable intrinsic dielectric images of the bacterial cells. Results for single Escherichia coli cells provide a relative electric permittivity of ∼4 in dry conditions and ∼20 in humid conditions, with no significant loss contributions. Present findings, together with the ability of microwaves to penetrate the cell membrane, open an important avenue in the microwave label-free imaging of single cells with nanoscale spatial resolution.

  8. A novel mechanism of bacterial toxin transfer within host blood cell-derived microvesicles.

    Directory of Open Access Journals (Sweden)

    Anne-lie Ståhl

    2015-02-01

    Full Text Available Shiga toxin (Stx is the main virulence factor of enterohemorrhagic Escherichia coli, which are non-invasive strains that can lead to hemolytic uremic syndrome (HUS, associated with renal failure and death. Although bacteremia does not occur, bacterial virulence factors gain access to the circulation and are thereafter presumed to cause target organ damage. Stx was previously shown to circulate bound to blood cells but the mechanism by which it would potentially transfer to target organ cells has not been elucidated. Here we show that blood cell-derived microvesicles, shed during HUS, contain Stx and are found within patient renal cortical cells. The finding was reproduced in mice infected with Stx-producing Escherichia coli exhibiting Stx-containing blood cell-derived microvesicles in the circulation that reached the kidney where they were transferred into glomerular and peritubular capillary endothelial cells and further through their basement membranes followed by podocytes and tubular epithelial cells, respectively. In vitro studies demonstrated that blood cell-derived microvesicles containing Stx undergo endocytosis in glomerular endothelial cells leading to cell death secondary to inhibited protein synthesis. This study demonstrates a novel virulence mechanism whereby bacterial toxin is transferred within host blood cell-derived microvesicles in which it may evade the host immune system.

  9. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing

    Science.gov (United States)

    Riba, J.; Gleichmann, T.; Zimmermann, S.; Zengerle, R.; Koltay, P.

    2016-09-01

    The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry.

  10. Photoinduced electron transfer in singly labeled thiouredopyrenetrisulfonate azurin derivatives

    DEFF Research Database (Denmark)

    Borovok, N; Kotlyar, A B; Pecht, I;

    1999-01-01

    efficiency. TUPS derivatives of azurin, singly labeled at specific lysine residues, were prepared and purified to homogeneity by ion exchange HPLC. Transient absorption spectroscopy was used to directly monitor the rates of the electron transfer reaction from the photoexcited triplet state of TUPS to Cu...... of the crystal structure of Pseudomonas aeruginosa azurin and molecular structure calculation of the TUPS modified proteins, electron transfer pathways were calculated. Analysis of the results revealed a good correlation between separation distance from donor to Cu ligating atom (His-N or Cys-S) and the observed...

  11. Single-molecular diodes based on opioid derivatives.

    Science.gov (United States)

    Siqueira, M R S; Corrêa, S M; Gester, R M; Del Nero, J; Neto, A M J C

    2015-12-01

    We propose an efficient single-molecule rectifier based on a derivative of opioid. Electron transport properties are investigated within the non-equilibrium Green's function formalism combined with density functional theory. The analysis of the current-voltage characteristics indicates obvious diode-like behavior. While heroin presents rectification coefficient R>1, indicating preferential electronic current from electron-donating to electron-withdrawing, 3 and 6-acetylmorphine and morphine exhibit contrary behavior, Rdiodes. In particular, the rectification rations for heroin diodes show microampere electron current with a maximum of rectification (R=9.1) at very low bias voltage of ∼0.6 V and (R=14.3)∼1.8 V with resistance varying between 0.4 and 1.5 M Ω. Once most of the current single-molecule diodes usually rectifies in nanoampere, are not stable over 1.0 V and present electrical resistance around 10 M. Molecular devices based on opioid derivatives are promising in molecular electronics.

  12. Stenotrophomonas maltophilia and Vermamoeba vermiformis relationships: bacterial multiplication and protection in amoebal-derived structures.

    Science.gov (United States)

    Cateau, Estelle; Maisonneuve, Elodie; Peguilhan, Samuel; Quellard, Nathalie; Hechard, Yann; Rodier, Marie-Helene

    2014-12-01

    Stenotrophomonas maltophilia, a bacteria involved in healthcare-associated infections, can be found in hospital water systems. Other microorganisms, such as Free Living amoebae (FLA), are also at times recovered in the same environment. Amongst these protozoa, many authors have reported the presence of Vermamoeba vermiformis. We show here that this amoeba enhances S. maltophilia growth and harbors the bacteria in amoebal-derived structures after 28 days in harsh conditions. These results highlight the fact that particular attention should be paid to the presence of FLA in hospital water systems, because of their potential implication in survival and growth of pathogenic bacterial species.

  13. Diverse bacterial PKS sequences derived from okadaic acid-producing dinoflagellates.

    Science.gov (United States)

    Perez, Roberto; Liu, Li; Lopez, Jose; An, Tianying; Rein, Kathleen S

    2008-05-22

    Okadaic acid (OA) and the related dinophysistoxins are isolated from dinoflagellates of the genus Prorocentrum and Dinophysis. Bacteria of the Roseobacter group have been associated with okadaic acid producing dinoflagellates and have been previously implicated in OA production. Analysis of 16S rRNA libraries reveals that Roseobacter are the most abundant bacteria associated with OA producing dinoflagellates of the genus Prorocentrum and are not found in association with non-toxic dinoflagellates. While some polyketide synthase (PKS) genes form a highly supported Prorocentrum clade, most appear to be bacterial, but unrelated to Roseobacter or Alpha-Proteobacterial PKSs or those derived from other Alveolates Karenia brevis or Crytosporidium parvum.

  14. Using llama derived single domain antibodies to target botulinum neurotoxins

    Science.gov (United States)

    Swain, Marla D.; Anderson, George P.; Bernstein, Rachael D.; Liu, Jinny L.; Goldman, Ellen R.

    2010-04-01

    Llama serum contains both conventional IgG as well as unique forms of antibody that contain only heavy chains where antigen binding is mediated through a single variable domain. These variable domains can be expressed recombinantly and are referred to as single domain antibodies (sdAb). SdAb are among the smallest known naturally derived antigen binding fragments, possess good solubility, thermal stability, and can refold after heat and chemical denaturation. Llamas were immunized with either BoNT A or B toxoid and phage display libraries prepared. Single domain antibodies (sdAb) that were able to detect botulinum neurotoxin (BoNT) serotypes A and B were selected from their respective libraries. Here, the binders obtained by panning the BoNT B library on either BoNT B toxoid or BoNT B complex toxoid coated plates or BoNT B toxin coupled microspheres are described. Using these panning methods, we selected for binders that showed specificity for BoNT B. Phage displayed binders were screened, moved to a protein expression vector and soluble sdAb was produced. Using a Luminex flow cytometer binders were evaluated in direct binding assays. We have exploited the unique properties of sdAb and used them as biological recognition elements in immuno-based sensors that can detect BoNT B.

  15. Bacterial symbionts: prospects for the sustainable production of invertebrate-derived pharmaceuticals.

    Science.gov (United States)

    Piel, J

    2006-01-01

    Invertebrate animals, such as sponges, tunicates and bryozoans, are among the most important sources of biomedically relevant natural products. However, as these animals generally contain only low quantities of the compounds, further pharmacological development is in most cases difficult. There is increasing evidence that many metabolites, in particular polyketides and nonribosomally synthesized peptides, are not produced by the animals themselves but by associated bacterial symbionts. This symbiont hypothesis currently attracts considerable interest, since it implicates that animal-independent production systems based on bacterial fermentation processes could be created. This review gives an overview about recent developments in the research on natural product symbiosis. Different techniques will be discussed that have been employed to pinpoint the actual producer. Since bacterial symbionts are highly fastidious and have been generally resistant to cultivation attempts, emphasis will be laid on culture-independent strategies, such as cell separation approaches and the cloning of biosynthetic genes. These strategies have provided insights into possible sources of several natural products, e.g. the bryostatins, pederin, the onnamides, swinholide A and theopalauamide. Finally, potential techniques for the generation of renewable supplies of symbiont-derived drug candidates will be discussed. Cultivation approaches and the heterologous expression of cloned biosynthesis genes from uncultured symbionts could in future provide access to several important marine drug candidates, including bryostatin 1, halichondrin or ET-743.

  16. Motion of single MreB bacterial actin proteins in Caulobacter show treadmilling in vivo

    Science.gov (United States)

    Moerner, W. E.; Kim, Soyeon; Gitai, Zemer; Kinkhabwala, Anika; McAdams, Harley; Shapiro, Lucy

    2006-03-01

    Ensemble imaging of a bacterial actin homologue, the MreB protein, suggests that the MreB proteins form a dynamic filamentous spiral along the long axis of the cell in Caulobacter crescentus. MreB contracts and expands along the cell axis and plays an important role in cell shape and polarity maintenance, as well as chromosome segregation and translocation of the origin of replication during cell division. In this study we investigated the real-time polymerization of MreB in Caulobacter crescentus using single-molecule fluorescence imaging. With time-lapse imaging, polymerized MreB could be distinguished from cytoplasmic MreB monomers, because single monomeric MreB showed fast motion characteristic of Brownian diffusion, while single polymerized MreB displayed slow, directed motion. This directional movement of labeled MreB in the growing polymer implies that treadmilling is the predominant mechanism in MreB filament formation. These single-molecule imaging experiments provide the first available information on the velocity of bacterial actin polymerization in a living cell.

  17. Design of benzimidazole- and benzoxazole-2-thione derivatives as inhibitors of bacterial hyaluronan lyase.

    Science.gov (United States)

    Braun, Stephan; Botzki, Alexander; Salmen, Sunnhild; Textor, Christian; Bernhardt, Günther; Dove, Stefan; Buschauer, Armin

    2011-09-01

    Bacterial hyaluronan lyases (Hyal) degrade hyaluronan, an important component of the extracellular matrix, and are involved in microbial spread. Hyal inhibitors may serve as tools to study the role of the enzyme, its substrates and products in the course of bacterial infections. Moreover, such enzyme inhibitors are potential candidates for antibacterial combination therapy. Based on crystal structures of Streptococcus pneumoniae Hyal in complex with a hexasaccharide substrate and with different inhibitors, 1-acylated benzimidazole-2-thiones and benzoxazole-2-thiones were derived as new leads for the inhibition of Streptococcus agalactiae strain 4755 Hyal. Structure-based optimization led to N-(3-phenylpropionyl)benzoxazole-2-thione, one of the most potent compounds known to date (IC(50) values: 24 μM at pH 7.4, 15 μM at pH 5). Among the 27 new derivatives, other N-acylated benzimidazoles and benzoxazoles are just as active at pH 7.4, but not at pH 5. The results support a binding mode characterized by interactions with residues in the catalytic site and with a hydrophobic patch.

  18. Radiation Protection Using Single-Wall Carbon Nanotube Derivatives

    Science.gov (United States)

    Tour, James M.; Lu, Meng; Lucente-Schultz, Rebecca; Leonard, Ashley; Doyle, Condell Dewayne; Kosynkin, Dimitry V.; Price, Brandi Katherine

    2011-01-01

    This invention is a means of radiation protection, or cellular oxidative stress mitigation, via a sequence of quenching radical species using nano-engineered scaffolds, specifically single-wall carbon nanotubes (SWNTs) and their derivatives. The material can be used as a means of radiation protection by reducing the number of free radicals within, or nearby, organelles, cells, tissue, organs, or living organisms, thereby reducing the risk of damage to DNA and other cellular components (i.e., RNA, mitochondria, membranes, etc.) that can lead to chronic and/or acute pathologies, including but not limited to cancer, cardiovascular disease, immuno-suppression, and disorders of the central nervous system. In addition, this innovation could be used as a prophylactic or antidote for accidental radiation exposure, during high-altitude or space travel where exposure to radiation is anticipated, or to protect from exposure from deliberate terrorist or wartime use of radiation- containing weapons.

  19. Observation of the dynamic germination of single bacterial spores using rapid Raman imaging

    Science.gov (United States)

    Kong, Lingbo; Setlow, Peter; Li, Yong-qing

    2014-01-01

    The dynamics of bacterial spore germination were successfully observed using a fast Raman imaging system, in combination with real-time phase contrast microscopy. By using a multifocus scan scheme, the spontaneous Raman-scattering imaging acquisition speed was increased to ˜30 s per frame while maintaining diffraction-limited resolution, which allowed monitoring of the dynamics of spore germination on a time scale of tens of seconds to a few minutes. This allowed simultaneous gathering of rich spatial distribution information on different cellular components including time-lapse molecular images of Ca-dipicolinic acid, protein, and nucleic acid during germination of single bacterial spores for the periods of 30 to 60 min.

  20. Designed to penetrate: Time-resolved interaction of single antibiotic molecules with bacterial pores

    Science.gov (United States)

    Nestorovich, Ekaterina M.; Danelon, Christophe; Winterhalter, Mathias; Bezrukov, Sergey M.

    2002-07-01

    Membrane permeability barriers are among the factors contributing to the intrinsic resistance of bacteria to antibiotics. We have been able to resolve single ampicillin molecules moving through a channel of the general bacterial porin, OmpF (outer membrane protein F), believed to be the principal pathway for the -lactam antibiotics. With ion channel reconstitution and high-resolution conductance recording, we find that ampicillin and several other efficient penicillins and cephalosporins strongly interact with the residues of the constriction zone of the OmpF channel. Therefore, we hypothesize that, in analogy to substrate-specific channels that evolved to bind certain metabolite molecules, antibiotics have "evolved" to be channel-specific. Molecular modeling suggests that the charge distribution of the ampicillin molecule complements the charge distribution at the narrowest part of the bacterial porin. Interaction of these charges creates a region of attraction inside the channel that facilitates drug translocation through the constriction zone and results in higher permeability rates.

  1. A comparative study of oral single dose of metronidazole, tinidazole, secnidazole and ornidazole in bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Jyoti Thulkar

    2012-01-01

    Full Text Available Objective: To compare the cure rates of oral single dose of metronidazole (2 g, tinidazole (2 g, secnidazole (2 g, and ornidazole (1.5 g in cases of bacterial vaginosis. Materials and Methods: This was a prospective, comparative, randomized clinical trial on 344 Indian women (86 women in each group who attended a gynecology outpatient department with complaint of abnormal vaginal discharge or who had abnormal vaginal discharge on Gynecological examination but they did not complaint of it. For diagnosis and cure rate of bacterial vaginosis, Amsel′s criteria were used. Statistical analysis was done by Chi-square test of proportions. The cure rate was compared considering metronidazole cure rate as gold standard. Results: At 1 week, the cure rate of tinidazole and ornidazole was 100% and at 4 weeks, it was 97.7% for both drugs (P<0.001. Secnidazole had cure rate of 80.2% at 4 weeks (P=NS. Metronidazole showed a cure rate of 77.9% at 4 weeks, which is the lowest of all four drugs. Conclusion: Tinidazole and ornidazole have better cure rate as compared to metronidazole in cases of bacterial vaginosis.

  2. In situ probing the interior of single bacterial cells at nanometer scale

    Science.gov (United States)

    Liu, Boyin; Hemayet Uddin, Md; Ng, Tuck Wah; Paterson, David L.; Velkov, Tony; Li, Jian; Fu, Jing

    2014-10-01

    We report a novel approach to probe the interior of single bacterial cells at nanometre resolution by combining focused ion beam (FIB) and atomic force microscopy (AFM). After removing layers of pre-defined thickness in the order of 100 nm on the target bacterial cells with FIB milling, AFM of different modes can be employed to probe the cellular interior under both ambient and aqueous environments. Our initial investigations focused on the surface topology induced by FIB milling and the hydration effects on AFM measurements, followed by assessment of the sample protocols. With fine-tuning of the process parameters, in situ AFM probing beneath the bacterial cell wall was achieved for the first time. We further demonstrate the proposed method by performing a spatial mapping of intracellular elasticity and chemistry of the multi-drug resistant strain Klebsiella pneumoniae cells prior to and after it was exposed to the ‘last-line’ antibiotic polymyxin B. Our results revealed increased stiffness occurring in both surface and interior regions of the treated cells, suggesting loss of integrity of the outer membrane from polymyxin treatments. In addition, the hydrophobicity measurement using a functionalized AFM tip was able to highlight the evident hydrophobic portion of the cell such as the regions containing cell membrane. We expect that the proposed FIB-AFM platform will help in gaining deeper insights of bacteria-drug interactions to develop potential strategies for combating multi-drug resistance.

  3. Single Plant Derived Nanotechnology for Synergistic Antibacterial Therapies

    Science.gov (United States)

    Kalluri, Jhansi R.; Gonzalez-Rodriguez, Roberto; Hartman, Phil S.; Loni, Armando; Canham, Leigh T.; Coffer, Jeffery L.

    2016-01-01

    Multiple new approaches to tackle multidrug resistant infections are urgently needed and under evaluation. One nanotechnology-based approach to delivering new relevant therapeutics involves silicon accumulator plants serving as a viable silicon source in green routes for the fabrication of the nanoscale drug delivery carrier porous silicon (pSi). If the selected plant leaf components contain medicinally-active species as well, then a single substance can provide not only the nanoscale high surface area drug delivery carrier, but the drug itself. With this idea in mind, porous silicon was fabricated from joints of the silicon accumulator plant Bambuseae (Tabasheer) and loaded with an antibacterial extract originating from leaves of the same type of plant (Bambuseae arundinacea). Preparation of porous silicon from Tabasheer includes extraction of biogenic silica from the ground plant by calcination, followed by reduction with magnesium in the presence of sodium chloride, thereby acting as a thermal moderator that helps to retain the mesoporous structure of the feedstock. The purified product was characterized by a combination of scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), X-ray diffraction (XRD), Raman spectroscopy, transmission electron microscopy (TEM), and low temperature nitrogen gas adsorption measurements. Antimicrobial activity and minimum inhibitory concentration of a leaf extract of Bambuseae arundinacea was tested against the bacteria Escherichia Coli (E. Coli) and Staphylococcus aureus (S. Aureus), along with the fungus Candida albicans (C. Albicans). A S. aureus active ethanolic leaf extract was loaded into the above Tabasheer-derived porous silicon. Initial studies indicate sustained in vitro antibacterial activity of the extract-loaded plant derived pSi (25 wt %, TGA), as measured by disk diffusion inhibitory zone assays. Subsequent chromatographic separation of this extract revealed that the active antimicrobial species

  4. Photodynamic antimicrobial chemotherapy using zinc phthalocyanine derivative for bacterial skin infection

    Science.gov (United States)

    Chen, Zhuo; Zhang, Yaxin; Li, Linsen; Zhou, Shanyong; Chen, Jincan; Hu, Ping; Huang, Mingdong

    2014-09-01

    Folliculitis, furunculosis and acne vulgaris are very common skin disorders of the hair follicles and are associated with large grease-producing (sebaceous) glands. Although the detailed mechanisms involved these skin disorders are not fully understood, it is believed that the bacteria Propionibacterium acnes and Staphylococcus aureus are the key pathogenic factors involved. Conventional treatments targeting the pathogenic factors include a variety of topical and oral medications such as antibiotics. The wide use of antibiotics leads to bacterial resistance, and hence there is a need for new alternatives in above bacterial skin treatment. Photodynamic antimicrobial chemotherapy (PACT) is based on an initial photosensitization of the infected area, followed by irradiation with visible light, producing singlet oxygen which is cytotoxic to bacteria. Herein we reported a zinc phthalocyanine derivative, pentalysine β-carbonylphthalocyanine zinc (ZnPc-(Lys)5) and its PACT effect for the bacteria involved in these skin infections. Our results demonstrated strong bactericidal effects of this photosensitizer on both strains of the bacteria, suggesting ZnPc-(Lys)5 as a promising antimicrobial photosensitizer for the treatment of infectious diseases caused by these bacteria.

  5. Ex Situ Formation of Metal Selenide Quantum Dots Using Bacterially Derived Selenide Precursors

    Energy Technology Data Exchange (ETDEWEB)

    Fellowes, Jonathan W.; Pattrick, Richard; Lloyd, Jon; Charnock, John M.; Coker, Victoria S.; Mosselmans, JFW; Weng, Tsu-Chien; Pearce, Carolyn I.

    2013-04-12

    Luminescent quantum dots were synthesized using bacterially derived selenide (SeII-) as the precursor. Biogenic SeII- was produced by the reduction of Se-IV by Veillonella atypica and compared directly against borohydride-reduced Se-IV for the production of glutathione-stabilized CdSe and beta-mercaptoethanol-stabilized ZnSe nanoparticles by aqueous synthesis. Biological SeII- formed smaller, narrower size distributed QDs under the same conditions. The growth kinetics of biologically sourced CdSe phases were slower. The proteins isolated from filter sterilized biogenic SeII- included a methylmalonyl-CoA decarboxylase previously characterized in the closely related Veillonella parvula. XAS analysis of the glutathione-capped CdSe at the S K-edge suggested that sulfur from the glutathione was structurally incorporated within the CdSe. A novel synchrotron based XAS technique was also developed to follow the nucleation of biological and inorganic selenide phases, and showed that biogenic SeII- is more stable and more resistant to beam-induced oxidative damage than its inorganic counterpart. The bacterial production of quantum dot precursors offers an alternative, 'green' synthesis technique that negates the requirement of expensive, toxic chemicals and suggests a possible link to the exploitation of selenium contaminated waste streams.

  6. Diverse Bacterial PKS Sequences Derived From Okadaic Acid-Producing Dinoflagellates

    Directory of Open Access Journals (Sweden)

    Kathleen S. Rein

    2008-05-01

    Full Text Available Okadaic acid (OA and the related dinophysistoxins are isolated from dinoflagellates of the genus Prorocentrum and Dinophysis. Bacteria of the Roseobacter group have been associated with okadaic acid producing dinoflagellates and have been previously implicated in OA production. Analysis of 16S rRNA libraries reveals that Roseobacter are the most abundant bacteria associated with OA producing dinoflagellates of the genus Prorocentrum and are not found in association with non-toxic dinoflagellates. While some polyketide synthase (PKS genes form a highly supported Prorocentrum clade, most appear to be bacterial, but unrelated to Roseobacter or Alpha-Proteobacterial PKSs or those derived from other Alveolates Karenia brevis or Crytosporidium parvum.

  7. Field evaluation of the bacterial volatile derivative 3-pentanol in priming for induced resistance in pepper.

    Science.gov (United States)

    Choi, Hye Kyung; Song, Geun Cheol; Yi, Hwe-Su; Ryu, Choong-Min

    2014-08-01

    Plants are defended from attack by emission of volatile organic compounds (VOCs) that can act directly against pathogens and herbivores or indirectly by recruiting natural enemies of herbivores. However, microbial VOC have been less investigated as potential triggers of plant systemic defense responses against pathogens in the field. Bacillus amyloliquefaciens strain IN937a, a plant growth-promoting rhizobacterium that colonizes plant tissues, stimulates induced systemic resistance (ISR) via its emission of VOCs. We investigated the ISR capacity of VOCs and derivatives collected from strain IN937a against bacterial spot disease caused by Xanthomonas axonopodis pv. vesicatoria in pepper. Of 15 bacterial VOCs and their derivatives, 3-pentanol, which is a C8 amyl alcohol reported to be a component of sex pheromones in insects, was selected for further investigation. Pathogens were infiltrated into pepper leaves 10, 20, 30, and 40 days after treatment and transplantation to the field. Disease severity was assessed 7 days after transplantation. Treatment with 3-pentanol significantly reduced disease severity caused by X. axonopodis and naturally occurring Cucumber mosaic virus in field trials over 2 years. We used quantitative real-time polymerase chain analysis to examine Pathogenesis-Related genes associated with salicylic acid (SA), jasmonic acid (JA), and ethylene defense signaling. The expression of Capsicum annuum Pathogenesis-Related protein 1 (CaPR1), CaPR2, and Ca protease inhibitor2 (CaPIN2) increased in field-grown pepper plants treated with 3-pentanol. Taken together, our results show that 3-pentanol triggers induced resistance by priming SA and JA signaling in pepper under field conditions.

  8. Influence of molecular noise on the growth of single cells and bacterial populations.

    Directory of Open Access Journals (Sweden)

    Mischa Schmidt

    Full Text Available During the last decades experimental studies have revealed that single cells of a growing bacterial population are significantly exposed to molecular noise. Important sources for noise are low levels of metabolites and enzymes that cause significant statistical variations in the outcome of biochemical reactions. In this way molecular noise affects biological processes such as nutrient uptake, chemotactic tumbling behavior, or gene expression of genetically identical cells. These processes give rise to significant cell-to-cell variations of many directly observable quantities such as protein levels, cell sizes or individual doubling times. In this study we theoretically explore if there are evolutionary benefits of noise for a growing population of bacteria. We analyze different situations where noise is either suppressed or where it affects single cell behavior. We consider two specific examples that have been experimentally observed in wild-type Escherichia coli cells: (i the precision of division site placement (at which molecular noise is highly suppressed and (ii the occurrence of noise-induced phenotypic variations in fluctuating environments. Surprisingly, our analysis reveals that in these specific situations both regulatory schemes [i.e. suppression of noise in example (i and allowance of noise in example (ii] do not lead to an increased growth rate of the population. Assuming that the observed regulatory schemes are indeed caused by the presence of noise our findings indicate that the evolutionary benefits of noise are more subtle than a simple growth advantage for a bacterial population in nutrient rich conditions.

  9. Real-time Bacterial Detection by Single Cell Based Sensors UsingSynchrotron FTIR Spectromicroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Bertozzi,Carolyn; Zhang, Miqin

    2005-08-10

    Microarrays of single macrophage cell based sensors weredeveloped and demonstrated for real time bacterium detection bysynchrotron FTIR microscopy. The cells were patterned on gold-SiO2substrates via a surface engineering technique by which the goldelectrodes were immobilized with fibronectin to mediate cell adhesion andthe silicon oxide background were passivated with PEG to resist proteinadsorption and cell adhesion. Cellular morphology and IR spectra ofsingle, double, and triple cells on gold electrodes exposed tolipopolysaccharide (LPS) of different concentrations were compared toreveal the detection capabilities of these biosensors. The single-cellbased sensors were found to generate the most significant IR wave numbervariation and thus provide the highest detection sensitivity. Changes inmorphology and IR spectrum for single cells exposed to LPS were found tobe time- and concentration-dependent and correlated with each other verywell. FTIR spectra from single cell arrays of gold electrodes withsurface area of 25 mu-m2, 100 mu-m2, and 400 mu-m2 were acquired usingboth synchrotron and conventional FTIR spectromicroscopes to study thesensitivity of detection. The results indicated that the developedsingle-cell platform can be used with conventional FTIRspectromicroscopy. This technique provides real-time, label-free, andrapid bacterial detection, and may allow for statistic and highthroughput analyses, and portability.

  10. Carboxyl-modified single-walled carbon nanotubes negatively affect bacterial growth and denitrification activity

    Science.gov (United States)

    Zheng, Xiong; Su, Yinglong; Chen, Yinguang; Wan, Rui; Li, Mu; Wei, Yuanyuan; Huang, Haining

    2014-07-01

    Single-walled carbon nanotubes (SWNTs) have been used in a wide range of fields, and the surface modification via carboxyl functionalization can further improve their physicochemical properties. However, whether carboxyl-modified SWNT poses potential risks to microbial denitrification after its release into the environment remains unknown. Here we present the possible effects of carboxyl-modified SWNT on the growth and denitrification activity of Paracoccus denitrificans (a model denitrifying bacterium). It was found that carboxyl-modified SWNT were present both outside and inside the bacteria, and thus induced bacterial growth inhibition at the concentrations of 10 and 50 mg/L. After 24 h of exposure, the final nitrate concentration in the presence of 50 mg/L carboxyl-modified SWNT was 21-fold higher than that in its absence, indicating that nitrate reduction was substantially suppressed by carboxyl-modified SWNT. The transcriptional profiling revealed that carboxyl-modified SWNT led to the transcriptional activation of the genes encoding ribonucleotide reductase in response to DNA damage and also decreased the gene expressions involved in glucose metabolism and energy production, which was an important reason for bacterial growth inhibition. Moreover, carboxyl-modified SWNT caused the significant down-regulation and lower activity of nitrate reductase, which was consistent with the decreased efficiency of nitrate reduction.

  11. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly.

    Science.gov (United States)

    García-Nafría, Javier; Watson, Jake F; Greger, Ingo H

    2016-06-06

    In vivo homologous recombination holds the potential for optimal molecular cloning, however, current strategies require specialised bacterial strains or laborious protocols. Here, we exploit a recA-independent recombination pathway, present in widespread laboratory E.coli strains, to develop IVA (In Vivo Assembly) cloning. This system eliminates the need for enzymatic assembly and reduces all molecular cloning procedures to a single-tube, single-step PCR, performed in IVA is a complete system, and offers significant advantages over alternative methods for all cloning procedures (insertions, deletions, site-directed mutagenesis and sub-cloning). Significantly, IVA allows unprecedented simplification of complex cloning procedures: five simultaneous modifications of any kind, multi-fragment assembly and library construction are performed in approximately half the time of current protocols, still in a single-step fashion. This system is efficient, seamless and sequence-independent, and requires no special kits, enzymes or proprietary bacteria, which will allow its immediate adoption by the academic and industrial molecular biology community.

  12. Making novel bio-interfaces through bacterial protein recrystallization on biocompatible polylactide derivative films

    Science.gov (United States)

    Lejardi, Ainhoa; López, Aitziber Eleta; Sarasua, José R.; Sleytr, U. B.; Toca-Herrera, José L.

    2013-09-01

    Fabrication of novel bio-supramolecular structures was achieved by recrystallizing the bacterial surface protein SbpA on amorphous and semicrystalline polylactide derivatives. Differential scanning calorimetry showed that the glass transition temperature (Tg) for (poly-L-lactide)-PLLA, poly(L,D-lactide)-PDLLA, poly(lactide-co-glycolide)-PLGA and poly(lactide-co-caprolactone)-PLCL was 63 °C, 53 °C, 49 °C and 15 °C, respectively. Tensile stress-strain tests indicated that PLLA, PLGA, and PDLLA had a glassy behaviour when tested below Tg. The obtained Young modulus were 1477 MPa, 1330 MPa, 1306 MPa, and 9.55 MPa for PLLA, PLGA, PDLLA, and PLCL, respectively. Atomic force microscopy results confirmed that SbpA recrystallized on every polymer substrate exhibiting the native S-layer P4 lattice (a = b = 13 nm, γ = 90°). However, the polymer substrate influenced the domain size of the S-protein crystal, with the smallest size for PLLA (0.011 μm2), followed by PDLLA (0.034 μm2), and PLGA (0.039 μm2), and the largest size for PLCL (0.09 μm2). quartz crystal microbalance with dissipation monitoring (QCM-D) measurements indicated that the adsorbed protein mass per unit area (˜1800 ng cm-2) was independent of the mechanical, thermal, and crystalline properties of the polymer support. The slowest protein adsorption rate was observed for amorphous PLCL (the polymer with the weakest mechanical properties and lowest Tg). QCM-D also monitored protein self-assembly in solution and confirmed that S-layer formation takes place in three main steps: adsorption, self-assembly, and crystal reorganization. Finally, this work shows that biodegradable polylactide derivatives films are a suitable support to form robust biomimetic S-protein layers.

  13. Making novel bio-interfaces through bacterial protein recrystallization on biocompatible polylactide derivative films.

    Science.gov (United States)

    Lejardi, Ainhoa; López, Aitziber Eleta; Sarasua, José R; Sleytr, U B; Toca-Herrera, José L

    2013-09-28

    Fabrication of novel bio-supramolecular structures was achieved by recrystallizing the bacterial surface protein SbpA on amorphous and semicrystalline polylactide derivatives. Differential scanning calorimetry showed that the glass transition temperature (T(g)) for (poly-L-lactide)-PLLA, poly(L,D-lactide)-PDLLA, poly(lactide-co-glycolide)-PLGA and poly(lactide-co-caprolactone)-PLCL was 63 °C, 53 °C, 49 °C and 15 °C, respectively. Tensile stress-strain tests indicated that PLLA, PLGA, and PDLLA had a glassy behaviour when tested below T(g). The obtained Young modulus were 1477 MPa, 1330 MPa, 1306 MPa, and 9.55 MPa for PLLA, PLGA, PDLLA, and PLCL, respectively. Atomic force microscopy results confirmed that SbpA recrystallized on every polymer substrate exhibiting the native S-layer P4 lattice (a = b = 13 nm, γ = 90°). However, the polymer substrate influenced the domain size of the S-protein crystal, with the smallest size for PLLA (0.011 μm(2)), followed by PDLLA (0.034 μm(2)), and PLGA (0.039 μm(2)), and the largest size for PLCL (0.09 μm(2)). quartz crystal microbalance with dissipation monitoring (QCM-D) measurements indicated that the adsorbed protein mass per unit area (~1800 ng cm(-2)) was independent of the mechanical, thermal, and crystalline properties of the polymer support. The slowest protein adsorption rate was observed for amorphous PLCL (the polymer with the weakest mechanical properties and lowest T(g)). QCM-D also monitored protein self-assembly in solution and confirmed that S-layer formation takes place in three main steps: adsorption, self-assembly, and crystal reorganization. Finally, this work shows that biodegradable polylactide derivatives films are a suitable support to form robust biomimetic S-protein layers.

  14. Evaluation of anti-bacterial effects of some novel thiazole and imidazole derivatives against some pathogenic bacteria

    Directory of Open Access Journals (Sweden)

    Behzad Ghasemi

    2015-12-01

    Full Text Available Background and Objectives: Bacterial resistance to antibiotics has motivated the researchers to evaluate the novel anti-bac- terial compounds such as some thiazole and imidazole derivatives. Thereby, in this work, we investigated the anti-bacterial effects of one new thiazole and two new imidazole derivatives on Bacillus cereus, Listeria monocytogenes, Escherichia coli, Salmonella typhimurium, Proteus mirabilis and Shigella dysenteriae.Materials and Methods: The thiazole and imidazole derivatives were dissolved in DMSO. The disk diffusion method was utilized to measure the growth inhibition zone diameter values, and the broth micro-dilution method was applied to deter- mine the minimum inhibitory concentration (MIC values.Results: The synthesized imidazole derivatives lacked any inhibitory effect against the tested bacteria. On the other hand, although the synthesized thiazole derivative showed no inhibitory effect against Bacillus cereus, Salmonella typhimurium, and Escherichia coli, it inhibited the growth of Proteus mirabilis, Shigella dysenteriae, and Listeria monocytogenes with the MIC values of 1000, 125, and 1000 µg/ml, respectively, and the growth inhibition zone diameter values of 9.3 ± 0.1, 15.6 ± 0.2, and 8.1 ± 0.0 mm, respectively.Conclusion: The anti-bacterial effect of the synthesized thiazole derivative on Shigella dysenteriae, Proteus mirabilis and Listeria monocytogenes was proven. However, its inhibition effect against Shigella dysenteriae was more than that against the others. Many in-vitro and in-vivo experiments are required to evaluate the effects of this compound on the bacteria and the human body. Keywords: Anti-bacterial effects, Thiazole, Imidazole

  15. Simultaneous determination of gene expression and bacterial identity in single cells in defined mixtures of pure cultures

    DEFF Research Database (Denmark)

    Poulsen, Lars K.; Dalton, Helen M.; Angels, Mark;

    1997-01-01

    A protocol was developed to achieve the simultaneous determination of gene expression and bacterial identity at the level of single cells: a chromogenic beta-galactosidase activity assay was combined with in situ hybridization of Fluorescently labelled oligonucleotide probes to rRNA. The method a...

  16. Optical tweezers for single molecule force spectroscopy on bacterial adhesion organelles

    Science.gov (United States)

    Andersson, Magnus; Axner, Ove; Uhlin, Bernt Eric; Fällman, Erik

    2006-08-01

    Instrumentation and methodologies for single molecule force spectroscopy on bacterial adhesion organelles by the use of force measuring optical tweezers have been developed. A thorough study of the biomechanical properties of fimbrial adhesion organelles expressed by uropathogenic E. coli, so-called pili, is presented. Steady-state as well as dynamic force measurements on P pili, expressed by E. coli causing pyelonephritis, have revealed, among other things, various unfolding and refolding properties of the helical structure of P pili, the PapA rod. Based on these properties an energy landscape model has been constructed by which specific biophysical properties of the PapA rod have been extracted, e.g. the number of subunits, the length of a single pilus, bond lengths and activation energies for bond opening and closure. Moreover, long time repetitive measurements have shown that the rod can be unfolded and refolded repetitive times without losing its intrinsic properties. These properties are believed to be of importance for the bacteria's ability to maintain close contact with host cells during initial infections. The results presented are considered to be of importance for the field of biopolymers in general and the development of new pharmaceuticals towards urinary tract infections in particular. The results show furthermore that the methodology can be used to gain knowledge of the intrinsic biomechanical function of adhesion organelles. The instrumentation is currently used for characterization of type 1 pili, expressed by E. coli causing cystitis, i.e. infections in the bladder. The first force spectrometry investigations of these pili will be presented.

  17. Unraveling the Secrets of Bacterial Adhesion Organelles Using Single-Molecule Force Spectroscopy

    Science.gov (United States)

    Axner, Ove; Björnham, Oscar; Castelain, Mickaël; Koutris, Efstratios; Schedin, Staffan; Fällman, Erik; Andersson, Magnus

    Many types of bacterium express micrometer-long attachment organelles (so-called pili) whose role is to mediate adhesion to host tissue. Until recently, little was known about their function in the adhesion process. Force-measuring optical tweezers (FMOT) have since then been used to unravel the biomechanical properties of various types of pili, primarily those from uropathogenic E. coli, in particular their force-vs.-elongation response, but lately also some properties of the adhesin are situated at the distal end of the pilus. This knowledge provides an understanding of how piliated bacteria can sustain external shear forces caused by rinsing processes, e.g., urine flow. It has been found that many types of pilus exhibit unique and complex force-vs.-elongation responses. It has been conjectured that their dissimilar properties impose significant differences in their ability to sustain external forces and that different types of pilus therefore have dissimilar predisposition to withstand different types of rinsing conditions. An understanding of these properties is of high importance since it can serve as a basis for finding new means to combat bacterial adhesion, including that caused by antibiotic-resistance bacteria. This work presents a review of the current status of the assessment of biophysical properties of individual pili on single bacteria exposed to strain/stress, primarily by the FMOT technique. It also addresses, for the first time, how the elongation and retraction properties of the rod couple to the adhesive properties of the tip adhesin.

  18. Chemical polyglycosylation and nanolitre detection enables single-molecule recapitulation of bacterial sugar export

    Science.gov (United States)

    Kong, Lingbing; Almond, Andrew; Bayley, Hagan; Davis, Benjamin G.

    2016-05-01

    The outermost protective layer of both Gram-positive and Gram-negative bacteria is composed of bacterial capsular polysaccharides. Insights into the interactions between the capsular polysaccharide and its transporter and the mechanism of sugar export would not only increase our understanding of this key process, but would also help in the design of novel therapeutics to block capsular polysaccharide export. Here, we report a nanolitre detection system that makes use of the bilayer interface between two droplets, and we use this system to study single-molecule recapitulation of sugar export. A synthetic strategy of polyglycosylation based on tetrasaccharide monomers enables ready synthetic access to extended fragments of K30 oligosaccharides and polysaccharides. Examination of the interactions between the Escherichia coli sugar transporter Wza and very small amounts of fragments of the K30 capsular polysaccharide substrate reveal the translocation of smaller but not larger fragments. We also observe capture events that occur only on the intracellular side of Wza, which would complement coordinated feeding by adjunct biosynthetic machinery.

  19. Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis.

    Science.gov (United States)

    Bienert, Ralf; Zeeb, Markus; Dostál, Lubomir; Feske, Anette; Magg, Christine; Max, Klaas; Welfle, Heinz; Balbach, Jochen; Heinemann, Udo

    2004-04-01

    The cold-shock response has been described for several bacterial species. It is characterized by distinct changes in intracellular protein patterns whereby a set of cold-shock-inducible proteins become abundant. The major cold-shock proteins of Bacillus subtilis (Bs-CspB) and Bacillus caldolyticus (Bc-Csp) are small oligonucleotide/oligosaccharide-binding (OB) fold proteins that have been described as binding single-stranded nucleic acids. Bs-CspB (Mr = 7365) and Bc-Csp (Mr = 7333) were crystallized in the presence of the deoxyhexanucleotide (dT)6. Crystals of (dT)6 with Bs-CspB grew in the orthorhombic space group C222(1), with unit-cell parameters a = 49.0, b = 53.2, c = 77.0 A. Crystals with Bc-Csp grew in the primitive orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 74.3, b = 64.9, c = 31.2 A. These crystals diffract to maximal resolutions of 1.78 and 1.29 A, respectively. The presence of protein and DNA in the crystals was demonstrated by Raman spectroscopy.

  20. Single-molecule approach to bacterial genomic comparisons via optical mapping.

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Shiguo [Univ. Wisc.-Madison; Kile, A. [Univ. Wisc.-Madison; Bechner, M. [Univ. Wisc.-Madison; Kvikstad, E. [Univ. Wisc.-Madison; Deng, W. [Univ. Wisc.-Madison; Wei, J. [Univ. Wisc.-Madison; Severin, J. [Univ. Wisc.-Madison; Runnheim, R. [Univ. Wisc.-Madison; Churas, C. [Univ. Wisc.-Madison; Forrest, D. [Univ. Wisc.-Madison; Dimalanta, E. [Univ. Wisc.-Madison; Lamers, C. [Univ. Wisc.-Madison; Burland, V. [Univ. Wisc.-Madison; Blattner, F. R. [Univ. Wisc.-Madison; Schwartz, David C. [Univ. Wisc.-Madison

    2004-01-01

    Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping.

  1. Molecular Docking Studies of Catechin and Its Derivatives as Anti-bacterial Inhibitor for Glucosamine-6-Phosphate Synthase

    Science.gov (United States)

    Fikrika, H.; Ambarsari, L.; Sumaryada, T.

    2016-01-01

    Molecular docking simulation of catechin and its derivatives on Glucosamine-6- Phosphate Synthase (GlmS) has been performed in this research. GlmS inhibition by a particular ligand will suppress the production of bacterial cell wall and significantly reduce the population of invading bacteria. In this study, catechin derivatives i.e epicatechin, galloatechin and epigalloatechin were found to have stronger binding affinities as compared to natural ligand of GlmS, Fructose-6-Phosphate (F6P). Those three ligands were docked on the same pocket in GlmS target as F6P, with 70% binding sites similarity. Based on the docking results, gallocatechin turns out to be the most potent ligand for anti-bacterial agent with ΔG= -8.00 kcal/mol. The docking between GlmS and catechin derivatives are characterized by a constant present of a strong hydrogen bond between functional group O3 and Ser-349. This hydrogen bond most likely plays a significant role in the docking mechanism and binding modes selection. The surprising result is catechin itself exhibited a quite strong binding with GlmS (ΔG= -7.80 kcal.mol), but docked on a completely different pocket compared to other ligands. This results suggest that catechin might still have a curing effect but with a completely different pathway and mechanism as compared to its derivatives.

  2. Graphene Quantum Dots Interfaced with Single Bacterial Spore for Bio-Electromechanical Devices: A Graphene Cytobot

    Science.gov (United States)

    Sreeprasad, T. S.; Nguyen, Phong; Alshogeathri, Ahmed; Hibbeler, Luke; Martinez, Fabian; McNeil, Nolan; Berry, Vikas

    2015-03-01

    The nanoarchitecture and micromachinery of a cell can be leveraged to fabricate sophisticated cell-driven devices. This requires a coherent strategy to derive cell's mechanistic abilities, microconstruct, and chemical-texture towards such microtechnologies. For example, a microorganism's hydrophobic membrane encapsulating hygroscopic constituents allows it to sustainably withhold a high aquatic pressure. Further, it provides a rich surface chemistry available for nano-interfacing and a strong mechanical response to humidity. Here we demonstrate a route to incorporate a complex cellular structure into microelectromechanics by interfacing compatible graphene quantum dots (GQDs) with a highly responsive single spore microstructure. A sensitive and reproducible electron-tunneling width modulation of 1.63 nm within a network of GQDs chemically-secured on a spore was achieved via sporal hydraulics with a driving force of 299.75 Torrs (21.7% water at GQD junctions). The electron-transport activation energy and the Coulomb blockade threshold for the GQD network were 35 meV and 31 meV, respectively; while the inter-GQD capacitance increased by 1.12 folds at maximum hydraulic force. This is the first example of nano/bio interfacing with spores and will lead to the evolution of next-generation bio-derived microarchitectures, probes for cellular/biochemical processes, biomicrorobotic-mechanisms, and membranes for micromechanical actuation.

  3. Graphene quantum dots interfaced with single bacterial spore for bio-electromechanical devices: a graphene cytobot.

    Science.gov (United States)

    Sreeprasad, T S; Nguyen, Phong; Alshogeathri, Ahmed; Hibbeler, Luke; Martinez, Fabian; McNeil, Nolan; Berry, Vikas

    2015-03-16

    The nanoarchitecture and micromachinery of a cell can be leveraged to fabricate sophisticated cell-driven devices. This requires a coherent strategy to derive cell's mechanistic abilities, microconstruct, and chemical-texture towards such microtechnologies. For example, a microorganism's hydrophobic membrane encapsulating hygroscopic constituents allows it to sustainably withhold a high aquatic pressure. Further, it provides a rich surface chemistry available for nano-interfacing and a strong mechanical response to humidity. Here we demonstrate a route to incorporate a complex cellular structure into microelectromechanics by interfacing compatible graphene quantum dots (GQDs) with a highly responsive single spore microstructure. A sensitive and reproducible electron-tunneling width modulation of 1.63 nm within a network of GQDs chemically-secured on a spore was achieved via sporal hydraulics with a driving force of 299.75 Torrs (21.7% water at GQD junctions). The electron-transport activation energy and the Coulomb blockade threshold for the GQD network were 35 meV and 31 meV, respectively; while the inter-GQD capacitance increased by 1.12 folds at maximum hydraulic force. This is the first example of nano/bio interfacing with spores and will lead to the evolution of next-generation bio-derived microarchitectures, probes for cellular/biochemical processes, biomicrorobotic-mechanisms, and membranes for micromechanical actuation.

  4. Synthesis and Anti-Bacterial Activities of Some Novel Schiff Bases Derived from Aminophenazone

    Directory of Open Access Journals (Sweden)

    Salman A Khan

    2010-10-01

    Full Text Available A series of 1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one-containing Schiff bases were synthesized, characterized and screened for their antibacterial activities. The structures of the synthesized compounds were established by spectroscopic (FT-IR, 1H-NMR, 13C-NMR, MS and elemental analyses. The anti-bacterial activities (with MIC values of compounds were evaluated. The anti-bacterial screening results reveal that among the six compounds screened, four compounds showed moderate to good anti-bacterial activity. Among the tested compounds, the most effective compounds against four bacterial strains, viz. Escherichia coli, Staphylococcus aureus, Salmonella typhimurium and Streptococcus pyogenes, are [(2-Chlorobenzylideneamino]-1,5-dimethyl-2-phenyl-1,2-dihydropyrazol-3-one (4 and [(1,5-Dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yliminomethyl]benzonitrile (5 with MIC values of 6.25 μg/mL.

  5. Acute Atrial Fibrillation Derived by Single-Doze Fentanyl Transdermal Usage

    Directory of Open Access Journals (Sweden)

    Mesut Gitmez

    2014-02-01

    Full Text Available Fentanyl is a selective and synthetic opiate agonist. Especially in cancer-derived pain treatment fentanyl transdermal usage is preferred. Clinic impacts occur related to several systems derived by fentanyl usage. However, respiratory failure, hypothermia and bradycardia are observed the most. In this article, we aimed at presenting a case which developed atrial fibrillation derived by single-dose fentanyl transdermal usage.

  6. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.

    Science.gov (United States)

    La Duc, Myron T; Vaishampayan, Parag; Nilsson, Henrik R; Torok, Tamas; Venkateswaran, Kasthuri

    2012-08-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.

  7. Microspectrometric insights on the uptake of antibiotics at the single bacterial cell level.

    Science.gov (United States)

    Cinquin, Bertrand; Maigre, Laure; Pinet, Elizabeth; Chevalier, Jacqueline; Stavenger, Robert A; Mills, Scott; Réfrégiers, Matthieu; Pagès, Jean-Marie

    2015-12-11

    Bacterial multidrug resistance is a significant health issue. A key challenge, particularly in Gram-negative antibacterial research, is to better understand membrane permeation of antibiotics in clinically relevant bacterial pathogens. Passing through the membrane barrier to reach the required concentration inside the bacterium is a pivotal step for most antibacterials. Spectrometric methodology has been developed to detect drugs inside bacteria and recent studies have focused on bacterial cell imaging. Ultimately, we seek to use this method to identify pharmacophoric groups which improve penetration, and therefore accumulation, of small-molecule antibiotics inside bacteria. We developed a method to quantify the time scale of antibiotic accumulation in living bacterial cells. Tunable ultraviolet excitation provided by DISCO beamline (synchrotron Soleil) combined with microscopy allows spectroscopic analysis of the antibiotic signal in individual bacterial cells. Robust controls and measurement of the crosstalk between fluorescence channels can provide real time quantification of drug. This technique represents a new method to assay drug translocation inside the cell and therefore incorporate rational drug design to impact antibiotic uptake.

  8. Do bacterial cell numbers follow a theoretical Poisson distribution? Comparison of experimentally obtained numbers of single cells with random number generation via computer simulation.

    Science.gov (United States)

    Koyama, Kento; Hokunan, Hidekazu; Hasegawa, Mayumi; Kawamura, Shuso; Koseki, Shigenobu

    2016-12-01

    We investigated a bacterial sample preparation procedure for single-cell studies. In the present study, we examined whether single bacterial cells obtained via 10-fold dilution followed a theoretical Poisson distribution. Four serotypes of Salmonella enterica, three serotypes of enterohaemorrhagic Escherichia coli and one serotype of Listeria monocytogenes were used as sample bacteria. An inoculum of each serotype was prepared via a 10-fold dilution series to obtain bacterial cell counts with mean values of one or two. To determine whether the experimentally obtained bacterial cell counts follow a theoretical Poisson distribution, a likelihood ratio test between the experimentally obtained cell counts and Poisson distribution which parameter estimated by maximum likelihood estimation (MLE) was conducted. The bacterial cell counts of each serotype sufficiently followed a Poisson distribution. Furthermore, to examine the validity of the parameters of Poisson distribution from experimentally obtained bacterial cell counts, we compared these with the parameters of a Poisson distribution that were estimated using random number generation via computer simulation. The Poisson distribution parameters experimentally obtained from bacterial cell counts were within the range of the parameters estimated using a computer simulation. These results demonstrate that the bacterial cell counts of each serotype obtained via 10-fold dilution followed a Poisson distribution. The fact that the frequency of bacterial cell counts follows a Poisson distribution at low number would be applied to some single-cell studies with a few bacterial cells. In particular, the procedure presented in this study enables us to develop an inactivation model at the single-cell level that can estimate the variability of survival bacterial numbers during the bacterial death process.

  9. Impact of bacteria and bacterial components on osteogenic and adipogenic differentiation of adipose-derived mesenchymal stem cells.

    Science.gov (United States)

    Fiedler, Tomas; Salamon, Achim; Adam, Stefanie; Herzmann, Nicole; Taubenheim, Jan; Peters, Kirsten

    2013-11-01

    Adult mesenchymal stem cells (MSC) are present in several tissues, e.g. bone marrow, heart muscle, brain and subcutaneous adipose tissue. In invasive infections MSC get in contact with bacteria and bacterial components. Not much is known about how bacterial pathogens interact with MSC and how contact to bacteria influences MSC viability and differentiation potential. In this study we investigated the impact of three different wound infection relevant bacteria, Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes, and the cell wall components lipopolysaccharide (LPS; Gram-negative bacteria) and lipoteichoic acid (LTA; Gram-positive bacteria) on viability, proliferation, and osteogenic as well as adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells (adMSC). We show that all three tested species were able to attach to and internalize into adMSC. The heat-inactivated Gram-negative E. coli as well as LPS were able to induce proliferation and osteogenic differentiation but reduce adipogenic differentiation of adMSC. Conspicuously, the heat-inactivated Gram-positive species showed the same effects on proliferation and adipogenic differentiation, while its cell wall component LTA exhibited no significant impact on adMSC. Therefore, our data demonstrate that osteogenic and adipogenic differentiation of adMSC is influenced in an oppositional fashion by bacterial antigens and that MSC-governed regeneration is not necessarily reduced under infectious conditions.

  10. Bone marrow-derived cells participate in stromal remodeling of the lung following acute bacterial pneumonia in mice.

    Science.gov (United States)

    Serikov, Vladimir B; Mikhaylov, Viatcheslav M; Krasnodembskay, Anna D; Matthay, Michael A

    2008-01-01

    Bone marrow-derived cells (BMDC) have been shown to graft injured tissues, differentiate in specialized cells, and participate in repair. The importance of these processes in acute lung bacterial inflammation and development of fibrosis is unknown. The goal of this study was to investigate the temporal sequence and lineage commitment of BMDC in mouse lungs injured by bacterial pneumonia. We transplanted GFP-tagged BMDC into 5-Gy-irradiated C57BL/6 mice. After 3 months of recovery, mice were subjected to LD(50) intratracheal instillation of live E. coli (controls received saline) which produced pneumonia and subsequent areas of fibrosis. Lungs were investigated by immunohistology for up to 6 months. At the peak of lung inflammation, the predominant influx of BMDC were GFP(+) leukocytes. Postinflammatory foci of lung fibrosis were evident after 1-2 months. The fibrotic foci in lung stroma contained clusters of GFP(+) CD45(+) cells, GFP(+) vimentin-positive cells, and GFP(+) collagen I-positive fibroblasts. GFP(+) endothelial or epithelial cells were not identified. These data suggest that following 5-Gy irradiation and acute bacterial pneumonia, BMDC may temporarily participate in lung postinflammatory repair and stromal remodeling without long-term engraftment as specialized endothelial or epithelial cells.

  11. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

    Science.gov (United States)

    Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

    2017-01-01

    Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

  12. Novel Steroidal (6R)-Spiro-1,3,4-thiadiazoline Derivatives as Anti-bacterial Agents

    Institute of Scientific and Technical Information of China (English)

    Khan Salman A.; Asiri, Abdullah M.

    2012-01-01

    Novel steroidal (6R)-spiro-1,3,4-thiadiazoline derivatives have been synthesized by the cyclization of steroidal thiosemiearbazones. Thiosemicarbazones have been synthesized by the reaction of steroidal ketones with thiosemi- carbazide. All the compounds have been characterized by IR, 1H NMR, mass and elemental analyses. The antibacterial activities of these compounds have been first tested in vitro by the disk diffusion assay against two Gram-positive and two Gram-negative bacteria, and then the minimum inhibitory concentration (MIC) values have been determined with the reference of standard drug amoxicillin. The results showed that steroidal thiadiazoline de- rivatives exhibited better antibacterial activity than the steroidal thiosemicarbazone derivatives. Chloro and acetoxy substituents on the 3β-position of the steroidal thiadiazoline ring increased the anti-bacterial activity. Among all the compounds, compounds 7 and 8 were found better inhibitors as compared to the respective drug amoxicillin.

  13. Cooperation between Monocyte-Derived Cells and Lymphoid Cells in the Acute Response to a Bacterial Lung Pathogen.

    Directory of Open Access Journals (Sweden)

    Andrew S Brown

    2016-06-01

    Full Text Available Legionella pneumophila is the causative agent of Legionnaires' disease, a potentially fatal lung infection. Alveolar macrophages support intracellular replication of L. pneumophila, however the contributions of other immune cell types to bacterial killing during infection are unclear. Here, we used recently described methods to characterise the major inflammatory cells in lung after acute respiratory infection of mice with L. pneumophila. We observed that the numbers of alveolar macrophages rapidly decreased after infection coincident with a rapid infiltration of the lung by monocyte-derived cells (MC, which, together with neutrophils, became the dominant inflammatory cells associated with the bacteria. Using mice in which the ability of MC to infiltrate tissues is impaired it was found that MC were required for bacterial clearance and were the major source of IL12. IL12 was needed to induce IFNγ production by lymphoid cells including NK cells, memory T cells, NKT cells and γδ T cells. Memory T cells that produced IFNγ appeared to be circulating effector/memory T cells that infiltrated the lung after infection. IFNγ production by memory T cells was stimulated in an antigen-independent fashion and could effectively clear bacteria from the lung indicating that memory T cells are an important contributor to innate bacterial defence. We also determined that a major function of IFNγ was to stimulate bactericidal activity of MC. On the other hand, neutrophils did not require IFNγ to kill bacteria and alveolar macrophages remained poorly bactericidal even in the presence of IFNγ. This work has revealed a cooperative innate immune circuit between lymphoid cells and MC that combats acute L. pneumophila infection and defines a specific role for IFNγ in anti-bacterial immunity.

  14. Cooperation between Monocyte-Derived Cells and Lymphoid Cells in the Acute Response to a Bacterial Lung Pathogen.

    Science.gov (United States)

    Brown, Andrew S; Yang, Chao; Fung, Ka Yee; Bachem, Annabell; Bourges, Dorothée; Bedoui, Sammy; Hartland, Elizabeth L; van Driel, Ian R

    2016-06-01

    Legionella pneumophila is the causative agent of Legionnaires' disease, a potentially fatal lung infection. Alveolar macrophages support intracellular replication of L. pneumophila, however the contributions of other immune cell types to bacterial killing during infection are unclear. Here, we used recently described methods to characterise the major inflammatory cells in lung after acute respiratory infection of mice with L. pneumophila. We observed that the numbers of alveolar macrophages rapidly decreased after infection coincident with a rapid infiltration of the lung by monocyte-derived cells (MC), which, together with neutrophils, became the dominant inflammatory cells associated with the bacteria. Using mice in which the ability of MC to infiltrate tissues is impaired it was found that MC were required for bacterial clearance and were the major source of IL12. IL12 was needed to induce IFNγ production by lymphoid cells including NK cells, memory T cells, NKT cells and γδ T cells. Memory T cells that produced IFNγ appeared to be circulating effector/memory T cells that infiltrated the lung after infection. IFNγ production by memory T cells was stimulated in an antigen-independent fashion and could effectively clear bacteria from the lung indicating that memory T cells are an important contributor to innate bacterial defence. We also determined that a major function of IFNγ was to stimulate bactericidal activity of MC. On the other hand, neutrophils did not require IFNγ to kill bacteria and alveolar macrophages remained poorly bactericidal even in the presence of IFNγ. This work has revealed a cooperative innate immune circuit between lymphoid cells and MC that combats acute L. pneumophila infection and defines a specific role for IFNγ in anti-bacterial immunity.

  15. Impact of bacteria and bacterial components on osteogenic and adipogenic differentiation of adipose-derived mesenchymal stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Fiedler, Tomas, E-mail: tomas.fiedler@med.uni-rostock.de [Institute for Medical Microbiology, Virology, and Hygiene, Rostock University Medical Center, Schillingallee 70, D-18057 Rostock (Germany); Salamon, Achim; Adam, Stefanie; Herzmann, Nicole [Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany); Taubenheim, Jan [Institute for Medical Microbiology, Virology, and Hygiene, Rostock University Medical Center, Schillingallee 70, D-18057 Rostock (Germany); Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany); Peters, Kirsten [Department of Cell Biology, Rostock University Medical Center, Schillingallee 69, D-18057 Rostock (Germany)

    2013-11-01

    Adult mesenchymal stem cells (MSC) are present in several tissues, e.g. bone marrow, heart muscle, brain and subcutaneous adipose tissue. In invasive infections MSC get in contact with bacteria and bacterial components. Not much is known about how bacterial pathogens interact with MSC and how contact to bacteria influences MSC viability and differentiation potential. In this study we investigated the impact of three different wound infection relevant bacteria, Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes, and the cell wall components lipopolysaccharide (LPS; Gram-negative bacteria) and lipoteichoic acid (LTA; Gram-positive bacteria) on viability, proliferation, and osteogenic as well as adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells (adMSC). We show that all three tested species were able to attach to and internalize into adMSC. The heat-inactivated Gram-negative E. coli as well as LPS were able to induce proliferation and osteogenic differentiation but reduce adipogenic differentiation of adMSC. Conspicuously, the heat-inactivated Gram-positive species showed the same effects on proliferation and adipogenic differentiation, while its cell wall component LTA exhibited no significant impact on adMSC. Therefore, our data demonstrate that osteogenic and adipogenic differentiation of adMSC is influenced in an oppositional fashion by bacterial antigens and that MSC-governed regeneration is not necessarily reduced under infectious conditions. - Highlights: • Staphylococcus aureus, Streptococcus pyogenes and Escherichia coli bind to and internalize into adMSC. • Heat-inactivated cells of these bacterial species trigger proliferation of adMSC. • Heat-inactivated E. coli and LPS induce osteogenic differentiation of adMSC. • Heat-inactivated E. coli and LPS reduce adipogenic differentiation of adMSC. • LTA does not influence adipogenic or osteogenic differentiation of adMSC.

  16. Physicochemical characterization of novel Schiff bases derived from developed bacterial cellulose 2,3-dialdehyde.

    Science.gov (United States)

    Keshk, Sherif M A S; Ramadan, Ahmed M; Bondock, Samir

    2015-08-20

    The synthesis of two novel Schiff's bases (cellulose-2,3-bis-[(4-methylene-amino)-benzene-sulfonamide] (5) & cellulose-2,3-bis-[(4-methylene-amino)-N-(thiazol-2-yl)-benzenesulfonamide] (6) via condensation reactions of periodate oxidized developed bacterial cellulose ODBC (2) with sulfa drugs [sulfanilamide (3) & sulfathiazole (4)] was reported. The physicochemical characterization of the condensation products was performed using FTIR, (1)H NMR, (13)C NMR spectral analyses, X-ray diffraction and DTA. The ODBC exhibited the highest degree of oxidation based on the aldehyde group number percentage (82.9%), which confirms the highest reactivity of developed bacterial cellulose [DBC (1)]. The X-ray diffractograms indicated an increase in the interplanar distance of the cellulose Schiff base (6) compared to ODBC (2) due to sulfathiazole (4) inclusion between ODBC (2) sheets corresponding to the 1 1 0 plane. In addition, the aldehyde content of Schiff base (6) was (20.8%) much lower than that of Schiff base (5) (41.5%). These results confirmed the high affinity of sulfathiazole (4) to the ODBC (2) chain, and the substantial changes in the original properties of ODBC were due to these chemical modifications rather than the sulfanilamide (3).

  17. Beetroot-pigment-derived colorimetric sensor for detection of calcium dipicolinate in bacterial spores.

    Directory of Open Access Journals (Sweden)

    Letícia Christina Pires Gonçalves

    Full Text Available In this proof-of-concept study, we describe the use of the main red beet pigment betanin for the quantification of calcium dipicolinate in bacterial spores, including Bacillus anthracis. In the presence of europium(III ions, betanin is converted to a water-soluble, non-luminescent orange 1∶1 complex with a stability constant of 1.4 × 10(5 L mol(-1. The addition of calcium dipicolinate, largely found in bacterial spores, changes the color of the aqueous solution of [Eu(Bn(+] from orange to magenta. The limit of detection (LOD of calcium dipicolinate is around 2.0 × 10(-6 mol L(-1 and the LOD determined for both spores, B. cereus and B. anthracis, is (1.1 ± 0.3× 10(6 spores mL(-1. This simple, green, fast and low cost colorimetric assay was selective for calcium dipicolinate when compared to several analogous compounds. The importance of this work relies on the potential use of betalains, raw natural pigments, as colorimetric sensors for biological applications.

  18. HISH-SIMS analysis of bacterial uptake of algal-derived carbon in the Río de la Plata estuary.

    Science.gov (United States)

    Alonso, Cecilia; Musat, Niculina; Adam, Birgit; Kuypers, Marcel; Amann, Rudolf

    2012-12-01

    One of the main goals of microbial ecologists is to assess the contribution of distinct bacterial groups to biogeochemical processes, e.g. carbon cycling. Until very recently, it was not possible to quantify the uptake of a given compound at single cell level. The advent of nano-scale secondary-ion mass spectrometry (nanoSIMS), and its combination with halogen in situ hybridization (HISH) opened up this possibility. Despite its power, difficulties in cell identification during analysis of environmental samples might render this approach challenging for certain applications. A pilot study, designed to quantify the incorporation of phytoplankton-derived carbon by the main clades of heterotrophic aquatic bacteria (i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes), is used to exemplify and suggest potential solutions to these technical difficulties. The results obtained indicate that the main aquatic bacterial clades quantitatively differ in the incorporation of algae-derived organic matter. From the methodological point of view, they highlight the importance of the concentration of the target cells, which needs to be sufficient to allow for a rapid mapping under the nanoSIMS. Moreover, when working with highly productive waters, organic and inorganic particles pose a serious problem for cell recognition based on HISH-SIMS. In this work several technical suggestions are presented to minimize the above mentioned difficulties, including alternatives to improve the halogen labeling of the cells and proposing the use of a combination of FISH and HISH along with a mapping system. This approach considerably enhances the reliability of cell identification and the speed of the subsequent nanoSIMS analysis in such complex samples.

  19. Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios.

    Science.gov (United States)

    Juottonen, Heli; Eiler, Alexander; Biasi, Christina; Tuittila, Eeva-Stiina; Yrjälä, Kim; Fritze, Hannu

    2017-02-15

    Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [(13)C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands.

  20. Prolonged exposure to bacterial toxins downregulated expression of toll-like receptors in mesenchymal stromal cell-derived osteoprogenitors

    Directory of Open Access Journals (Sweden)

    Lau Yu

    2008-09-01

    Full Text Available Abstract Background Human mesenchymal stromal cells (MSCs, also known as mesenchymal stem cells are multipotent cells with potential therapeutic value. Owing to their osteogenic capability, MSCs may be clinically applied for facilitating osseointegration in dental implants or orthopedic repair of bony defect. However, whether wound infection or oral microflora may interfere with the growth and osteogenic differentiation of human MSCs remains unknown. This study investigated whether proliferation and osteogenic differentiation of MSCs would be affected by potent gram-positive and gram-negative derived bacterial toxins commonly found in human settings. Results We selected lipopolysaccharide (LPS from Escherichia coli and lipoteichoic acid (LTA from Streptococcus pyogenes as our toxins of choice. Our findings showed both LPS and LTA did not affect MSC proliferation, but prolonged LPS challenge upregulated the osteogenic differentiation of MSCs, as assessed by alkaline phosphatase activity and calcium deposition. Because toll-like receptors (TLRs, in particularly TLR4 and TLR2, are important for the cellular responsiveness to LPS and LTA respectively, we evaluated their expression profiles serially from MSCs to osteoblasts by quantitative PCR. We found that during osteogenic differentiation, MSC-derived osteoprogenitors gradually expressed TLR2 and TLR4 by Day 12. But under prolonged incubation with LPS, MSC-derived osteoprogenitors had reduced TLR2 and TLR4 gene expression. This peculiar response to LPS suggests a possible adaptive mechanism when MSCs are subjected to continuous exposure with bacteria. Conclusion In conclusion, our findings support the potential of using human MSCs as a biological graft, even under a bacterial toxin-rich environment.

  1. Biomass derived solvents for the scalable production of single layered graphene from graphite.

    Science.gov (United States)

    Sharma, Mukesh; Mondal, Dibyendu; Singh, Nripat; Prasad, Kamalesh

    2016-07-12

    Among four different biomass derived green and sustainable solvents namely levulinic acid (LA), ethyl lactate (EL), γ-valerolactone (GVL) and formic acid (FA) only LA was found to exfoliate graphite to single and few layered graphene sheets. During exfoliation, the formation of LA crystals embedded with single layered graphene sheets was observed. The process is scalable and the solvent can be recovered and reused in five subsequent cycles of exfoliation for the large scale production of graphene sheets.

  2. Sulfoalkyl ether β-cyclodextrin derivatives synthesized by a single step method as pharmaceutical biomaterials

    Institute of Scientific and Technical Information of China (English)

    SONG AiJing; WANG JianHua; LIU ChunDong; DENG LinHong

    2009-01-01

    We report a simple "one pot" single step method to synthesize sulfoalkyl ether β-cyclodextrin (β-CD)derivatives in aqueous solution,which avoids the limitations associated with commonly used organic synthesis of such derivatives including multi-step reactions,use of expensive,toxic,and often environmentally hazardous organic solvents and/or reagents. Using this method,we obtained sulfopropyl and sulfobutyl ethyl β-CDs. We characterized these two derivatives and evaluated their ability to enhance solubility of fluconazole,s commonly used antifungal drug with poor water solubility. Experimental results indicate that these derivatives are structurally analogous to some of the commercially available β-CD derivatives. More importantly,when they formed supramolecular inclusion complexes with fluconazole,they demonstrated similar,if not better,capacity to enhance fluconazole solubility compared with commercially available β-CD derivatives,suggesting that the simple "one pot" single step synthesis may provide an effective alternative approach to produce large quantity of β-CD derivatives as pharmaceutical biomaterials for medicinal applications.

  3. New Systematic CFD Methods to Calculate Static and Single Dynamic Stability Derivatives of Aircraft

    Directory of Open Access Journals (Sweden)

    Bai-gang Mi

    2017-01-01

    Full Text Available Several new systematic methods for high fidelity and reliability calculation of static and single dynamic derivatives are proposed in this paper. Angle of attack step response is used to obtain static derivative directly; then translation acceleration dynamic derivative and rotary dynamic derivative can be calculated by employing the step response motion of rate of the angle of attack and unsteady motion of pitching angular velocity step response, respectively. Longitudinal stability derivative calculations of SACCON UCAV are taken as test cases for validation. Numerical results of all cases achieve good agreement with reference values or experiments data from wind tunnel, which indicate that the proposed methods can be considered as new tools in the process of design and production of advanced aircrafts for their high efficiency and precision.

  4. Detection and quantification of bacterial autofluorescence at the single-cell level by a laboratory-built high-sensitivity flow cytometer.

    Science.gov (United States)

    Yang, Lingling; Zhou, Yingxing; Zhu, Shaobin; Huang, Tianxun; Wu, Lina; Yan, Xiaomei

    2012-02-07

    Cellular autofluorescence can affect the sensitivity of fluorescence microscopic or flow cytometric assays by interfering with or even precluding the detection of low-level specific fluorescence. Here we developed a method to detect and quantify bacterial autofluorescence in the green region of the spectrum at the single-cell level using a laboratory-built high-sensitivity flow cytometer (HSFCM). The detection of the very weak bacterial autofluorescence was confirmed by analyzing polystyrene beads of comparable and larger size than bacteria in parallel. Dithionite reduction and air re-exposure experiments verified that the green autofluorescence mainly originates from endogenous flavins. Bacterial autofluorescence was quantified by calibrating the fluorescence intensity of nanospheres with known FITC equivalents, and autofluorescence distribution was generated by analyzing thousands of bacterial cells in 1 min. Among the eight bacterial strains tested, it was found that bacterial autofluorescence can vary from 80 to 1400 FITC equivalents per cell, depending on the bacterial species, and a relatively large cell-to-cell variation in autofluorescence intensity was observed. Quantitative measurements of bacterial autofluorescence provide a reference for the background signals that can be expected with bacteria, which is important in guiding studies of low-level gene expression and for the detection of low-abundance biological molecules in individual bacterial cells. This paper presents the first quantification of bacterial autofluorescence in FITC equivalents.

  5. Spatial distribution of bacterial communities on volumetric and planar anodes in single-chamber air-cathode microbial fuel cells

    KAUST Repository

    Vargas, Ignacio T.

    2013-05-29

    Pyrosequencing was used to characterize bacterial communities in air-cathode microbial fuel cells across a volumetric (graphite fiber brush) and a planar (carbon cloth) anode, where different physical and chemical gradients would be expected associated with the distance between anode location and the air cathode. As expected, the stable operational voltage and the coulombic efficiency (CE) were higher for the volumetric anode than the planar anode (0.57V and CE=22% vs. 0.51V and CE=12%). The genus Geobacter was the only known exoelectrogen among the observed dominant groups, comprising 57±4% of recovered sequences for the brush and 27±5% for the carbon-cloth anode. While the bacterial communities differed between the two anode materials, results showed that Geobacter spp. and other dominant bacterial groups were homogenously distributed across both planar and volumetric anodes. This lends support to previous community analysis interpretations based on a single biofilm sampling location in these systems. © 2013 Wiley Periodicals, Inc.

  6. Single-phase Phase-locked Loop Based on Derivative Elements

    DEFF Research Database (Denmark)

    Guan, Qingxin; Zhang, Yu; Kang, Yong;

    2017-01-01

    High performance phase locked loops (PLLs) are critical for power control in grid-connected systems. This paper presents a new method of designing a PLL for single-phase systems based on derivative elements (DEs). The quadrature signal generator (QSG) is constructed by two DEs with the same main ...

  7. Potential of protoporphyrin IX and metal derivatives for single molecule fluorescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Hu Yi; Geissinger, Peter [Department of Chemistry and Biochemistry, Laboratory for Surface Studies, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211 (United States); Woehl, Joerg C., E-mail: woehl@uwm.ed [Department of Chemistry and Biochemistry, Laboratory for Surface Studies, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211 (United States)

    2011-03-15

    Metalloporphyrins are cofactors of a variety of proteins, and are often used as spectroscopic probes of the active site. Many high resolution techniques, such as single molecule spectroscopy, are based on fluorescence contrast and require the replacement of the native metalloporphyrin by a fluorescent analog. We have investigated the potential of several fluorescent analogs of heme, namely free-base protoporphyrin IX and its metal derivatives containing Zn, Sn, and Mg, for single molecule fluorescence studies by determining their room-temperature molecular absorption cross sections and fluorescence quantum yields. According to these data, free-base protoporphyrin IX and its Zn derivative, which have the highest fluorescence quantum yields, are the most suitable heme analogs for single molecule fluorescence studies. - Research highlights: Protoporphyrin IX and fluorescent metal derivatives for single molecule detection. Measurement of room temperature absorption cross sections for Q bands. Measurement of room temperature fluorescence quantum yields for Q bands. PPIX and Zn derivative have highest quantum yields for lowest-energy transition.

  8. Bacterial inactivation using atmospheric pressure single pin electrode microplasma jet with a ground ring

    Science.gov (United States)

    Kim, Sun Ja; Chung, T. H.; Bae, S. H.; Leem, S. H.

    2009-04-01

    Bacterial inactivation experiment was performed using atmospheric pressure microplasma jets driven by radio-frequency wave of 13.56 MHz and by low frequency wave of several kilohertz. With addition of a ground ring electrode, the discharge current, the optical emission intensities from reactive radicals, and the sterilization efficiency were enhanced significantly. When oxygen gas was added to helium at the flow rate of 5 SCCM, the sterilization efficiency was enhanced. From the survival curve of Escherichia coli, the primary role in the inactivation was played by reactive species with minor aid from heat, UV photons, charged particles, and electric fields.

  9. Design, synthesis and antibacterial activity of cinnamaldehyde derivatives as inhibitors of the bacterial cell division protein FtsZ.

    Science.gov (United States)

    Li, Xin; Sheng, Juzheng; Huang, Guihua; Ma, Ruixin; Yin, Fengxin; Song, Di; Zhao, Can; Ma, Shutao

    2015-06-05

    In an attempt to discover potential antibacterial agents against the increasing bacterial resistance, novel cinnamaldehyde derivatives as FtsZ inhibitors were designed, synthesized and evaluated for their antibacterial activity against nine significant pathogens using broth microdilution method, and their cell division inhibitory activity against four representative strains. In the in vitro antibacterial activity, the newly synthesized compounds generally displayed better efficacy against Staphylococcus aureus ATCC25923 than the others. In particular, compounds 3, 8 and 10 exerted superior or comparable activity to all the reference drugs. In the cell division inhibitory activity, all the compounds showed the same trend as their in vitro antibacterial activity, exhibiting better activity against S. aureus ATCC25923 than the other strains. Additionally, compounds 3, 6, 7 and 8 displayed potent cell division inhibitory activity with an MIC value of below 1 μg/mL, over 256-fold better than all the reference drugs.

  10. The Motion of a Single Molecule, the Lambda-Receptor, in the Bacterial Outer Membrane

    DEFF Research Database (Denmark)

    Oddershede, Lene; Dreyer, Jakob Kisbye; Grego, Sonia

    2002-01-01

    Using optical tweezers and single particle tracking, we have revealed the motion of a single protein, the lambda-receptor, in the outer membrane of living Escherichia coli bacteria. We genetically modified the lambda-receptor placing a biotin on an extracellular site of the receptor in vivo...

  11. Direct detection of single-nucleotide polymorphisms in bacterial DNA by SNPtrap

    DEFF Research Database (Denmark)

    Grønlund, Hugo Ahlm; Moen, Birgitte; Hoorfar, Jeffrey

    2011-01-01

    A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. Single-nucleotide extension by the minisequencing principle represents a technolo...

  12. Recombinant production of bacterial toxins and their derivatives in the methylotrophic yeast Pichia pastoris

    OpenAIRE

    Gurkan Cemal; Ellar David J

    2005-01-01

    RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Abstract The meth...

  13. Measuring bacterial adaptation dynamics at the single-cell level using a microfluidic chemostat and time-lapse fluorescence microscopy.

    Science.gov (United States)

    Long, Zhicheng; Olliver, Anne; Brambilla, Elisa; Sclavi, Bianca; Lagomarsino, Marco Cosentino; Dorfman, Kevin D

    2014-10-21

    We monitored the dynamics of cell dimensions and reporter GFP expression in individual E. coli cells growing in a microfluidic chemostat using time-lapse fluorescence microscopy. This combination of techniques allows us to study the dynamical responses of single bacterial cells to nutritional shift-down or shift-up for longer times and with more precision over the chemical environment than similar experiments performed on conventional agar pads. We observed two E. coli strains containing different promoter-reporter gene constructs and measured how both their cell dimensions and the GFP expression change after nutritional upshift and downshift. As expected, both strains have similar adaptation dynamics for cell size rearrangement. However, the strain with a ribosomal RNA promoter dependent reporter has a faster GFP production rate than the strain with a constitutive promoter reporter. As a result, the mean GFP concentration in the former strain changes rapidly with the nutritional shift, while that in the latter strain remains relatively stable. These findings characterize the present microfluidic chemostat as a versatile platform for measuring single-cell bacterial dynamics and physiological transitions.

  14. Anisotropic surface hole-transport property of triphenylamine-derivative single crystal prepared by solution method

    Science.gov (United States)

    Umeda, Minoru; Katagiri, Mitsuhiko; Shironita, Sayoko; Nagayama, Norio

    2016-12-01

    This paper reports the anisotropic hole transport at the triphenylamine-derivative single crystal surface prepared by a solution method. Triphenylamine derivatives are commonly used in a hole-transport material for organic photoconductors of laser-beam printers, in which the materials are used as an amorphous form. For developing organic photovoltaics using the photoconductor's technology, preparation of a single crystal seems to be a specific way by realizing the high mobility of an organic semiconductor. In this study, a single crystal of 4-(2,2-diphenylethenyl)-N,N-bis(4-methylphenyl)-benzenamine (TPA) was prepared and its anisotropic hole-transport property measured. First, the hole-transport property of the TPA was investigated based on its chemical structure and electrochemical redox characteristics. Next, a large-scale single crystal formation at a high rate was developed by employing a solution method based on its solubility and supersolubility curves. The grown TPA was found to be a single crystal based on the polarization micrograph observation and crystallographic analysis. For the TPA single crystal, an anisotropic surface conduction was found, which was well explained by its molecular stack structure. The measured current in the long-axis direction is one order of magnitude greater than that of amorphous TPA.

  15. Organic loading rates affect composition of soil-derived bacterial communities during continuous, fermentative biohydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Yonghua; Bruns, Mary Ann [Department of Crop and Soil Sciences, The Pennsylvania State University, University Park, PA 16802 (United States); Zhang, Husen; Salerno, Michael; Logan, Bruce E. [Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802 (United States)

    2008-11-15

    Bacterial community composition during steady-state, fermentative H{sub 2} production was compared across a range of organic loading rates (OLRs) of 0.5-19 g COD l{sup -1} h{sup -1} in a 2-l continuous flow reactor at 30 C. The varied OLRs were achieved with glucose concentrations of 2.5-10 g l{sup -1} and hydraulic retention times of 1-10 h. The synthetic wastewater feed was amended with L-cysteine and maintained at a pH of 5.5. For each run at a given glucose concentration, the reactor was inoculated with an aliquot of well-mixed agricultural topsoil that had been heat-treated to reduce numbers of vegetative cells. At OLRs less than 2 g COD l{sup -1} h{sup -1}, DNA sequences from ribosomal RNA intergenic spacer analysis profiles revealed more diverse and variable populations (Selenomonas, Enterobacter, and Clostridium spp.) than were observed above 2 g COD l{sup -1} h{sup -1} (Clostridium spp. only). An isolate, LYH1, was cultured from a reactor sample (10 g glucose l{sup -1} at a 10-h HRT) on medium containing L-cysteine. In confirming H{sub 2} production by LYH1 in liquid batch culture, lag periods for H{sub 2} production in the presence and absence of L-cysteine were 5 and 50 h, respectively. The 16S rRNA gene sequence of LYH1 indicated that the isolate was a Clostridium sp. affiliated with RNA subcluster Ic, with >99% similarity to Clostridium sp. FRB1. In fluorescent in situ hybridization tests, an oligonucleotide probe complementary to the 16S rRNA of LYH1 hybridized with 90% of cells observed at an OLR of 2 g COD h{sup -1}, compared to 26% of cells at an OLR of 0.5 g COD l{sup -1} h{sup -1}. An OLR of 2 g COD l{sup -1} h{sup -1} appeared to be a critical threshold above which clostridia were better able to outcompete Enterobacteriaceae and other organisms in the mixed soil inoculum. Our results are discussed in light of other biohydrogen studies employing pure cultures and mixed inocula. (author)

  16. A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene.

    Science.gov (United States)

    Stallforth, Pierre; Brock, Debra A; Cantley, Alexandra M; Tian, Xiangjun; Queller, David C; Strassmann, Joan E; Clardy, Jon

    2013-09-03

    Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria's host is a "farmer" clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer's spore production and depresses a nonfarmer's spore production. Genome sequence and phylogenetic analyses identify a derived point mutation in the food strain that generates a premature stop codon in a global activator (gacA), encoding the response regulator of a two-component regulatory system. Generation of a knockout mutant of this regulatory gene in the nonfood bacterial strain altered its secondary metabolite profile to match that of the food strain, and also, independently, converted it into a food source. These results suggest that a single mutation in an inedible ancestral strain that served a protective role converted it to a "domesticated" food source.

  17. A Generic Topology Derivation Method for Single-phase Converters with Active Capacitive DC-links

    DEFF Research Database (Denmark)

    Wang, Haoran; Wang, Huai; Zhu, Guorong;

    2016-01-01

    capacitive DCDC- link solutions, but important aspects of the topology assess-ment, such as the total energy storage, overall capacitive energy buffer ratio, cost, and reliability are still not available. This paper proposes a generic topology derivation method of single-phase power converters...... with capacitive DC-links, which derives all existing topologies to our best knowledge, and identify a few new topologies. A reliability-oriented design process is applied to compare the cost of different solutions with the lifetime target of 10 years and 35 years, respectively. It reveals that the most cost...

  18. Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Macek, B;

    2006-01-01

    Single-stranded DNA-binding proteins (SSBs) are required for repair, recombination and replication in all organisms. Eukaryotic SSBs are regulated by phosphorylation on serine and threonine residues. To our knowledge, phosphorylation of SSBs in bacteria has not been reported. A systematic search ...

  19. Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo

    Directory of Open Access Journals (Sweden)

    Nathan D. McDonald

    2016-04-01

    Full Text Available A major challenge facing bacterial intestinal pathogens is competition for nutrient sources with the host microbiota. Vibrio cholerae is an intestinal pathogen that causes cholera, which affects millions each year; however, our knowledge of its nutritional requirements in the intestinal milieu is limited. In this study, we demonstrated that V. cholerae can grow efficiently on intestinal mucus and its component sialic acids and that a tripartite ATP-independent periplasmic SiaPQM strain, transporter-deficient mutant NC1777, was attenuated for colonization using a streptomycin-pretreated adult mouse model. In in vivo competition assays, NC1777 was significantly outcompeted for up to 3 days postinfection. NC1777 was also significantly outcompeted in in vitro competition assays in M9 minimal medium supplemented with intestinal mucus, indicating that sialic acid uptake is essential for fitness. Phylogenetic analyses demonstrated that the ability to utilize sialic acid was distributed among 452 bacterial species from eight phyla. The majority of species belonged to four phyla, Actinobacteria (members of Actinobacillus, Corynebacterium, Mycoplasma, and Streptomyces, Bacteroidetes (mainly Bacteroides, Capnocytophaga, and Prevotella, Firmicutes (members of Streptococcus, Staphylococcus, Clostridium, and Lactobacillus, and Proteobacteria (including Escherichia, Shigella, Salmonella, Citrobacter, Haemophilus, Klebsiella, Pasteurella, Photobacterium, Vibrio, and Yersinia species, mostly commensals and/or pathogens. Overall, our data demonstrate that the ability to take up host-derived sugars and sialic acid specifically allows V. cholerae a competitive advantage in intestinal colonization and that this is a trait that is sporadic in its occurrence and phylogenetic distribution and ancestral in some genera but horizontally acquired in others.

  20. Skin-Derived C-Terminal Filaggrin-2 Fragments Are Pseudomonas aeruginosa-Directed Antimicrobials Targeting Bacterial Replication.

    Directory of Open Access Journals (Sweden)

    Britta Hansmann

    2015-09-01

    Full Text Available Soil- and waterborne bacteria such as Pseudomonas aeruginosa are constantly challenging body surfaces. Since infections of healthy skin are unexpectedly rare, we hypothesized that the outermost epidermis, the stratum corneum, and sweat glands directly control the growth of P. aeruginosa by surface-provided antimicrobials. Due to its high abundance in the upper epidermis and eccrine sweat glands, filaggrin-2 (FLG2, a water-insoluble 248 kDa S100 fused-type protein, might possess these innate effector functions. Indeed, recombinant FLG2 C-terminal protein fragments display potent antimicrobial activity against P. aeruginosa and other Pseudomonads. Moreover, upon cultivation on stratum corneum, P. aeruginosa release FLG2 C-terminus-containing FLG2 fragments from insoluble material, indicating liberation of antimicrobially active FLG2 fragments by the bacteria themselves. Analyses of the underlying antimicrobial mechanism reveal that FLG2 C-terminal fragments do not induce pore formation, as known for many other antimicrobial peptides, but membrane blebbing, suggesting an alternative mode of action. The association of the FLG2 fragment with the inner membrane of treated bacteria and its DNA-binding implicated an interference with the bacterial replication that was confirmed by in vitro and in vivo replication assays. Probably through in situ-activation by soil- and waterborne bacteria such as Pseudomonads, FLG2 interferes with the bacterial replication, terminates their growth on skin surface and thus may contributes to the skin's antimicrobial defense shield. The apparent absence of FLG2 at certain body surfaces, as in the lung or of burned skin, would explain their higher susceptibility towards Pseudomonas infections and make FLG2 C-terminal fragments and their derivatives candidates for new Pseudomonas-targeting antimicrobials.

  1. Graphene Quantum Dots Interfaced with Single Bacterial Spore for Bio-Electromechanical Devices: A Graphene Cytobot

    OpenAIRE

    Sreeprasad, T.S; Phong Nguyen; Ahmed Alshogeathri; Luke Hibbeler; Fabian Martinez; Nolan McNeil; Vikas Berry

    2015-01-01

    The nanoarchitecture and micromachinery of a cell can be leveraged to fabricate sophisticated cell-driven devices. This requires a coherent strategy to derive cell's mechanistic abilities, microconstruct, and chemical-texture towards such microtechnologies. For example, a microorganism's hydrophobic membrane encapsulating hygroscopic constituents allows it to sustainably withhold a high aquatic pressure. Further, it provides a rich surface chemistry available for nano-interfacing and a strong...

  2. The oral immunogenicity of BioProtein, a bacterial single-cell protein, is affected by its particulate nature

    DEFF Research Database (Denmark)

    Christensen, Hanne Risager; Larsen, L.C.; Frøkiær, Hanne

    2003-01-01

    The bacterial single-cell protein BioProtein (BP; Norferm Danmark, Odense, Denmark), produced by fermentation of natural gas with methanotrophic bacteria, is a potential protein source for man and animals. For human consumption, removal of the nucleic acid is necessary. Preliminary studies have...... shown that ingested BP induces a specific immune response. The objective of the present study was to characterize the type of response, its development over time and product-related causative factors. Mice were fed with diets containing 60 g nucleic acid-reduced BP/kg, 240 g nucleic acid-reduced BP...... and saliva. Ingested BP induced a steady specific mucosal and systemic immune response, characterized by a dose-dependent production of immunoglobulin and immunoglobulin A in blood and immunoglobulin A in saliva. Basic BP and nucleic acid-reduced BP induced identical responses. However, feeding mice BP...

  3. Donor-Derived Myeloid Sarcoma in Two Kidney Transplant Recipients from a Single Donor

    Directory of Open Access Journals (Sweden)

    Amudha Palanisamy

    2015-01-01

    Full Text Available We report the rare occurrence of donor-derived myeloid sarcoma in two kidney transplant patients who received organs from a single deceased donor. There was no evidence of preexisting hematologic malignancy in the donor at the time of organ recovery. Both recipients developed leukemic involvement that appeared to be limited to the transplanted organ. Fluorescence in situ hybridization (FISH and molecular genotyping analyses confirmed that the malignant cells were of donor origin in each patient. Allograft nephrectomy and immediate withdrawal of immunosuppression were performed in both cases; systemic chemotherapy was subsequently administered to one patient. Both recipients were in remission at least one year following the diagnosis of donor-derived myeloid sarcoma. These cases suggest that restoration of the immune system after withdrawal of immunosuppressive therapy and allograft nephrectomy may be sufficient to control HLA-mismatched donor-derived myeloid sarcoma without systemic involvement.

  4. A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

    Science.gov (United States)

    Xie, Sunney; Choi, Paul; Cai, Long

    2009-03-01

    By monitoring fluorescently labeled lactose permease with single-molecule sensitivity, we investigated the molecular mechanism of how an Escherichia coli cell with the lac operon switches from one phenotype to another. At intermediate inducer concentrations, a population of genetically identical cells exhibits two phenotypes: induced cells with highly fluorescent membranes and uninduced cells with a small number of membrane-bound permeases. We found that this basal-level expression results from partial dissociation of the tetrameric lactose repressor from one of its operators on looped DNA. In contrast, infrequent events of complete dissociation of the repressor from DNA result in large bursts of permease expression that trigger induction of the lac operon. Hence, a stochastic single-molecule event determines a cell's phenotype.

  5. Whole genome amplification and de novo assembly of single bacterial cells.

    Directory of Open Access Journals (Sweden)

    Sébastien Rodrigue

    Full Text Available BACKGROUND: Single-cell genome sequencing has the potential to allow the in-depth exploration of the vast genetic diversity found in uncultured microbes. We used the marine cyanobacterium Prochlorococcus as a model system for addressing important challenges facing high-throughput whole genome amplification (WGA and complete genome sequencing of individual cells. METHODOLOGY/PRINCIPAL FINDINGS: We describe a pipeline that enables single-cell WGA on hundreds of cells at a time while virtually eliminating non-target DNA from the reactions. We further developed a post-amplification normalization procedure that mitigates extreme variations in sequencing coverage associated with multiple displacement amplification (MDA, and demonstrated that the procedure increased sequencing efficiency and facilitated genome assembly. We report genome recovery as high as 99.6% with reference-guided assembly, and 95% with de novo assembly starting from a single cell. We also analyzed the impact of chimera formation during MDA on de novo assembly, and discuss strategies to minimize the presence of incorrectly joined regions in contigs. CONCLUSIONS/SIGNIFICANCE: The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.

  6. Monitoring Dynamic Protein Expression in Single Living E. Coli. Bacterial Cells by Laser Tweezers Raman Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chan, J W; Winhold, H; Corzett, M H; Ulloa, J M; Cosman, M; Balhorn, R; Huser, T

    2007-01-09

    Laser tweezers Raman spectroscopy (LTRS) is a novel, nondestructive, and label-free method that can be used to quantitatively measure changes in cellular activity in single living cells. Here, we demonstrate its use to monitor changes in a population of E. coli cells that occur during overexpression of a protein, the extracellular domain of myelin oligodendrocyte glycoprotein (MOG(1-120)) Raman spectra were acquired of individual E. coli cells suspended in solution and trapped by a single tightly focused laser beam. Overexpression of MOG(1-120) in transformed E. coli Rosetta-Gami (DE3)pLysS cells was induced by addition of isopropyl thiogalactoside (IPTG). Changes in the peak intensities of the Raman spectra from a population of cells were monitored and analyzed over a total duration of three hours. Data was also collected for concentrated purified MOG(1-120) protein in solution, and the spectra compared with that obtained for the MOG(1-120) expressing cells. Raman spectra of individual, living E. coli cells exhibit signatures due to DNA and protein molecular vibrations. Characteristic Raman markers associated with protein vibrations, such as 1257 cm{sup -1}, 1340 cm{sup -1}, 1453 cm{sup -1} and 1660 cm{sup -1}, are shown to increase as a function of time following the addition of IPTG. Comparison of these spectra and the spectra of purified MOG protein indicates that the changes are predominantly due to the induction of MOG protein expression. Protein expression was found to occur mostly within the second hour, with a 470% increase relative to the protein expressed in the first hour. A 230% relative increase between the second and third hour indicates that protein expression begins to level off within the third hour. It is demonstrated that LTRS has sufficient sensitivity for real-time, nondestructive, and quantitative monitoring of biological processes, such as protein expression, in single living cells. Such capabilities, which are not currently available in

  7. Thermal stability and refolding capability of shark derived single domain antibodies.

    Science.gov (United States)

    Liu, Jinny L; Zabetakis, Dan; Brown, Jazmine C; Anderson, George P; Goldman, Ellen R

    2014-06-01

    Single-domain antibodies (sdAb) from camelids and sharks represent the smallest immunoglobulin-based functional binding domains, and are known for their thermal stability and ability to refold after denaturation. Whereas target-binding sdAb have been derived from both immunized and naïve sharks and camelids, the stability of camelid-derived sdAb have been evaluated much more extensively. To address this disparity we characterized 20 sdAb derived from spiny dogfish shark and smooth dogfish shark in terms of their protein production, melting temperature and ability to refold after heat denaturation. Using the same expression system and protocol as we follow to produce camelid sdAb, production of the shark sdAb was quite poor, often resulting in less than a tenth of the typical yield for camelid sdAb. We measured the melting temperature of each of the sdAb. Similar to camelid sdAb, the shark-derived sdAb, showed a range of melting temperature values from 42°C to 77°C. Also similar to what has been observed in camelids, the sdAb from both shark species showed a range of ability to refold after heat denaturation. This work demonstrated that although shark sdAb can possess high melting temperatures and refolding ability, no clear advantage over sdAb derived from camelids in terms of thermostability and renaturation was obtained.

  8. Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification

    Directory of Open Access Journals (Sweden)

    David H. Keating

    2014-08-01

    Full Text Available Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass, phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH. To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(PH, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5-hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.

  9. Structure-Activity Relationships of Antimicrobial Gallic Acid Derivatives from Pomegranate and Acacia Fruit Extracts against Potato Bacterial Wilt Pathogen.

    Science.gov (United States)

    Farag, Mohamed A; Al-Mahdy, Dalia A; Salah El Dine, Riham; Fahmy, Sherifa; Yassin, Aymen; Porzel, Andrea; Brandt, Wolfgang

    2015-06-01

    Bacterial wilts of potato, tomato, pepper, and or eggplant caused by Ralstonia solanacearum are among the most serious plant diseases worldwide. In this study, the issue of developing bactericidal agents from natural sources against R. solanacearum derived from plant extracts was addressed. Extracts prepared from 25 plant species with antiseptic relevance in Egyptian folk medicine were screened for their antimicrobial properties against the potato pathogen R. solancearum by using the disc-zone inhibition assay and microtitre plate dilution method. Plants exhibiting notable antimicrobial activities against the tested pathogen include extracts from Acacia arabica and Punica granatum. Bioactivity-guided fractionation of A. arabica and P. granatum resulted in the isolation of bioactive compounds 3,5-dihydroxy-4-methoxybenzoic acid and gallic acid, in addition to epicatechin. All isolates displayed significant antimicrobial activities against R. solanacearum (MIC values 0.5-9 mg/ml), with 3,5-dihydroxy-4-methoxybenzoic acid being the most effective one with a MIC value of 0.47 mg/ml. We further performed a structure-activity relationship (SAR) study for the inhibition of R. solanacearum growth by ten natural, structurally related benzoic acids.

  10. Single-cell level based approach to investigate bacterial metabolism during batch industrial fermentation

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Eriksen, Niels T.

    Escherichia coli fermentations have been studied for decades, but most results are based on average measurements of the whole populations of cells, whilst averaged data can mask the distribution of activities at the sub-population or single-cell level. A population of genetically identical cells...... can exhibit different phenotypes under specific environmental conditions that show significant differences in physiological parameters from the population average. However, studies concerning segregation of populations into metabolically diversified subpopulations are scarce. Acetate is a product...... of Escherichia coli overflow metabolism when the bacteria are grown under aerobic conditions and glucose is present in excessive concentrations. Acetate accumulation is of the utmost importance in batch fermentation processes as it is an undesirable byproduct that negatively affects growth, physiology...

  11. In vitro high-resolution structural dynamics of single germinating bacterial spores

    Energy Technology Data Exchange (ETDEWEB)

    Plomp, M; Leighton, T; Wheeler, K; Malkin, A

    2006-11-14

    Although significant progress has been achieved in understanding the genetic and biochemical bases of the spore germination process, the structural basis for breaking the dormant spore state remains poorly understood. We have used atomic force microscopy (AFM) to probe the high-resolution structural dynamics of single Bacillus atrophaeus spores germinating under native conditions. Here we show that AFM can reveal previously unrecognized germination-induced alterations in spore coat architecture and topology as well as the disassembly of outer spore coat rodlet structures. These results and previous studies in other microorganisms suggest that the spore coat rodlets are structurally similar to amyloid fibrils. AFM analysis of the nascent surface of the emerging germ cell revealed a porous network of peptidoglycan fibers. The results are consistent with a honeycomb model structure for synthetic peptidoglycan oligomers determined by nuclear magnetic resonance. AFM is a promising experimental tool for investigating the morphogenesis of spore germination and cell wall peptidoglycan structure.

  12. In vitro high-resolution structural dynamics of single germinating bacterial spores

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence Livermore National Laboratory

    2006-12-11

    Although significant progress has been achieved in understanding the genetic and biochemical bases of the spore germination process, the structural basis for breaking the dormant spore state remains poorly understood. We have used atomic force microscopy (AFM) to probe the high-resolution structural dynamics of single Bacillus atrophaeus spores germinating under native conditions. Here we show that AFM can reveal previously unrecognized germination-induced alterations in spore coat architecture and topology as well as the disassembly of outer spore coat rodlet structures. These results and previous studies in other microorganisms suggest that the spore coat rodlets are structurally similar to amyloid fibrils. AFM analysis of the nascent surface of the emerging germ cell revealed a porous network of peptidoglycan fibers. The results are consistent with a honeycomb model structure for synthetic peptidoglycan oligomers determined by nuclear magnetic resonance. AFM is a promising experimental tool for investigating the morphogenesis of spore germination and cell wall peptidoglycan structure.

  13. Scaling laws governing stochastic growth and division of single bacterial cells

    CERN Document Server

    Iyer-Biswas, Srividya; Henry, Jonathan T; Lo, Klevin; Burov, Stanislav; Lin, Yihan; Crooks, Gavin E; Crosson, Sean; Dinner, Aaron R; Scherer, Norbert F

    2014-01-01

    Uncovering the quantitative laws that govern the growth and division of single cells remains a major challenge. Using a unique combination of technologies that yields unprecedented statistical precision, we find that the sizes of individual Caulobacter crescentus cells increase exponentially in time. We also establish that they divide upon reaching a critical multiple ($\\approx$1.8) of their initial sizes, rather than an absolute size. We show that when the temperature is varied, the growth and division timescales scale proportionally with each other over the physiological temperature range. Strikingly, the cell-size and division-time distributions can both be rescaled by their mean values such that the condition-specific distributions collapse to universal curves. We account for these observations with a minimal stochastic model that is based on an autocatalytic cycle. It predicts the scalings, as well as specific functional forms for the universal curves. Our experimental and theoretical analysis reveals a ...

  14. Timescales and Frequencies of Reversible and Irreversible Adhesion Events of Single Bacterial Cells.

    Science.gov (United States)

    Hoffman, Michelle D; Zucker, Lauren I; Brown, Pamela J B; Kysela, David T; Brun, Yves V; Jacobson, Stephen C

    2015-12-15

    In the environment, most bacteria form surface-attached cell communities called biofilms. The attachment of single cells to surfaces involves an initial reversible stage typically mediated by surface structures such as flagella and pili, followed by a permanent adhesion stage usually mediated by polysaccharide adhesives. Here, we determine the absolute and relative timescales and frequencies of reversible and irreversible adhesion of single cells of the bacterium Caulobacter crescentus to a glass surface in a microfluidic device. We used fluorescence microscopy of C. crescentus expressing green fluorescent protein to track the swimming behavior of individual cells prior to adhesion, monitor the cell at the surface, and determine whether the cell reversibly or irreversibly adhered to the surface. A fluorescently labeled lectin that binds specifically to polar polysaccharides, termed holdfast, discriminated irreversible adhesion events from reversible adhesion events where no holdfast formed. In wild-type cells, the holdfast production time for irreversible adhesion events initiated by surface contact (23 s) was 30-times faster than the holdfast production time that occurs through developmental regulation (13 min). Irreversible adhesion events in wild-type cells (3.3 events/min) are 15-times more frequent than in pilus-minus mutant cells (0.2 events/min), indicating the pili are critical structures in the transition from reversible to irreversible surface-stimulated adhesion. In reversible adhesion events, the dwell time of cells at the surface before departing was the same for wild-type cells (12 s) and pilus-minus mutant cells (13 s), suggesting the pili do not play a significant role in reversible adhesion. Moreover, reversible adhesion events in wild-type cells (6.8 events/min) occur twice as frequently as irreversible adhesion events (3.3 events/min), demonstrating that most cells contact the surface multiple times before transitioning from reversible to

  15. Scaling and automation of a high-throughput single-cell-derived tumor sphere assay chip.

    Science.gov (United States)

    Cheng, Yu-Heng; Chen, Yu-Chih; Brien, Riley; Yoon, Euisik

    2016-10-07

    Recent research suggests that cancer stem-like cells (CSCs) are the key subpopulation for tumor relapse and metastasis. Due to cancer plasticity in surface antigen and enzymatic activity markers, functional tumorsphere assays are promising alternatives for CSC identification. To reliably quantify rare CSCs (1-5%), thousands of single-cell suspension cultures are required. While microfluidics is a powerful tool in handling single cells, previous works provide limited throughput and lack automatic data analysis capability required for high-throughput studies. In this study, we present the scaling and automation of high-throughput single-cell-derived tumor sphere assay chips, facilitating the tracking of up to ∼10 000 cells on a chip with ∼76.5% capture rate. The presented cell capture scheme guarantees sampling a representative population from the bulk cells. To analyze thousands of single-cells with a variety of fluorescent intensities, a highly adaptable analysis program was developed for cell/sphere counting and size measurement. Using a Pluronic® F108 (poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol)) coating on polydimethylsiloxane (PDMS), a suspension culture environment was created to test a controversial hypothesis: whether larger or smaller cells are more stem-like defined by the capability to form single-cell-derived spheres. Different cell lines showed different correlations between sphere formation rate and initial cell size, suggesting heterogeneity in pathway regulation among breast cancer cell lines. More interestingly, by monitoring hundreds of spheres, we identified heterogeneity in sphere growth dynamics, indicating the cellular heterogeneity even within CSCs. These preliminary results highlight the power of unprecedented high-throughput and automation in CSC studies.

  16. Single daily amikacin versus cefotaxime in the short-course treatment of spontaneous bacterial peritonitis in cirrhotics

    Institute of Scientific and Technical Information of China (English)

    Tai-An Chen; Gin-Ho Lo; Kwok-Hung Lai; Whey-Jen Lin

    2005-01-01

    AIM: To compare the efficacy and safety of single daily amikacin vs. cefotaxime in the 5-d treatment of spontaneous bacterial peritonitis (SBP).METHODS: Thirty-seven cirrhotic patients with SBP,19 in group A and 18 in group B, were studied. Group A received 1 g of cefotaxime every 6 h, and group B received 500 mg of amikacin qd. Both antibiotics were administered up to 5 d and the responses were compared.RESULTS: Infection was cured in 15 of 19 patients (78.9%) treated with cefotaxime and in 11 of 18 (61.1%)treated with amikacin. Four patients of the Cefotaxime group (21.1%) and five patients of the Amikacin group (27.8%) died. Two in each group (10.5% vs 11.1%)had renal impairment during study period. One in each group (5.3% vs 5.6%) may be considered to suffer from nephrotoxicity due to increased urinary β2-microglobulin concentration.CONCLUSION: In this study, single daily doses of amikacin in the treatment of SBP in cirrhotics were not associated with an increased incidence of renal impairment or nephrotoxicity. However, a 5-d regimen of amikacin is less effective than a 5-d regimen of cefotaxime in the SBP treatment.

  17. Characterization of a Single Magnetotactic Bacterial Species from Devil's Bathtub, Mendon Ponds Park, Honeoye Falls, NY

    Science.gov (United States)

    Wagner, C.; Tarduno, J. A.; Stein, A.; Sia, E.

    2015-12-01

    Magnetotactic bacteria (MTB) belong to a lineage of prokaryotic bacteria that synthesize magnetosomes, single domain magnetic particles (typically magnetite or greigite) with an average size of 50 nanometers. MTB utilize magnetosomes through magnetotaxis, the alignment and movement along magnetic field lines to navigate towards preferred environmental conditions. MTB are sensitive to different environments and are thought to exhibit varying magnetosome morphologies, compositions, sizes, and quantities in regards to the environments which they inhabit. These characteristics allow MTB and magnetofossils (preserved magnetosomes) to be used as modern/paleoenvironmental recorders and biomarkers for environmental change(s). Devil's Bathtub (Mendon Ponds Park, Honeoye Falls, NY) is a meromictic glacial kettle pond surrounded by deciduous tree cover. Here we examine one species of MTB based on prominence of this particular morphology at this locale. Magnetotaxis and morphology of this species have been observed using light microscopy. Micrographs have also been taken using Transmission Electron Microscopy (TEM) to verify cell morphology and to determine magnetosome morphology. TEM and magnetic hysteresis measurements were done to find and test the composition of magnetosomes. In this study we also focus on DNA sequencing and characterization of this MTB, as there are few MTB species which have been DNA sequenced successfully. Data from these experiments are directly applicable to this up-and-coming area of research as it will aid in the understanding and correlation of magnetosome and magnetofossils with environmental characteristics.

  18. The Design of Simple Bacterial Microarrays: Development towards Immobilizing Single Living Bacteria on Predefined Micro-Sized Spots on Patterned Surfaces.

    Directory of Open Access Journals (Sweden)

    Nina Bjørk Arnfinnsdottir

    Full Text Available In this paper we demonstrate a procedure for preparing bacterial arrays that is fast, easy, and applicable in a standard molecular biology laboratory. Microcontact printing is used to deposit chemicals promoting bacterial adherence in predefined positions on glass surfaces coated with polymers known for their resistance to bacterial adhesion. Highly ordered arrays of immobilized bacteria were obtained using microcontact printed islands of polydopamine (PD on glass surfaces coated with the antiadhesive polymer polyethylene glycol (PEG. On such PEG-coated glass surfaces, bacteria were attached to 97 to 100% of the PD islands, 21 to 62% of which were occupied by a single bacterium. A viability test revealed that 99% of the bacteria were alive following immobilization onto patterned surfaces. Time series imaging of bacteria on such arrays revealed that the attached bacteria both divided and expressed green fluorescent protein, both of which indicates that this method of patterning of bacteria is a suitable method for single-cell analysis.

  19. Single-step production of a recyclable nanobiocatalyst for organophosphate pesticides biodegradation using functionalized bacterial magnetosomes.

    Directory of Open Access Journals (Sweden)

    Nicolas Ginet

    Full Text Available Enzymes are versatile catalysts in laboratories and on an industrial scale; improving their immobilization would be beneficial to broadening their applicability and ensuring their (reuse. Lipid-coated nano-magnets produced by magnetotactic bacteria are suitable for a universally applicable single-step method of enzyme immobilization. By genetically functionalizing the membrane surrounding these magnetite particles with a phosphohydrolase, we engineered an easy-to-purify, robust and recyclable biocatalyst to degrade ethyl-paraoxon, a commonly used pesticide. For this, we genetically fused the opd gene from Flavobacterium sp. ATCC 27551 encoding a paraoxonase to mamC, an abundant protein of the magnetosome membrane in Magnetospirillum magneticum AMB-1. The MamC protein acts as an anchor for the paraoxonase to the magnetosome surface, thus producing magnetic nanoparticles displaying phosphohydrolase activity. Magnetosomes functionalized with Opd were easily recovered from genetically modified AMB-1 cells: after cellular disruption with a French press, the magnetic nanoparticles are purified using a commercially available magnetic separation system. The catalytic properties of the immobilized Opd were measured on ethyl-paraoxon hydrolysis: they are comparable with the purified enzyme, with K(m (and k(cat values of 58 µM (and 178 s(-1 and 43 µM (and 314 s(-1 for the immobilized and purified enzyme respectively. The Opd, a metalloenzyme requiring a zinc cofactor, is thus properly matured in AMB-1. The recycling of the functionalized magnetosomes was investigated and their catalytic activity proved to be stable over repeated use for pesticide degradation. In this study, we demonstrate the easy production of functionalized magnetic nanoparticles with suitably genetically modified magnetotactic bacteria that are efficient as a reusable nanobiocatalyst for pesticides bioremediation in contaminated effluents.

  20. Use of single-molecule spectroscopy to tackle fundamental problems in biochemistry: using studies on purple bacterial antenna complexes as an example.

    Science.gov (United States)

    Cogdell, Richard J; Köhler, Jürgen

    2009-08-13

    Optical single-molecule techniques can be used in two modes to investigate fundamental questions in biochemistry, namely single-molecule detection and single-molecule spectroscopy. This review provides an overview of how single-molecule spectroscopy can be used to gain detailed information on the electronic structure of purple bacterial antenna complexes and to draw conclusions about the underlying physical structure. This information can be used to understand the energy-transfer reactions that are responsible for the earliest reactions in photosynthesis.

  1. Circulating bacterial-derived DNA fragment level is a strong predictor of cardiovascular disease in peritoneal dialysis patients.

    Directory of Open Access Journals (Sweden)

    Cheuk-Chun Szeto

    Full Text Available Circulating bacterial DNA fragment is related to systemic inflammatory state in peritoneal dialysis (PD patients. We hypothesize that plasma bacterial DNA level predicts cardiovascular events in new PD patients.We measured plasma bacterial DNA level in 191 new PD patients, who were then followed for at least a year for the development of cardiovascular event, hospitalization, and patient survival.The average age was 59.3 ± 11.8 years; plasma bacterial DNA level 34.9 ± 1.5 cycles; average follow up 23.2 ± 9.7 months. At 24 months, the event-free survival was 86.1%, 69.8%, 55.4% and 30.8% for plasma bacterial DNA level quartiles I, II, III and IV, respectively (p < 0.0001. After adjusting for confounders, plasma bacterial DNA level, baseline residual renal function and malnutrition-inflammation score were independent predictors of composite cardiovascular end-point; each doubling in plasma bacterial DNA level confers a 26.9% (95% confidence interval, 13.0 - 42.5% excess in risk. Plasma bacterial DNA also correlated with the number of hospital admission (r = -0.379, p < 0.0001 and duration of hospitalization for cardiovascular reasons (r = -0.386, p < 0.0001. Plasma bacterial DNA level did not correlate with baseline arterial pulse wave velocity (PWV, but with the change in carotid-radial PWV in one year (r = -0.238, p = 0.005.Circulating bacterial DNA fragment level is a strong predictor of cardiovascular event, need of hospitalization, as well as the progressive change in arterial stiffness in new PD patients.

  2. Vesicular Stomatitis Virus-Vectored Multi-Antigen Tuberculosis Vaccine Limits Bacterial Proliferation in Mice following a Single Intranasal Dose

    Science.gov (United States)

    Zhang, Ming; Dong, Chunsheng; Xiong, Sidong

    2017-01-01

    Tuberculosis (TB) remains a serious health problem worldwide, and an urgent need exists to improve or replace the available vaccine, Mycobacterium bovis bacillus Calmette-Guérin (BCG). Most vaccination protocols adapt two or three doses to induce long-term lasting immunity. Our previous study showed that the naked DNA encoding the triple-antigen fusion TFP846 (Rv3615c-Mtb10.4-Rv2660c) induced robust T cellular immune responses accompanying four inoculations against mycobacteria infection. However, a number of compliance issues exist in some areas lacking the appropriate medical infrastructure with multiple administrations. In this study, a novel vesicular stomatitis virus expressing TFP846 (VSV-846) was developed and the immune responses elicited by VSV-846 were evaluated. We observed that intranasal delivery of VSV-846 induced a potent antigen-specific T cell response following a single dose and VSV-846 efficiently controlled bacterial growth to levels ~10-fold lower than that observed in the mock group 6 weeks post-infection in BCG-infected mice. Importantly, mice immunized with VSV-846 provided long-term protection against mycobacteria infection compared with those receiving p846 or BCG immunization. Increased memory T cells were also observed in the spleens of VSV-846-vaccinated mice, which could be a potential mechanism associated with long-term protective immune response. These findings supported the use of VSV as an antigen delivery vector with the potential for TB vaccine development. PMID:28224119

  3. Tricyclic dihydrobenzoxazepine and tetracyclic indole derivatives can specifically target bacterial DNA ligases and can distinguish them from human DNA ligase I.

    Science.gov (United States)

    Yadav, Nisha; Khanam, Taran; Shukla, Ankita; Rai, Niyati; Hajela, Kanchan; Ramachandran, Ravishankar

    2015-05-21

    DNA ligases are critical components for DNA metabolism in all organisms. NAD(+)-dependent DNA ligases (LigA) found exclusively in bacteria and certain entomopoxviruses are drawing increasing attention as therapeutic targets as they differ in their cofactor requirement from ATP-dependent eukaryotic homologs. Due to the similarities in the cofactor binding sites of the two classes of DNA ligases, it is necessary to find determinants that can distinguish between them for the exploitation of LigA as an anti-bacterial target. In the present endeavour, we have synthesized and evaluated a series of tricyclic dihydrobenzoxazepine and tetracyclic indole derivatives for their ability to distinguish between bacterial and human DNA ligases. The in vivo inhibition assays that employed LigA deficient E. coli GR501 and S. typhimurium LT2 bacterial strains, rescued by ATP-dependent T4 DNA ligase or Mycobacterium tuberculosis NAD(+)-dependent DNA ligase (Mtb LigA), respectively, showed that the compounds can specifically inhibit bacterial LigA. The in vitro enzyme inhibition assays using purified MtbLigA, human DNA ligase I & T4 DNA ligase showed specific inhibition of MtbLigA at low micromolar range. Our results demonstrate that tricyclic dihydrobenzoxazepine and tetracyclic indole derivatives can distinguish between bacterial and human DNA ligases by ∼5-folds. In silico docking and enzyme inhibition assays identified that the compounds bind to the cofactor binding site and compete with the cofactor. Ethidium bromide displacement and gel-shift assays showed that the inhibitors do not exhibit any unwanted general interactions with the substrate DNA. These results set the stage for the detailed exploration of this compound class for development as antibacterials.

  4. Derivative Threshold Actuation for Single Phase Wormhole Detection With Reduced False Alarm Rate

    Directory of Open Access Journals (Sweden)

    K.Aathi Dharshini

    2014-06-01

    Full Text Available Communication in mobile Ad hoc networks is completed via multi-hop ways. Owing to the distributed specification and restricted resource of nodes, MANET is a lot prone to wormhole attacks i.e. wormhole attacks place severe threats to each Ad hoc routing protocol and a few security enhancements. Thus, so as to discover wormholes, totally different techniques are in use. In all those techniques fixation of threshold is merely by trial & error methodology or by random manner. Conjointly wormhole detection is in twin part by putting the nodes that is higher than the edge in a suspicious set, however predicting the node as a wormhole by using some other algorithms. Our aim in this paper is to deduce the traffic threshold level by derivational approach for identifying wormholes in a very single phase in relay network having dissimilar characteristics.

  5. Atomic force microscope observation of branching in single transcript molecules derived from human cardiac muscle

    Energy Technology Data Exchange (ETDEWEB)

    Reed, Jason; Hsueh, Carlin; Gimzewski, James K [Department of Chemistry and Biochemistry, UCLA, 607 Charles Young Drive East, Los Angeles, CA 90095 (United States); Mishra, Bud [Courant Institute of Mathematical Sciences, NYU, 251 Mercer Street, New York, NY 10012 (United States)], E-mail: jreed@chem.ucla.edu, E-mail: gim@chem.ucla.edu

    2008-09-24

    We have used an atomic force microscope to examine a clinically derived sample of single-molecule gene transcripts, in the form of double-stranded cDNA, (c: complementary) obtained from human cardiac muscle without the use of polymerase chain reaction (PCR) amplification. We observed a log-normal distribution of transcript sizes, with most molecules being in the range of 0.4-7.0 kilobase pairs (kb) or 130-2300 nm in contour length, in accordance with the expected distribution of mRNA (m: messenger) sizes in mammalian cells. We observed novel branching structures not previously known to exist in cDNA, and which could have profound negative effects on traditional analysis of cDNA samples through cloning, PCR and DNA sequencing.

  6. Single stage to orbit mass budgets derived from propellant density and specific impulse

    Energy Technology Data Exchange (ETDEWEB)

    Whitehead, J.C.

    1996-06-06

    The trade between specific impulse (Isp) and density is examined in view of Single Stage To Orbit (SSTO) requirements. Mass allocations for vehicle hardware are derived from these two properties, for several propellant combinations and a dual-fuel case. This comparative analysis, based on flight-proven hardware, indicates that the higher density of several alternative propellants compensates for reduced Isp, when compared with cryogenic oxygen and hydrogen. Approximately half the orbiting mass of a rocket- propelled SSTO vehicle must be allocated to propulsion hardware and residuals. Using hydrogen as the only fuel requires a slightly greater fraction of orbiting mass for propulsion, because hydrogen engines and tanks are heavier than those for denser fuels. The advantage of burning both a dense fuel and hydrogen in succession depends strongly on tripropellant engine weight. The implications of the calculations for SSTO vehicle design are discussed, especially with regard to the necessity to minimize non-tankage structure.

  7. Hail statistics for Germany derived from single-polarization radar data

    Science.gov (United States)

    Puskeiler, Marc; Kunz, Michael; Schmidberger, Manuel

    2016-09-01

    Despite the considerable damage potential related to severe hailstorms, knowledge about the local hail probability in Germany is very limited. Constructing a reliable hail probability map is challenging due largely to the lack of direct hail observations. In our study, we suggest a reasonable method by which to estimate hail signals from 3D radar reflectivity measured by conventional single-polarization radars between 2005 and 2011. Evaluating the radar-derived hail days with loss data from a building and an agricultural insurance company confirmed the reliability of the method and the results as expressed, for example, by a Heidke Skill Score HSS of 0.7. Overall, radar-derived hail days demonstrate very high spatial variability, which reflects the local-scale nature of deep moist convection. Nonetheless, systematic patterns related to climatic conditions and orography can also be observed. On the large scale, the number of hail days substantially increases from north to south, which may plausibly be explained by the higher thermal instability in the south. At regional and local scales, several hot spots with elevated hail frequency can be identified, in most cases downstream of the mountains. Several other characteristics including convective energy related to the events identified, differences in track lengths, and seasonal cycles are discussed.

  8. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

    Science.gov (United States)

    Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

    2015-09-01

    A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures.

  9. Anti-bacterial and Anti-biofilm Evaluation of Thiazolopyrimidinone Derivatives Targeting the Histidine Kinase YycG Protein of Staphylococcus epidermidis

    Science.gov (United States)

    Lv, Zhihui; Zhao, Dan; Chang, Jun; Liu, Huayong; Wang, Xiaofei; Zheng, Jinxin; Huang, Renzheng; Lin, Zhiwei; Shang, Yongpeng; Ye, Lina; Wu, Yang; Han, Shiqing; Qu, Di

    2017-01-01

    Staphylococcus epidermidis is one of the most important opportunistic pathogens in nosocomial infections. The main pathogenicity associated with S. epidermidis involves the formation of biofilms on implanted medical devices, biofilms dramatically decrease the efficacy of conventional antibiotics and the host immune system. This emphasizes the urgent need for designing novel anti-staphylococcal biofilm agents. Based on the findings that compound 5, targeting the histidine kinase domain of S. epidermidis YycG, possessed bactericidal activity against staphylococci, 39 derivatives of compound 5 with intact thiazolopyrimidinone core structures were newly designed, 7 derivatives were further screened to explore their anti-bacterial and anti-biofilm activities. The seven derivatives strongly inhibited the growth of S. epidermidis and Staphylococcus aureus in the minimal inhibitory concentration range of 1.56–6.25 μM. All the derivatives reduced the proportion of viable cells in mature biofilms. They all displayed low cytotoxicity on mammalian cells and were not hemolytic to human erythrocytes. The biofilm inhibition activities of four derivatives (H5-32, H5-33, H5-34, and H5-35) were further investigated under shearing forces, they all led to significant decreases in the biofilm formation of S. epidermidis. These results were suggestive that the seven derivatives of compound 5 have the potential to be developed into agents for eradicating biofilm-associated infections.

  10. Plasma gasification of refuse derived fuel in a single-stage system using different gasifying agents.

    Science.gov (United States)

    Agon, N; Hrabovský, M; Chumak, O; Hlína, M; Kopecký, V; Masláni, A; Bosmans, A; Helsen, L; Skoblja, S; Van Oost, G; Vierendeels, J

    2016-01-01

    The renewable evolution in the energy industry and the depletion of natural resources are putting pressure on the waste industry to shift towards flexible treatment technologies with efficient materials and/or energy recovery. In this context, a thermochemical conversion method of recent interest is plasma gasification, which is capable of producing syngas from a wide variety of waste streams. The produced syngas can be valorized for both energetic (heat and/or electricity) and chemical (ammonia, hydrogen or liquid hydrocarbons) end-purposes. This paper evaluates the performance of experiments on a single-stage plasma gasification system for the treatment of refuse-derived fuel (RDF) from excavated waste. A comparative analysis of the syngas characteristics and process yields was done for seven cases with different types of gasifying agents (CO2+O2, H2O, CO2+H2O and O2+H2O). The syngas compositions were compared to the thermodynamic equilibrium compositions and the performance of the single-stage plasma gasification of RDF was compared to that of similar experiments with biomass and to the performance of a two-stage plasma gasification process with RDF. The temperature range of the experiment was from 1400 to 1600 K and for all cases, a medium calorific value syngas was produced with lower heating values up to 10.9 MJ/Nm(3), low levels of tar, high levels of CO and H2 and which composition was in good agreement to the equilibrium composition. The carbon conversion efficiency ranged from 80% to 100% and maximum cold gas efficiency and mechanical gasification efficiency of respectively 56% and 95%, were registered. Overall, the treatment of RDF proved to be less performant than that of biomass in the same system. Compared to a two-stage plasma gasification system, the produced syngas from the single-stage reactor showed more favourable characteristics, while the recovery of the solid residue as a vitrified slag is an advantage of the two-stage set-up.

  11. A mathematical model of T lymphocyte calcium dynamics derived from single transmembrane protein properties

    Directory of Open Access Journals (Sweden)

    Christine Dorothee Schmeitz

    2013-09-01

    Full Text Available Fate decision processes of T lymphocytes are crucial for health and disease. Whether a T lymphocyte is activated, divides, gets anergic or initiates apoptosis depends on extracellular triggers and intracellular signalling. Free cytosolic calcium dynamics plays an important role in this context. The relative contributions of store-derived calcium entry and calcium entry from extracellular space to T lymphocyte activation are still a matter of debate. Here we develop a quantitative mathematical model of T lymphocyte calcium dynamics in order to establish a tool which allows to disentangle cause-effect relationships between ion fluxes and observed calcium time courses. The model is based on single transmembrane protein characteristics which have been determined in independent experiments. This reduces the number of unknown parameters in the model to a minimum and ensures the predictive power of the model. Simulation results are subsequently used for an analysis of whole cell calcium dynamics measured under various experimental conditions. The model accounts for a variety of these conditions, which supports the suitability of the modelling approach. The simulation results suggest a model in which calcium dynamics dominantly relies on the opening of channels in calcium stores while calcium entry through calcium-release activated channels (CRAC is more associated with the maintenance of the T lymphocyte calcium levels and prevents the cell from calcium depletion. Our findings indicate that CRAC guarantees a long-term stable calcium level which is required for cell survival and sustained calcium enhancement.

  12. A single molecule study of a fluorescently labeled telomestatin derivative and G-quadruplex interactions

    Science.gov (United States)

    Maleki, Parastoo; Ma, Yue; Iida, Keisuke; Nagasawa, Kazuo; Balci, Hamza

    2017-01-01

    The potential use of G-quadruplex (GQ) stabilizing small molecules as anti-cancer drugs has created a flurry of activity on various aspects of these molecules. Telomestatin and oxazole telomestatin derivatives (OTD) are some of the most prominent of such molecules, yet the underlying dynamics of their interactions with GQ and the extent of heterogeneities in these interactions are not known. We performed single molecule measurements to study binding kinetics, rotational freedom, and dwell time distributions of a Cy5-labeled OTD (L1Cy5–7OTD) as it interacted with several different GQ structures. Our measurements show that L1Cy5–7OTD dwells on more stable GQ for longer times and binds to such GQ with higher frequency. The dwell times showed a broad distribution, but were longer than a minute for a significant fraction of molecules (characteristic dwell time τ = 192 ± 15 s and τ = 98 ± 15 s for the more and less stable GQ, respectively). In addition, L1Cy5–7OTD might be able to bind to GQ in at least two different primary orientations and occasionally transition between these orientations. The dwell time in one of these orientations was significantly longer than that in the other one, suggesting different stabilities for different binding orientations. PMID:27899628

  13. Efficient dispersion and exfoliation of single-walled nanotubes in 3-aminopropyltriethoxysilane and its derivatives.

    Science.gov (United States)

    Sun, Zhenyu; Nicolosi, Valeria; Bergin, Shane D; Coleman, Jonathan N

    2008-12-03

    A novel amine solvent, 3-aminopropyltriethoxysilane, has been used to disperse single-walled carbon nanotubes. Well-dispersed nanotubes in the form of small bundles coexist in the liquid phase with large nanotube aggregates. A mild centrifugation step can be used to remove the aggregates. By measurement of the absorbance before and after centrifugation as a function of concentration, the fraction of the dispersed nanotube phase can be estimated. As measured by atomic force microscopy, the mean bundle diameter tends to decrease with decreasing concentration and levels off below a concentration of ∼0.012 mg ml(-1). Individual nanotubes are always observed, whose population increases with decreasing concentration before saturating at a concentration of ∼0.012 mg ml(-1). The absolute number of individual nanotubes per volume of dispersion initially increases with decreasing concentration, and then reaches a peak at a concentration of ∼0.024 mg ml(-1). Further experimental results showed that nanotubes can also be effectively dispersed in a series of aminoalkoxylsilane derivatives. In the light of these findings, possible solvent-nanotube interaction mechanisms are discussed.

  14. The effect of polyhexamethylene guanidine hydrochloride (PHMG) derivatives introduced into polylactide (PLA) on the activity of bacterial enzymes.

    Science.gov (United States)

    Walczak, Maciej; Richert, Agnieszka; Burkowska-But, Aleksandra

    2014-11-01

    The present study was aimed at investigating bactericidal properties of polylactide (PLA) films containing three different polyhexamethylene guanidine hydrochloride (PHMG) derivatives and effect of the derivatives on extracellular hydrolytic enzymes and intracellular dehydrogenases. All PHMG derivatives had a slightly stronger bactericidal effect on Staphylococcus aureus than on E. coli but only PHMG granular polyethylene wax (at the concentration of at least 0.6 %) has a bactericidal effect. PHMG derivatives introduced into PLA affected the activity of microbial hydrolases to a small extent. This means that the introduction of PHMG derivatives into PLA will not reduce its enzymatic biodegradation significantly. On the other hand, PHMG derivatives introduced into PLA strongly affected dehydrogenases activity in S. aureus than in E. coli.

  15. Chlamydia trachomatis intercepts Golgi-derived sphingolipids through a Rab14-mediated transport required for bacterial development and replication.

    Directory of Open Access Journals (Sweden)

    Anahí Capmany

    Full Text Available Chlamydia trachomatis are obligate intracellular bacteria that survive and replicate in a bacterial-modified phagosome called inclusion. As other intracellular parasites, these bacteria subvert the phagocytic pathway to avoid degradation in phagolysosomes and exploit trafficking pathways to acquire both energy and nutrients essential for their survival. Rabs are host proteins that control intracellular vesicular trafficking. Rab14, a Golgi-related Rab, controls Golgi to endosomes transport. Since Chlamydia establish a close relationship with the Golgi apparatus, the recruitment and participation of Rab14 on inclusion development and bacteria growth were analyzed. Time course analysis revealed that Rab14 associated with inclusions by 10 h post infection and was maintained throughout the entire developmental cycle. The recruitment was bacterial protein synthesis-dependent but independent of microtubules and Golgi integrity. Overexpression of Rab14 dominant negative mutants delayed inclusion enlargement, and impaired bacteria replication as determined by IFU. Silencing of Rab14 by siRNA also decreased bacteria multiplication and infectivity. By electron microscopy, aberrant bacteria were observed in cells overexpressing the cytosolic negative Rab14 mutant. Our results showed that Rab14 facilitates the delivery of sphingolipids required for bacterial development and replication from the Golgi to chlamydial inclusions. Novel anti-chlamydial therapies could be developed based on the knowledge of how bacteria subvert host vesicular transport events through Rabs manipulation.

  16. Synthesis and characterization of cellulose derivatives obtained from bacterial cellulose; Sintese e caracterizacao de derivados celulosicos obtidos a partir da celulose bacteriana

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Rafael L. de; Barud, Hernane; Ribeiro, Sidney J.L.; Messaddeq, Younes, E-mail: rafael.tu@gmail.com [Instituto de Quimica - Universidade Estadual Paulista Julio de Mesquita Filho - UNESP, Araraquara, SP (Brazil)

    2011-07-01

    The chemical modification of cellulose leads to production of derivatives with different properties from those observed for the original cellulose, for example, increased solubility in more traditional solvents. In this work we synthesized four derivatives of cellulose: microcrystalline cellulose, cellulose acetate, methylcellulose and carboxymethylcellulose using bacterial cellulose as a source. These were characterized in terms of chemical and structural changes by examining the degree of substitution (DS), infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy - NMR {sup 13}C. The molecular weight and degree of polymerization were evaluated by viscometry. The characterization of the morphology of materials and thermal properties were performed with the techniques of X-ray diffraction, electron microscopy images, differential scanning calorimetry (DSC) and thermogravimetric analysis. (author)

  17. Screening of bacterial strains capable of converting biodiesel-derived raw glycerol into 1,3-propanediol, 2,3-butanediol and ethanol

    Energy Technology Data Exchange (ETDEWEB)

    Metsoviti, Maria; Paramithiotis, Spiros; Drosinos, Eleftherios H.; Galiotou-Panayotou, Maria; Nychas, George-John E.; Papanikolaou, Seraphim [Department of Food Science and Technology, Agricultural University of Athens, Athens (Greece); Zeng, An-Ping [Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology (TUHH), Hamburg (Germany)

    2012-02-15

    The ability of bacterial strains to assimilate glycerol derived from biodiesel facilities to produce metabolic compounds of importance for the food, textile and chemical industry, such as 1,3-propanediol (PD), 2,3-butanediol (BD) and ethanol (EtOH), was assessed. The screening of 84 bacterial strains was performed using glycerol as carbon source. After initial trials, 12 strains were identified capable of consuming raw glycerol under anaerobic conditions, whereas 5 strains consumed glycerol under aerobiosis. A plethora of metabolic compounds was synthesized; in anaerobic batch-bioreactor cultures PD in quantities up to 11.3 g/L was produced by Clostridium butyricum NRRL B-23495, while the respective value was 10.1 g/L for a newly isolated Citrobacter freundii. Adaptation of Cl. butyricum at higher initial glycerol concentration resulted in a PD{sub max} concentration of {proportional_to}32 g/L. BD was produced by a new Enterobacter aerogenes isolate in shake-flask experiments, under fully aerobic conditions, with a maximum concentration of {proportional_to}22 g/L which was achieved at an initial glycerol quantity of 55 g/L. A new Klebsiella oxytoca isolate converted waste glycerol into mixtures of PD, BD and EtOH at various ratios. Finally, another new C. freundii isolate converted waste glycerol into EtOH in anaerobic batch-bioreactor cultures with constant pH, achieving a final EtOH concentration of 14.5 g/L, a conversion yield of 0.45 g/g and a volumetric productivity of {proportional_to}0.7 g/L/h. As a conclusion, the current study confirmed the utilization of biodiesel-derived raw glycerol as an appropriate substrate for the production of PD, BD and EtOH by several newly isolated bacterial strains under different experimental conditions. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Dynamics of bacterial communities during the ripening process of different Croatian cheese types derived from raw ewe's milk cheeses.

    Science.gov (United States)

    Fuka, Mirna Mrkonjić; Wallisch, Stefanie; Engel, Marion; Welzl, Gerhard; Havranek, Jasmina; Schloter, Michael

    2013-01-01

    Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a

  19. Dynamics of bacterial communities during the ripening process of different Croatian cheese types derived from raw ewe's milk cheeses.

    Directory of Open Access Journals (Sweden)

    Mirna Mrkonjić Fuka

    Full Text Available Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB, mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all

  20. CD8(+) T cells specific to a single Yersinia pseudotuberculosis epitope restrict bacterial replication in the liver but fail to provide sterilizing immunity.

    Science.gov (United States)

    Shen, Haiqian; Gonzalez-Juarbe, Norberto; Blanchette, Krystle; Crimmins, Gregory; Bergman, Molly A; Isberg, Ralph R; Orihuela, Carlos J; Dube, Peter H

    2016-09-01

    CD8(+) T cells use contact-dependent cytolysis of target cells to protect the host against intracellular pathogens. We have previously shown that CD8(+) T cells and perforin are required to protect against the extracellular pathogen Yersinia pseudotuberculosis. Here we establish an experimental system where CD8(+) T cells specific to a single model antigen are the only memory response present at time of challenge. Using mice immunized with a vaccine strain of Listeria monocytogenes that expresses secreted ovalbumin (Lm-OVA), we show that OVA-specific CD8(+) T cells are generated and provide limited protection against challenge with virulent OVA(+)Y. pseudotuberculosis. Perforin expression by OVA-specific CD8(+) T cells was required, as Lm-OVA-immunized perforin-deficient mice showed higher bacterial burden as compared to Lm-OVA-immunized perforin-sufficient mice. Surprisingly, antigen-specific T cell protection waned over time, as Lm-OVA-immune mice eventually succumbed to Yersinia infection. Kinetic analysis of infection in mice with and without OVA-specific CD8(+) T cells revealed that bacterial numbers increased sharply in OVA-naïve mice until death, while OVA-immune mice held bacterial burden to a lower level throughout the duration of illness until death. Clonal analysis of bacterial populations in OVA-naïve and OVA-immune mice at distinct time points revealed equivalent and severe bottle-neck effects for bacteria in both sets of mice immediately after intravenous challenge, demonstrating a dominant role for other aspects of the immune system regardless of CD8(+) T cell status. These studies indicate that CD8(+) T cells against a single antigen can restrict Y. pseudotuberculosis colonization in a perforin-dependent manner, but ultimately are insufficient in their ability to provide sterilizing immunity and protect against death.

  1. The role of brain-derived neurotrophic factor and its single nucleotide polymorphisms in stroke patients.

    Science.gov (United States)

    Kotlęga, Dariusz; Peda, Barbara; Zembroń-Łacny, Agnieszka; Gołąb-Janowska, Monika; Nowacki, Przemysław

    2017-03-06

    Stroke is the main cause of motoric and neuropsychological disability in adults. Recent advances in research into the role of the brain-derived neurotrophic factor in neuroplasticity, neuroprotection and neurogenesis might provide important information for the development of new poststroke-rehabilitation strategies. It plays a role as a mediator in motor learning and rehabilitation after stroke. Concentrations of BDNF are lower in acute ischemic-stroke patients compared to controls. Lower levels of BDNF are correlated with an increased risk of stroke, worse functional outcomes and higher mortality. BDNF signalling is dependent on the genetic variation which could affect an individual's response to recovery after stroke. Several single nucleotide polymorphisms of the BDNF gene have been studied with regard to stroke patients, but most papers analyse the rs6265 which results in a change from valine to methionine in the precursor protein. Subsequently a reduction in BDNF activity is observed. There are studies indicating the role of this polymorphism in brain plasticity, functional and morphological changes in the brain. It may affect the risk of ischemic stroke, post-stroke outcomes and the efficacy of the rehabilitation process within physical exercise and transcranial magnetic stimulation. There is a consistent trend of Met alleles' being connected with worse outcomes and prognoses after stroke. However, there is no satisfactory data confirming the importance of Met allele in stroke epidemiology and the post-stroke rehabilitation process. We present the current data on the role of BDNF and polymorphisms of the BDNF gene in stroke patients, concentrating on human studies.

  2. Facile synthesis, single crystal analysis, and computational studies of sulfanilamide derivatives

    Science.gov (United States)

    Tahir, Muhammad Nawaz; Khalid, Muhammad; Islam, Ayesha; Ali Mashhadi, Syed Muddassir; Braga, Ataualpa A. C.

    2017-01-01

    Antibacterial resistance is a worldwide problem. Sulfanilamide is widely used antibacterial. For the first time, we report here a simple method for the derivative synthesis of the title drugs, single crystal XRD and density functional theory (DFT) studies. The optimized molecular structure, natural bond orbital (NBO), frontier molecular orbitals (FMOs) molecular electrostatic potential studies (MEP) and Mulliken population analysis (MPA) have been performed using M06-2X/6-31G(d, p). The FT-IR spectra and thermodynamic parameters were calculated at M06-2X/6-311 + G(2d,p) and B3LYP/6-31G(d, p) levels respectively, while, the UV-Vis analysis was performed using TD-DFT/B3LYP/6-31G(d, p) method. The experimental FT-IR spectra of both compounds were also carried out to reconfirm sbnd H⋯Osbnd hydrogen bonds. The DFT optimized parameters exhibiting good agreement with the experimental data. NBO analysis explored the hyper conjugative interaction and stability of title crystals, especially, reconfirmed the existence of sbnd H⋯Osbnd hydrogen bonds between the dimers. The FT-IR, thermodynamic parameters, MEP and MPA also revealed the hydrogen bonding detail is harmonious to XRD data. As a matter of the fact, the hydrogen bonding is a significant parameter for the understanding and design of molecular crystals, subsequently; it can also play a vital role in the supramolecular chemistry. Moreover, the global reactivity descriptors suggest that title compounds might be bioactive.

  3. Integrated Analysis of Contractile Kinetics, Force Generation, and Electrical Activity in Single Human Stem Cell-Derived Cardiomyocytes

    NARCIS (Netherlands)

    Kijlstra, Jan David; Hu, Dongjian; Mittal, Nikhil; Kausel, Eduardo; van der Meer, Peter; Garakani, Arman; Domian, Ibrahim J.

    2015-01-01

    The quantitative analysis of cardiomyocyte function is essential for stem cell-based approaches for the in vitro study of human cardiac physiology and pathophysiology. We present a method to comprehensively assess the function of single human pluripotent stem cell-derived cardiomyocyte (hPSC-CMs) th

  4. Different Types of Diatom-Derived Extracellular Polymeric Substances Drive Changes in Heterotrophic Bacterial Communities from Intertidal Sediments

    Science.gov (United States)

    Bohórquez, Julio; McGenity, Terry J.; Papaspyrou, Sokratis; García-Robledo, Emilio; Corzo, Alfonso; Underwood, Graham J. C.

    2017-01-01

    Intertidal areas support extensive diatom-rich biofilms. Such microphytobenthic (MPB) diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides, glycoproteins and other biopolymers, which represent a substantial carbon pool. However, degradation rates of different EPS components, and how they shape heterotrophic communities in sediments, are not well understood. An aerobic mudflat-sediment slurry experiment was performed in the dark with two different EPS carbon sources from a diatom-dominated biofilm: colloidal EPS (cEPS) and the more complex hot-bicarbonate-extracted EPS. Degradation rate constants determined over 9 days for three sediment fractions [dissolved organic carbon (DOC), total carbohydrates (TCHO), and (cEPS)] were generally higher in the colloidal-EPS slurries (0.105–0.123 d−1) compared with the hot-bicarbonate-extracted-EPS slurries (0.060–0.096 d−1). Addition of hot-bicarbonate-EPS resulted in large increases in dissolved nitrogen and phosphorous by the end of the experiment, indicating that the more complex EPS is an important source of regenerated inorganic nutrients. Microbial biomass increased ~4–6-fold over 9 days, and pyrosequencing of bacterial 16S rRNA genes revealed that the addition of both types of EPS greatly altered the bacterial community composition (from 0 to 9 days) compared to a control with no added EPS. Bacteroidetes (especially Tenacibaculum) and Verrucomicrobia increased significantly in relative abundance in both the hot-bicarbonate-EPS and colloidal-EPS treatments. These differential effects of EPS fractions on carbon-loss rates, nutrient regeneration and microbial community assembly improve our understanding of coastal-sediment carbon cycling and demonstrate the importance of diverse microbiota in processing this abundant pool of organic carbon. PMID:28289404

  5. Object-oriented identification of forested landslides with derivatives of single pulse LiDAR data

    NARCIS (Netherlands)

    Eeckhaut, van den M.; Kerle, N.; Poesen, J.; Hervas, J.

    2012-01-01

    In contrast to the many studies that use expert-based analysis of LiDAR derivatives for landslide mapping in forested terrain, only few studies have attempted to develop (semi-)automatic methods for extracting landslides from LiDAR derivatives. While all these studies are pixel-based, it has not yet

  6. Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance.

    Science.gov (United States)

    Fatehi, Shervin; Alguire, Ethan; Shao, Yihan; Subotnik, Joseph E

    2011-12-21

    We present a method for analytically calculating the derivative couplings between a pair of configuration-interaction-singles (CIS) excited states obtained in an atom-centered basis. Our theory is exact and has been derived using two completely independent approaches: one inspired by the Hellmann-Feynman theorem and the other following from direct differentiation. (The former is new, while the latter is in the spirit of existing approaches in the literature.) Our expression for the derivative couplings incorporates all Pulay effects associated with the use of an atom-centered basis, and the computational cost is minimal, roughly comparable to that of a single CIS energy gradient. We have validated our method against CIS finite-difference results and have applied it to the lowest lying excited states of naphthalene; we find that naphthalene derivative couplings include Pulay contributions sufficient to have a qualitative effect. Going beyond standard problems in analytic gradient theory, we have also constructed a correction, based on perturbative electron-translation factors, for including electronic momentum and eliminating spurious components of the derivative couplings that break translational symmetry. This correction is general and can be applied to any level of electronic structure theory.

  7. Abundance and single-cell activity of heterotrophic bacterial groups in the western Arctic Ocean in summer and winter.

    Science.gov (United States)

    Nikrad, Mrinalini P; Cottrell, M T; Kirchman, D L

    2012-04-01

    Environmental conditions in the western Arctic Ocean range from constant light and nutrient depletion in summer to complete darkness and sea ice cover in winter. This seasonal environmental variation is likely to have an effect on the use of dissolved organic matter (DOM) by heterotrophic bacteria in surface water. However, this effect is not well studied and we know little about the activity of specific bacterial clades in the surface oceans. The use of DOM by three bacterial subgroups in both winter and summer was examined by microautoradiography combined with fluorescence in situ hybridization. We found selective use of substrates by these groups, although the abundances of Ant4D3 (Antarctic Gammaproteobacteria), Polaribacter (Bacteroidetes), and SAR11 (Alphaproteobacteria) were not different between summer and winter in the Beaufort and Chukchi Seas. The number of cells taking up glucose within all three bacterial groups decreased significantly from summer to winter, while the percentage of cells using leucine did not show a clear pattern between seasons. The uptake of the amino acid mix increased substantially from summer to winter by the Ant4D3 group, although such a large increase in uptake was not seen for the other two groups. Use of glucose by bacteria, but not use of leucine or the amino acid mix, related strongly to inorganic nutrients, chlorophyll a, and other environmental factors. Our results suggest a switch in use of dissolved organic substrates from summer to winter and that the three phylogenetic subgroups examined fill different niches in DOM use in the two seasons.

  8. Hot topic: Bovine milk samples yielding negative or nonspecific results in bacterial culturing--the possible role of PCR-single strand conformation polymorphism in mastitis diagnosis.

    Science.gov (United States)

    Schwaiger, K; Wimmer, M; Huber-Schlenstedt, R; Fehlings, K; Hölzel, C S; Bauer, J

    2012-01-01

    A large proportion of mastitis milk samples yield negative or nonspecific results (i.e., no mastitis pathogen can be identified) in bacterial culturing. Therefore, the culture-independent PCR-single strand conformation polymorphism method was applied to the investigation of bovine mastitis milk samples. In addition to the known mastitis pathogens, the method was suitable for the detection of fastidious bacteria such as Mycoplasma spp., which are often missed by conventional culturing methods. The detection of Helcococcus ovis in 4 samples might indicate an involvement of this species in pathogenesis of bovine mastitis. In conclusion, PCR-single-strand conformation polymorphism is a promising tool for gaining new insights into the bacteriological etiology of mastitis.

  9. Inhibition of bacterial adhesion and salmonella infection in BALB/c mice by sialyloligosaccharides and their derivatives from chicken egg yolk.

    Science.gov (United States)

    Sugita-Konishi, Yoshiko; Sakanaka, Senji; Sasaki, Ken; Juneja, Lekh Raj; Noda, Tetsuji; Amano, Fumio

    2002-06-05

    The effects of an egg-yolk-derived sialyloligosaccharide (YDS), asialo-YDS, and a sialylglycopeptide of YDS (SGP) on bacterial adhesion to intestinal epithelial cells and on Salmonella infection in BALB/c mice were examined. YDS, its derivative asialo-YDS, and SGP strongly inhibited the binding of Salmonella enteritidis but not E. coli K-88 to a human epithelial cell line, Caco-2. In a Salmonella infection experiment using BALB/c mice, oral administration of these reagents effectively prevented the bacteria from proliferating in spleen, as well as preventing lethality. An experiment using radioactive SGP orally administered to mice revealed that the compound was absorbed from the intestine into blood and eliminated via urine within 8 h. However, these reagents did not influence the production of TNF-alpha or NO. in culture macrophages. The results suggest that they inhibit Salmonella infection not by activating macrophages but by inhibiting the entry of bacteria through the gut, suggesting that YDS and its derivatives are useful for preventing Salmonella infection when ingested continuously.

  10. In vitro antibacterial activity of sphaeropsidins and chemical derivatives toward Xanthomonas oryzae pv. oryzae, the causal agent of rice bacterial blight.

    Science.gov (United States)

    Evidente, Antonio; Venturi, Vittorio; Masi, Marco; Degrassi, Giuliano; Cimmino, Alessio; Maddau, Lucia; Andolfi, Anna

    2011-12-27

    Sphaeropsidin A, the main phytotoxin produced by Diplodia cupressi, as well as the two natural analogues sphaeropsidins B and C and 14 derivatives obtained by chemical modifications were assayed for antibacterial activity against Xanthomonas oryzae pv. oryzae, Pseudomonas fuscovaginae, and Burkholderia glumae, the causal agents of severe bacterial rice diseases. The results showed a strong and specific activity of sphaeropsidin A against X. oryzae pv. oryzae, while no activity was observed against the other two pathogens. The results of structure-activity relationship studies showed that structural features important to impart this antibacterial activity are the presence of the C-7 carbonyl group and the hemiketalic lactone functionality. The C-13 vinyl group, the double bond of ring C, and/or the tertiary C-9 hydroxy group, as well as the pimarane arrangement of the tricylic carbon skeleton, were also important for the antibacterial activity. These findings may be useful in designing novel compounds for practical applications in agriculture.

  11. Integrated Analysis of Contractile Kinetics, Force Generation, and Electrical Activity in Single Human Stem Cell-Derived Cardiomyocytes

    OpenAIRE

    Jan David Kijlstra; Dongjian Hu; Nikhil Mittal; Eduardo Kausel; Peter van der Meer; Arman Garakani; Ibrahim J. Domian

    2015-01-01

    Summary The quantitative analysis of cardiomyocyte function is essential for stem cell-based approaches for the in vitro study of human cardiac physiology and pathophysiology. We present a method to comprehensively assess the function of single human pluripotent stem cell-derived cardiomyocyte (hPSC-CMs) through simultaneous quantitative analysis of contraction kinetics, force generation, and electrical activity. We demonstrate that statistical analysis of movies of contracting hPSC-CMs can b...

  12. Namibia's transition from whole blood-derived pooled platelets to single-donor apheresis platelet collections

    NARCIS (Netherlands)

    Pitman, John P.; Basavaraju, Sridhar V.; Shiraishi, Ray W.; Wilkinson, Robert; von Finckenstein, Bjorn; Lowrance, David W.; Marfin, Anthony A.; Postma, Maarten; Mataranyika, Mary; Smit Sibinga, Cees Th.

    2015-01-01

    BACKGROUNDFew African countries separate blood donations into components; however, demand for platelets (PLTs) is increasing as regional capacity to treat causes of thrombocytopenia, including chemotherapy, increases. Namibia introduced single-donor apheresis PLT collections in 2007 to increase PLT

  13. Chromosome 9 ALS and FTD locus is probably derived from a single founder.

    Science.gov (United States)

    Mok, Kin; Traynor, Bryan J; Schymick, Jennifer; Tienari, Pentti J; Laaksovirta, Hannu; Peuralinna, Terhi; Myllykangas, Liisa; Chiò, Adriano; Shatunov, Aleksey; Boeve, Bradley F; Boxer, Adam L; DeJesus-Hernandez, Mariely; Mackenzie, Ian R; Waite, Adrian; Williams, Nigel; Morris, Huw R; Simón-Sánchez, Javier; van Swieten, John C; Heutink, Peter; Restagno, Gabriella; Mora, Gabriele; Morrison, Karen E; Shaw, Pamela J; Rollinson, Pamela Sara; Al-Chalabi, Ammar; Rademakers, Rosa; Pickering-Brown, Stuart; Orrell, Richard W; Nalls, Michael A; Hardy, John

    2012-01-01

    We and others have recently reported an association between amyotrophic lateral sclerosis (ALS) and single nucleotide polymorphisms on chromosome 9p21 in several populations. Here we show that the associated haplotype is the same in all populations and that several families previously shown to have genetic linkage to this region also share this haplotype. The most parsimonious explanation of these data are that there is a single founder for this form of disease.

  14. Derivation of the density matrix of a single photon produced in parametric down-conversion

    Science.gov (United States)

    Kolenderski, Piotr; Wasilewski, Wojciech

    2009-07-01

    We discuss an effective numerical method of density matrix determination of fiber coupled single photon generated in process of spontaneous parametric down conversion in type I noncollinear configuration. The presented theory has been successfully applied in case of source utilized to demonstrate the experimental characterization of spectral state of single photon, what was reported in Wasilewski, Kolenderski, and Frankowski [Phys. Rev. Lett. 99, 123601 (2007)].

  15. Laboratory studies with cloud-derived Bacterial Cells acting as Ice Nuclei in the Immersion and Deposition Mode

    Science.gov (United States)

    Oehm, C.; Chou, C.; Amato, P.; Attard, E.; Delort, A.-M.; Morris, C.; Kiselev, A.; Stetzer, O.; Möhler, O.; Leisner, T.

    2012-04-01

    Atmospheric aerosol particles play an important role in cloud microphysics. Aerosols of biological origin are a subgroup, and some of them are able to act as heterogeneous ice nuclei and thus influence cloud life cycles and the climate. Some bacteria species have been found to act as ice nuclei at relatively high temperatures up to -2 degree Celsius and are therefore of particular importance as "high temperature" ice nuclei. Recently, ice nucleation experiments with bacterial cells from different sources were performed at the aerosol and cloud simulation chamber AIDA at the Karlsruhe Institute of Technology. At the AIDA facility, microphysical cloud processes can be simulated and investigated in laboratory at realistic atmospheric cloud conditions. Different ice nucleation active (INA) bacteria strains were isolated from cloud water, glacier melt water and phyllosphere and examined in AIDA experiments. The living cells were suspended in nanopure or artificial cloud water and injected into the cloud chamber through a dispersion nozzle. The injected droplets evaporated in the chamber and the bacterial cells were transformed into the aerosol phase. After the spraying, the cloud formation was started by expansion cooling. Experiments were performed in the temperature range from -2 down to -20 degree Celsius. Detailed measurements of the number concentration and size distribution of the aerosol particles as well as of the droplets and ice particles were carried out during the AIDA experiments. A minor fraction of the bacteria cells was observed to act as ice nuclei in the immersion nucleation mode at higher temperatures as well as in the deposition nucleation mode at lower temperatures. The ice activity started at -6 degree Celsius. The most efficient INA bacteria species were Pseudomonas syringae 32b74 and Pseudomonas fluorescens Antarctica1. The ice active number fraction with respect to the cells varied from 0,01 to 0,1, and it does not change at different

  16. Comparison of single cell culture derived Solanum tuberosum L. plants and a model for their application in breeding programs.

    Science.gov (United States)

    Wenzel, G; Schieder, O; Przewozny, T; Sopory, S K; Melchers, G

    1979-03-01

    The techniques of microspore and protoplast regeneration starting from dihaploid Solanum tuberosum plants has been improved to such an extent that the production of more than 2000 microspore derived A1 plant lines and of several hundred protoplast derived plantlets has become possible. Further, from the dihaploid Solanum species S. phureja the regeneration of microspores to plants, and from the species S. infundibuliforme, S. sparsipilum and S. tarijense the regeneration of protoplasts to calluses, has been achieved. The plants descending from the two single cell culture systems are compared with reference to phenotypic markers and economic qualities. Some principles characteristic for either microspore or protoplast derived plants are examined and their significance is discussed. The results are compiled into an extended analytical synthetic breeding scheme based on a stepwise reduction of the autotetraploid to the monohaploid level and a subsequent controlled combination to a new synthetic completely heterozygous tetraploid potato.

  17. ONIOM studies of interaction between single-walled carbon nanotube and gallates derivatives as anticancer agents

    Directory of Open Access Journals (Sweden)

    Nosrat Madadi Mahani

    2017-01-01

    Full Text Available Objective(s: The novel 7-hydroxycoumarinyl gallates derivatives are detected in many pharmaceutical compounds like anticancer and antimicrobial agents. Whereas carbon nanotubes (CNTs have been discussed for nanomedicine applications and in particular as drug delivery systems. The capability of armchair (5, 5 SWCNT -based drug delivery system in the therapy of anticancer has been investigated by quantum mechanics/molecular mechanics method.Materials and Methods: Theoretical investigation of the interaction between armchair (5, 5 SWCNT with gallates derivatives has been fulfilled by quantum mechanics/molecular mechanics (QM/MM method by ONIOM2 (DFT: UFF using the program of GAUSSIAN 03 suite.Results: The results derived from this study, demonstrate  that armchair (5, 5 SWCNT has weak interaction that these interactions contain Vander Waals interactions and indicated clearly that these systems have relatively low durability and so armchair (5, 5 SWCNT is appropriate drug delivery that have been investigated for anti-cancer drug.Conclusion: Analysis of ONIOM2 calculations and the interaction energies of the armchair (5, 5 SWCNT and gallates derivatives represented that this carrier can be utilized to improve the biological and anti-cancer activity of gallates derivatives.

  18. PET image reconstruction with system matrix based on point spread function derived from single photon incidence response

    CERN Document Server

    Xin, Fan; Ming-Kai, Yun; Xiao-Li, Sun; Xue-Xiang, Cao; Shuang-Quanm, Liu; Pei, Chai; Dao-Wu, Li; Long, Wei

    2014-01-01

    In positron emission tomography (PET) imaging, statistical iterative reconstruction (IR) techniques appear particularly promising since they can provide accurate physical model and geometric system description. The reconstructed image quality mainly depends on the system matrix model which describes the relationship between image space and projection space for the IR method. The system matrix can contain some physics factors of detection such as geometrical component and blurring component. Point spread function (PSF) is generally used to describe the blurring component. This paper proposes an IR method based on the PSF system matrix, which is derived from the single photon incidence response function. More specifically, the gamma photon incidence on a crystal array is simulated by the Monte Carlo (MC) simulation, and then the single photon incidence response functions are obtained. Subsequently, using the single photon incidence response functions, the coincidence blurring factor is acquired according to the...

  19. Dissecting contact mechanics from quantum interference in single-molecule junctions of stilbene derivatives.

    Science.gov (United States)

    Aradhya, Sriharsha V; Meisner, Jeffrey S; Krikorian, Markrete; Ahn, Seokhoon; Parameswaran, Radha; Steigerwald, Michael L; Nuckolls, Colin; Venkataraman, Latha

    2012-03-14

    Electronic factors in molecules such as quantum interference and cross-conjugation can lead to dramatic modulation and suppression of conductance in single-molecule junctions. Probing such effects at the single-molecule level requires simultaneous measurements of independent junction properties, as conductance alone cannot provide conclusive evidence of junction formation for molecules with low conductivity. Here, we compare the mechanics of the conducting para-terminated 4,4'-di(methylthio)stilbene and moderately conducting 1,2-bis(4-(methylthio)phenyl)ethane to that of insulating meta-terminated 3,3'-di(methylthio)stilbene single-molecule junctions. We simultaneously measure force and conductance across single-molecule junctions and use force signatures to obtain independent evidence of junction formation and rupture in the meta-linked cross-conjugated molecule even when no clear low-bias conductance is measured. By separately quantifying conductance and mechanics, we identify the formation of atypical 3,3'-di(methylthio)stilbene molecular junctions that are mechanically stable but electronically decoupled. While theoretical studies have envisaged many plausible systems where quantum interference might be observed, our experiments provide the first direct quantitative study of the interplay between contact mechanics and the distinctively quantum mechanical nature of electronic transport in single-molecule junctions.

  20. A derivative based simplified phase tracker for a single fringe pattern demodulation

    Science.gov (United States)

    Deepan, B.; Quan, C.; Tay, C. J.

    2016-08-01

    In this paper, a novel fringe demodulation method for the estimation of phase and its first-order derivative from a closed-fringe interferogram is proposed. The proposed method determines the phase derivatives in both x&y directions from fringe orientation and density. The phase derivatives are subsequently used to determine phase values using a novel simplified phase tracker. In the phase tracking model, the complexity of the cost function is reduced using predetermined derivatives so computation time required for phase tracking is reduced considerably. The proposed model is more robust while dealing with saddle points in fringes than the conventional phase tracker model. Hence it does not require any specialized scanning strategy. The proposed method is validated with simulated and experimental fringe patterns (obtained using electronic speckle pattern interferometry and optical holographic interferometry) and a comparison study is carried out with conventional regularized phase tracker. The simulation results show that the proposed method has good accuracy and requires less computation time than existing phase-tracking algorithms. The experimental results demonstrate the robustness of the proposed method against speckle noise and its practical applicability for static and dynamic applications.

  1. Enhanced sunlight photocatalytic activity of Ag3PO4 decorated novel combustion synthesis derived TiO2 nanobelts for dye and bacterial degradation.

    Science.gov (United States)

    Eswar, Neerugatti KrishnaRao; Ramamurthy, Praveen Chandrashekarapura; Madras, Giridhar

    2015-07-01

    This study demonstrates the synthesis of TiO2 nanobelts using solution combustion derived TiO2 with enhanced photocatalytic activity for dye degradation and bacterial inactivation. Hydrothermal treatment of combustion synthesized TiO2 resulted in unique partially etched TiO2 nanobelts and Ag3PO4 was decorated using the co-precipitation method. The catalyst particles were characterized using X-ray diffraction analysis, BET surface area analysis, diffuse reflectance and electron microscopy. The photocatalytic properties of the composites of Ag3PO4 with pristine combustion synthesized TiO2 and commercial TiO2 under sunlight were compared. Therefore the studies conducted proved that the novel Ag3PO4/unique combustion synthesis derived TiO2 nanobelt composites exhibited extended light absorption, better charge transfer mechanism and higher generation of hydroxyl and hole radicals. These properties resulted in enhanced photodegradation of dyes and bacteria when compared to the commercial TiO2 nanocomposite. These findings have important implications in designing new photocatalysts for water purification.

  2. Imaging and Intracellular Tracking of Cancer-Derived Exosomes Using Single-Molecule Localization-Based Super-Resolution Microscope.

    Science.gov (United States)

    Chen, Chen; Zong, Shenfei; Wang, Zhuyuan; Lu, Ju; Zhu, Dan; Zhang, Yizhi; Cui, Yiping

    2016-10-05

    Exosomes are small membrane vesicles secreted by cells and enriched with plenty of proteins. Considering their significant roles in different physical activities and potential value for diagnostic drug delivery, researchers have put great efforts in in vitro tracking and content analysis of exosomes. Recently, the emergence of different kinds of super-resolution microscopy provides powerful tools for exosome study. Here, we demonstrate the application of single-molecule localization based super-resolution imaging technique in the imaging and tracking of cancer-derived exosomes. In the experiment, first, cancer-derived exosomes are extracted from the culture media of tumor cells. Then the exosome membrane receptors are labeled with photoswitchable probes, which allow super-resolution imaging of these membrane receptors via photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). By using human breast cancer cell-derived exosomes, we demonstrated simultaneous dual-color PALM/STORM imaging of two kinds of membrane receptors on the exosome membrane. Moreover, the successful labeling and imaging of exosomes make it possible to observe the interaction between cancer-derived exosomes and normal cells. Meanwhile, we realized the colocalization of cancer-derived exosomes and lysosomes in recipient cells with PALM/STORM imaging. Since exosomes play a vital role in intercellular communications, we anticipate that the presented PALM/STORM-based imaging and tracking of exosomes holds a great potential in the investigation of the mechanism of exosome-mediated cancer metastasis.

  3. Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory.

    Science.gov (United States)

    Zhang, Xing; Herbert, John M

    2014-08-14

    We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H3 near its D(3h) geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state.

  4. Effectiveness of sorting single-walled carbon nanotubes by diameter using polyfluorene derivatives

    NARCIS (Netherlands)

    Gao, J.; Kwak, M.; Wildeman, J.; Hermann, A.; Loi, M. A.; Herrmann, A.

    2011-01-01

    Semiconducting single-walled carbon nanotubes (SWCNTs) sorted by conjugated polymers are of great interest for electronic and optoelectronic applications Here we demonstrate by optical methods that the selectivity of conjugated polymers for semiconducting SWCNTs is influenced by the structure of the

  5. Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters.

    Science.gov (United States)

    Bao, Weichen; Mi, Zhihui; Xu, Haiyan; Zheng, Yi; Kwok, Lai Yu; Zhang, Heping; Zhang, Wenyi

    2016-06-24

    The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.

  6. Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters

    Science.gov (United States)

    Bao, Weichen; Mi, Zhihui; Xu, Haiyan; Zheng, Yi; Kwok, Lai Yu; Zhang, Heping; Zhang, Wenyi

    2016-01-01

    The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage. PMID:27340760

  7. Oral-derived bacterial flora defends its domain by recognizing and killing intruders--a molecular analysis using Escherichia coli as a model intestinal bacterium.

    Science.gov (United States)

    He, Xuesong; Tian, Yan; Guo, Lihong; Lux, Renate; Zusman, David R; Shi, Wenyuan

    2010-10-01

    Within the same human gastrointestinal tract, substantial differences in the bacterial species that inhabit oral cavity and intestinal tract have been noted. Previous research primarily attributed the differences to the influences of host environments and nutritional availabilities ("host habitat" effect). Our recent study indicated that, other than the host habitat effect, an existing microbial community could impose a selective pressure on incoming foreign bacterial species independent of host-mediated selection ("community selection" effect). In this study, we employed in vitro microbial floras representing microorganisms that inhabit the oral cavities and intestinal tract of mice in combination with Escherichia coli as a model intestinal bacterium and demonstrated that E. coli displays a striking community preference. It thrived when introduced into the intestinal microbial community and survived poorly in the microbial flora of foreign origin (oral community). A more detailed examination of this phenomenon showed that the oral community produced oxygen-free radicals in the presence of wild-type E. coli while mutants deficient in lipopolysaccharides (LPS) did not trigger significant production of these cell-damaging agents. Furthermore, mutants of E. coli defective in the oxidative stress response experienced a more drastic reduction in viability when cocultivated with the oral flora, while the exogenous addition of the antioxidant vitamin C was able to rescue it. We concluded that the oral-derived microbial community senses the E. coli LPS and kills the bacterium with oxygen-free radicals. This study reveals a new mechanism of community invasion resistance employed by established microflora to defend their domains.

  8. High-Throughput Single-Cell Derived Sphere Formation for Cancer Stem-Like Cell Identification and Analysis

    Science.gov (United States)

    Chen, Yu-Chih; Ingram, Patrick N.; Fouladdel, Shamileh; McDermott, Sean P.; Azizi, Ebrahim; Wicha, Max S.; Yoon, Euisik

    2016-06-01

    Considerable evidence suggests that many malignancies are driven by a cellular compartment that displays stem cell properties. Cancer stem-like cells (CSCs) can be identified by expression of cell surface markers or enzymatic activity, but these methods are limited by phenotypic heterogeneity and plasticity of CSCs. An alternative phenotypic methodology based on in-vitro sphere formation has been developed, but it is typically labor-intensive and low-throughput. In this work, we present a 1,024-microchamber microfluidic platform for single-cell derived sphere formation. Utilizing a hydrodynamic capturing scheme, more than 70% of the microchambers capture only one cell, allowing for monitoring of sphere formation from heterogeneous cancer cell populations for identification of CSCs. Single-cell derived spheres can be retrieved and dissociated for single-cell analysis using a custom 96-gene panel to probe heterogeneity within the clonal CSC spheres. This microfluidic platform provides reliable and high-throughput sphere formation for CSC identification and downstream clonal analysis.

  9. Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates

    OpenAIRE

    Hedrich Hans J; Wedekind Dirk; Zeegers Dimphy; Guryev Victor; Smits Bart MG; Cuppen Edwin

    2005-01-01

    Abstract Background The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies. Results We show that Single Nucleotide Polymorphisms (SNPs) in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun ...

  10. A zeta potential value determines the aggregate’s size of penta-substituted [60]fullerene derivatives in aqueous suspension whereas positive charge is required for toxicity against bacterial cells

    OpenAIRE

    Deryabin, Dmitry G.; Ludmila V. Efremova; Vasilchenko, Alexey S.; Saidakova, Evgeniya V; Sizova, Elena A.; Pavel A. Troshin; Zhilenkov, Alexander V; Khakina, Ekaterina E

    2015-01-01

    Background The cause–effect relationships between physicochemical properties of amphiphilic [60]fullerene derivatives and their toxicity against bacterial cells have not yet been clarified. In this study, we report how the differences in the chemical structure of organic addends in 10 originally synthesized penta-substituted [60]fullerene derivatives modulate their zeta potential and aggregate’s size in salt-free and salt-added aqueous suspensions as well as how these physicochemical characte...

  11. Barbiturate bearing aroylhydrazine derivatives: Synthesis, NMR investigations, single crystal X-ray studies and biological activity

    Science.gov (United States)

    Giziroglu, Emrah; Sarikurkcu, Cengiz; Aygün, Muhittin; Basbulbul, Gamze; Soyleyici, H. Can; Firinci, Erkan; Kirkan, Bulent; Alkis, Ayse; Saylica, Tayfur; Biyik, Halil

    2016-03-01

    A series of barbituric acid aroylhydrazine derivatives have been prepared from their corresponding 1,3-dimethyl-5-acetyl barbituric acid and aroylhydrazines. All compounds have been fully characterized by using FT-IR, multinuclear NMR (1H, 13C) and Mass (MS) spectrometry. We also describe the X-ray crystal structure of 3a, which crystallizes in the monoclinic P21/n space group. The crystal structure is stabilized with infinite linear chains of dimeric units. Furthermore, all compounds were investigated for their tyrosinase inhibition, antioxidative and antimicrobial activies. The results from biological activity assays have shown that all of compounds have excellent antioxidant, significant tyrosinase inhibition and moderate antimicrobial activity.

  12. Dynamical Analysis on Single Degree-of-Freedom Semiactive Control System by Using Fractional-Order Derivative

    Directory of Open Access Journals (Sweden)

    Yongjun Shen

    2015-01-01

    Full Text Available The single degree-of-freedom (SDOF system under the control of three semiactive methods is analytically studied in this paper, where a fractional-order derivative is used in the mathematical model. The three semiactive control methods are on-off control, limited relative displacement (LRD control, and relative control, respectively. The averaging method is adopted to provide an analytical study on the performance of the three different control methods. Based on the comparison between the analytical solutions with the numerical ones, it could be proved that the analytical solutions are accurate enough. The effects of the fractional-order parameters on the control performance, especially the relative and absolute displacement transmissibility, are analyzed. The research results indicate that the steady-state amplitudes of the three semiactive systems with fractional-order derivative in the model could be significantly reduced and the control performance can be greatly improved.

  13. Cellulose derivatives as excellent dispersants for single-wall carbon nanotubes as demonstrated by absorption and photoluminescence spectroscopy

    Science.gov (United States)

    Minami, Nobutsugu; Kim, Yeji; Miyashita, Kanae; Kazaoui, Said; Nalini, Balakrishnan

    2006-02-01

    Sodium carboxymethylcellulose, an etherified derivative of cellulose, has been found to realize stable aqueous dispersion of single-wall carbon nanotubes (SWNTs) that is twenty times more concentrated than when a surfactant is used under the same condition. The dispersion as well as thin films prepared from it exhibits well-resolved near-infrared photoluminescence peaks originating from band-gap transitions in semiconducting SWNTs, a sign of isolated individual tubes. Mechanical stretching of the film strongly aligns the tubes, as demonstrated by considerable dichroism in their absorption spectra. Possessing high optical quality and uniformity, these densely dispersed SWNT films are expected to serve as an important platform for SWNTs' optical, electrical, and optoelectronic applications, especially because cellulose derivatives are cheap, mass-produced, safe, water-processable, and environmentally benign.

  14. Multilineage potential and proteomic profiling of human dental stem cells derived from a single donor

    Energy Technology Data Exchange (ETDEWEB)

    Patil, Rajreddy; Kumar, B. Mohana; Lee, Won-Jae; Jeon, Ryoung-Hoon; Jang, Si-Jung; Lee, Yeon-Mi [Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701 (Korea, Republic of); Park, Bong-Wook; Byun, June-Ho [Department of Oral and Maxillofacial Surgery, School of Medicine and Institute of Health Science, Gyeongsang National University, Jinju 660-702 (Korea, Republic of); Ahn, Chun-Seob; Kim, Jae-Won [Department of Microbiology, Division of Life Sciences, Research Institute of Life Science, Gyeongsang National University, Jinju 660-701 (Korea, Republic of); Rho, Gyu-Jin, E-mail: jinrho@gnu.ac.kr [Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 660-701 (Korea, Republic of); Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701 (Korea, Republic of)

    2014-01-01

    Dental tissues provide an alternative autologous source of mesenchymal stem cells (MSCs) for regenerative medicine. In this study, we isolated human dental MSCs of follicle, pulp and papilla tissue from a single donor tooth after impacted third molar extraction by excluding the individual differences. We then compared the morphology, proliferation rate, expression of MSC-specific and pluripotency markers, and in vitro differentiation ability into osteoblasts, adipocytes, chondrocytes and functional hepatocyte-like cells (HLCs). Finally, we analyzed the protein expression profiles of undifferentiated dental MSCs using 2DE coupled with MALDI-TOF-MS. Three types of dental MSCs largely shared similar morphology, proliferation potential, expression of surface markers and pluripotent transcription factors, and differentiation ability into osteoblasts, adipocytes, and chondrocytes. Upon hepatogenic induction, all MSCs were transdifferentiated into functional HLCs, and acquired hepatocyte functions by showing their ability for glycogen storage and urea production. Based on the proteome profiling results, we identified nineteen proteins either found commonly or differentially expressed among the three types of dental MSCs. In conclusion, three kinds of dental MSCs from a single donor tooth possessed largely similar cellular properties and multilineage potential. Further, these dental MSCs had similar proteomic profiles, suggesting their interchangeable applications for basic research and call therapy. - Highlights: • Isolated and characterized three types of human dental MSCs from a single donor. • MSCs of dental follicle, pulp and papilla had largely similar biological properties. • All MSCs were capable of transdifferentiating into functional hepatocyte-like cells. • 2DE proteomics with MALDI-TOF/MS identified 19 proteins in three types of MSCs. • Similar proteomic profiles suggest interchangeable applications of dental MSCs.

  15. A New Method to Derive Low-Lying N-dimensional Quantum Wave Functions by Quadratures Along a Single Trajectory

    CERN Document Server

    Friedberg, R; Zhao Wei Qin

    2000-01-01

    We present a new method to derive low-lying N-dimensional quantum wave functions by quadrature along a single trajectory. The N-dimensional Schroedinger equation is cast into a series of readily integrable first order ordinary differential equations. Our approach resembles the familiar W.K.B. approximation in one dimension, but is designed to explore the classically forbidden region and has a much wider applicability than W.K.B.. The method also provides a perturbation series expansion and the Green's functions of the wave equation in N-dimension, all by quadratures along a single trajectory. A number of examples are given for illustration, including a simple algorithm to evaluate the Stark effect in closed form to any finite order of the electric field.

  16. Integrated Analysis of Contractile Kinetics, Force Generation, and Electrical Activity in Single Human Stem Cell-Derived Cardiomyocytes

    Directory of Open Access Journals (Sweden)

    Jan David Kijlstra

    2015-12-01

    Full Text Available The quantitative analysis of cardiomyocyte function is essential for stem cell-based approaches for the in vitro study of human cardiac physiology and pathophysiology. We present a method to comprehensively assess the function of single human pluripotent stem cell-derived cardiomyocyte (hPSC-CMs through simultaneous quantitative analysis of contraction kinetics, force generation, and electrical activity. We demonstrate that statistical analysis of movies of contracting hPSC-CMs can be used to quantify changes in cellular morphology over time and compute contractile kinetics. Using a biomechanical model that incorporates substrate stiffness, we calculate cardiomyocyte force generation at single-cell resolution and validate this approach with conventional traction force microscopy. The addition of fluorescent calcium indicators or membrane potential dyes allows the simultaneous analysis of contractility and calcium handling or action potential morphology. Accordingly, our approach has the potential for broad application in the study of cardiac disease, drug discovery, and cardiotoxicity screening.

  17. Entropy-enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF.

    Science.gov (United States)

    Alcaraz, Antonio; Queralt-Martín, María; Verdiá-Báguena, Carmina; Aguilella, Vicente M; Mafé, Salvador

    2014-12-21

    The pH sensing mechanism of the OmpF channel operates via ligand modification: increasing acidity induces the replacement of cations with protons in critical binding sites decreasing the channel conductance. Aside from the change in enthalpy associated with the binding, there is also a change in the microscopic arrangements of ligands, receptors and the surrounding solvent. We show that the pH-modulation of the single channel conduction involves small free energy changes because large enthalpic and entropic contributions change in opposite ways, demonstrating an approximate enthalpy-entropy compensation for different salts and concentrations.

  18. Reverse and Multiple Stable Isotope Probing to Study Bacterial Metabolism and Interactions at the Single Cell Level.

    Science.gov (United States)

    Wang, Yun; Song, Yizhi; Tao, Yifan; Muhamadali, Howbeer; Goodacre, Royston; Zhou, Ning-Yi; Preston, Gail M; Xu, Jian; Huang, Wei E

    2016-10-04

    The interactions between microorganisms driven by substrate metabolism and energy flow are important to shape diversity, abundance, and structure of a microbial community. Single cell technologies are useful tools for dissecting the functions of individual members and their interactions in microbial communities. Here, we developed a novel Raman stable isotope probing (Raman-SIP), which uses Raman microspectroscopy coupled with reverse and D2O colabeling to study metabolic interactions in a two-species community consisting of Acinetobacter baylyi ADP1 and Escherichia coli DH5α-GFP. This Raman-SIP approach is able to detect carbon assimilation and general metabolic activity simultaneously. Taking advantage of Raman shift of single cell Raman spectra (SCRS) mediated by incorporation of stable-isotopic substrates, Raman-SIP with reverse labeling has been applied to detect initially (13)C-labeled bands of ADP1 SCRS reverting back to (12)C positions in the presence of (12)C citrate. Raman-SIP with D2O labeling has been employed to probe metabolic activity of single cells without the need of cell replication. Our results show that E. coli alone in minimal medium with citrate as the sole carbon source had no metabolic activity, but became metabolically active in the presence of ADP1. Mass spectrometry-based metabolite footprint analysis suggests that putrescine and phenylalanine excreted by ADP1 cells may support the metabolic activity of E. coli. This study demonstrates that Raman-SIP with reverse labeling would be a useful tool to probe metabolism of any carbon substrate, overcoming limitations when stable isotopic substrates are not readily available. It is also found that Raman-SIP with D2O labeling is a sensitive and reliable approach to distinguish metabolically active cells but not quiescent cells. This novel approach extends the application of Raman-SIP and demonstrates its potential application as a valuable strategic approach for probing cellular metabolism

  19. Multiple breast cancer cell-lines derived from a single tumor differ in their molecular characteristics and tumorigenic potential.

    Directory of Open Access Journals (Sweden)

    Goar Mosoyan

    Full Text Available BACKGROUND: Breast cancer cell lines are widely used tools to investigate breast cancer biology and to develop new therapies. Breast cancer tissue contains molecularly heterogeneous cell populations. Thus, it is important to understand which cell lines best represent the primary tumor and have similarly diverse phenotype. Here, we describe the development of five breast cancer cell lines from a single patient's breast cancer tissue. We characterize the molecular profiles, tumorigenicity and metastatic ability in vivo of all five cell lines and compare their responsiveness to 4-hydroxytamoxifen (4-OHT treatment. METHODS: Five breast cancer cell lines were derived from a single patient's primary breast cancer tissue. Expression of different antigens including HER2, estrogen receptor (ER, CK8/18, CD44 and CD24 was determined by flow cytometry, western blotting and immunohistochemistry (IHC. In addition, a Fluorescent In Situ Hybridization (FISH assay for HER2 gene amplification and p53 genotyping was performed on all cell lines. A xenograft model in nude mice was utilized to assess the tumorigenic and metastatic abilities of the breast cancer cells. RESULTS: We have isolated, cloned and established five new breast cancer cell lines with different tumorigenicity and metastatic abilities from a single primary breast cancer. Although all the cell lines expressed low levels of ER, their growth was estrogen-independent and all had high-levels of expression of mutated non-functional p53. The HER2 gene was rearranged in all cell lines. Low doses of 4-OHT induced proliferation of these breast cancer cell lines. CONCLUSIONS: All five breast cancer cell lines have different antigenic expression profiles, tumorigenicity and organ specific metastatic abilities although they derive from a single tumor. None of the studied markers correlated with tumorigenic potential. These new cell lines could serve as a model for detailed genomic and proteomic analyses to

  20. Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates

    Directory of Open Access Journals (Sweden)

    Hedrich Hans J

    2005-11-01

    Full Text Available Abstract Background The laboratory rat (Rattus norvegicus is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies. Results We show that Single Nucleotide Polymorphisms (SNPs in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun sequencing of 814 Kbp in one wild rat resulted in the identification of 485 SNPs as compared with the Brown Norway genome sequence. Genotyping 36 commonly used inbred rat strains showed that 84% of these alleles are also polymorphic in a representative set of laboratory rat strains. Conclusion We postulate that shotgun sequencing in a wild rat sample and subsequent genotyping in multiple laboratory or domesticated strains rather than direct shotgun sequencing of multiple strains, could be the most efficient SNP discovery approach. For the rat, laboratory strains still harbor a large portion of the haplotypes present in wild isolates, suggesting a relatively recent common origin and supporting the idea that rat inbred strains, in contrast to mouse inbred strains, originate from a single species, R. norvegicus.

  1. Modeling and CFD simulation of nutrient distribution in picoliter bioreactors for bacterial growth studies on single-cell level.

    Science.gov (United States)

    Westerwalbesloh, Christoph; Grünberger, Alexander; Stute, Birgit; Weber, Sophie; Wiechert, Wolfgang; Kohlheyer, Dietrich; von Lieres, Eric

    2015-11-01

    A microfluidic device for microbial single-cell cultivation of bacteria was modeled and simulated using COMSOL Multiphysics. The liquid velocity field and the mass transfer within the supply channels and cultivation chambers were calculated to gain insight in the distribution of supplied nutrients and metabolic products secreted by the cultivated bacteria. The goal was to identify potential substrate limitations or product accumulations within the cultivation device. The metabolic uptake and production rates, colony size, and growth medium composition were varied covering a wide range of operating conditions. Simulations with glucose as substrate did not show limitations within the typically used concentration range, but for alternative substrates limitations could not be ruled out. This lays the foundation for further studies and the optimization of existing picoliter bioreactor systems.

  2. Effect of TiO2 nanoparticles on adipose derived stromal cell differentiation, morphology, ECM deposition and its susceptibility to bacterial infections

    Science.gov (United States)

    Mironava, Tatsiana; Xu, Yan; Rafailovich, Miriam

    The growing annual production of Titanium dioxide (TiO2) nanoparticles is proportional to an increase in the chances of occupational and consumer exposure. Considering, that these nanoparticles are currently being used in multiple personal care products many concerns have arisen about their health impact. Human skin is in constant contact with the external environment and is one of the most important routes of exposure to TiO2. In this study we have investigated the effect of two forms of TiO2, rutile and anatase, on human adipose derived stromal cells (ADSCs). Here, we focus on the effects of TiO2 exposure on intracellular lipid accumulation and expression of adipogenic markers; on whether different forms of TiO2 have similar effects on cell function; and whether nanoparticle localization inside cells correlates with loss of cell function. In addition presence of bacteria on the skin is taken into account in its complex interaction with ADSCs and TiO2 nanoparticles. Altogether, the present study indicates that nanosized TiO2 particles adversely effects the differentiation of ADSCs, have profound effects on cell function and increase the rate of bacterial infection.

  3. Electrostatic Potential as a Descriptor of Anti-Bacterial Activities of Some Anacardic Acid Derivatives: A Study Using Density Functional Theory

    CERN Document Server

    Tiwari, Manish K

    2015-01-01

    Structures and minimum molecular electrostatic potential (MEP) distributions in anacardic acid and some of its derivatives have been studied by full geometry optimization at the M06-2X/6-31G(d,p), WB97XD/6-31G(d,p) and B3LYP/6-31G(d,p) levels of density functional theory (DFT) in gas phase as well as in DMSO and aqueous solutions. Solvent effect was treated employing the integral equation formalism of the polarizable continuum model. Effects of modifications of the C1-side chain on the minimum MEP values in various regions were studied. Minimum MEP values near the oxygen atoms of the C2-OH group, oxygen or sulfur atoms of the C1-attached urea or thiourea groups and above or below the ring plane considered to be involved in interaction with the receptor were used to perform multiple linear regression. Experimentally observed anti-bacterial activities of these molecules against S. aureus are thus shown to be related to minimum MEP values in the above mentioned regions. Among the three DFT functionals used in th...

  4. Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable "Clean" Mutant Selection in Clostridium beijerinckii as an Example.

    Science.gov (United States)

    Wang, Yi; Zhang, Zhong-Tian; Seo, Seung-Oh; Lynn, Patrick; Lu, Ting; Jin, Yong-Su; Blaschek, Hans P

    2016-07-15

    CRISPR-Cas9 has been demonstrated as a transformative genome engineering tool for many eukaryotic organisms; however, its utilization in bacteria remains limited and ineffective. Here we explored Streptococcus pyogenes CRISPR-Cas9 for genome editing in Clostridium beijerinckii (industrially significant but notorious for being difficult to metabolically engineer) as a representative attempt to explore CRISPR-Cas9 for genome editing in microorganisms that previously lacked sufficient genetic tools. By combining inducible expression of Cas9 and plasmid-borne editing templates, we successfully achieved gene deletion and integration with high efficiency in single steps. We further achieved single nucleotide modification by applying innovative two-step approaches, which do not rely on availability of Protospacer Adjacent Motif sequences. Severe vector integration events were observed during the genome engineering process, which is likely difficult to avoid but has never been reported by other researchers for the bacterial genome engineering based on homologous recombination with plasmid-borne editing templates. We then further successfully employed CRISPR-Cas9 as an efficient tool for selecting desirable "clean" mutants in this study. The approaches we developed are broadly applicable and will open the way for precise genome editing in diverse microorganisms.

  5. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    Directory of Open Access Journals (Sweden)

    Matheus Costa dos Reis

    2014-01-01

    Full Text Available This study was carried out to obtain the estimates of genetic variance and covariance components related to intra- and interpopulation in the original populations (C0 and in the third cycle (C3 of reciprocal recurrent selection (RRS which allows breeders to define the best breeding strategy. For that purpose, the half-sib progenies of intrapopulation (P11 and P22 and interpopulation (P12 and P21 from populations 1 and 2 derived from single-cross hybrids in the 0 and 3 cycles of the reciprocal recurrent selection program were used. The intra- and interpopulation progenies were evaluated in a 10×10 triple lattice design in two separate locations. The data for unhusked ear weight (ear weight without husk and plant height were collected. All genetic variance and covariance components were estimated from the expected mean squares. The breakdown of additive variance into intrapopulation and interpopulation additive deviations (στ2 and the covariance between these and their intrapopulation additive effects (CovAτ found predominance of the dominance effect for unhusked ear weight. Plant height for these components shows that the intrapopulation additive effect explains most of the variation. Estimates for intrapopulation and interpopulation additive genetic variances confirm that populations derived from single-cross hybrids have potential for recurrent selection programs.

  6. Synthesis, structure analysis, anti-bacterial and in vitro anti-cancer activity of new Schiff base and its copper complex derived from sulfamethoxazole

    Indian Academy of Sciences (India)

    I Rama; R Selvameena

    2015-04-01

    A new bidentate Schiff base ligand (HL1), containing O,N donors was prepared by the reaction of sulfamethoxazole with 5-nitrosalicylaldehyde and characterized by elemental analysis, FT-IR, 1H and 13C NMR. The copper complex of this ligand was synthesised by treating DMF-ethanolic mixture solution of the ligand of two equivalents with one equivalent of copper acetate. The complex was characterized on the basis of UV, FT-IR, molar conductance, EPR, magnetic moment and single crystal X-ray diffraction. Interestingly, the crystal structure of the octahedral complex showed two solvent molecules (DMF) as ligands at their axial positions. The molar conductance data revealed that the complex is a non-electrolyte. The Schiff base and its copper complex have been investigated as anti-bacterial and anti-fungal agents against various microorganisms. The in vitro cytotoxicity tests of the ligand and its copper complex were carried out in two different human tumour cell lines, HCT-116 and MDA – MB - 231. The cytotoxicity studies showed that the complex exhibited higher activity than cisplatin and carboplatin towards MDA – MB – 231.

  7. Single-Molecule Tribology: Force Microscopy Manipulation of a Porphyrin Derivative on a Copper Surface.

    Science.gov (United States)

    Pawlak, Rémy; Ouyang, Wengen; Filippov, Alexander E; Kalikhman-Razvozov, Lena; Kawai, Shigeki; Glatzel, Thilo; Gnecco, Enrico; Baratoff, Alexis; Zheng, Quanshui; Hod, Oded; Urbakh, Michael; Meyer, Ernst

    2016-01-26

    The low-temperature mechanical response of a single porphyrin molecule attached to the apex of an atomic force microscope (AFM) tip during vertical and lateral manipulations is studied. We find that approach-retraction cycles as well as surface scanning with the terminated tip result in atomic-scale friction patterns induced by the internal reorientations of the molecule. With a joint experimental and computational effort, we identify the dicyanophenyl side groups of the molecule interacting with the surface as the dominant factor determining the observed frictional behavior. To this end, we developed a generalized Prandtl-Tomlinson model parametrized using density functional theory calculations that includes the internal degrees of freedom of the side group with respect to the core and its interactions with the underlying surface. We demonstrate that the friction pattern results from the variations of the bond length and bond angles between the dicyanophenyl side group and the porphyrin backbone as well as those of the CN group facing the surface during the lateral and vertical motion of the AFM tip.

  8. Single-molecule derivation of salt dependent base-pair free energies in DNA

    CERN Document Server

    Huguet, J M; Forns, N; Smith, S B; Bustamante, C; Ritort, F; 10.1073/pnas.1001454107

    2010-01-01

    Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol-1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our new energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melt...

  9. Single step reconstitution of multifunctional high-density lipoprotein-derived nanomaterials using microfluidics.

    Science.gov (United States)

    Kim, YongTae; Fay, Francois; Cormode, David P; Sanchez-Gaytan, Brenda L; Tang, Jun; Hennessy, Elizabeth J; Ma, Mingming; Moore, Kathryn; Farokhzad, Omid C; Fisher, Edward Allen; Mulder, Willem J M; Langer, Robert; Fayad, Zahi A

    2013-11-26

    High-density lipoprotein (HDL) is a natural nanoparticle that transports peripheral cholesterol to the liver. Reconstituted high-density lipoprotein (rHDL) exhibits antiatherothrombotic properties and is being considered as a natural treatment for cardiovascular diseases. Furthermore, HDL nanoparticle platforms have been created for targeted delivery of therapeutic and diagnostic agents. The current methods for HDL reconstitution involve lengthy procedures that are challenging to scale up. A central need in the synthesis of rHDL, and multifunctional nanomaterials in general, is to establish large-scale production of reproducible and homogeneous batches in a simple and efficient fashion. Here, we present a large-scale microfluidics-based manufacturing method for single-step synthesis of HDL-mimicking nanomaterials (μHDL). μHDL is shown to have the same properties (e.g., size, morphology, bioactivity) as conventionally reconstituted HDL and native HDL. In addition, we were able to incorporate simvastatin (a hydrophobic drug) into μHDL, as well as gold, iron oxide, quantum dot nanocrystals or fluorophores to enable its detection by computed tomography (CT), magnetic resonance imaging (MRI), or fluorescence microscopy, respectively. Our approach may contribute to effective development and optimization of lipoprotein-based nanomaterials for medical imaging and drug delivery.

  10. Electronic properties of Cs-intercalated single-walled carbon nanotubes derived from nuclear magnetic resonance

    KAUST Repository

    Abou-Hamad, E

    2011-05-24

    We report on the electronic properties of Cs-intercalated single-walled carbon nanotubes (SWNTs). A detailed analysis of the 13C and 133Cs nuclear magnetic resonance (NMR) spectra reveals an increased metallization of the pristine SWNTs under Cs intercalation. The \\'metallization\\' of CsxC materials where x=0–0.144 is evidenced from the increased local electronic density of states (DOS) n(EF) at the Fermi level of the SWNTs as determined from spin–lattice relaxation measurements. In particular, there are two distinct electronic phases called α and β and the transition between these occurs around x=0.05. The electronic DOS at the Fermi level increases monotonically at low intercalation levels x<0.05 (α-phase), whereas it reaches a plateau in the range 0.05≤x≤0.143 at high intercalation levels (β-phase). The new β-phase is accompanied by a hybridization of Cs(6s) orbitals with C(sp2) orbitals of the SWNTs. In both phases, two types of metallic nanotubes are found with a low and a high local n(EF), corresponding to different local electronic band structures of the SWNTs.

  11. Virus-binding proteins recovered from bacterial culture derived from activated sludge by affinity chromatography assay using a viral capsid peptide.

    Science.gov (United States)

    Sano, Daisuke; Matsuo, Takahiro; Omura, Tatsuo

    2004-06-01

    The contamination of water environments by pathogenic viruses has raised concerns about outbreaks of viral infectious diseases in our society. Because conventional water and wastewater treatment systems are not effective enough to inactivate or remove pathogenic viruses, a new technology for virus removal needs to be developed. In this study, the virus-binding proteins (VBPs) in a bacterial culture derived from activated sludge were successfully recovered. The recovery of VBPs was achieved by applying extracted crude proteins from a bacterial culture to an affinity column in which a custom-made peptide of capsid protein from the poliovirus type 1 (PV1) Mahoney strain (H(2)N-DNPASTTNKDKL-COOH) was immobilized as a ligand. VBPs exhibited the ability to adsorb infectious particles of PV1 Sabin 1 as determined by enzyme-linked immunosorbent assay. The evaluation of surface charges of VBPs with ion-exchange chromatography found that a majority of VBP molecules had a net negative charge under the conditions of affinity chromatography. On the other hand, a calculated isoelectric point implied that the viral peptide in the affinity column was also charged negatively. As a result, the adsorption of the VBPs to the viral peptide in the affinity column occurred with a strong attractive force that was able to overcome the electrostatic repulsive force. Two-dimensional electrophoresis revealed that the isolated VBPs include a number of proteins, and their molecular masses were widely distributed but smaller than 100 kDa. Amino acid sequences of N termini of five VBPs were determined. Homology searches for the N termini against all protein sequences in the National Center for Biotechnology Information (NCBI) database showed that the isolated VBPs in this study were newly discovered proteins. These VBPs that originated with bacteria in activated sludge might be stable, because they are existing in the environment of wastewater treatments. Therefore, a virus removal technology

  12. Optimization of single plate-serial dilution spotting (SP-SDS with sample anchoring as an assured method for bacterial and yeast cfu enumeration and single colony isolation from diverse samples

    Directory of Open Access Journals (Sweden)

    Pious Thomas

    2015-12-01

    Full Text Available We propose a simple technique for bacterial and yeast cfu estimations from diverse samples with no prior idea of viable counts, designated as single plate-serial dilution spotting (SP-SDS with the prime recommendation of sample anchoring (100 stocks. For pure cultures, serial dilutions were prepared from 0.1 OD (100 stock and 20 μl aliquots of six dilutions (101–106 were applied as 10–15 micro-drops in six sectors over agar-gelled medium in 9-cm plates. For liquid samples 100–105 dilutions, and for colloidal suspensions and solid samples (10% w/v, 101–106 dilutions were used. Following incubation, at least one dilution level yielded 6–60 cfu per sector comparable to the standard method involving 100 μl samples. Tested on diverse bacteria, composite samples and Saccharomyces cerevisiae, SP-SDS offered wider applicability over alternative methods like drop-plating and track-dilution for cfu estimation, single colony isolation and culture purity testing, particularly suiting low resource settings.

  13. Inter- and Intraspecific Variation in Wild-type and Single Female-derived Populations of Xiphinema americanum-group Nematodes.

    Science.gov (United States)

    Halbrendt, J M; Brown, D J

    1994-06-01

    Ten populations of Xiphinema americanum-group nematodes were reared from individual females to evaluate inter- and intraspecific variation under identical host and environmental conditions. Data indicated that morphometric variability of X. americanum was the result of genetic variation rather than phenotypic plasticity and that genetic heterogeneity was greater than previously thought. Morphometrics of single female derived (SFD) populations identified different genotypes present in the field populations. Stylet length was the least variable morphometric character of SFD populations, but collectively stylet measurements of all individuals formed an uninterrupted continuum ranging from 107-148 mum. Range and frequency of stylet measurements of field populations could be accounted for by the relative proportion of different genotypes in the population. Nine SFD populations were identified as X. americanum sensu stricto, and one SFD population was similar to X. californicum.

  14. Phase-derivative-based estimation of a digital reference wave from a single off-axis digital hologram.

    Science.gov (United States)

    Khodadad, Davood

    2016-03-01

    This paper describes a method to obtain an estimated digital reference wave from a single off-axis digital hologram that matches the actual experimental reference wave as closely as possible. The proposed method is independent of a reference flat plate and speckles. The digital reference wave parameters are estimated directly from the recorded phase information. The parameters include both the off-axis tilt angle and the curvature of the reference wave. Phase derivatives are used to extract the digital reference wave parameters without the need for a phase unwrapping process. Thus, problems associated with phase wrapping are avoided. Experimental results for the proposed method are provided. The simulated effect of the digital reference wave parameters on the reconstructed image phase distribution is shown. The pseudo phase gradient originating from incorrect estimation of the digital reference wave parameters and its effect on object reconstruction are discussed.

  15. Cloning and characterization of the biosynthetic gene cluster of the bacterial RNA polymerase inhibitor tirandamycin from marine-derived Streptomyces sp. SCSIO1666.

    Science.gov (United States)

    Mo, Xuhua; Wang, Zhongwen; Wang, Bo; Ma, Junying; Huang, Hongbo; Tian, Xinpeng; Zhang, Si; Zhang, Changsheng; Ju, Jianhua

    2011-03-18

    Tirandamycins are bacterial RNA polymerase inhibitors holding great potential for antibacterial agent design. To elucidate the biosynthetic machinery and generate new derivatives, the tirandamycin biosynthetic gene cluster was cloned and sequenced from marine-derived Streptomyces sp. SCSIO1666. The biosynthetic gene cluster of tirandamycin spans a DNA region of ∼56kb and consists of 15 open reading frames (ORFs) which encode three type I polyketide synthases (TrdAI, AII, AIII), one non-ribosomal peptide synthetase (TrdD), one phosphopantetheinyl transferase (TrdM), one Type II thioesterase (TrdB), one FAD-dependent oxidoreductase (TrdL), one cytochrome P450 monooxygenase (TrdI), three proteins related to resistance and regulations (TrdHJK), and four proteins with unknown function (TrdCEFG). To investigate the roles of the genes played in the biosynthetic machinery, seven genes (trdAI and trdBDFHIK) were inactivated via in frame replacement with an apramycin gene cassette using λ-RED recombination technology. The ΔtrdAI and ΔtrdD mutants targeting the ketosynthase and adenylation domain of TrdAI and TrdD, respectively, abolished the production of tirandamycins, confirming their involvement in the tirandamycin biosynthesis. TrdH showed high homology to LuxR family transcriptional regulatory proteins, disruption of which abolished the production of tirandamycins, indicating that TrdH is a positive regulator for tirandamycin biosynthesis. On the other hand, TrdK showed high homology to TetR-family transcriptional regulatory proteins, disruption of which significantly increased the yields of tirandamycins almost one-fold, implicating that TrdK is a negative regulator for tirandamycin biosynthesis. Disruption of the gene trdI resulted in the accumulation of the intermediate tirandamycin C (3) and a trace amount of new product tirandamycin C2 (5). A model of tirandamycin biosynthesis was proposed based on bioinformatics analyses, gene inactivation experiments and

  16. RNA- and single-stranded DNA-binding (SSB) proteins expressed during Drosophila melanogaster oogenesis: a homolog of bacterial and eukaryotic mitochondrial SSBs.

    Science.gov (United States)

    Stroumbakis, N D; Li, Z; Tolias, P P

    1994-06-10

    Little is known about the identity and involvement of single-stranded (ss) DNA-binding (SSB) and RNA-binding proteins in developmental processes that occur during oogenesis in Drosophila melanogaster (Dm). Here, we describe a molecular approach designed to identify such proteins by virtue of their ssDNA-binding activity. We have constructed a directional ovarian cDNA library and conducted expression cloning screens which identified five unique cDNAs that encode proteins capable of binding ssDNA. All five represent previously unreported sequences. The remainder of this paper focuses on one of these cDNAs which encodes a Dm protein displaying significant sequence homology to Escherichia coli ssDNA-binding protein (SSB, involved in DNA replication, repair and recombination), as well as eukaryotic SSBs isolated from the mitochondria (mt) of rats, frogs, humans and yeast. The deduced amino acid (aa) sequence of this 15.6-kDa protein, which we will refer to as Dm mtSSB, displays average identities of 38.3% with eukaryotic mtSSBs and 23.4% with bacterial SSBs. Gel retardation analysis with an affinity-purified GST fusion protein confirms that Dm mtSSB specifically binds ss, but not double stranded DNA. Dm mtSSB is encoded by a nuclear gene whose expression appears to be developmentally regulated. It is expressed as a single 600-nucleotide (nt) transcript during oogenesis and embryogenesis. A larger transcript of 1500 nt is prevalent in some later stages of Dm development.

  17. Start-up and bacterial communities of single-stage nitrogen removal using anammox and partial nitritation (SNAP) for treatment of high strength ammonia wastewater.

    Science.gov (United States)

    Zhang, Jianbing; Zhou, Jian; Han, Yi; Zhang, Xiaoguang

    2014-10-01

    In this study, a lab-scale sequencing batch biofilm reactor (SBBR) was used to start up the single-stage nitrogen removal system using anammox and partial nitritation (SNAP) process seeding from surplus activated sludge. The volumetric nitrogen loading rate (vNLR) was firstly 0.075 kg N m(-3) d(-1) and then gradually increased to 0.60 kg N m(-3) d(-1). A maximal total nitrogen (TN) removal rate of 0.54 kg N m(-3) d(-1) was achieved by the SNAP process after 132 days operation with NH4(+)-N and TN removal efficiency of 99.4% and 90.5%, respectively. This reactor may have applications for the SNAP process treating high strength ammonia wastewater. And dewatered surplus activated sludge was recommended as the seed sludge for engineering applications. The dominant bacterial strains were Xanthomonas campestris, Nitrosomonas europaea and Ignavibacterium album, corresponding to the percentage of 24%, 22% and 20%, respectively, based on the 16S rDNA amplicon pyrosequencing of the SNAP sludge.

  18. A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Deal Karin R

    2009-01-01

    Full Text Available Abstract Background Current techniques of screening bacterial artificial chromosome (BAC libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a single locus on a genetic map. These limitations are the principal impediment in the construction of physical maps of large eukaryotic genomes. It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly parallel Illumina GoldenGate™ assay. Results To test the efficacy of the Golden Gate assay in BAC library screening, multidimensional pools involving 302976 Aegilops tauschii BAC clones were genotyped for the presence/absence of specific gene sequences with multiplexed Illumina GoldenGate oligonucleotide assays previously used to place single nucleotide polymorphisms on an Ae. tauschii genetic map. Of 1384 allele-informative oligonucleotide assays, 87.6% successfully clustered BAC pools into those positive for a BAC clone harboring a specific gene locus and those negative for it. The location of the positive BAC clones within contigs assembled from 199190 fingerprinted Ae. tauschii BAC clones was used to evaluate the precision of anchoring of BAC clones and contigs on the Ae. tauschii genetic map. For 41 (95% assays, positive BAC clones were neighbors in single contigs. Those contigs could be unequivocally assigned to loci on the genetic map. For two (5% assays, positive clones were in two different contigs and the relationships of these contigs to loci on the Ae. tauschii genetic map were equivocal. Screening of BAC libraries with a simple five-dimensional BAC pooling strategy was evaluated and shown to allow direct detection of positive BAC clones without the need for manual deconvolution of BAC clone pools. Conclusion The highly parallel Illumina oligonucleotide assay is shown here to be an efficient tool for screening BAC libraries and a strategy for high

  19. Proposal for defining the relevance of drug accumulation derived from single dose study data for modified release dosage forms.

    Science.gov (United States)

    Scheerans, Christian; Heinig, Roland; Mueck, Wolfgang

    2015-03-01

    Recently, the European Medicines Agency (EMA) published the new draft guideline on the pharmacokinetic and clinical evaluation of modified release (MR) formulations. The draft guideline contains the new requirement of performing multiple dose (MD) bioequivalence studies, in the case when the MR formulation is expected to show 'relevant' drug accumulation at steady state (SS). This new requirement reveals three fundamental issues, which are discussed in the current work: first, measurement for the extent of drug accumulation (MEDA) predicted from single dose (SD) study data; second, its relationship with the percentage residual area under the plasma concentration-time curve (AUC) outside the dosing interval (τ) after SD administration, %AUC(τ-∞)SD ; and third, the rationale for a threshold of %AUC(τ-∞)SD that predicts 'relevant' drug accumulation at SS. This work revealed that the accumulation ratio RA,AUC , derived from the ratio of the time-averaged plasma concentrations during τ at SS and after SD administration, respectively, is the 'preferred' MEDA for MR formulations. A causal relationship was derived between %AUC(τ-∞)SD and RA,AUC , which is valid for any drug (product) that shows (dose- and time-) linear pharmacokinetics regardless of the shape of the plasma concentration-time curve. Considering AUC thresholds from other guidelines together with the causal relationship between %AUC(τ-∞)SD and RA,AUC indicates that values of %AUC(τ-∞)SD ≤ 20%, resulting in RA,AUC ≤ 1.25, can be considered as leading to non-relevant drug accumulation. Hence, the authors suggest that 20% for %AUC(τ-∞)SD is a reasonable threshold and selection criterion between SD or MD study designs for bioequivalence studies of new MR formulations.

  20. Evaluation of single amino acid chelate derivatives and regioselective radiolabelling of a cyclic peptide for the urokinase plasminogen activator receptor

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Andrea F.; Lemon, Jennifer A. [McMaster Institute for Applied Radiation Sciences, McMaster University, ON, L8S 4M1 (Canada); Czorny, Shannon K. [McMaster Institute for Applied Radiation Sciences, McMaster University, ON, L8S 4M1 (Canada); Juravinski Cancer Centre, Hamilton, ON, L8V 5C2 (Canada); Singh, Gurmit [Juravinski Cancer Centre, Hamilton, ON, L8V 5C2 (Canada); Valliant, John F. [Department of Chemistry, McMaster University, Hamilton, ON, L8S 4M1 (Canada); Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, ON, L8S 4M1 (Canada)], E-mail: valliant@mcmaster.ca

    2009-11-15

    Introduction: The aim of this work was to investigate the relative radiolabelling kinetics and affinity of a series of ligands for the [{sup 99m}Tc(CO){sub 3}]{sup +} core, both in the absence and in the presence of competing donors. This information was used to select a suitable ligand for radiolabelling complex peptide-based targeting vectors in high yield under mild conditions. Methods: A series of {alpha}-N-Fmoc-protected lysine derivatives bearing two heterocyclic donor groups at the {epsilon}-amine (, 2-pyridyl; , quinolyl; , 6-methoxy-2-pyridyl; 1d, 2-thiazolyl; 1e, N-methylimidazolyl; , 3-pyridyl) were synthesized and labelled with {sup 99m}Tc. A resin-capture purification strategy for the separation of residual ligand from the radiolabelled product was also developed. The binding affinities of targeted peptides 4, 5a and 5b for uPAR were determined using flow cytometry. Results: Variable temperature radiolabelling reactions using - and [{sup 99m}Tc(CO){sub 3}]{sup +} revealed optimal kinetics and good selectivity for compounds and 1d; in the case of , 1d, and 1e, the labelling can be conducted at ambient temperature. The utility of this class of ligands was further demonstrated by the radiolabelling of a cyclic peptide that is known to target the serine protease receptor uPAR; essentially quantitative incorporation of {sup 99m}Tc occurred exclusively at the SAAC site, despite the presence of a His residue, and without disruption of the disulfide bond. Conclusion: A series of single amino acid chelate (SAAC) ligands have been evaluated for their ability to incorporate {sup 99m}Tc into peptides. The lead agent to emerge from this work is the thiazole SAAC derivative 1d which has demonstrated the ability to regioselectively label the widest range of peptides.

  1. Bacterial Vaginosis

    Science.gov (United States)

    ... Issues > Conditions > Sexually Transmitted > Bacterial Vaginosis Health Issues Listen Español Text Size Email Print Share Bacterial Vaginosis Page Content Bacterial vaginosis (BV) is the most common vaginal infection in sexually active teenaged girls . It appears to be caused by ...

  2. Feed consumption, growth and growth efficiency of rainbow trout (Oncorhynchus mykiss (Walbaum)) fed on diets containing a bacterial single-cell protein.

    Science.gov (United States)

    Perera, W M; Carter, C G; Houlihan, D F

    1995-04-01

    The aim of the present study was to compare the nutritive value of bacterial single-cell protein (BSCP) with that of fishmeal in rainbow trout (Oncorhynchus mykiss (Walbaum)). Four diets were formulated to contain a total of 458 g crude protein/kg of which 0% was from BSCP in diet 1 (BSCP-0), 25% in diet 2 (BSCP-25), 62.5% in diet 3 (BSCP-62.5) and 100% in diet 4 (BSCP-100); the remainder of the protein was from fishmeal. There were two studies: in study 1, duplicate groups of twenty-five fish were fed on one of the four experimental diets at the rate of 20 g/kg body weight per d for 132 d. Feed consumption rates of individual fish were measured using radiography and the overall apparent absorption efficiency for N in each group was measured over a 2-week period. In study 2, N intake, consumption, absorption and accretion were measured for each fish under controlled environmental conditions (12 h: 12 h light-dark regime; 14 degrees). Higher dietary levels of BSCP resulted in significantly higher feed consumption rates but reduced N absorption efficiency and growth rates. However, a diet containing 25% BSCP (75% fishmeal) did not significantly influence growth rates, feed consumption and absorption efficiency compared with a 100% fishmeal diet. The N growth efficiencies were highest in fish fed on the diet containing the highest level of fishmeal and significantly decreased with increasing BSCP content. Construction of N budgets demonstrated that the reduction in growth in fish eating an increasingly larger proportion of BSCP was due to a decrease in N absorption and an increase in the excretion of urea.

  3. Selection and design of high affinity DNA ligands for mutant single-chain derivatives of the bacteriophage 434 repressor

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Single-chain repressor RRTRES is a derivative of bacteriophage 434 repressor, which contains covalently dimerized DNA-binding domains (amino acids 1-69) of the phage 434 repressor. In this single-chain molecule, the wild type domain R is connected to the mutant domain RTRES by a recombinant linker in a head-to-tail arrangement. The DNA-contacting amino acids of RTRES at the -1, 1, 2, and 5 positions of the a3 helix are T, R, E, S respectively. By using a randomized DNA pool containing the central sequence -CATACAAGAAAGNNNNNNTTT-, a cyclic, in vitro DNA-binding site selection was performed. The selected population was cloned and the individual members were characterized by determining their binding affinities to RRTRES. The results showed that the optimal operators contained the TTAC or TTCC sequences in the underlined positions as above, and that the Kd values were in the 1×10-12 mol/L-1×10-11mol/L concentration range. Since the affinity of the natural 434 repressor to its natural operator sites is in the 1×10-9 mol/L range, the observed binding affinity increase is remarkable. It was also found that binding affinity was strongly affected by the flanking bases of the optimal tetramer binding sites, especially by the base at the 5′ position. We constructed a new homodimeric single-chain repressor RTRESRTRES and its DNA-binding specificity was tested by using a series of new operators designed according to the recog-nition properties previously determined for the RTRES domain. These operators containing the con-sensus sequence GTAAGAAARNTTACN or GGAAGAAARNTTCCN (R is A or G) were recognized by RTRESRTRES specifically, and with high binding affinity. Thus, by using a combination of random selection and rational design principles, we have discovered novel, high affinity protein-DNA inter-actions with new specificity. This method can potentially be used to obtain new binding specificity for other DNA-binding proteins.

  4. Single Particle Dynamic Imaging and Fe3+ Sensing with Bright Carbon Dots Derived from Bovine Serum Albumin Proteins

    Science.gov (United States)

    Yang, Qingxiu; Wei, Lin; Zheng, Xuanfang; Xiao, Lehui

    2015-12-01

    In this work, we demonstrated a convenient and green strategy for the synthesis of highly luminescent and water-soluble carbon dots (Cdots) by carbonizing carbon precursors, i.e., Bovine serum albumin (BSA) nanoparticles, in water solution. Without post surface modification, the as-synthesized Cdots exhibit fluorescence quantum yield (Q.Y.) as high as 34.8% and display superior colloidal stability not only in concentrated salt solutions (e.g. 2 M KCl) but also in a wide range of pH solutions. According to the FT-IR measurements, the Cdots contain many carboxyl groups, providing a versatile route for further chemical and biological functionalization. Through conjugation of Cdots with the transacting activator of transcription (TAT) peptide (a kind of cell penetration peptide (CPP)) derived from human immunodeficiency virus (HIV), it is possible to directly monitor the dynamic interactions of CPP with living cell membrane at single particle level. Furthermore, these Cdots also exhibit a dosage-dependent selectivity toward Fe3+ among other metal ions, including K+, Na+, Mg2+, Hg2+, Co2+, Cu2+, Pb2+ and Al3+. We believed that the Cdots prepared by this strategy would display promising applications in various areas, including analytical chemistry, nanomedicine, biochemistry and so on.

  5. [Risk Assessment of Single-Donor (Apheresis) Platelet Concentrates and Pooled Whole-Blood-Derived Platelet Concentrates].

    Science.gov (United States)

    Hitzler, Walter; Hutschenreuter, Gabriele; Wartensleben, Herbert

    2015-01-01

    According to the risk estimates of the Robert-Koch-Institute (RKI) and the Paul Ehrlich-Institute (PEI) an equivalence cannot be assumed to exist between the two different platelet preparations. Differences between single-donor (apheresis) platelet concentrates (ATK) and pooled whole-blood-derived platelet concentrates (PTK) result from donor populations, donation intervals, and preparation techniques. There are no prospective randomized studies with regard to the clinical efficacy, which would unambiguously demonstrate equivalence of the therapeutic efficacy of PTK (buffy coat method) in comparison to ATK. The German Association of Blood Transfusion Services (StKB) points out that, due to the non-equivalence of PTK and ATK, it is incumbent on the transfusion physician to select the platelet concentrate, make the appropriate disclosures, and assume treatment responsibility. Proper compensation for ATK and PTK must be ensured by the health insurance companies, whereby a special indication for the selection of either PTK or ATK is not given. Exceptions are patients with known HLA antibodies in which only selected platelet concentrates may be administered. Otherwise, no indication exists in the selection of the different platelet concentrates (Article is in German).

  6. Association analysis of bacterial leaf spot resistance and SNP markers derived from expressed sequence tags (ESTs) in lettuce (Lactuca sativa L.)

    Science.gov (United States)

    Bacterial leaf spot of lettuce, caused by Xanthomonas campestris pv. vitians, is a devastating disease of lettuce worldwide. Since there are no chemicals available for effective control of the disease, host-plant resistance is highly desirable to protect lettuce production. A total of 179 lettuce ge...

  7. Multiple Genes in a Single Host: Cost-Effective Production of Bacterial Laccase (cotA), Pectate Lyase (pel), and Endoxylanase (xyl) by Simultaneous Expression and Cloning in Single Vector in E. coli

    Science.gov (United States)

    Kumar, Sandeep; Jain, Kavish Kumar; Bhardwaj, Kailash N.; Chakraborty, Subhojit; Kuhad, Ramesh Chander

    2015-01-01

    This study attempted to reduce the enzyme production cost for exploiting lignocellulosic materials by expression of multiple genes in a single host. Genes for bacterial laccase (CotA), pectate lyase (Pel) and endoxylanase (Xyl), which hold significance in lignocellulose degradation, were cloned in pETDuet-1 vector containing two independent cloning sites (MCS). CotA and xyl genes were cloned in MCS1 and MCS 2, respectively. Pel gene was cloned by inserting complete cassette (T7 promoter, ribosome binding site, pel gene, His tag and complete gene ORF) preceded by cotA open reading frame in the MCS1. IPTG induction of CPXpDuet-1 construct in E. coli BL21(DE3) resulted in expression of all three heterologous proteins of ~65 kDa (CotA), ~45 kDa (Pel) and ~25 kDa (Xyl), confirmed by SDS-PAGE and western blotting. Significant portions of the enzymes were also found in culture supernatant (~16, ~720 and ~370 IU/ml activities of CotA, Pel and Xyl, respectively). Culture media optimization resulted in 2, 3 and 7 fold increased secretion of recombinant CotA, Pel and Xyl, respectively. Bioreactor level optimization of the recombinant cocktail expression resulted in production of 19 g/L dry cell biomass at OD600nm 74 from 1 L induced culture after 15 h of cultivation, from which 9, 627 and 1090 IU/ml secretory enzyme activities of CotA, Xyl and Pel were obtained, respectively. The cocktail was also found to increase the saccharification of orange peel in comparison to the xylanase alone. Thus, simultaneous expression as well as extra cellular secretion of these enzymes as cocktail can reduce the enzyme production cost which increases their applicability specially for exploiting lignocellulosic materials for their conversion to value added products like alcohol and animal feed. PMID:26642207

  8. Construction and characterization of single-chain variable fragment antibody library derived from germline rearranged immunoglobulin variable genes.

    Directory of Open Access Journals (Sweden)

    Man Cheng

    Full Text Available Antibody repertoires for library construction are conventionally harvested from mRNAs of immune cells. To examine whether germline rearranged immunoglobulin (Ig variable region genes could be used as source of antibody repertoire, an immunized phage-displayed scFv library was prepared using splenocytic genomic DNA as template. In addition, a novel frame-shifting PCR (fsPCR step was introduced to rescue stop codon and to enhance diversity of the complementarity-determining region 3 (CDR3. The germline scFv library was initially characterized against the hapten antigen phenyloxazolone (phOx. Sequence analysis of the phOx-selective scFvs indicated that the CDRs consisted of novel as well as conserved motifs. In order to illustrate that the diversity of CDR3 was increased by the fsPCR step, a second scFv library was constructed using a single scFv clone L3G7C as a template. Despite showing similar binding characteristics towards phOx, the scFv clones that were obtained from the L3G7C-derived antibody library gave a lower non-specific binding than that of the parental L3G7C clone. To determine whether germline library represented the endogenous immune status, specific scFv clones for nucleocapsid (N protein of SARS-associated coronavirus (SCoV were obtained both from naïve and immunized germline scFv libraries. Both libraries yielded specific anti-N scFvs that exhibited similar binding characteristics towards recombinant N protein, except the immunized library gave a larger number of specific anti-N scFv, and clones with identical nucleotide sequences were found. In conclusion, highly diversified antibody library can be efficiently constructed using germline rearranged immunoglobulin variable genes as source of antibody repertoires and fsPCR to diversify the CDR3.

  9. Introducing a single-cell-derived human mesenchymal stem cell line expressing hTERT after lentiviral gene transfer.

    Science.gov (United States)

    Böcker, Wolfgang; Yin, Zhanhai; Drosse, Inga; Haasters, Florian; Rossmann, Oliver; Wierer, Matthias; Popov, Cvetan; Locher, Melanie; Mutschler, Wolf; Docheva, Denitsa; Schieker, Matthias

    2008-08-01

    Human mesenchymal stem cells (hMSCs) can be readily isolated from bone marrow and differentiate into multiple tissues, making them a promising target for future cell and gene therapy applications. The low frequency of hMSCs in bone marrow necessitates their isolation and expansion in vitro prior to clinical use, but due to senescence-associated growth arrest during culture, limited cell numbers can be generated. The lifespan of hMSCs has been extended by ectopic expression of human telomerase reverse transcriptase (hTERT) using retroviral vectors. Since malignant transformation was observed in hMSCs and retroviral vectors cause insertional mutagenesis, we ectopically expressed hTERT using lentiviral gene transfer. Single-cell-derived hMSC clones expressing hTERT did not show malignant transformation in vitro and in vivo after extended culture periods. There were no changes observed in the expression of tumour suppressor genes and karyotype. Cultured hMSCs lack telomerase activity, but it was significantly increased by ectopic expression of hTERT. HTERT expression prevented hMSC senescence and the cells showed significantly higher and unlimited proliferation capacity. Even after an extended culture period, hMSCs expressing hTERT preserved their stem cells character as shown by osteogenic, adipogenic and chondrogenic differentiation. In summary, extending the lifespan of human mesenchymal stem cells by ectopic expression of hTERT using lentiviral gene transfer may be an attractive and safe way to generate appropriate cell numbers for cell and gene therapy applications.

  10. The long persistence of pyrrolizidine alkaloid-derived DNA adducts in vivo: kinetic study following single and multiple exposures in male ICR mice.

    Science.gov (United States)

    Zhu, Lin; Xue, Junyi; Xia, Qingsu; Fu, Peter P; Lin, Ge

    2017-02-01

    Pyrrolizidine alkaloid (PA)-containing plants are widespread in the world and the most common poisonous plants affecting livestock, wildlife, and humans. Our previous studies demonstrated that PA-derived DNA adducts can potentially be a common biological biomarker of PA-induced liver tumor formation. In order to validate the use of these PA-derived DNA adducts as a biomarker, it is necessary to understand the basic kinetics of the PA-derived DNA adducts formed in vivo. In this study, we studied the dose-dependent response and kinetics of PA-derived DNA adduct formation and removal in male ICR mice orally administered with a single dose (40 mg/kg) or multiple doses (10 mg/kg/day) of retrorsine, a representative carcinogenic PA. In the single-dose exposure, the PA-derived DNA adducts exhibited dose-dependent linearity and persisted for up to 4 weeks. The removal of the adducts following a single-dose exposure to retrorsine was biphasic with half-lives of 9 h (t 1/2α) and 301 h (~12.5 days, t 1/2β). In the 8-week multiple exposure study, a marked accumulation of PA-derived DNA adducts without attaining a steady state was observed. The removal of adducts after the multiple exposure also demonstrated a biphasic pattern but with much extended half-lives of 176 h (~7.33 days, t 1/2α) and 1736 h (~72.3 days, t 1/2β). The lifetime of PA-derived DNA adducts was more than 8 weeks following the multiple-dose treatment. The significant persistence of PA-derived DNA adducts in vivo supports their role in serving as a biomarker of PA exposure.

  11. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  12. A combined metabolomic and phylogenetic study reveals putatively prebiotic effects of high molecular weight arabino-oligosaccharides when assessed by in vitro fermentation in bacterial communities derived from humans.

    Science.gov (United States)

    Sulek, Karolina; Vigsnaes, Louise Kristine; Schmidt, Line Rieck; Holck, Jesper; Frandsen, Henrik Lauritz; Smedsgaard, Jørn; Skov, Thomas Hjort; Meyer, Anne S; Licht, Tine Rask

    2014-08-01

    Prebiotic oligosaccharides are defined by their selective stimulation of growth and/or activity of bacteria in the digestive system in ways claimed to be beneficial for health. However, apart from the short chain fatty acids, little is known about bacterial metabolites created by fermentation of prebiotics, and the significance of the size of the oligosaccharides remains largely unstudied. By in vitro fermentations in human fecal microbial communities (derived from six different individuals), we studied the effects of high-mass (HA, >1 kDa), low-mass (LA, prebiotic impact on human health.

  13. A new approach to counteract bacteria resistance: a comparative study between moxifloxacin and a new moxifloxacin derivative in different model systems of bacterial membrane.

    Science.gov (United States)

    Lopes, Silvia C; Ribeiro, Carla; Gameiro, Paula

    2013-02-01

    New drug design has been one of the major challenges to combat bacterial resistance over the past decade. Conventional antibiotics act by destroying bacterial cell wall or by blocking biosynthetic pathways necessary for its survival. Unfortunately, there has been a fast increase in multiresistance, to several conventional antibiotics, in clinical bacterial strains. Previous studies have shown that metalloantibiotics, ternary complexes of antibiotic-metal-phenanthroline, present an increased potential as antimicrobial agents. In this work moxifloxacin, a fourth-generation quinolone, with a broad spectrum of action, and its copper ternary complex (metalloantibiotic) have been study by fluorescence spectroscopy. Partition coefficients were determined and showed that while free moxifloxacin exhibits the same behaviour independently of the lipidic system tested, the metalloantibiotic presents higher partition to liposomes, in a lipid composition-dependent way. These significant differences in the interaction of the metalloantibiotic with model bacteria membranes point out for a putative change in its uptake mechanism with increased drug-lipid interaction potentiating metalloantibiotic influx.

  14. Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages

    Science.gov (United States)

    Murakami, Takumi; Segawa, Takahiro; Dial, Roman; Takeuchi, Nozomu; Kohshima, Shiro; Hongoh, Yuichi

    2017-01-01

    The community structure of bacteria associated with the glacier ice worm Mesenchytraeus solifugus was analyzed by amplicon sequencing of 16S rRNA genes and their transcripts. Ice worms were collected from two distinct glaciers in Alaska, Harding Icefield and Byron Glacier, and glacier surfaces were also sampled for comparison. Marked differences were observed in bacterial community structures between the ice worm and glacier surface samples. Several bacterial phylotypes were detected almost exclusively in the ice worms, and these bacteria were phylogenetically affiliated with either animal-associated lineages or, interestingly, clades mostly consisting of glacier-indigenous species. The former included bacteria that belong to Mollicutes, Chlamydiae, Rickettsiales, and Lachnospiraceae, while the latter included Arcicella and Herminiimonas phylotypes. Among these bacteria enriched in ice worm samples, Mollicutes, Arcicella, and Herminiimonas phylotypes were abundantly and consistently detected in the ice worm samples; these phylotypes constituted the core microbiota associated with the ice worm. A fluorescence in situ hybridization analysis showed that Arcicella cells specifically colonized the epidermis of the ice worms. Other bacterial phylotypes detected in the ice worm samples were also abundantly recovered from the respective habitat glaciers; these bacteria may be food for ice worms to digest or temporary residents. Nevertheless, some were overrepresented in the ice worm RNA samples; they may also function as facultative gut bacteria. Our results indicate that the community structure of bacteria associated with ice worms is distinct from that in the associated glacier and includes worm-specific and facultative, glacier-indigenous lineages. PMID:28302989

  15. Petroleum and derivatives emulsification by bacterial consortium of sea meeds from Enseada do Forno-Armacao de Buzios (RJ); Emulsificacao de petroleo e seus derivados pelos consorcios bacterianos de algas da Enseada do Forno-Armacao dos Buzios (RJ)

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Frederico S. da; Crapez, Mirian A.C.; Krepsky, Natascha; Fontana, Luiz F.; Baptista-Neto, Jose Antonio [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil)]. E-mail: fred@igeo.uff.br

    2004-07-01

    Constant petroleum spill over natural habitats made necessary alternatives for environmental damage mitigation and recuperation. Bio surfactants can be used as an alternative for oil spill once they reduce surface oil tension, making them soluble in water or can make it available from the sediments. Bacterial consortia were isolated and bio amplified from Caulerpa (C), Laurencia (L) and Dictyota (D) algae biofilm. Bacterial carbon (CB); surface tension (TS); Emulsification index (E{sub 24}) and non-aqueous (A) and aqueous (B) emulsification of gasoline, kerosene and Arabian Light were estimated in 0, 7, 15 and 30 days of incubation. Results show a decrease of Laurencia and Caulerpa CB. However, Dictyota showed an increase at CB. Laurencia TS showed no significant reduction at days 7 and 15. For Dictyota and Caulerpa there was a increase at day 7 and reduction at day 15. E{sub 24} was higher than 70% for all the three substances and consortia tested. Laurencia bacteria consortia presented emulsification B for Arabian Light and emulsification A for gasoline and kerosene. Caulerpa consortia emulsified all compounds. All bacterial consortia isolated were surfactant producer, with emulsification A and B, being indicated for recuperation of environments contaminated with oil and its derivatives compounds. (author)

  16. Deriving concentrations of oxygen and carbon in human tissues using single- and dual-energy CT for ion therapy applications

    Science.gov (United States)

    Landry, Guillaume; Parodi, Katia; Wildberger, Joachim E.; Verhaegen, Frank

    2013-08-01

    Dedicated methods of in-vivo verification of ion treatment based on the detection of secondary emitted radiation, such as positron-emission-tomography and prompt gamma detection require high accuracy in the assignment of the elemental composition. This especially concerns the content in carbon and oxygen, which are the most abundant elements of human tissue. The standard single-energy computed tomography (SECT) approach to carbon and oxygen concentration determination has been shown to introduce significant discrepancies in the carbon and oxygen content of tissues. We propose a dual-energy CT (DECT)-based approach for carbon and oxygen content assignment and investigate the accuracy gains of the method. SECT and DECT Hounsfield units (HU) were calculated using the stoichiometric calibration procedure for a comprehensive set of human tissues. Fit parameters for the stoichiometric calibration were obtained from phantom scans. Gaussian distributions with standard deviations equal to those derived from phantom scans were subsequently generated for each tissue for several values of the computed tomography dose index (CTDIvol). The assignment of %weight carbon and oxygen (%wC,%wO) was performed based on SECT and DECT. The SECT scheme employed a HU versus %wC,O approach while for DECT we explored a Zeff versus %wC,O approach and a (Zeff, ρe) space approach. The accuracy of each scheme was estimated by calculating the root mean square (RMS) error on %wC,O derived from the input Gaussian distribution of HU for each tissue and also for the noiseless case as a limiting case. The (Zeff, ρe) space approach was also compared to SECT by comparing RMS error for hydrogen and nitrogen (%wH,%wN). Systematic shifts were applied to the tissue HU distributions to assess the robustness of the method against systematic uncertainties in the stoichiometric calibration procedure. In the absence of noise the (Zeff, ρe) space approach showed more accurate %wC,O assignment (largest error of

  17. Same-Single-Cell Analysis of Pacemaker-Specific Markers in Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Subtypes Classified by Electrophysiology.

    Science.gov (United States)

    Yechikov, Sergey; Copaciu, Raul; Gluck, Jessica M; Deng, Wenbin; Chiamvimonvat, Nipavan; Chan, James W; Lieu, Deborah K

    2016-07-19

    Insights into the expression of pacemaker-specific markers in human induced pluripotent stem cell (hiPSC)-derived cardiomyocyte subtypes can facilitate the enrichment and track differentiation and maturation of hiPSC-derived pacemaker-like cardiomyocytes. To date, no study has directly assessed gene expression in each pacemaker-, atria-, and ventricular-like cardiomyocyte subtype derived from hiPSCs since currently the subtypes of these immature cardiomyocytes can only be identified by action potential profiles. Traditional acquisition of action potentials using patch-clamp recordings renders the cells unviable for subsequent analysis. We circumvented these issues by acquiring the action potential profile of a single cell optically followed by assessment of protein expression through immunostaining in that same cell. Our same-single-cell analysis for the first time revealed expression of proposed pacemaker-specific markers-hyperpolarization-activated cyclic nucleotide-modulated (HCN)4 channel and Islet (Isl)1-at the protein level in all three hiPSC-derived cardiomyocyte subtypes. HCN4 expression was found to be higher in pacemaker-like hiPSC-derived cardiomyocytes than atrial- and ventricular-like subtypes but its downregulation over time in all subtypes diminished the differences. Isl1 expression in pacemaker-like hiPSC-derived cardiomyocytes was initially not statistically different than the contractile subtypes but did become statistically higher than ventricular-like cells with time. Our observations suggest that although HCN4 and Isl1 are differentially expressed in hiPSC-derived pacemaker-like relative to ventricular-like cardiomyocytes, these markers alone are insufficient in identifying hiPSC-derived pacemaker-like cardiomyocytes. Stem Cells 2016.

  18. A comparison of effects of broad-spectrum antibiotics and biosurfactants on established bacterial biofilms.

    Science.gov (United States)

    Quinn, Gerry A; Maloy, Aaron P; Banat, Malik M; Banat, Ibrahim M

    2013-11-01

    Current antibiofilm solutions based on planktonic bacterial physiology have limited efficacy in clinical and occasionally environmental settings. This has prompted a search for suitable alternatives to conventional therapies. This study compares the inhibitory properties of two biological surfactants (rhamnolipids and a plant-derived surfactant) against a selection of broad-spectrum antibiotics (ampicillin, chloramphenicol and kanamycin). Testing was carried out on a range of bacterial physiologies from planktonic and mixed bacterial biofilms. Rhamnolipids (Rhs) have been extensively characterised for their role in the development of biofilms and inhibition of planktonic bacteria. However, there are limited direct comparisons with antimicrobial substances on established biofilms comprising single or mixed bacterial strains. Baseline measurements of inhibitory activity using planktonic bacterial assays established that broad-spectrum antibiotics were 500 times more effective at inhibiting bacterial growth than either Rhs or plant surfactants. Conversely, Rhs and plant biosurfactants reduced biofilm biomass of established single bacterial biofilms by 74-88 and 74-98 %, respectively. Only kanamycin showed activity against biofilms of Bacillus subtilis and Staphylococcus aureus. Broad-spectrum antibiotics were also ineffective against a complex biofilm of marine bacteria; however, Rhs and plant biosurfactants reduced biofilm biomass by 69 and 42 %, respectively. These data suggest that Rhs and plant-derived surfactants may have an important role in the inhibition of complex biofilms.

  19. Bacterial toxin-inducible gene expression of cathelicidin-B1 in the chicken bursal lymphoma-derived cell line DT40: functional characterization of cathelicidin-B1.

    Science.gov (United States)

    Takeda, Asuna; Tsubaki, Takashi; Sagae, Nozomi; Onda, Yumiko; Inada, Yuri; Mochizuki, Takuya; Okumura, Kazuo; Kikuyama, Sakae; Kobayashi, Tetsuya; Iwamuro, Shawichi

    2014-09-01

    Chicken cathelicidin-B1 (chCATH-B1) is a major host defense peptide of the chicken bursa of Fabricius (BF). To investigate the mechanisms of chCATH-B1 gene expression in the BF, we focused on the DT40 cell line derived from chicken bursal lymphoma as a model for analysis. A cDNA encoding chCATH-B1 precursor was cloned from DT40 cells. The nucleotide sequence of the cDNA was identical with that of the BF chCATH-B1. A broth dilution analysis showed that the synthetic chCATH-B1 exhibited a significant defensive activity against both Escherichia coli and Staphylococcus aureus. A scanning microscopic analysis demonstrated that chCATH-B1 inhibited bacterial growth through membrane destruction with formation of blebs and spheroplasts. Limulus amoebocyte lysate assay and electromobility shift assay results revealed that chCATH-B1 bound to lipopolysaccharide (LPS) and lipoteichoic acid (LTA), which are the surface substances of the E. coli and S. aureus cell, respectively. A chemotactic assay results revealed that chCATH-B1 showed mouse-derived P-815 mastocytoma migrating activity dose-dependently but with a higher concentration, resulting in a loss of the activity. A semi-quantitative real-time RT-PCR analysis revealed that LPS stimulated chCATH-B1 gene expression in a dose-dependent manner and that the LPS-inducible chCATH-B1 gene expression was inhibited by the administration of dexamethasone. The chCATH-B1 mRNA levels in DT40 cells were also increased by the administration of bacterial LTA. The results indicate that bacterial toxins induce chCATH-B1 gene expression in the chicken BF and the peptide expressed in the organ would act against pathogenic microorganisms not only directly but also indirectly by attracting mast cells.

  20. Effect of bacterial mineralization of phytoplankton-derived phytodetritus on the release of arsenic, cobalt and manganese from muddy sediments in the Southern North Sea. A microcosm study.

    Science.gov (United States)

    Gillan, David C; Pede, Annelies; Sabbe, Koen; Gao, Yue; Leermakers, Martine; Baeyens, Willy; Louriño Cabana, Beatriz; Billon, Gabriel

    2012-03-01

    Muddy sediments of the Belgian Continental Zone (BCZ) are contaminated by metals such as Co, As, Cd, Pb, and Ni. Previous studies have suggested that mineralization of phytodetritus accumulating each year on sediments might cause secondary contaminations of the overlying seawater (metal effluxes). The aim of the present research was to investigate these effluxes using a microcosm approach. Muddy sediments were placed in microcosms (diameter: 15 cm) and overlaid by phytodetritus (a mix of Phaeocystis globosa with the diatom Skeletonema costatum). The final suspension was 130.6 mg L(-1) (dw) and the final chlorophyll a content was 750 ± 35 μg L(-1) (mean ± SD). Natural seawater was used for controls. Microcosms were then incubated in the dark at 15°C during 7 days. Metals were monitored in overlying waters and microbial communities were followed using bacterial and nanoflagellate DAPI counts, thymidine incorporation, community level physiological profiling (CLPP) and fluorescein diacetate analysis (FDA). Benthic effluxes observed in sediments exposed to phytodetritus were always more elevated than those observed in controls. Large effluxes were observed for Mn, Co and As, reaching 1084 nmol m(-2)day(-1) (As), 512 nmol m(-2)day(-1) (Co), and 755 μmol m(-2)day(-1) (Mn). A clear link was established between heterotrophic microbial activity and metal effluxes. The onset of mineralization was very fast and started within 2h of deposition as revealed by CLPP. An increased bacterial production was observed after two days (8.7 mg Cm(-2)day(-2)) and the bacterial biomass appeared controlled by heterotrophic nanoflagellates. Calculations suggest that during phytoplankton blooms the microbial activity alone may release substantial amounts of dissolved arsenic in areas of the BCZ covered by muddy sediments.

  1. Distribution of Triplet Separators in Bacterial Genomes

    Institute of Scientific and Technical Information of China (English)

    HU Rui; ZHENG Wei-Mou

    2001-01-01

    Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared with the distributions of the bacterial genomes. A prominent double band structure, which does not exist in the theoretical distributions, is observed in the bacterial distributions for most triplets.``

  2. Selection and design of high affinity DNA ligands for mutant single-chain derivatives of the bacteriophage 434 repressor

    Institute of Scientific and Technical Information of China (English)

    LIANG; Tiebing

    2001-01-01

    ., 1996, 255: 373-386.[13]Kim, J. -S., Pabo, C. O., Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants, Proc. Natl. Acad. Sci. USA, 1998, 95: 2812-2817.[14]Wu, H., Yang, W. -P., BarbasIII, C. F., Building zinc fingers by selection: toward a therapeutic application, Proc. Natl. Acad. Sci. USA, 1995, 92: 344-348.[15]Wang, B. S., Pabo, C. O., Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences, Proc. Natl. Acad. Sci. USA, 1999, 96: 9568-9573.[16]Choo, Y., Sánchez-García, I., Klug, A., In vivo repression by a site-specific DNA-binding protein designed against an on-cogenic sequence, Nature, 1994, 372: 642-645.[17]Wolfe, S. A., Greisman, H. A., Ramm, E. I. et al., Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code, J. Mol. Biol., 1999, 285: 1917-1934.[18]Chen, J. -Q., Pongor, S., Simoncsits, A., Recognition of DNA by single-chain derivatives of the phage 434 repressor: high affinity binding depends on both the contacted and non-contacted base pairs, Nucleic Acids Research, 1997, 25: 2047-2054.[19]Simoncsits, A., Tj?rnhammar, M. -L., Wang, S. -L. et al., Isolation of altered specificity mutants of the single-chain 434 repressor that recognize asymmetric DNA sequences containing the TTAA and TTAC subsites, Nucleic Acids Research, 1999, 27: 3474-3480.[20]Zhou, Y. -H., Busby, S., Ebright, R. H., Identification of the functional subunit of a dimeric transcription activator protein by use of oriented heterodimers, Cell, 1993, 73: 375-379.[21]Studier, F. W., Rosenberg, A. H., Dunn, J. J. et al., Use of T7 RNA polymerase to direct expression of cloned genes, Methods Enzymol., 1990, 185: 60-89.[22]Simoncsits, A., Bristulf, J., Tj?rnhammar, M. -L. et al., Deletion mutants of human interleukin 1? with significantly re-duced agonist properties: search for agonist/ antagonist switch in ligands to the interleukin 1

  3. One bacterial cell, one complete genome.

    Directory of Open Access Journals (Sweden)

    Tanja Woyke

    Full Text Available While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA. Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs, indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  4. One Bacterial Cell, One Complete Genome

    Energy Technology Data Exchange (ETDEWEB)

    Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos; Clum, Alicia; Copeland, Alex; Schackwitz, Wendy; Lapidus, Alla; Wu, Dongying; McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.; Bristow, James; Cheng, Jan-Fang

    2010-04-26

    While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  5. Bacterial gastroenteritis

    Science.gov (United States)

    Bacterial gastroenteritis is present when bacteria cause an infection of the stomach and intestines ... has not been treated Many different types of bacteria can cause ... Campylobacter jejuni E coli Salmonella Shigella Staphylococcus ...

  6. Growh performance, nitrogen balance and urinary purine derivatives in growing-furring mink (Mustela vison) fed bacterial protein produced from natural gas

    DEFF Research Database (Denmark)

    Ahlstrøm, Ø.; Tauson, Anne-Helene; Hellwing, Anne Louise Frydendahl

    2006-01-01

    A bacterial protein meal (BPM), containing 70% crude protein and produced on natural gas, was evaluated versus fish meal as protein source for mink in the growing-furring period (June 29-November 26). BPM, rich in nucleic acids, accounted for 0 (control), 20 and 40% of dietary crude protein......, except for males on the 8% BPM diet. Balance experiments carried out with 18 and 28 weeks old males, revealed similar digestibility of main nutrients except for fat that were reduced with BPM inclusion. N-retentions were similar for the dietary groups. Daily excretion of urine was lower with the 8% BPM...... not affected by diet, except for shorter hair length with inclusion of BPM. In conclusion, the experiment showed that BPM can account for 40% of dietary protein in growing-furring mink without negative effects on N metabolism, body weight gain or fur quality....

  7. Derivation of factors to estimate daily yield from single milkings for Holsteins milked two or three times daily

    Science.gov (United States)

    The objective was to derive factors to predict daily yield when milk weights are recorded once when cows are milked twice (2x) or once or twice when cows are milked thrice (3x) per d. Data was from herds enrolled in DHI and automatically recording milking weights and times. Following edits, 83,690...

  8. Manufacture of Clinical-Grade Human Clonal Mesenchymal Stem Cell Products from Single Colony Forming Unit-Derived Colonies Based on the Subfractionation Culturing Method.

    Science.gov (United States)

    Yi, TacGhee; Kim, Si-na; Lee, Hyun-Joo; Kim, Junghee; Cho, Yun-Kyoung; Shin, Dong-Hee; Tak, Sun-Ji; Moon, Sun-Hwa; Kang, Ji-Eun; Ji, In-Mi; Lim, Huyn-Ja; Lee, Dong-Soon; Jeon, Myung-Shin; Song, Sun U

    2015-12-01

    Stem cell products derived from mesenchymal stem cells (MSCs) have been widely used in clinical trials, and a few products have been already commercialized. However, the therapeutic effects of clinical-grade MSCs are still controversial owing to mixed results from recent clinical trials. A potential solution to overcome this hurdle may be to use clonal stem cells as the starting cell material to increase the homogeneity of the final stem cell products. We have previously developed an alternative isolation and culture protocol for establishing a population of clonal MSCs (cMSCs) from single colony forming unit (CFU)-derived colonies. In this study, we established a good manufacturing practice (GMP)-compatible procedure for the clinical-grade production of human bone marrow-derived cMSCs based on the subfractionation culturing method. We optimized the culture procedures to expand and obtain a clonal population of final MSC products from single CFU-derived colonies in a GMP facility. The characterization results of the final cMSC products met our preset criteria. Animal toxicity tests were performed in a good laboratory practice facility, and showed no toxicity or tumor formation in vivo. These tests include single injection toxicity, multiple injection toxicity, biodistribution analysis, and tumorigenicity tests in vivo. No chromosomal abnormalities were detected by in situ karyotyping using oligo-fluorescence in situ hydridization (oligo-FISH), providing evidence of genetic stability of the clinical-grade cMSC products. The manufacture and quality control results indicated that our GMP methodology could produce sufficient clonal population of MSC products from a small amount of bone marrow aspirate to treat a number of patients.

  9. Bacterial transformation of terpenoids

    Science.gov (United States)

    Grishko, V. V.; Nogovitsina, Y. M.; Ivshina, I. B.

    2014-04-01

    Data on the bacterial transformation of terpenoids published in the literature in the past decade are analyzed. Possible pathways for chemo-, regio- and stereoselective modifications of terpenoids are discussed. Considerable attention is given to new technological approaches to the synthesis of terpenoid derivatives suitable for the use in the perfume and food industry and promising as drugs and chiral intermediates for fine organic synthesis. The bibliography includes 246 references.

  10. Pair distribution function-derived mechanism of a single-crystal to disordered to single-crystal transformation in a hemilabile metal-organic framework

    Energy Technology Data Exchange (ETDEWEB)

    Allan, P. K.; Chapman, K. W.; Chupas, P. J.; Hriljac, J. A.; Renouf, C. L.; Lucas, T. C. A.; Morris, R. E. (X-Ray Science Division); (Univ. of St. Andrews); (Univ. of Birmingham)

    2012-01-01

    Flexible metal-organic frameworks (MOFs) are materials of great current interest. A small class of MOFs show flexibility driven by reversible bonding rearrangements that lead directly to unusual properties. Cu-SIP-3 is a MOF based on the 5-sulfoisophthalate ligand, where the strong copper-carboxylate bonds ensure that the three-dimensional integrity of the structure is retained while allowing bonding changes to occur at the more weakly bonding sulfonate group leading to unusual properties such as the ultra-selective adsorption of only certain gases. While the integrity of the framework remains intact during bonding changes, crystalline order is not retained at all times during the transformations. X-Ray diffraction reveals that highly crystalline single crystals lose order during the transformation before regaining crystallinity once it is complete. Here we show how X-ray pair distribution function analysis can be used to reveal the mechanism of the transformations in Cu-SIP-3, identifying the sequence of atomic displacements that occur in the disordered phase. A similar approach reveals the underlying mechanism of Cu-SIP-3's ultra-selective gas adsorption.

  11. A combined metabolomic and phylogenetic study reveals putatively prebiotic effects of high molecular weight arabino-oligosaccharides when assessed by in vitro fermentation in bacterial communities derived from humans

    DEFF Research Database (Denmark)

    Sulek, Karolina; Vigsnæs, Louise Kristine; Schmidt, Line Rieck

    2014-01-01

    Prebiotic oligosaccharides are defined by their selective stimulation of growth and/or activity of bacteria in the digestive system in ways claimed to be beneficial for health. However, apart from the short chain fatty acids, little is known about bacterial metabolites created by fermentation...... plant structures. Additionally, the combination of qPCR and LC–MS revealed a number of other putative interactions between intestinal microbes and the oligosaccharides, which contributes to the understanding of the mechanisms behind prebiotic impact on human health....... of prebiotics, and the significance of the size of the oligosaccharides remains largely unstudied. By in vitro fermentations in human fecal microbial communities (derived from six different individuals), we studied the effects of high-mass (HA, >1 kDa), low-mass (LA,

  12. Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

    Science.gov (United States)

    Someya, Tatsuhiko; Baba, Seiki; Fujimoto, Mai; Kawai, Gota; Kumasaka, Takashi; Nakamura, Kouji

    2012-01-01

    Bacterial Hfq is a protein that plays an important role in the regulation of genes in cooperation with sRNAs. Escherichia coli Hfq (EcHfq) has two or more sites that bind RNA(s) including U-rich and/or the poly(A) tail of mRNA. However, functional and structural information about Bacillus subtilis Hfq (BsHfq) including the RNA sequences that specifically bind to it remain unknown. Here, we describe RNA aptamers including fragment (AG)3A that are recognized by BsHfq and crystal structures of the BsHfq–(AG)3A complex at 2.2 Å resolution. Mutational and structural studies revealed that the RNA fragment binds to the distal site, one of the two binding sites on Hfq, and identified amino acid residues that are critical for sequence-specific interactions between BsHfq and (AG)3A. In particular, R32 appears to interact with G bases in (AG)3A. Poly(A) also binds to the distal site of EcHfq, but the overall RNA structure and protein–RNA interaction patterns engaged in the R32 residues of BsHfq–(AG)3A differ from those of EcHfq–poly(A). These findings provide novel insight into how the Hfq homologue recognizes RNA. PMID:22053080

  13. Change in viable bacterial count during preservation of milk derived from dairy cows with subclinical mastitis and its relationship with antimicrobial components in milk

    Science.gov (United States)

    HISAEDA, Keiichi; KOSHIISHI, Tomoko; WATANABE, Masako; MIYAKE, Hajime; YOSHIMURA, Yukinori; ISOBE, Naoki

    2016-01-01

    The objectives of the present study were to investigate the change in the number of viable pathogens during preservation of milk obtained from cows with subclinical mastitis and the association between the decreasing ratio of viable bacteria during preservation and the somatic cell count (SCC) and the values of lingual antimicrobial peptide (LAP), lactoferrin (LF) and lactoperoxidase (LPO). After preservation of milk at room temperature for 0, 0.5, 1, 2, 3, 4 and 5 hr, the bacterial colonies in the milk were counted to determine the number of colony forming units (CFUs). Fresh skim milk was used to determine the values of LAP, LPO and LF. Bacteria were not detected in 19.4% of milk samples, and this percentage increased up to 30% after 5 hr of preservation. The number of Staphylococcus aureus and Streptococcus uberis in milk did not change significantly during the 5-hr incubation, whereas significant decreases were observed in the number of coliforms, coagulase-negative staphylococci, yeasts and Corynebacterium bovis. High SCC significantly decreased CFUs of S. aureus and yeast after preservation of milk for 4 to 5 hr. High LF concentration in milk was associated with decrease in CFU of S. aureus during 4-hr preservation. These results suggest that the viable counts of some pathogens in milk decreased during preservation at room temperature after collection, which may be attributed to the leukocytes and antimicrobial components present in milk. PMID:27109069

  14. The origin of emissive states of carbon nanoparticles derived from ensemble-averaged and single-molecular studies.

    Science.gov (United States)

    Demchenko, Alexander P; Dekaliuk, Mariia O

    2016-08-01

    At present, there is no consensus understanding on the origin of photoluminescence of carbon nanoparticles, particularly the so-called carbon dots. Providing comparative analysis of spectroscopic studies in solution and on a single-molecular level, we demonstrate that these particles behave collectively as fixed single dipoles and probably are the quantum emitter entities. Their spectral and lifetime heterogeneity in solutions is explained by variation of the local chemical environment within and around luminescence centers. Hence, the carbon dots possess a unique hybrid combination of fluorescence properties peculiar to dye molecules, their conjugates and semiconductor nanocrystals. It is proposed that their optical properties are due to generation of H-aggregate-type excitonic states with their coherence spreading over the whole nanoparticles.

  15. The origin of emissive states of carbon nanoparticles derived from ensemble-averaged and single-molecular studies

    Science.gov (United States)

    Demchenko, Alexander P.; Dekaliuk, Mariia O.

    2016-07-01

    At present, there is no consensus understanding on the origin of photoluminescence of carbon nanoparticles, particularly the so-called carbon dots. Providing comparative analysis of spectroscopic studies in solution and on a single-molecular level, we demonstrate that these particles behave collectively as fixed single dipoles and probably are the quantum emitter entities. Their spectral and lifetime heterogeneity in solutions is explained by variation of the local chemical environment within and around luminescence centers. Hence, the carbon dots possess a unique hybrid combination of fluorescence properties peculiar to dye molecules, their conjugates and semiconductor nanocrystals. It is proposed that their optical properties are due to generation of H-aggregate-type excitonic states with their coherence spreading over the whole nanoparticles.

  16. DERIVATION OF A SINGLE-BAND MODEL FOR CUO2 PLANES BY A CELL-PERTURBATION METHOD

    NARCIS (Netherlands)

    JEFFERSON, JH; ESKES, H; FEINER, LF

    1992-01-01

    A cell-perturbation method is developed for CuO2 planes in the cuprate superconductors described by a d-p model. It is shown that a single-band t-t'-J-J' model accurately describes the low-energy physics and how the parameters of this model vary with those of the underlying d-p model. The method is

  17. The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content

    Directory of Open Access Journals (Sweden)

    Zachery T. Lewis

    2016-01-01

    Full Text Available Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides. No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status. However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.

  18. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion...... is the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental parameters......, which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to significantly...

  19. Bacterial lipases

    NARCIS (Netherlands)

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    1994-01-01

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation, mea

  20. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    Bacterial ecology is concerned with the interactions between bacteria and their biological and nonbiological environments and with the role of bacteria in biogeochemical element cycling. Many fundamental properties of bacteria are consequences of their small size. Thus, they can efficiently exploit...

  1. DNA-damaging activity in vivo and bacterial mutagenicity of sixteen aromatic amines and azo-derivatives, as related quantitatively to their carcinogenicity.

    Science.gov (United States)

    Parodi, S; Taningher, M; Russo, P; Pala, M; Tamaro, M; Monti-Bragadin, C

    1981-01-01

    Sixteen aromatic amines and azo-derivatives were studied. They were: benzidine; 2-acetylaminofluorene; 3'-methyl-p-dimethylaminobenzene; o-aminoazo-toluene; p-dimethylaminoazobenzene; 2,4-diamino-toluene; 4,4'-oxydianiline; 2,4-diaminoanisole; 4,4'-methylenedianiline; 2-naphthylamine; Auramine O; Rhodamine B; Ponceau MX; 1-naphthylamine; p-aminoazobenzene and aniline. The compounds were examined for their capability to induce alkaline DNA fragmentation in rat liver after treatment in vivo, for their mutagenicity in the Salmonella strains TA 98 and TA 100, for their acute toxicity and for their carcinogenicity in mice and rats. For each parameter a quantitative potency index was established, and the correlation existing amongst the different parameters investigated. Only mutagenicity in the strain TA 98 was slightly correlated with carcinogenic potency (r = 0.408). DNA fragmentation and toxicity were not correlated with carcinogenicity. A significant correlation was found between DNA fragmentation and toxicity (r = 0.539). No correlation was found between DNA fragmentation and mutagenicity. The lack of correlation between DNA fragmentation and carcinogenicity is in contrast with previous results obtained with a family of hydrazine derivatives (12) and a group of nitrosocompounds (22). For these two groups of chemicals correlation between DNA fragmentation and carcinogenicity existed, but not between carcinogenicity and mutagenicity in the Ames' test. It is suggested that short term tests can perform very differently for different classes of chemicals.

  2. Expanded Large-Scale Forcing Properties Derived from the Multiscale Data Assimilation System and Its Application to Single-Column Models

    Science.gov (United States)

    Feng, S.; Li, Z.; Liu, Y.; Lin, W.; Toto, T.; Vogelmann, A. M.; Fridlind, A. M.

    2013-12-01

    We present an approach to derive large-scale forcing that is used to drive single-column models (SCMs) and cloud resolving models (CRMs)/large eddy simulation (LES) for evaluating fast physics parameterizations in climate models. The forcing fields are derived by use of a newly developed multi-scale data assimilation (MS-DA) system. This DA system is developed on top of the NCEP Gridpoint Statistical Interpolation (GSI) System and is implemented in the Weather Research and Forecasting (WRF) model at a cloud resolving resolution of 2 km. This approach has been applied to the generation of large scale forcing for a set of Intensive Operation Periods (IOPs) over the Atmospheric Radiation Measurement (ARM) Climate Research Facility's Southern Great Plains (SGP) site. The dense ARM in-situ observations and high-resolution satellite data effectively constrain the WRF model. The evaluation shows that the derived forcing displays accuracies comparable to the existing continuous forcing product and, overall, a better dynamic consistency with observed cloud and precipitation. One important application of this approach is to derive large-scale hydrometeor forcing and multiscale forcing, which is not provided in the existing continuous forcing product. It is shown that the hydrometeor forcing poses an appreciable impact on cloud and precipitation fields in the single-column model simulations. The large-scale forcing exhibits a significant dependency on domain-size that represents SCM grid-sizes. Subgrid processes often contribute a significant component to the large-scale forcing, and this contribution is sensitive to the grid-size and cloud-regime.

  3. Facile synthesis of single-crystalline microwires based on anthracene derivative and their efficient optical waveguides and linearly polarized emission

    Science.gov (United States)

    Peng, Hong-Dan; Wang, Juan-Ye; Liu, Zheng-Hui; Pan, Ge-Bo

    2016-05-01

    The well-defined single-crystalline microwires of a solid-emissive organic functional molecule, 2-(anthracen-9-yl)-4, 5-diphenyl-1H-imidozole (ADPI) were successfully prepared by a facile solution process without the use of surfactant or additional templates. In addition, the optical loss coefficient is as low as 0.1 dB μm-1 for the as-prepared ADPI microwires, which is lower than most previous reported organic optical waveguides. Meanwhile, these microwires also show optically uniaxial properties as demonstrated by the linearly polarized emission, providing potentially orientation-sensitive applications as optical waveguides with low optical loss.

  4. Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5+ Intestinal Stem Cells

    Directory of Open Access Journals (Sweden)

    Tae-Hee Kim

    2016-08-01

    Full Text Available Lgr5+ intestinal stem cells (ISCs drive epithelial self-renewal, and their immediate progeny—intestinal bipotential progenitors—produce absorptive and secretory lineages via lateral inhibition. To define features of early transit from the ISC compartment, we used a microfluidics approach to measure selected stem- and lineage-specific transcripts in single Lgr5+ cells. We identified two distinct cell populations, one that expresses known ISC markers and a second, abundant population that simultaneously expresses markers of stem and mature absorptive and secretory cells. Single-molecule mRNA in situ hybridization and immunofluorescence verified expression of lineage-restricted genes in a subset of Lgr5+ cells in vivo. Transcriptional network analysis revealed that one group of Lgr5+ cells arises from the other and displays characteristics expected of bipotential progenitors, including activation of Notch ligand and cell-cycle-inhibitor genes. These findings define the earliest steps in ISC differentiation and reveal multilineage gene priming as a fundamental property of the process.

  5. Effect of purified β-glucans derived from Laminaria digitata, Laminaria hyperborea and Saccharomyces cerevisiae on piglet performance, selected bacterial populations, volatile fatty acids and pro-inflammatory cytokines in the gastrointestinal tract of pigs.

    Science.gov (United States)

    Sweeney, T; Collins, C B; Reilly, P; Pierce, K M; Ryan, M; O'Doherty, J V

    2012-10-01

    β-Glucans have been identified as natural biomolecules with immunomodulatory activity. The first objective of the present study was to compare the effects of purified β-glucans derived from Laminaria digitata, L. hyperborea and Saccharomyces cerevisiae on piglet performance, selected bacterial populations and intestinal volatile fatty acid (VFA) production. The second aim was to compare the gene expression profiles of the markers of pro- and anti-inflammation in both unchallenged and lipopolysaccharide (LPS)-challenged ileal and colonic tissues. β-Glucans were included at 250 mg/kg in the diets. The β-glucans derived from L. hyperborea, L. digitata and S. cerevisiae all reduced the Enterobacteriaceae population (P0·05) in the ileum and colon. There was a significant interaction between gastrointestinal region and β-glucan source in the expression of cytokine markers, IL-1α (yeast sources reduce Enterobacteriaceae counts and pro-inflammatory markers in the colon, though the mechanisms of action may be different between the soluble and insoluble fibre sources.

  6. Synthesis and single crystal x-ray diffraction study of a Schiff base derived from 4-acylpyrazolone and 2-aminophenol

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Naresh; Kant, Rajni, E-mail: vivek-gupta2k2@hotmail.com; Gupta, Vivek K., E-mail: vivek-gupta2k2@hotmail.com [Department of Physics and Electronics, University of Jammu, Jammu Tawi - 180006 (India); Jadeja, R. N. [Department of Chemistry, Faculty of Science, The M. S. University of Baroda, Vadodara-390002 (India)

    2014-04-24

    The title compound, (Z)-1-(3-chlorophenyl)-4[1((2hydroxyphenyl)amino)propylidene] -3-methyl-1H-pyrazol-5(4H)-one was synthesized by refluxing compound 1-(m-chlorophenyl)-3-methyl-4-propionyl-5-pyrazolone, with 2-aminophenol in ethanol. The compound crystallizes in the orthorhombic crystal system with space group Pca2{sub 1} having unit cell parameters: a = 26.2993(8), b = 7.0724(2) and c = 18.7170(5)Å. The structure contains two crystallographically independent molecules, A, and, B, in the asymmetric unit cell. The crystal structure was solved by direct method using single crystal X-ray diffraction data collected at room temperature and refined by full-matrix least-squares procedures to a final R- value of 0.049 for 5207 observed reflections.

  7. Synthesis, spectral characterization, single crystal and conformational study of 1,5-dimethyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-one derivatives

    Science.gov (United States)

    Venkateswaramoorthi, R.; John Francis Xavier, J.; Krishnasamy, K.; Saleem, H.

    2012-03-01

    1,5-Dimethyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-one 1 and their derivatives 2-8 were obtained by condensation of 2,6-dimethyl cyclohexanone, Ammonium acetate and substituted aromatic aldehydes and characterized by FT-IR, FT-Raman, 1H NMR, 13C NMR, GC-MS, HOMOCOSY, HSQC, NOESY, single crystal X-ray diffraction analysis and theoretical DFT calculation. Compound 1 crystallized in the Triclinic system, space group P-1 with a = 6.8950(5) Ǻ, b = 11.5889(9) Ǻ, c = 11.9172(9) Ǻ, α = 76.277(4)°, β = 78.000(3)°, γ = 72.920(4)°, V = 874.41(12) Ǻ3 and Z = 2. 1,5-Dimethyl-2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-one 1 and their derivatives 2-8 were exist in boat-chair conformation with equatorial orientation of all the substituents at piperidine ring (two phenyl rings at C-2 and C-4 position, two methyl substituents at C-1 and C-5 position) of compound 1. In the crystal structure of compound 1, the molecules are connected by Nsbnd H⋯Odbnd C intermolecular hydrogen bonds. The existence of boat-chair conformation was confirmed by single crystal X-ray diffraction analysis and theoretical DFT calculation.

  8. [Bacterial vaginosis].

    Science.gov (United States)

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists.

  9. Bacterial-Derived Polymer Poly-γ-Glutamic Acid (γ-PGA)-Based Micro/Nanoparticles as a Delivery System for Antimicrobials and Other Biomedical Applications

    Science.gov (United States)

    Khalil, Ibrahim R.; Burns, Alan T. H.; Radecka, Iza; Kowalczuk, Marek; Khalaf, Tamara; Adamus, Grazyna; Johnston, Brian; Khechara, Martin P.

    2017-01-01

    In the past decade, poly-γ-glutamic acid (γ-PGA)-based micro/nanoparticles have garnered remarkable attention as antimicrobial agents and for drug delivery, owing to their controlled and sustained-release properties, low toxicity, as well as biocompatibility with tissue and cells. γ-PGA is a naturally occurring biopolymer produced by several gram-positive bacteria that, due to its biodegradable, non-toxic and non-immunogenic properties, has been used successfully in the medical, food and wastewater industries. Moreover, its carboxylic group on the side chains can offer an attachment point to conjugate antimicrobial and various therapeutic agents, or to chemically modify the solubility of the biopolymer. The unique characteristics of γ-PGA have a promising future for medical and pharmaceutical applications. In the present review, the structure, properties and micro/nanoparticle preparation methods of γ-PGA and its derivatives are covered. Also, we have highlighted the impact of micro/nanoencapsulation or immobilisation of antimicrobial agents and various disease-related drugs on biodegradable γ-PGA micro/nanoparticles. PMID:28157175

  10. A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene

    OpenAIRE

    2013-01-01

    Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria’s host is a “farmer” clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves a...

  11. Neutralization Analysis of a Chicken Single-Chain Variable Fragment Derived from an Immune Antibody Library Against Infectious Bronchitis Virus.

    Science.gov (United States)

    Lin, Yuan; Li, Benqiang; Ye, Jiaxin; Wang, Man; Wang, Jianhua; Zhang, Ying; Zhu, Jianguo

    2015-09-01

    Avian infectious bronchitis virus (IBV), which is prevalent in many countries causing severe economic loss to the poultry industry, causes infectious bronchitis (IB) in birds. Recombinant single-chain variable fragments (scFvs) have been proven to effectively inhibit many viruses, both in vitro and in vivo, and they could be a potential diagnostic and therapeutic reagent to control IB. In this study, six anti-IBV chicken scFvs, ZL.10, ZL.64, ZL.78, ZL.80, ZL.138, and ZL.256, were obtained by screening random clones from an immune antibody library. An analysis of nucleotide sequences revealed that they represented distinctive genetic sequences and greatly varied in complementarity-determining region three of the heavy chain. Neutralization tests showed that ZL.10, which bound the S1 protein in western blots, inhibited the formation of syncytia in Vero cells 48 h post IBV infection and decreased the transcriptional level of nucleoprotein mRNA to 17.2%, while the other five scFvs, including ZL.78 and ZL.256, that bound the N protein did not. In conclusion, the results suggested that specific and neutralizing chicken scFvs against IBV, which can be safe and economical antibody reagents, can be produced in vitro through prokaryotic expression.

  12. The Fingerprint of Rapid Eye Movement: Its Algorithmic Detection in the Sleep Electroencephalogram Using a Single Derivation.

    Science.gov (United States)

    McCarty, David E; Kim, Paul Y; Frilot, Clifton; Chesson, Andrew L; Marino, Andrew A

    2016-10-01

    The strong associations of rapid eye movement (REM) sleep with dreaming and memory consolidation imply the existence of REM-specific brain electrical activity, notwithstanding the visual similarity of the electroencephalograms (EEGs) in REM and wake states. Our goal was to detect REM sleep by means of algorithmic analysis of the EEG. We postulated that novel depth and fragmentation variables, defined in relation to temporal changes in the signal (recurrences), could be statistically combined to allow disambiguation of REM epochs. The cohorts studied were consecutive patients with obstructive sleep apnea (OSA) recruited from a sleep medicine clinic, and clinically normal participants selected randomly from a national database (N = 20 in each cohort). Individual discriminant analyses were performed, for each subject based on 4 recurrence biomarkers, and used to classify every 30-second epoch in the subject's overnight polysomnogram as REM or NotREM (wake or any non-REM sleep stage), using standard clinical staging as ground truth. The primary outcome variable was the accuracy of algorithmic REM classification. Average accuracies of 90% and 87% (initial and cross-validation analyses) were achieved in the OSA cohort; corresponding results in the normal cohort were 87% and 85%. Analysis of brain recurrence allowed identification of REM sleep, disambiguated from wake and all other stages, using only a single EEG lead, in subjects with or without OSA.

  13. Identification and characterization of a new type of asymmetrical dicentric chromosome derived from a single maternal chromosome 18.

    Science.gov (United States)

    Lin, C C; Li, Y-C; Liu, P-P; Hsieh, L-J; Cheng, Y-M; Teng, R-H; Shi, S-L; Tsai, F-J

    2007-01-01

    Molecular cytogenetic analysis identified a new type of dicentric chromosome involving different breakpoints at 18q in a female fetus. The chromosome anomaly was designated as an asymmetrical pseudoisodicentric chromosome 18, 46,XX,psu dic(18)(pter-->q11.2::q21.3-->pter)mat. A series of BAC clones for 18q11.2 and q21.3 regions were used to identify one breakpoint within the region q11.2 between 19.8 and 21.6 Mb from the telomere of 18p and another breakpoint within q21.3 between 55.4 and 56.9 Mb from the telomere of 18p by FISH analysis. Real-time quantitative PCR and microsatellite analysis further verified that the dicentric chromosome was maternal in origin and resulted from a break-reunion between sister chromatids of a single maternal chromosome. We propose that a loop-type configuration of sister chromatids took place and that the break-reunion occurred at cross sites of the loop to form an asymmetrical isodicentric chromosome during either mitosis or meiosis. In this case, the asymmetrical pseudoisodicentric resulted in an 18pter--> q11.2 duplication and an 18q21.3-->qter deletion, which could have led to certain dysmorphic features of 18q- syndrome in this fetus.

  14. Characterization of Recombinant Dengue-2 Virus Derived from a Single Nucleotide Substitution in the 5′ Noncoding Region

    Directory of Open Access Journals (Sweden)

    Vijittra Leardkamolkarn

    2010-01-01

    Full Text Available Variants of wild-type dengue serotype 2 (DEN-2 virus containing nucleotide substitutions at positions 14, 15, or 57 in the 5′ NCR were constructed by PCR-mediated site-directed mutagenesis. All three viruses containing a single point substitution demonstrated attenuation phenotype as evidenced by decreases replication and plaque size in cell culture assay. All three variants were less neurovirulent in newborn mice compared to the wild type. The mutants were immunogenic in adult mice immunogenicity and maintained stable replication characteristics following passage in mice. The variant viruses were competent for replication in Aedes aegypi mosquito vector, albeit at lower levels of infection and dissemination in the mosquito than the wild-type Den-2 16681 virus. Although all of the viruses, including the wild type, were found transmissible in mosquito life cycles, they were found subsequentially decreased in efficiency of infection, transmission, and dissemination rates along the mosquito generations and all of them remained genetically stable.

  15. Characterization of rice black-streaked dwarf virus- and rice stripe virus-derived siRNAs in singly and doubly infected insect vector Laodelphax striatellus.

    Directory of Open Access Journals (Sweden)

    Junmin Li

    Full Text Available Replication of RNA viruses in insect cells triggers an antiviral defense that is mediated by RNA interference (RNAi which generates viral-derived small interfering RNAs (siRNAs. However, it is not known whether an antiviral RNAi response is also induced in insects by reoviruses, whose double-stranded RNA genome replication is thought to occur within core particles. Deep sequencing of small RNAs showed that when the small brown planthopper (Laodelphax striatellus was infected by Rice black-streaked dwarf virus (RBSDV (Reoviridae; Fijivirus, more viral-derived siRNAs accumulated than when the vector insect was infected by Rice stripe virus (RSV, a negative single-stranded RNA virus. RBSDV siRNAs were predominantly 21 and 22 nucleotides long and there were almost equal numbers of positive and negative sense. RBSDV siRNAs were frequently generated from hotspots in the 5'- and 3'-terminal regions of viral genome segments but these hotspots were not associated with any predicted RNA secondary structures. Under laboratory condition, L. striatellus can be infected simultaneously with RBSDV and RSV. Double infection enhanced the accumulation of particular genome segments but not viral coat protein of RBSDV and correlated with an increase in the abundance of siRNAs derived from RBSDV. The results of this study suggest that reovirus replication in its insect vector potentially induces an RNAi-mediated antiviral response.

  16. Aminoglycoside antibiotics for NIH category II chronic bacterial prostatitis: A single-cohort study with one-year follow-up.

    Science.gov (United States)

    Magri, Vittorio; Montanari, Emanuele; Marras, Emanuela; Perletti, Gianpaolo

    2016-10-01

    Although fluoroquinolones are first-line agents for the treatment of National Institutes of Health (NIH) category II chronic bacterial prostatitis (CBP), therapy with these agents is not always feasible due to the increasing worldwide resistance of causative uropathogens. New therapeutic options are urgently required, as drugs such as β-lactam antibiotics distribute poorly to prostatic sites of infection and trimethoprim therapy is often unfeasible due to high resistance rates. The present study aimed to analyze the efficacy of aminoglycosides, administered to a cohort of 78 patients affected by fluoroquinolone-resistant CBP, or excluded from fluoroquinolone therapy due to various contraindications. Patients received netilmicin (4.5 mg/kg, once-daily, intramuscular), combined or not with a β-lactam antibiotic, for 4 weeks. Follow-up visits were scheduled 6 and 12 months after the end of treatment. Fifty-five out of 70 patients (78.6%) showed eradication of the causative pathogen, and a significant reduction of the NIH-Chronic Prostatitis Symptom Index (NIH-CPSI) total score from a baseline median value of 21 to 14 at the end of therapy, and to 9 and 8 at 6-month and 12-month follow-up assessments, respectively. The pain, voiding and quality of life subdomains of the NIH-CPSI decreased accordingly. In 15 patients showing persistence of infection, NIH-CPSI total and subdomain scores did not decrease at the end of therapy. Additional clinical parameters, such as the urinary peak flow rate, percentage voided bladder, serum prostate-specific antigen concentration, International Prostate Symptom Score and prostate volume improved significantly only in the group of patients in which the infection was eradicated. Therapy was well tolerated, and genetic testing for deafness-predisposing mitochondrial mutations allowed safer administration of aminoglycosides. These results suggest that aminoglycosides may become a therapeutic alternative for the treatment of CBP. These

  17. Aminoglycoside antibiotics for NIH category II chronic bacterial prostatitis: A single-cohort study with one-year follow-up

    Science.gov (United States)

    Magri, Vittorio; Montanari, Emanuele; Marras, Emanuela; Perletti, Gianpaolo

    2016-01-01

    Although fluoroquinolones are first-line agents for the treatment of National Institutes of Health (NIH) category II chronic bacterial prostatitis (CBP), therapy with these agents is not always feasible due to the increasing worldwide resistance of causative uropathogens. New therapeutic options are urgently required, as drugs such as β-lactam antibiotics distribute poorly to prostatic sites of infection and trimethoprim therapy is often unfeasible due to high resistance rates. The present study aimed to analyze the efficacy of aminoglycosides, administered to a cohort of 78 patients affected by fluoroquinolone-resistant CBP, or excluded from fluoroquinolone therapy due to various contraindications. Patients received netilmicin (4.5 mg/kg, once-daily, intramuscular), combined or not with a β-lactam antibiotic, for 4 weeks. Follow-up visits were scheduled 6 and 12 months after the end of treatment. Fifty-five out of 70 patients (78.6%) showed eradication of the causative pathogen, and a significant reduction of the NIH-Chronic Prostatitis Symptom Index (NIH-CPSI) total score from a baseline median value of 21 to 14 at the end of therapy, and to 9 and 8 at 6-month and 12-month follow-up assessments, respectively. The pain, voiding and quality of life subdomains of the NIH-CPSI decreased accordingly. In 15 patients showing persistence of infection, NIH-CPSI total and subdomain scores did not decrease at the end of therapy. Additional clinical parameters, such as the urinary peak flow rate, percentage voided bladder, serum prostate-specific antigen concentration, International Prostate Symptom Score and prostate volume improved significantly only in the group of patients in which the infection was eradicated. Therapy was well tolerated, and genetic testing for deafness-predisposing mitochondrial mutations allowed safer administration of aminoglycosides. These results suggest that aminoglycosides may become a therapeutic alternative for the treatment of CBP. These

  18. Synthesis, growth, optical and DFT calculation of 2-naphthol derived Mannich base organic non linear optical single crystal for frequency conversion applications

    Science.gov (United States)

    Raj, A. Dennis; Jeeva, M.; Shankar, M.; Purusothaman, R.; Prabhu, G. Venkatesa; Potheher, I. Vetha

    2016-11-01

    2-naphthol derived Mannich base 1-((4-methylpiperazin-1-yl) (phenyl) methyl) naphthalen-2-ol (MPN) - a nonlinear optical single crystal was synthesized and successfully grown by slow evaporation technique at room temperature. The molecular structure was confirmed by single crystal XRD, FT-IR, 1H NMR and 13C NMR spectral studies. The single crystal X-ray diffraction analysis reveals that the crystal belongs to orthorhombic crystal system with non-centrosymmetric space group Pna21. The chemical shift of 5.34 ppm (singlet methine CH proton) in 1H NMR and signal for the CH carbon around δ70.169 ppm in 13C NMR confirms the formation of the title compound. The crystal growth pattern and dislocations of crystal are analyzed using chemical etching technique. UV cut off wavelength of the material was found to be 212 nm. The second harmonic generation (SHG) of MPN was determined from Kurtz Perry powder technique and the efficiency is almost equal to that of standard KDP crystal. The laser damage threshold was measured by passing Nd: YAG laser beam through the sample and it was found to be 1.1974 GW/cm2. The material was thermally stable up to 142 °C. The relationship between the molecular structure and the optical properties was also studied from quantum chemical calculations using Density Functional Theory (DFT) and reported for the first time.

  19. Comparison of Aerosol Single Scattering Albedo Derived from the Ozone Monitoring Instrument with Aerosol Robotic Network Observations

    Institute of Scientific and Technical Information of China (English)

    LIU Qi; HONG Yu-Lan

    2012-01-01

    The single-scattering albedo (SSA), which quantifies radiative absorption capability, is an important optical property of aerosols. Ground-based methods have been extensively exploited to determine aerosol SSA but there were no satellite-based SSA measurements available until the advent of advanced remote sensing techniques, such as the Ozone Monitoring Instrument (OMI). Although the overall accuracy of OMI SSA is estimated to approach 0.1, its regional availability is unclear. Four-year SSA daily measurements from three Aerosol Robotic Network (AERONET) sites in China (Xianghe, Taihu, and Hong Kong) are chosen to determine the accuracy of OMI SSA in specific locations. The results show that on a global scale, the OMI SSA is systematically higher (with a mean relative bias of 3.5% and a RMS difference of ~0.06) and has poor correlation with the AERONET observations. In the Xianghe, Taihu, and Hong Kong sites, the correlation coefficients are 0.16, 0.47, and 0.44, respectively, suggesting that the distinct qualities of OMI SSA depend on geographic locations and/or dominant aerosol environments. The two types of SSA data yield the best agreement in Taihu and the worst in Hong Kong; the differing behavior is likely caused by varying levels of cloud contamination. The good consistency of the aerosol variation between the two SSA datasets on a seasonal scale is promising. These findings suggest that the current-version OMI SSA product can be applied to qualitatively characterize climatological variations of aerosol properties despite its limited accuracy as an instantaneous measurement.

  20. A Single-Tube, Functional Marker-Based Multiplex PCR Assay for Simultaneous Detection of Major Bacterial Blight Resistance GenesXa21, xa13 andxa5 in Rice

    Institute of Scientific and Technical Information of China (English)

    S. K. HAJIRA; M. ANILA; S. BHASKAR; V. ABHILASH; H. K. MAHADEVASWAMY; M. KOUSIK; T. DILIPKUMAR; G. HARIKA; G. REKHA; R. M. SUNDARAM; G. S. LAHA; A. YUGANDER; S. M. BALACHANDRAN; B. C. VIRAKTAMATH; K. SUJATHA; C. H. BALACHIRANJEEVI; K. PRANATHI

    2016-01-01

    In marker-assisted breeding for bacterial blight (BB) resistance in rice, three major resistance genes, viz.,Xa21, xa13andxa5,are routinely deployed either singly or in combinations. As efficient and functional markers are yet to be developed forxa13 andxa5,we have developed simple PCR-based functional markers for both the genes.Forxa13,we designed a functional PCR-based marker, xa13-prom targeting the InDel polymorphism in the promoter of candidate geneOs8N3 located on chromosome 8 of rice. With respect toxa5, a multiplex-PCR based functional marker system, named xa5FM, consisting of two sets of primer pairs targeting the 2-bp functional nucleotide polymorphism in the exon II of the geneTFIIAɤ5 (candidate forxa5), has been developed. Both xa13-prom and xa5FM can differentiate the resistant and susceptible alleles forxa13 andxa5, respectively, in a co-dominant fashion. Using these two functional markers along with the already reported functional PCR-based marker forXa21 (pTA248),we designed a single-tube multiplex PCR based assay for simultaneous detection of all the three major resistance genes and demonstrated the utility of the multiplex marker system in a segregating population.

  1. Construction and Analysis of Three-dimensional Graphic Model of Single-chain Fv Derived from an Anti-human Placental Acidic Isoferritin Monoclonal Antibody by Computer

    Institute of Scientific and Technical Information of China (English)

    ZHOU Chun; SHEN Guanxin; ZHU Huifen; YANG Jing; ZHANG Yue; FENG Jiannan; SHEN Beifen

    2000-01-01

    A three-dimensional (3D) graphic model of a single-chain Fv (scFv) which was derived from an anti-human placental acidic isoferritin (PAF) monoclonal antibody (Mab) was constructed by a homologous protein-predicting computer algorithm on Silicon graphic computer station.The structure, surface static electricity and hydrophobicity of scFv were investigated. Computer graphic modelling indicated that all regions of scFv including the linker, variable regions of the heavy (VH) and light (VL) chains were suitable. The VH region and the VL region were involved in composing the "hydrophobic pocket". The linker was drifted away VH and VL regions. The complementarity determining regions (CDRs) of VH and VL regions surrounded the "hydrophobic pocket". This study provides a theory basis for improving antibody affinity, investigating antibody structure and analyzing the functions of VH and VL regions in antibody activity.

  2. Synthesis and conformational analysis of muramic acid delta-lactam structures and their 4-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl) derivatives, characteristic of bacterial spore peptidoglycan.

    Science.gov (United States)

    Keglević, D; Kojić-Prodić, B; Banić, Z; Tomić, S; Puntarec, V

    1993-03-17

    1,6-Anhydro-4-O-benzyl-beta-muramic acid 1',2-lactam (2) was prepared by reduction of 1,6-anhydro-2-azido-4-O-benzyl-2-deoxy-3-O-[(R)-1- methoxycarbonylethyl]-beta-D-glucopyranose (1) followed by cyclisation. Debenzylation of 2 (-->3) and glycosylation of HO-4 with 3,4,6-tri-O-acetyl-2- deoxy-2-phthalimido-beta-D-glucopyranosyl chloride afforded 75% of a beta-(1-->4)-linked disaccharide derivative (7). Removal of the Phth group from 7, then acetylation, and O-deacetylation yielded 4-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-amino-1,6-anhydro-3-O- [(R)- 1-carboxyethyl]-2-deoxy-beta-D-glucopyranose 1',2-lactam (10) Acetolysis of the 1,6-anhydro ring in the 4-acetate (4) of 3 and the 3',4',6'-triacetate (9) of 10, with saponification of the products 5 and 11, afforded 2-amino-3-O- [(R)-1-carboxyethyl]-2-deoxy-D-glucopyranose 1',2-lactam (6) and 4-O-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-2-amino-3- O-[(R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranose 1',2-lactam (12), respectively. The structure of 12 corresponds to that of the disaccharide unit characteristic of the glycan chains of bacterial spore peptidoglycan. 1H NMR spectroscopy indicated that the beta-D-glucopyranose ring in the 1,6-anhydro 1',2-lactam derivatives adopts the BO,3 conformation. On cleavage of the 1,6-anhydro ring by acetolysis, the D-glucopyranose ring adopts the 4C1 conformation. X-ray analysis of 2, 4, and 5 confirmed the proposed structures. Molecular mechanics and molecular dynamics simulations were used to follow the transformation of the BO,3 conformation of the D-glucopyranose ring via transition states to the 4C1 form.

  3. [Single-donor (apheresis) platelets and pooled whole-blood-derived platelets--significance and assessment of both blood products].

    Science.gov (United States)

    Hitzler, Walter E

    2014-01-01

    The transfusion efficacy of ATK, which contain fully functional platelets, is beyond all doubt. The equivalence of ATK and PTK has been subject of many studies. Some of those studies show the superiority of ATK's, while others do not, but there have been no studies that demonstrated a superiority of PTK's. The superiority of platelets stored in plasma and in third generation additive solution was demonstrated in clinical studies; therefore, it cannot be said that all the platelet concentrates on the German market are equivalent in efficacy. Of decisive importance, above all, is the risk of transfusion-transmitted infections with known pathogens, or those not yet discovered. This risk is different for ATK compared to PTK. Taking this difference in risk and the difference in donor exposure of transfused patients into account, it can definitely be said that ATK and PTK are not equivalent. In 2012, the Robert-Koch-Institute (RKI) published a mathematical risk model for different platelet concentrates and assessed the risk of transmitting known pathogens such as HIV, HCV, and HBV. The risk was higher for PTK compared to ATK. The relative risks for PTK derived from 4BCs were 2.2 (95%--CI: 2.1-2.4) for HIV, 2.7 (95%--CI: 2.5-3.0) for HCV, and 2.2 (95%--CI: 2.8-3.7) for HBV. At the present time, these are the relative risks of transfusion-transmitted infections with the traditional pathogens for PTK compared to ATK. In addition to the RKI assessed risks, there is the theoretical risk of a new, unknown agent, transmitted through blood exposure. The magnitude of this risk is hardly predictable for PTK. The experience gathered so far, especially in the last three decades, with the emergence of HIV, prions, and West Nil virus, shows that the biological nature of a next transfusion-transmissible infectious agent cannot be predictable. This agent, if we think at a conventional sexually transmissible agent with nucleic acid and long latent period, would spread first in areas with

  4. Imperfect DNA lesion repair in the semiconservative quasispecies model: Derivation of the Hamming class equations and solution of the single-fitness peak landscape

    Science.gov (United States)

    Tannenbaum, Emmanuel; Sherley, James L.; Shakhnovich, Eugene I.

    2004-12-01

    This paper develops a Hamming class formalism for the semiconservative quasispecies equations with imperfect lesion repair, first presented and analytically solved in Y. Brumer and E.I. Shakhnovich (q-bio.GN/0403018, 2004). Starting from the quasispecies dynamics over the space of genomes, we derive an equivalent dynamics over the space of ordered sequence pairs. From this set of equations, we are able to derive the infinite sequence length form of the dynamics for a class of fitness landscapes defined by a master genome. We use these equations to solve for a generalized single-fitness-peak landscape, where the master genome can sustain a maximum number of lesions and remain viable. We determine the mean equilibrium fitness and error threshold for this class of landscapes, and show that when lesion repair is imperfect, semiconservative replication displays characteristics from both conservative replication and semiconservative replication with perfect lesion repair. The work presented here provides a formulation of the model which greatly facilitates the analysis of a relatively broad class of fitness landscapes, and thus serves as a convenient springboard into biological applications of imperfect lesion repair.

  5. Effect of Single and Double Administration of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells Following Focal Cerebral Ischemia in Rats

    Science.gov (United States)

    Park, Hyung Woo; Kim, Yona; Chang, Jong Wook; Yang, Yoon Sun; Oh, Wonil; Lee, Jae Min; Park, Hye Ran; Kim, Dong Gyu

    2017-01-01

    Stem cell therapies are administered during the acute phase of stroke to preserve the penumbral tissues from ischemic injury. However, the effect of repeated cell therapy during the acute phase remains unclear. In this study, we investigated and compared the functional outcome of single (two days post-injury) and repeated (two and nine days post-injury) treatment with human umbilical cord derived mesenchymal stem cells (hUCB-MSCs) after middle cerebral artery occlusion (MCAO). The rotarod and limb placement tests were utilized to investigate functional outcomes, while infarct volume and tissue damage were measured by immunofluorescent staining for neovascularization, neurogenesis, apoptosis, and inflammation in the penumbral zones. We observed notable motor dysfunction and a significant decrease in infarcted brain volume, as well as increases in neurons and vessels in both single and repeated hUCB-MSC treatments compared to the control group. Interestingly, repeated administration of hUCB-MSCs was not found to elicit additional or synergistic improvements over monotherapy. This study suggests that a clearer understanding of the therapeutic window after stroke will facilitate the development of more efficient treatment protocols in the clinical application of stem cell therapy. PMID:28243167

  6. Deriving Sensitivity Kernels of Coda-Wave Travel Times to Velocity Changes Based on the Three-Dimensional Single Isotropic Scattering Model

    Science.gov (United States)

    Nakahara, Hisashi; Emoto, Kentaro

    2016-08-01

    Recently, coda-wave interferometry has been used to monitor temporal changes in subsurface structures. Seismic velocity changes have been detected by coda-wave interferometry in association with large earthquakes and volcanic eruptions. To constrain the spatial extent of the velocity changes, spatial homogeneity is often assumed. However, it is important to locate the region of the velocity changes correctly to understand physical mechanisms causing them. In this paper, we are concerned with the sensitivity kernels relating travel times of coda waves to velocity changes. In previous studies, sensitivity kernels have been formulated for two-dimensional single scattering and multiple scattering, three-dimensional multiple scattering, and diffusion. In this paper, we formulate and derive analytical expressions of the sensitivity kernels for three-dimensional single-scattering case. These sensitivity kernels show two peaks at both source and receiver locations, which is similar to the previous studies using different scattering models. The two peaks are more pronounced for later lapse time. We validate our formulation by comparing it with finite-difference simulations of acoustic wave propagation. Our formulation enables us to evaluate the sensitivity kernels analytically, which is particularly useful for the analysis of body waves from deeper earthquakes.

  7. Deriving Sensitivity Kernels of Coda-Wave Travel Times to Velocity Changes Based on the Three-Dimensional Single Isotropic Scattering Model

    Science.gov (United States)

    Nakahara, Hisashi; Emoto, Kentaro

    2017-01-01

    Recently, coda-wave interferometry has been used to monitor temporal changes in subsurface structures. Seismic velocity changes have been detected by coda-wave interferometry in association with large earthquakes and volcanic eruptions. To constrain the spatial extent of the velocity changes, spatial homogeneity is often assumed. However, it is important to locate the region of the velocity changes correctly to understand physical mechanisms causing them. In this paper, we are concerned with the sensitivity kernels relating travel times of coda waves to velocity changes. In previous studies, sensitivity kernels have been formulated for two-dimensional single scattering and multiple scattering, three-dimensional multiple scattering, and diffusion. In this paper, we formulate and derive analytical expressions of the sensitivity kernels for three-dimensional single-scattering case. These sensitivity kernels show two peaks at both source and receiver locations, which is similar to the previous studies using different scattering models. The two peaks are more pronounced for later lapse time. We validate our formulation by comparing it with finite-difference simulations of acoustic wave propagation. Our formulation enables us to evaluate the sensitivity kernels analytically, which is particularly useful for the analysis of body waves from deeper earthquakes.

  8. Bacterial hydrodynamics

    CERN Document Server

    Lauga, Eric

    2015-01-01

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells yet they represent the bulk of the world's biomass, and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds-number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micron scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically-complex environments. Using hydrodynamics as an organizing framework, we review the biomechanics of bacterial motility and look ahead to future challenges.

  9. Bacterial derived proteoliposome for allergy vaccines.

    Science.gov (United States)

    Lastre, Miriam; Pérez, Oliver; Labrada, Alexis; Bidot, Igor; Pérez, Jorge; Bracho, Gustavo; del Campo, Judith; Pérez, Dainerys; Facenda, Elisa; Zayas, Caridad; Rodríguez, Claudio; Sierra, Gustavo

    2006-04-12

    One current approach in developing anti allergic vaccines is the use of potent adjuvants, capable of inducing Th1 or T regulatory cells. Proteoliposomes (PL) could be a suitable adjuvant. Purified Dermatophagoides siboney (Ds) allergens were mixed with PL and adsorbed into Al(OH)3 and evaluated in mice. The Th1/Th2 responses were measured at classes, subclasses, cytokines, and DTH levels. Anti Ds response was deviated to a Thl pattern, with the production of IgG2a and gamma1FN. A positive DTH response and a dramatic decrease of specific IgE and IL5 were not detected. The low dose was more effective than high dose. These results clearly support the potential use of PL as possible adjuvants for anti-allergic vaccines.

  10. Bacterial vaginosis -- aftercare

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000687.htm Bacterial vaginosis - aftercare To use the sharing features on this ... to back after you use the bathroom. Preventing Bacterial Vaginosis You can help prevent bacterial vaginosis by: Not ...

  11. Pregnancy Complications: Bacterial Vaginosis

    Science.gov (United States)

    ... Complications & Loss > Pregnancy complications > Bacterial vaginosis and pregnancy Bacterial vaginosis and pregnancy E-mail to a friend Please ... this page It's been added to your dashboard . Bacterial vaginosis (also called BV or vaginitis) is an infection ...

  12. 5-Arylidene derivatives of Meldrum's acid: Synthesis, structural characterization using single crystal and powder crystal X-ray diffraction, and electronic properties

    Science.gov (United States)

    Dey, Tanusri; Ghosh, Soumen; Ghosh, Somnath; Mukherjee, Alok Kumar

    2015-07-01

    Four 5-arylidene derivatives of Meldrum's acid, 5-(4-chlorobenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (2), 5-(3-hydroxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (3), 5-(3,4-dimethoxybenzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (4) and 5-(2,4-dimethoxy benzylidene)-2,2-dimethyl-1,3-dioxane-4,6-dione (5) have been synthesized and their crystal structures have been determined using single crystal X-ray diffractometry for 2, 4 and 5 and X-ray powder diffraction for 3. The nature of intermolecular interactions in 2-5 has been analyzed through Hirshfeld surfaces and 2D fingerprint plots. The DFT optimized molecular geometries in 2-5 agree closely with those obtained from the crystallographic studies. The crystal packing in 2-5 exhibits an interplay of Osbnd H⋯O, Csbnd H⋯O, Csbnd H⋯Cl and Csbnd H⋯π (arene) hydrogen bonds and π⋯π interactions, which assemble molecules into three-dimensional architecture in 2, 3 and 5 and two-dimensional framework in 4. The Hirshfeld surface analyses of 2-5, Meldrum's acid (1) and a few related 5-arylidene derivatives of Meldrum's acid retrieved from the Cambridge Structural Database (CSD) indicate that about 85% of the Hirshfeld surface area (72% in 2 where H⋯Cl contribution is about 13%) in this class of compounds are due to H⋯H, O⋯H and C⋯H contacts. The HOMO-LUMO energy gap (>2.2 eV) in 2-5 indicates a significant degree of internal charge transfer within the molecule.

  13. Llama-derived single variable domains (nanobodies) directed against chemokine receptor CXCR7 reduce head and neck cancer cell growth in vivo.

    Science.gov (United States)

    Maussang, David; Mujić-Delić, Azra; Descamps, Francis J; Stortelers, Catelijne; Vanlandschoot, Peter; Stigter-van Walsum, Marijke; Vischer, Henry F; van Roy, Maarten; Vosjan, Maria; Gonzalez-Pajuelo, Maria; van Dongen, Guus A M S; Merchiers, Pascal; van Rompaey, Philippe; Smit, Martine J

    2013-10-11

    The chemokine receptor CXCR7, belonging to the membrane-bound G protein-coupled receptor superfamily, is expressed in several tumor types. Inhibition of CXCR7 with either small molecules or small interference (si)RNA has shown promising therapeutic benefits in several tumor models. With the increased interest and effectiveness of biologicals inhibiting membrane-bound receptors we made use of the "Nanobody platform" to target CXCR7. Previously we showed that Nanobodies, i.e. immunoglobulin single variable domains derived from naturally occurring heavy chain-only camelids antibodies, represent new biological tools to efficiently tackle difficult drug targets such as G protein-coupled receptors. In this study we developed and characterized highly selective and potent Nanobodies against CXCR7. Interestingly, the CXCR7-targeting Nanobodies displayed antagonistic properties in contrast with previously reported CXCR7-targeting agents. Several high affinity CXCR7-specific Nanobodies potently inhibited CXCL12-induced β-arrestin2 recruitment in vitro. A wide variety of tumor biopsies was profiled, showing for the first time high expression of CXCR7 in head and neck cancer. Using a patient-derived CXCR7-expressing head and neck cancer xenograft model in nude mice, tumor growth was inhibited by CXCR7-targeting Nanobody therapy. Mechanistically, CXCR7-targeting Nanobodies did not inhibit cell cycle progression but instead reduced secretion of the angiogenic chemokine CXCL1 from head and neck cancer cells in vitro, thus acting here as inverse agonists, and subsequent angiogenesis in vivo. Hence, with this novel class of CXCR7 inhibitors, we further substantiate the therapeutic relevance of targeting CXCR7 in head and neck cancer.

  14. General derivation of the Green's functions for the atomic approach of the Anderson model: application to a single electron transistor (SET

    Directory of Open Access Journals (Sweden)

    M. E. Foglio

    2012-09-01

    Full Text Available We consider the cumulant expansion of the periodic Anderson model (PAM in the case of a finite electronic correlation U, employing the hybridization as perturbation, and obtain a formal expression of the exact one-electron Green's function (GF. This expression contains effective cumulants that are as difficult to calculate as the original GF, and the atomic approach consists in substituting the effective cumulants by the ones that correspond to the atomic case, namely by taking a conduction band of zeroth width and local hybridization. In a previous work (T. Lobo, M. S. Figueira, and M. E. Foglio, Nanotechnology 21, 274007 (201010.1088/0957-4484/21/27/274007 we developed the atomic approach by considering only one variational parameter that is used to adjust the correct height of the Kondo peak by imposing the satisfaction of the Friedel sum rule. To obtain the correct width of the Kondo peak in the present work, we consider an additional variational parameter that guarantees this quantity. The two constraints now imposed on the formalism are the satisfaction of the Friedel sum rule and the correct Kondo temperature. In the first part of the work, we present a general derivation of the method for the single impurity Anderson model (SIAM, and we calculate several density of states representative of the Kondo regime for finite correlation U, including the symmetrical case. In the second part, we apply the method to study the electronic transport through a quantum dot (QD embedded in a quantum wire (QW, which is realized experimentally by a single electron transistor (SET. We calculate the conductance of the SET and obtain a good agreement with available experimental and theoretical results.

  15. Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study.

    Science.gov (United States)

    Ganji, Masoud Darvish; Mohseni, Maryam; Bakhshandeh, Anahita

    2013-03-01

    We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp (2)-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The -0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.

  16. Protein nanopore-based, single-molecule exploration of copper binding to an antimicrobial-derived, histidine-containing chimera peptide.

    Science.gov (United States)

    Mereuta, Loredana; Schiopu, Irina; Asandei, Alina; Park, Yoonkyung; Hahm, Kyung-Soo; Luchian, Tudor

    2012-12-11

    Metal ions binding exert a crucial influence upon the aggregation properties and stability of peptides, and the propensity of folding in various substates. Herein, we demonstrate the use of the α-HL protein as a powerful nanoscopic tool to probe Cu(2+)-triggered physicochemical changes of a 20 aminoacids long, antimicrobial-derived chimera peptide with a His residue as metal-binding site, and simultaneously dissect the kinetics of the free- and Cu(2+)-bound peptide interaction to the α-HL pore. Combining single-molecule electrophysiology on reconstituted lipid membranes and fluorescence spectroscopy, we show that the association rate constant between the α-HL pore and a Cu(2+)-free peptide is higher than that of a Cu(2+)-complexed peptide. We posit that mainly due to conformational changes induced by the bound Cu(2+) on the peptide, the resulting complex encounters a higher energy barrier toward its association with the protein pore, stemming most likely from an extra entropy cost needed to fit the Cu(2+)-complexed peptide within the α-HL lumen region. The lower dissociation rate constant of the Cu(2+)-complexed peptide from α-HL pore, as compared to that of Cu(2+)-free peptide, supports the existence of a deeper free energy well for the protein interaction with a Cu(2+)-complexed peptide, which may be indicative of specific Cu(2+)-mediated contributions to the binding of the Cu(2+)-complexed peptide within the pore lumen.

  17. DNA translocation by type III restriction enzymes: a comparison of current models of their operation derived from ensemble and single-molecule measurements.

    Science.gov (United States)

    Dryden, David T F; Edwardson, J M; Henderson, Robert M

    2011-06-01

    Much insight into the interactions of DNA and enzymes has been obtained using a number of single-molecule techniques. However, recent results generated using two of these techniques-atomic force microscopy (AFM) and magnetic tweezers (MT)-have produced apparently contradictory results when applied to the action of the ATP-dependent type III restriction endonucleases on DNA. The AFM images show extensive looping of the DNA brought about by the existence of multiple DNA binding sites on each enzyme and enzyme dimerisation. The MT experiments show no evidence for looping being a requirement for DNA cleavage, but instead support a diffusive sliding of the enzyme on the DNA until an enzyme-enzyme collision occurs, leading to cleavage. Not only do these two methods appear to disagree, but also the models derived from them have difficulty explaining some ensemble biochemical results on DNA cleavage. In this 'Survey and Summary', we describe several different models put forward for the action of type III restriction enzymes and their inadequacies. We also attempt to reconcile the different models and indicate areas for further experimentation to elucidate the mechanism of these enzymes.

  18. Synthesis of single-walled carbon nanotubes by the pyrolysis of a compression activated iron(II) phthalocyanine/phthalocyanine metal-free derivative/ferric acetate mixture

    Indian Academy of Sciences (India)

    Tawanda Mugadza; Edith Antunes; Tebello Nyokong

    2015-07-01

    This paper reports on the synthesis of single walled carbon nanotubes (SWCNTs) from an activated mixture of iron (II) phthalocyanine, its metal-free derivative and ferric acetate. The powdered mixture was activated by compression into a tablet by applying a force of 300 kN, followed by re-grinding into powder and heating it to high temperatures (1000°C). The activation by compression resulted in more than 50% debundling of SWCNTs as judged by transition electron microscopy. Acid functionalization of the SWCNTs was confirmed by the increase in the D:G ratio from 0.56 to 0.87 in the Raman spectra and the observation of an average of one carboxylic acid group per 13 carbon atoms from thermogravimetric analysis (TGA). TGA also showed that the initial decomposition temperatures for the activated and non-activated mixtures to be 205°C and 245°C, respectively. Hence, activation leads to the lowering of the pyrolysis temperature of the phthalocyanines. X-ray diffraction, electronic absorption and Fourier transform infrared spectra were also employed to characterize the SWCNT.

  19. Bacterial Degradation of Aromatic Compounds

    Directory of Open Access Journals (Sweden)

    Qing X. Li

    2009-01-01

    Full Text Available Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

  20. Large atmospheric shortwave radiative forcing by Mediterranean aerosols derived from simultaneous ground-based and spaceborne observations and dependence on the aerosol type and single scattering albedo

    Science.gov (United States)

    di Biagio, Claudia; di Sarra, Alcide; Meloni, Daniela

    2010-05-01

    Aerosol optical properties and shortwave irradiance measurements at the island of Lampedusa (central Mediterranean) during 2004-2007 are combined with Clouds and the Earth's Radiant Energy System observations of the outgoing shortwave flux at the top of the atmosphere (TOA). The measurements are used to estimate the surface (FES), the top of the atmosphere (FETOA), and the atmospheric (FEATM) shortwave aerosol forcing efficiencies for solar zenith angle (θ) between 15° and 55° for desert dust (DD), urban/industrial-biomass burning aerosols (UI-BB), and mixed aerosols (MA). The forcing efficiency at the different atmospheric levels is derived by applying the direct method, that is, as the derivative of the shortwave net flux versus the aerosol optical depth at fixed θ. The diurnal average forcing efficiency at the surface/TOA at the equinox is (-68.9 ± 4.0)/(-45.5 ± 5.4) W m-2 for DD, (-59.0 ± 4.3)/(-19.2 ± 3.3) W m-2 for UI-BB, and (-94.9 ± 5.1)/(-36.2 ± 1.7) W m-2 for MA. The diurnal average atmospheric radiative forcing at the equinox is (+7.3 ± 2.5) W m-2 for DD, (+8.4 ± 1.9) W m-2 for UI-BB, and (+8.2 ± 1.9) W m-2 for MA, suggesting that the mean atmospheric forcing is almost independent of the aerosol type. The largest values of the atmospheric forcing may reach +35 W m-2 for DD, +23 W m-2 for UI-BB, and +34 W m-2 for MA. FETOA is calculated for MA and 25° ≤ θ ≤ 35° for three classes of single scattering albedo (0.7 ≤ ω < 0.8, 0.8 ≤ ω < 0.9, and 0.9 ≤ ω ≤ 1) at 415.6 and 868.7 nm: FETOA increases, in absolute value, for increasing ω. A 0.1 increment in ω determines an increase in FETOA by 10-20 W m-2.

  1. Electrical characterization of single molecule and Langmuir–Blodgett monomolecular films of a pyridine-terminated oligo(phenylene-ethynylene derivative

    Directory of Open Access Journals (Sweden)

    Henrry M. Osorio

    2015-05-01

    Full Text Available Monolayer Langmuir–Blodgett (LB films of 1,4-bis(pyridin-4-ylethynylbenzene (1 together with the “STM touch-to-contact” method have been used to study the nature of metal–monolayer–metal junctions in which the pyridyl group provides the contact at both molecule–surface interfaces. Surface pressure vs area per molecule isotherms and Brewster angle microscopy images indicate that 1 forms true monolayers at the air–water interface. LB films of 1 were fabricated by deposition of the Langmuir films onto solid supports resulting in monolayers with surface coverage of 0.98 × 10−9 mol·cm−2. The morphology of the LB films that incorporate compound 1 was studied using atomic force microscopy (AFM. AFM images indicate the formation of homogeneous, monomolecular films at a surface pressure of transference of 16 mN·m−1. The UV–vis spectra of the Langmuir and LB films reveal that 1 forms two dimensional J-aggregates. Scanning tunneling microscopy (STM, in particular the “STM touch-to-contact” method, was used to determine the electrical properties of LB films of 1. From these STM studies symmetrical I–V curves were obtained. A junction conductance of 5.17 × 10−5 G0 results from the analysis of the pseudolinear (ohmic region of the I–V curves. This value is higher than that of the conductance values of LB films of phenylene-ethynylene derivatives contacted by amines, thiols, carboxylate, trimethylsilylethynyl or acetylide groups. In addition, the single molecule I–V curve of 1 determined using the I(s method is in good agreement with the I–V curve obtained for the LB film, and both curves fit well with the Simmons model. Together, these results not only indicate that the mechanism of transport through these metal–molecule–metal junctions is non-resonant tunneling, but that lateral interactions between molecules within the LB film do not strongly influence the molecule conductance. The results presented here

  2. Spontaneous bacterial peritonitis

    Institute of Scientific and Technical Information of China (English)

    Anastasios Koulaouzidis; Shivaram Bhat; Athar A Saeed

    2009-01-01

    Since its initial description in 1964, research has transformed spontaneous bacterial peritonitis (SBP) from a feared disease (with reported mortality of 90%) to a treatable complication of decompensated cirrhosis,albeit with steady prevalence and a high recurrence rate. Bacterial translocation, the key mechanism in the pathogenesis of SBP, is only possible because of the concurrent failure of defensive mechanisms in cirrhosis.Variants of SBP should be treated. Leucocyte esterase reagent strips have managed to shorten the 'tap-toshot' time, while future studies should look into their combined use with ascitic fluid pH. Third generation cephalosporins are the antibiotic of choice because they have a number of advantages. Renal dysfunction has been shown to be an independent predictor of mortality in patients with SBP. Albumin is felt to reduce the risk of renal impairment by improving effective intravascular volume, and by helping to bind proinflammatory molecules. Following a single episode of SBP, patients should have long-term antibiotic prophylaxis and be considered for liver transplantation.

  3. Complete Genomes of Classical Swine Fever Virus Cloned into Bacterial Artificial Chromosomes

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Reimann, I.; Uttenthal, Åse;

    Complete genome amplification of viral RNA provides a new tool for the generation of modified pestiviruses. We have used our full-genome amplification strategy for generation of amplicons representing complete genomes of classical swine fever virus. The amplicons were cloned directly into a stabl...... single-copy bacterial artificial chromosome (BAC) generating full-length pestivirus DNAs from which infectious RNA transcripts could be also derived. Our strategy allows construction of stable infectious BAC DNAs from a single full-length PCR product....

  4. Cloning, bacterial expression and biological characterization of recombinant human granulocyte chemotactic protein-2 and differential expression of granulocyte chemotactic protein-2 and epithelial cell-derived neutrophil activating peptide-78 mRNAs.

    Science.gov (United States)

    Froyen, G; Proost, P; Ronsse, I; Mitera, T; Haelens, A; Wuyts, A; Opdenakker, G; Van Damme, J; Billiau, A

    1997-02-01

    Human osteosarcoma cells secrete a novel C-X-C chemokine called granulocyte chemotactic protein-2 (GCP-2), which was previously identified by amino acid sequencing of the purified natural protein. In order to understand the role of this new protein in inflammatory reactions, we cloned GCP-2 DNA sequences to generate recombinant protein and specific DNA probes and primers. By means of PCR on cloned cDNA of osteosarcoma cells induced by interleukin-1 beta and fibroblasts induced by lipopolysaccharide plus dsRNA, the complete coding domain of GCP-2 was isolated. This sequence was cloned into the bacterial expression vector pHEN1 and, after induction, GCP-2 was secreted into the periplasm of Escherichia coli. Recombinant GCP-2 (rGCP-2) was purified and characterized by SDS/PAGE as a monomeric 6.5-kDa protein and by amino-terminal sequencing. The chemoattractive potency of GCP-2 for neutrophilic granulocytes was about 10-times less than that of interleukin-8 and the minimal effective dose was 10 ng/ml. However, at optimal dose (100 ng/ml) the maximal chemotactic response was comparable with that of interleukin-8. Both characteristics correspond with those of natural GCP-2. In addition, intracellular calcium release in neutrophils by recombinant GCP-2 was achieved with as little as 10 ng/ml. Quantitation studies using reverse transcriptase and the polymerase chain reaction revealed higher GCP-2 mRNA production in normal fibroblasts than in tumor cells. When compared with epithelial-cell-derived neutrophil-activating peptide-78 (ENA-78) mRNA, the GCP-2 mRNA levels were higher in all cell lines tested. In addition, GCP-2 and ENA-78 expression seem to be differentially regulated in that phorbol ester and lipopolysaccharide have opposing effects on their mRNA induction in diploid fibroblasts and epithelial cells, respectively. Interleukin-1 was demonstrated to be a general inducer for both chemokines, while interferon-gamma down-regulates their mRNA expression. The

  5. Patient-specific and genome-edited induced pluripotent stem cell-derived cardiomyocytes elucidate single cell phenotype of Brugada Syndrome

    Science.gov (United States)

    Liang, Ping; Sallam, Karim; Wu, Haodi; Li, Yingxin; Itzhaki, Ilanit; Garg, Priyanka; Zhang, Ying; Vermglinchan, Vittavat; Lan, Feng; Gu, Mingxia; Gong, Tingyu; Zhuge, Yan; He, Chunjiang; Ebert, Antje D.; Sanchez-Freire, Veronica; Churko, Jared; Hu, Shijun; Sharma, Arun; Lam, Chi Keung; Scheinman, Melvin M.; Bers, Donald M.; Wu, Joseph C.

    2017-01-01

    Background Brugada Syndrome is a disorder associated with characteristic ECG precordial ST elevation and predisposes afflicted patients to ventricular fibrillation and sudden cardiac death. Despite marked achievements in outlining the organ level pathophysiology of the disorder, the understanding of human cellular phenotype has lagged due to lack of adequate human cellular models of the disorder. Methods and Results We recruited two patients with Type 1 Brugada Syndrome (BrS) carrying two different SCN5A variants and two healthy controls. We generated induced pluripotent stem cells (iPSCs) from their skin fibroblasts by using integration-free Sendai virus. We utilized directed differentiation to create purified populations of iPSC-derived cardiomyocytes (iPSC-CMs). BrS iPSC-CMs showed reductions in inward Na+ current density and reduced maximal upstroke velocity of action potential compared to healthy control iPSC-CMs. Furthermore, BrS iPSC-CMs showed increased burden of triggered activity, abnormal Ca2+ transients, and beating interval variation. Correction of the causative variant by genome editing was performed and resultant iPSC-CMs showed resolution of triggered activity and abnormal Ca2+ transients. Gene expression profiling of iPSC-CMs showed clustering of BrS compared to controls. Furthermore, BrS iPSC-CM gene expression correlated with gene expression from BrS human cardiac tissue gene expression. Conclusions Patient-specific iPSC-CMs are able to recapitulate single cell phenotype features of BrS, including blunted inward sodium current, increased triggered activity and abnormal Ca2+ handling. This novel human cellular model creates future opportunities to further elucidate cellular disease mechanism and identify novel therapeutic targets. PMID:27810048

  6. Three-dimensional culture of single embryonic stem-derived neural/stem progenitor cells in fibrin hydrogels: neuronal network formation and matrix remodelling.

    Science.gov (United States)

    Bento, Ana R; Quelhas, Pedro; Oliveira, Maria J; Pêgo, Ana P; Amaral, Isabel F

    2016-12-29

    In an attempt to improve the efficacy of neural stem/progenitor cell (NSPC) based therapies, fibrin hydrogels are being explored to provide a favourable microenvironment for cell survival and differentiation following transplantation. In the present work, the ability of fibrin to support the survival, proliferation, and neuronal differentiation of NSPCs derived from embryonic stem (ES) cells under monolayer culture was explored. Single mouse ES-NSPCs were cultured within fibrin (fibrinogen concentration: 6 mg/ml) under neuronal differentiation conditions up to 14 days. The ES-NSPCs retained high cell viability and proliferated within small-sized spheroids. Neuronal differentiation was confirmed by an increase in the levels of βIII-tubulin and NF200 over time. At day 14, cell-matrix constructs mainly comprised NSPCs and neurons (46.5% βIII-tubulin(+) cells). Gamma-aminobutyric acid (GABA)ergic and dopaminergic/noradrenergic neurons were also observed, along with a network of synaptic proteins. The ES-NSPCs expressed matriptase and secreted MMP-2/9, with MMP-2 activity increasing along time. Fibronectin, laminin and collagen type IV deposition was also detected. Fibrin gels prepared with higher fibrinogen concentrations (8/10 mg/ml) were less permissive to neurite extension and neuronal differentiation, possibly owing to their smaller pore area and higher rigidity. Overall, it is shown that ES-NSPCs within fibrin are able to establish neuronal networks and to remodel fibrin through MMP secretion and extracellular matrix (ECM) deposition. This three-dimensional (3D) culture system was also shown to support cell viability, neuronal differentiation and ECM deposition of human ES-NSPCs. The settled 3D platform is expected to constitute a valuable tool to develop fibrin-based hydrogels for ES-NSPC delivery into the injured central nervous system. Copyright © 2016 John Wiley & Sons, Ltd.

  7. Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain.

    Science.gov (United States)

    Lima, Fabio Mitsuo; Souza, Renata Torres; Santori, Fábio Rinaldo; Santos, Michele Fernandes; Cortez, Danielle Rodrigues; Barros, Roberto Moraes; Cano, Maria Isabel; Valadares, Helder Magno Silva; Macedo, Andréa Mara; Mortara, Renato Arruda; da Silveira, José Franco

    2013-01-01

    Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure.

  8. The Impact of Aerobic Exercise on Brain-Derived Neurotrophic Factor and Neurocognition in Individuals With Schizophrenia: A Single-Blind, Randomized Clinical Trial.

    Science.gov (United States)

    Kimhy, David; Vakhrusheva, Julia; Bartels, Matthew N; Armstrong, Hilary F; Ballon, Jacob S; Khan, Samira; Chang, Rachel W; Hansen, Marie C; Ayanruoh, Lindsey; Lister, Amanda; Castrén, Eero; Smith, Edward E; Sloan, Richard P

    2015-07-01

    Individuals with schizophrenia display substantial neurocognitive deficits for which available treatments offer only limited benefits. Yet, findings from studies of animals, clinical and nonclinical populations have linked neurocognitive improvements to increases in aerobic fitness (AF) via aerobic exercise training (AE). Such improvements have been attributed to up-regulation of brain-derived neurotrophic factor (BDNF). However, the impact of AE on neurocognition, and the putative role of BDNF, have not been investigated in schizophrenia. Employing a proof-of-concept, single-blind, randomized clinical trial design, 33 individuals with schizophrenia were randomized to receive standard psychiatric treatment (n = 17; "treatment as usual"; TAU) or attend a 12-week AE program (n = 16) utilizing active-play video games (Xbox 360 Kinect) and traditional AE equipment. Participants completed assessments of AF (indexed by VO2 peak ml/kg/min), neurocognition (MATRICS Consensus Cognitive Battery), and serum-BDNF before and after and 12-week period. Twenty-six participants (79%) completed the study. At follow-up, the AE participants improved their AF by 18.0% vs a -0.5% decline in the TAU group (P = .002) and improved their neurocognition by 15.1% vs -2.0% decline in the TAU group (P = .031). Hierarchical multiple regression analyses indicated that enhancement in AF and increases in BDNF predicted 25.4% and 14.6% of the neurocognitive improvement variance, respectively. The results indicate AE is effective in enhancing neurocognitive functioning in people with schizophrenia and provide preliminary support for the impact of AE-related BDNF up-regulation on neurocognition in this population. Poor AF represents a modifiable risk factor for neurocognitive dysfunction in schizophrenia for which AE training offer a safe, nonstigmatizing, and side-effect-free intervention.

  9. A Single Nucleotide Polymorphism in the Stromal Cell-Derived Factor 1 Gene Is Associated with Coronary Heart Disease in Chinese Patients

    Directory of Open Access Journals (Sweden)

    Lei Feng

    2014-06-01

    Full Text Available Coronary heart disease (CHD is highly prevalent globally and a major cause of mortality. Genetic predisposition is a non-modifiable risk factor associated with CHD. Eighty-four Chinese patients with CHD and 253 healthy Chinese controls without CHD were recruited. Major clinical data were collected, and a single nucleotide polymorphism (SNP in the stromal cell-derived factor 1 (SDF-1 gene at position 801 (G to A, rs1801157 in the 3'-untranslated region was identified. The correlation between rs1801157 genotypes and CHD was evaluated by a multivariate logistic regression analysis. The allele frequency in the CHD and control groups was in Hardy-Weinberg equilibrium (HWE (p > 0.05. The frequency of the GG genotype in the CHD group (59.5% was significantly higher than that in the control group (49.8% (p = 0.036. A number of variables, including male sex, age, presence of hypertension, and the levels of low-density lipoprotein cholesterol (LDL-C, high-density lipoprotein cholesterol (HDL-C, triglycerides (TG, uric acid, and total bilirubin, were associated with CHD in a primary univariate analysis. In a multivariable logistic regression analysis, the GG genotype (GG:AA, odds ratio (OR = 2.31, 95% confidence interval (CI = 1.21–5.23, male sex, advanced age (≥60 years, presence of hypertension, LDL-C level ≥ 3.33 mg/dL, HDL-C level < 1.03 mg/dL, and TG level ≥ 1.7 mg/dL were independent risk factors for CHD.

  10. Heterogeneous intracellular trafficking dynamics of brain-derived neurotrophic factor complexes in the neuronal soma revealed by single quantum dot tracking.

    Directory of Open Access Journals (Sweden)

    Anke Vermehren-Schmaedick

    Full Text Available Accumulating evidence underscores the importance of ligand-receptor dynamics in shaping cellular signaling. In the nervous system, growth factor-activated Trk receptor trafficking serves to convey biochemical signaling that underlies fundamental neural functions. Focus has been placed on axonal trafficking but little is known about growth factor-activated Trk dynamics in the neuronal soma, particularly at the molecular scale, due in large part to technical hurdles in observing individual growth factor-Trk complexes for long periods of time inside live cells. Quantum dots (QDs are intensely fluorescent nanoparticles that have been used to study the dynamics of ligand-receptor complexes at the plasma membrane but the value of QDs for investigating ligand-receptor intracellular dynamics has not been well exploited. The current study establishes that QD conjugated brain-derived neurotrophic factor (QD-BDNF binds to TrkB receptors with high specificity, activates TrkB downstream signaling, and allows single QD tracking capability for long recording durations deep within the soma of live neurons. QD-BDNF complexes undergo internalization, recycling, and intracellular trafficking in the neuronal soma. These trafficking events exhibit little time-synchrony and diverse heterogeneity in underlying dynamics that include phases of sustained rapid motor transport without pause as well as immobility of surprisingly long-lasting duration (several minutes. Moreover, the trajectories formed by dynamic individual BDNF complexes show no apparent end destination; BDNF complexes can be found meandering over long distances of several microns throughout the expanse of the neuronal soma in a circuitous fashion. The complex, heterogeneous nature of neuronal soma trafficking dynamics contrasts the reported linear nature of axonal transport data and calls for models that surpass our generally limited notions of nuclear-directed transport in the soma. QD-ligand probes are

  11. Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

    Science.gov (United States)

    Hewitt, Krissi M; Mannino, Frank L; Gonzalez, Antonio; Chase, John H; Caporaso, J Gregory; Knight, Rob; Kelley, Scott T

    2013-01-01

    Infants in Neonatal Intensive Care Units (NICUs) are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs) in the spread of infections. We used culture-independent next-generation sequencing to survey bacterial diversity in two San Diego NICUs and to track the sources of microbes in these environments. Thirty IHE samples were collected from two Level-Three NICU facilities. We extracted DNA from these samples and amplified the bacterial small subunit (16S) ribosomal RNA gene sequence using 'universal' barcoded primers. The purified PCR products were pooled into a single reaction for pyrosequencing, and the data were analyzed using QIIME. On average, we detected 93+/-39 (mean +/- standard deviation) bacterial genera per sample in NICU IHEs. Many of the bacterial genera included known opportunistic pathogens, and many were skin-associated (e.g., Propionibacterium). In one NICU, we also detected fecal coliform bacteria (Enterobacteriales) in a high proportion of the surface samples. Comparison of these NICU-derived sequences to previously published high-throughput 16S rRNA amplicon studies of other indoor environments (offices, restrooms and healthcare facilities), as well as human- and soil-associated environments, found the majority of the NICU samples to be similar to typical building surface and air samples, with the notable exception of the IHEs which were dominated by Enterobacteriaceae. Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs.

  12. Bacterial diversity in two Neonatal Intensive Care Units (NICUs.

    Directory of Open Access Journals (Sweden)

    Krissi M Hewitt

    Full Text Available Infants in Neonatal Intensive Care Units (NICUs are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs in the spread of infections. We used culture-independent next-generation sequencing to survey bacterial diversity in two San Diego NICUs and to track the sources of microbes in these environments. Thirty IHE samples were collected from two Level-Three NICU facilities. We extracted DNA from these samples and amplified the bacterial small subunit (16S ribosomal RNA gene sequence using 'universal' barcoded primers. The purified PCR products were pooled into a single reaction for pyrosequencing, and the data were analyzed using QIIME. On average, we detected 93+/-39 (mean +/- standard deviation bacterial genera per sample in NICU IHEs. Many of the bacterial genera included known opportunistic pathogens, and many were skin-associated (e.g., Propionibacterium. In one NICU, we also detected fecal coliform bacteria (Enterobacteriales in a high proportion of the surface samples. Comparison of these NICU-derived sequences to previously published high-throughput 16S rRNA amplicon studies of other indoor environments (offices, restrooms and healthcare facilities, as well as human- and soil-associated environments, found the majority of the NICU samples to be similar to typical building surface and air samples, with the notable exception of the IHEs which were dominated by Enterobacteriaceae. Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs.

  13. Pattern Formation in a Bacterial Colony Model

    Directory of Open Access Journals (Sweden)

    Xinze Lian

    2014-01-01

    Full Text Available We investigate the spatiotemporal dynamics of a bacterial colony model. Based on the stability analysis, we derive the conditions for Hopf and Turing bifurcations. Furthermore, we present novel numerical evidence of time evolution of patterns controlled by parameters in the model and find that the model dynamics exhibit a diffusion controlled formation growth to spots, holes and stripes pattern replication, which show that the bacterial colony model is useful in revealing the spatial predation dynamics in the real world.

  14. Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds

    DEFF Research Database (Denmark)

    Barh, Debmalya; Gupta, Krishnakant; Jain, Neha;

    2013-01-01

    Although attempts have been made to unveil protein-protein and host-pathogen interactions based on molecular insights of important biological events and pathogenesis in various organisms, these efforts have not yet been reported in Corynebacterium pseudotuberculosis (Cp), the causative agent......-species bacterial PPI using conserved proteins in multiple pathogens (Y. pestis, M. tuberculosis, C. diphtheriae, C. ulcerans, E. coli, and all four Cp strains) and E. Coli based experimentally validated PPI data. Furthermore, the interacting proteins in the common conserved inter-species bacterial PPI were used...

  15. DNA methylation and single nucleotide variants in the brain-derived neurotrophic factor (BDNF and oxytocin receptor (OXTR genes are associated with anxiety/depression in older women

    Directory of Open Access Journals (Sweden)

    Yvon eChagnon

    2015-06-01

    Full Text Available Background: Environmental effects and personal experiences could be expressed in individuals through epigenetic non-structural changes such as DNA methylation. This methylation could up- regulate or down-regulate corresponding gene expressions and modify related phenotypes. DNA methylation increases with ageing and could be related to the late expression of some forms of mental disease. The objective of this study was to evaluate the association between anxiety disorders and/or depression in older women and DNA methylation for four genes related to anxiety or depression. Methods: Women aged 65 and older with (n =19 or without (n =24 anxiety disorders and/or major depressive episode (DSM-IV, were recruited. DNA methylation and single nucleotide variant (SNV were evaluated from saliva, respectively by pyrosequencing and by PCR, for the following genes: brain-derived neurotrophic factor (BDNF; rs6265, oxytocin receptor (OXTR; rs53576, serotonin transporter (SLC6A4; rs25531 and apolipoprotein E (APOE; rs429358 and rs7412. Results: A greater BDNF DNA methylation was observed in subjects with anxiety/depression compared to control group subjects(Mean: 2.92 SD: 0.74 vs. 2.34 SD: 0.42; p=0.0026.This difference was more pronounced in subjects carrying the BDNF rs6265 CT genotype (2.99 SD: 0.41 vs.2.27 SD: 0.26; p=0.0006 than those carrying the CC genotype (p=0.0332; no subjects with the TT genotype were observed. For OXTR, a greater DNA methylation was observed in subjects with anxiety/depression, but only for those carrying the AA genotype of the OXTR rs53576SNV, more particularly at one out of the seven CpGs studied (7.01 SD: 0.94 vs. 4.44 SD: 1.11; p=0.0063. No significant differences were observed for APOE and SLC6A4.Conclusion: These results suggest that DNA methylation in interaction with SNV variations in BDNF and OXTR, are associated with the occurrence of anxiety/depression in older women.

  16. Neuronal-like differentiation of single versus multiple treatments with human amnion-derived mesenchymal stem cells induced by basic fibroblast growth factor

    Institute of Scientific and Technical Information of China (English)

    Hongliang Jiao; Fangxia Guan; Xiang Hu; Jianbin Li; Hong Shan; Wei Li; Jun Li; Ying Du; Bo Yang; Yunfan Zhou

    2009-01-01

    BACKGROUND: Cultures from multiple portions of umbilical cord blood mesenchymal stem cells have been shown to undergo more rapid proliferation and attachment than single portions. OBJECTIVE: To observe growth of basic fibroblast growth factor (bFGF)-induced cultures of human amnion-derived mesenchymal stem cells (AMSCs) and differentiation into neuronal-like cells. DESIGN, TIME AND SETTING: Comparative observation. The study was performed at the Laboratory of Microbiology and Immunology, Basic Medical School of Zhengzhou University from January to May 2008.METHODS: Amnia from full-term, uterine-incision delivery were donated by 12 healthy women. AMSCs were obtained by cell separation and culture techniques, and were passaged and induced by bFGF. From the third passage, a total of 1 mL AMSCs, at a density of 1.0 ×10 4/mL, was separately harvested from six samples, which served as group A. A total of 1 mL AMSCs, at a density of 1.0×10 4 /mL, was harvested separately from the remaining six samples, which served as group B. A total of 0.5 mL from the six samples of group A and 0.5 mL from the six samples of group B were combined to form group C. MAIN OUTCOME MEASURES: Differences in cell quantity among the three groups were compared by cell quantification and 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT)analysis. Expression of a glial cell marker, neuron-specific enolase, and nestin was detected in the three groups by immunocytochemistry. RESULTS: Cell quantification and MTT analysis of live cells, as well as AMSC absorbance, were significantly greater in group C compared with groups A and B at 18 days of culture (P<0.05), and no significant difference was observed between groups A and B. Glial fibrillary acidic protein, neuron-specific enolase, and nestin were expressed in all groups following bFGF induction. CONCLUSION: Mixed AMSC cultures promoted proliferation, and bFGF-induced AMSCs differentiated into neuronal-like cells.

  17. DNA sequences and composition from 12 BAC clones-derived MUSB SSR markers mapped to cotton (Gossypium Hirsutum L. x G. Barbadense L.)chromosomes 11 and 21

    Science.gov (United States)

    To discover resistance (R) and/or pathogen-induced (PR) genes involved in disease response, 12 bacterial artificial chromosome (BAC) clones from cv. Acala Maxxa (G. hirsutum) were sequenced at the Clemson University, Genomics Institute, Clemson, SC. These BACs derived MUSB single sequence repeat (SS...

  18. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach...... that imposes selection pressure for resistant bacteria. New approaches are urgently needed. Targeting bacterial virulence functions directly is an attractive alternative. An obvious target is bacterial adhesion. Bacterial adhesion to surfaces is the first step in colonization, invasion, and biofilm formation....... As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will become...

  19. Bacterial degradation of aminopyrine.

    Science.gov (United States)

    Blecher, H; Blecher, R; Wegst, W; Eberspaecher, J; Lingens, F

    1981-11-01

    1. Four strains of bacteria growing with aminopyrine as sole source of carbon were isolated from soil and were identified as strains of Phenylobacterium immobilis. 2. Strain M13 and strain E, the type species of Phenylobacterium immobilis (DSM 1986), which had been isolated by enrichment with chloridazon (5-amino-4-chloro-2-phenyl-2H-pyridazin-3-one) were used to investigate the bacterial degradation of aminopyrine. 3. Three metabolites were isolated and identified as: 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydro-2,3-dihydroxy-4,6-cyc lohexadien-1-yl)-3H-pyrazol-3-one, 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydroxyphenyl)-3H-pyrazol-3 -one and 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-3H-pyrazol-3-one. 4. An enzyme extract from cells of strain m13 was shown to further metabolize the catechol derivative of aminopyrine, with the formation of 2-pyrone-6-carboxylic acid. 5. Results indicate that the benzene ring of aminopyrine is the principal site of microbial metabolism.

  20. Arabidopsis lysin-motif proteins LYM1 LYM3 CERK1 mediate bacterial peptidoglycan sensing and immunity to bacterial infection

    Science.gov (United States)

    Willmann, Roland; Lajunen, Heini M.; Erbs, Gitte; Newman, Mari-Anne; Kolb, Dagmar; Tsuda, Kenichi; Katagiri, Fumiaki; Fliegmann, Judith; Bono, Jean-Jacques; Cullimore, Julie V.; Jehle, Anna K.; Götz, Friedrich; Kulik, Andreas; Molinaro, Antonio; Lipka, Volker; Gust, Andrea A.; Nürnberger, Thorsten

    2011-01-01

    Recognition of microbial patterns by host pattern recognition receptors is a key step in immune activation in multicellular eukaryotes. Peptidoglycans (PGNs) are major components of bacterial cell walls that possess immunity-stimulating activities in metazoans and plants. Here we show that PGN sensing and immunity to bacterial infection in Arabidopsis thaliana requires three lysin-motif (LysM) domain proteins. LYM1 and LYM3 are plasma membrane proteins that physically interact with PGNs and mediate Arabidopsis sensitivity to structurally different PGNs from Gram-negative and Gram-positive bacteria. lym1 and lym3 mutants lack PGN-induced changes in transcriptome activity patterns, but respond to fungus-derived chitin, a pattern structurally related to PGNs, in a wild-type manner. Notably, lym1, lym3, and lym3 lym1 mutant genotypes exhibit supersusceptibility to infection with virulent Pseudomonas syringae pathovar tomato DC3000. Defects in basal immunity in lym3 lym1 double mutants resemble those observed in lym1 and lym3 single mutants, suggesting that both proteins are part of the same recognition system. We further show that deletion of CERK1, a LysM receptor kinase that had previously been implicated in chitin perception and immunity to fungal infection in Arabidopsis, phenocopies defects observed in lym1 and lym3 mutants, such as peptidoglycan insensitivity and enhanced susceptibility to bacterial infection. Altogether, our findings suggest that plants share with metazoans the ability to recognize bacterial PGNs. However, as Arabidopsis LysM domain proteins LYM1, LYM3, and CERK1 form a PGN recognition system that is unrelated to metazoan PGN receptors, we propose that lineage-specific PGN perception systems have arisen through convergent evolution. PMID:22106285

  1. One Pot Single Step Synthesis and Biological Evaluation of Some Novel Bis(1,3,4-thiadiazole Derivatives as Potential Cytotoxic Agents

    Directory of Open Access Journals (Sweden)

    Sobhi M. Gomha

    2016-11-01

    Full Text Available A novel series of bis(1,3,4-thiadiazole derivatives were synthesized in one step methodology with good yields by condensation reaction between bis-hydrazonoyl chloride 1 and various reagents. The structures of the prepared compounds were confirmed by spectral data (IR, NMR, and MS, and elemental analysis. The anticancer activity against human breast carcinoma (MCF-7 cancer cell lines was evaluated in MTT assay. The results revealed that the bis-thiadiazole derivatives 5c,d, 7b,c and 9c had higher antitumor activity than the standard drug Imatinib.

  2. Evolution of Bacterial Suicide

    Science.gov (United States)

    Tchernookov, Martin; Nemenman, Ilya

    2013-03-01

    While active, controlled cellular suicide (autolysis) in bacteria is commonly observed, it has been hard to argue that autolysis can be beneficial to an individual who commits it. We propose a theoretical model that predicts that bacterial autolysis is evolutionarily advantageous to an individualand would fixate in physically structured environments for stationary phase colonies. We perform spatially resolved agent-based simulations of the model, which predict that lower mixing in the environment results in fixation of a higher autolysis rate from a single mutated cell, regardless of the colony's genetic diversity. We argue that quorum sensing will fixate as well, even if initially rare, if it is coupled to controlling the autolysis rate. The model does not predict a strong additional competitive advantage for cells where autolysis is controlled by quorum sensing systems that distinguish self from nonself. These predictions are broadly supported by recent experimental results in B. subtilisand S. pneumoniae. Research partially supported by the James S McDonnell Foundation grant No. 220020321 and by HFSP grant No. RGY0084/2011.

  3. The bacterial microbiota in inflammatory lung diseases.

    Science.gov (United States)

    Huffnagle, Gary B; Dickson, Robert P

    2015-08-01

    Numerous lines of evidence, ranging from recent studies back to those in the 1920s, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined.

  4. The Bacterial Microbiota in Inflammatory Lung Diseases

    Science.gov (United States)

    Huffnagle, Gary B.; Dickson, Robert P.

    2016-01-01

    Numerous lines of evidence, ranging from recent studies back to those in the 1920's, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined. PMID:26122174

  5. Peritonitis - spontaneous bacterial

    Science.gov (United States)

    Spontaneous bacterial peritonitis (SBP); Ascites - peritonitis; Cirrhosis - peritonitis ... who are on peritoneal dialysis for kidney failure. Peritonitis may have other causes . These include infection from ...

  6. The bacterial lux reporter system: applications in bacterial localisation studies.

    Science.gov (United States)

    Gahan, Cormac G M

    2012-02-01

    Bacterial production of visible light is a natural phenomenon occurring in marine (Vibrio and Photobacterium) and terrestrial (Photorhabdus) species. The mechanism underpinning light production in these organisms is similar and involves the oxidation of an aldehyde substrate in a reaction catalysed by the bacterial luciferase enzyme. The genes encoding the luciferase and a fatty acid reductase complex which synthesizes the substrate are contained in a single operon (the lux operon). This provides a useful reporter system as cloning the operon into a recipient host bacterium will generate visible light without the requirement to add exogenous substrate. The light can be detected in vivo in the living animal using a sensitive detection system and is therefore ideally suited to bioluminescence imaging protocols. The system has therefore been widely used to track bacteria during infection or colonisation of the host. As bacteria are currently being examined as bactofection vectors for gene delivery, particularly to tumour tissue, the use of bioluminescence imaging offers a powerful means to investigate vector amplification in situ. The implications of this technology for bacterial localization, tumour targeting and gene transfer (bactofection) studies are discussed.

  7. Intercomparison of aerosol single-scattering albedo derived from AERONET surface radiometers and LARGE in situ aircraft profiles during the 2011 DRAGON-MD and DISCOVER-AQ experiments

    Science.gov (United States)

    Schafer, J. S.; Eck, T. F.; Holben, B. N.; Thornhill, K. L.; Anderson, B. E.; Sinyuk, A.; Giles, D. M.; Winstead, E. L.; Ziemba, L. D.; Beyersdorf, A. J.; Kenny, P. R.; Smirnov, A.; Slutsker, I.

    2014-06-01

    Single-scattering albedo (SSA) retrievals obtained with CIMEL Sun-sky radiometers from the Aerosol Robotic Network (AERONET) aerosol monitoring network were used to make comparisons with simultaneous in situ sampling from aircraft profiles carried out by the NASA Langley Aerosol Group Experiment (LARGE) team in the summer of 2011 during the coincident DRAGON-MD (Distributed Regional Aerosol Gridded Observational Network-Maryland) and DISCOVER-AQ (Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality) experiments. The single-scattering albedos (interpolated to 550 nm) derived from AERONET measurements for aerosol optical depth (AOD) at 440 nm ≥ 0.4 (mean SSA: 0.979) were on average 0.011 lower than the values derived from the LARGE profile measurements (mean SSA: 0.99). The maximum difference observed was 0.023 with all the observed differences within the combined uncertainty for the stated SSA accuracy (0.03 for AERONET; 0.02 for LARGE). Single-scattering albedo averages were also analyzed for lower aerosol loading conditions (AOD ≥ 0.2) and a dependence on aerosol optical depth was noted with significantly lower single-scattering albedos observed for lower AOD in both AERONET and LARGE data sets. Various explanations for the SSA trend were explored based on other retrieval products including volume median radius and imaginary refractive index as well as column water vapor measurements. Additionally, these SSA trends with AOD were evaluated for one of the DRAGON-MD study sites, Goddard Space Flight Center, and two other Mid-Atlantic AERONET sites over the long-term record dating to 1999.

  8. Growth kinetics and in vivo radiosensitivity in nude mice of two subpopulations derived from a single human small cell carcinoma of the lung

    DEFF Research Database (Denmark)

    Spang-Thomsen, M; Clerici, M; Engelholm, S A;

    1986-01-01

    were described according to a transformed Gompertz function, and the cell kinetics were examined by flow cytometric DNA analysis (FCM) and by the technique of labelled mitoses. The effect of single-dose irradiation was estimated by the specific growth delay calculated from the growth curves...

  9. A bacterial tyrosine phosphatase inhibits plant pattern recognition receptor activation.

    Science.gov (United States)

    Macho, Alberto P; Schwessinger, Benjamin; Ntoukakis, Vardis; Brutus, Alexandre; Segonzac, Cécile; Roy, Sonali; Kadota, Yasuhiro; Oh, Man-Ho; Sklenar, Jan; Derbyshire, Paul; Lozano-Durán, Rosa; Malinovsky, Frederikke Gro; Monaghan, Jacqueline; Menke, Frank L; Huber, Steven C; He, Sheng Yang; Zipfel, Cyril

    2014-03-28

    Innate immunity relies on the perception of pathogen-associated molecular patterns (PAMPs) by pattern-recognition receptors (PRRs) located on the host cell's surface. Many plant PRRs are kinases. Here, we report that the Arabidopsis receptor kinase EF-TU RECEPTOR (EFR), which perceives the elf18 peptide derived from bacterial elongation factor Tu, is activated upon ligand binding by phosphorylation on its tyrosine residues. Phosphorylation of a single tyrosine residue, Y836, is required for activation of EFR and downstream immunity to the phytopathogenic bacterium Pseudomonas syringae. A tyrosine phosphatase, HopAO1, secreted by P. syringae, reduces EFR phosphorylation and prevents subsequent immune responses. Thus, host and pathogen compete to take control of PRR tyrosine phosphorylation used to initiate antibacterial immunity.

  10. Cytochemical Differences in Bacterial Glycocalyx

    Science.gov (United States)

    Krautgartner, Wolf Dietrich; Vitkov, Ljubomir; Hannig, Matthias; Pelz, Klaus; Stoiber, Walter

    2005-02-01

    To examine new cytochemical aspects of the bacterial adhesion, a strain 41452/01 of the oral commensal Streptococcus sanguis and a wild strain of Staphylococcus aureus were grown with and without sucrose supplementation for 6 days. Osmiumtetraoxyde (OsO4), uranyl acetate (UA), ruthenium red (RR), cupromeronic blue (CB) staining with critical electrolytic concentrations (CECs), and the tannic acid-metal salt technique (TAMST) were applied for electron microscopy. Cytochemically, only RR-positive fimbriae in S. sanguis were visualized. By contrast, some types of fimbriae staining were observed in S. aureus glycocalyx: RR-positive, OsO4-positive, tannophilic and CB-positive with ceasing point at 0.3 M MgCl2. The CB staining with CEC, used for the first time for visualization of glycoproteins of bacterial glycocalyx, also reveals intacellular CB-positive substances-probably the monomeric molecules, that is, subunits forming the fimbriae via extracellular assembly. Thus, glycosylated components of the biofilm matrix can be reliably related to single cells. The visualization of intracellular components by CB with CEC enables clear distinction between S. aureus and other bacteria, which do not produce CB-positive substances. The small quantities of tannophilic substances found in S. aureus makes the use of TAMST for the same purpose difficult. The present work protocol enables, for the first time, a partial cytochemical differentiation of the bacterial glycocalyx.

  11. Targeted Large-Scale Deletion of Bacterial Genomes Using CRISPR-Nickases.

    Science.gov (United States)

    Standage-Beier, Kylie; Zhang, Qi; Wang, Xiao

    2015-11-20

    Programmable CRISPR-Cas systems have augmented our ability to produce precise genome manipulations. Here we demonstrate and characterize the ability of CRISPR-Cas derived nickases to direct targeted recombination of both small and large genomic regions flanked by repetitive elements in Escherichia coli. While CRISPR directed double-stranded DNA breaks are highly lethal in many bacteria, we show that CRISPR-guided nickase systems can be programmed to make precise, nonlethal, single-stranded incisions in targeted genomic regions. This induces recombination events and leads to targeted deletion. We demonstrate that dual-targeted nicking enables deletion of 36 and 97 Kb of the genome. Furthermore, multiplex targeting enables deletion of 133 Kb, accounting for approximately 3% of the entire E. coli genome. This technology provides a framework for methods to manipulate bacterial genomes using CRISPR-nickase systems. We envision this system working synergistically with preexisting bacterial genome engineering methods.

  12. The Preignition and Autoignition Oxidation of Alternatives to Petroleum Derived JP-8 and their Surrogate Components in a Pressurized Flow Reactor and Single Cylinder Research Engine

    Science.gov (United States)

    2009-09-01

    designs such as HCCI engines , where ignition relies on the chemistry of the fuel. An initial mixture of 59.4% n-decane/40.6% iso-octane was...Octane Oxidation for HCCI Engines . Fuel, Vol. 85, 2593-2604. Koert, D. N., N. P. Cernansky. (1992). A Flow Reactor for the Study of...Reactor and Single Cylinder Research Engine A Thesis Submitted to the Faculty of Drexel University by Matthew S. Kurman in partial

  13. Quantification of nucleated cells, CD34-positive cells and CFU-GM colonies in single bone marrow samples and bone marrow harvests derived from healthy children.

    Science.gov (United States)

    Schündeln, Michael M; Walde, Gabriele; Basu, Oliver; Havers, Werner; Kremens, Bernhard

    2014-05-01

    Little is known regarding bone marrow (BM) cellularity, CD34+ fraction, and CFU-GM colony formation in relation to age and whether healthy children require a reference range distinct from healthy adults. We therefore analyzed a series of single BM aspirates from 45 healthy children who were evaluated as potential BM donors. Thirty-three of these children subsequently donated BM. We quantified the nucleated cell count, fraction of CD34+ cells, and number of CFU-GM colonies in single aspirates and BM harvests. Single aspirates displayed a mean nucleated cell count of 31.3 × 10(6) cells/mL, a mean fraction of 1.17% CD34+ cells, and a mean colony forming potential of 66.6 CFU-GM/10(5) cells. Harvests yielded the same number of nucleated cells but increased numbers of CD34+ cells and CFU-GM compared with single aspirates. The mean nucleated cell count in BM harvests was 31.1 × 10(6) /mL with a mean fraction of 1.95% CD34+ cells and a mean of 112.4 CFU-GM colonies/10(5) cells. The concentration of nucleated cells was elevated compared with reported adult counts, while CD34+ percentage and CFU-GM counts were similar. In this series of healthy children, the fraction of CD34+ cells, CFU-GM colonies, and nucleated cells decreased with age. We did not identify gender specific differences. To our knowledge, this represents the first comprehensive study of CD34+ cell fraction, CFU-GM counts, and nucleated cell numbers in the BM of healthy children. The findings provide valuable information for practical use for BM transplantation and contribute to the understanding of hematopoiesis from birth to adulthood.

  14. Coupled-Mode Theory derivation of the formal equivalence between a three-mode waveguide and a set of three mutually coupled single-mode waveguides

    Directory of Open Access Journals (Sweden)

    Boucher Yann G.

    2017-01-01

    Full Text Available The formal identification between a two-mode waveguide and a system of two mutually coupled single-mode waveguides stems from the symmetries of the evolution operator. When the gap tends to zero, the super-modes of the coupled system merge continuously into the modes of the multimode waveguide. For modelling purposes, it is very tempting to extend the analogy to three-mode waveguides (and beyond. But not without some precautions…

  15. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach that ...... valuable weapons for preventing pathogen contamination and fighting infectious diseases in the future....

  16. Vimentin in Bacterial Infections

    DEFF Research Database (Denmark)

    Mak, Tim N; Brüggemann, Holger

    2016-01-01

    Despite well-studied bacterial strategies to target actin to subvert the host cell cytoskeleton, thus promoting bacterial survival, replication, and dissemination, relatively little is known about the bacterial interaction with other components of the host cell cytoskeleton, including intermediate...... filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge...... about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria...

  17. Synthesis, characterization and biological evaluation of thiazolopyrimidine derivatives

    Indian Academy of Sciences (India)

    H Nagarajaiah; I M Khazi; Noor Shahina Begum

    2012-07-01

    Different substituted diesters of thiazolopyrimidine were prepared by the treatment of 3,4 dihydropyrimidine2-thione with -haloesters using ethanol under reflux condition affording 71-85% yield. IR, 1HNMR, 13CNMR and elemental analyses were used for the characterization of these compounds. The crystal and molecular structure of one of the product, 5-phenyl-3,7-dimethyl-5H-thiazolo[3,2-a]pyrimidine-2,6-dicarboxylic acid diethyl ester (3e) was verified by single crystal X-ray diffraction method. The antimicrobial activity was evaluated against four bacterial strains and one fungal species. Few of the derivatives exhibited antibacterial and antifungal activities.

  18. Single-ion-magnet behavior in a two-dimensional coordination polymer constructed from Co(II) nodes and a pyridylhydrazone derivative.

    Science.gov (United States)

    Liu, Xiangyu; Sun, Lin; Zhou, Huiliang; Cen, Peipei; Jin, Xiaoyong; Xie, Gang; Chen, Sanping; Hu, Qilin

    2015-09-21

    A novel two-dimensional (2D) coordination polymer, [Co(ppad)2]n (1), resulted from the assembly of Co(II) ions based on a versatile ligand termed N(3)-(3-pyridoyl)-3-pyridinecarboxamidrazone. Alternating/direct-current magnetic studies of compound 1 indicate that the spatially separated high-spin Co(II) ions act as single-ion magnets (SIMs). The present work represents the first case of a 2D Co(II)-based SIM composed of a monocomponent organic spacer.

  19. Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment*

    OpenAIRE

    Canul-Tec, Juan Carlos; Riaño-Umbarila, Lidia; Rudiño-Piñera, Enrique; Becerril, Baltazar; Possani, Lourival D.; Torres-Larios, Alfredo

    2011-01-01

    It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 Å resolution. A 15-residue span of the toxin is recognized by th...

  20. Luminescence, magnetocaloric effect and single-molecule magnet behavior in lanthanide complexes based on a tridentate ligand derived from 8-hydroxyquinoline.

    Science.gov (United States)

    Shen, Hai-Yun; Wang, Wen-Min; Bi, Yan-Xia; Gao, Hong-Ling; Liu, Shuang; Cui, Jian-Zhong

    2015-11-21

    A new family of lanthanide complexes, [Ln2(hfac)4L2] (Ln = Eu (1), Gd (2), Tb (3), Dy (4), Ho (5), Er (6), Lu (7); hfac = hexafluoroacetylacetonate, HL = 2-(2′-benzothiazole)-8-hydroxyquinoline), was synthesized and characterized using single-crystal X-ray diffraction, elemental analysis (EA), thermal gravimetric analysis (TGA), powder X-ray diffraction (PXRD) and UV-vis spectra. X-ray crystallographic analyses reveal that 1–7 are isomorphous and crystallize in the monoclinic space group C2/c. In these dinuclear complexes, each LnШ ion is eight-coordinated with two bidentate hfac and two μ-phenol bridging L ligands. The TGA results show that the complexes have relatively high thermal stabilities. Complexes 1 and 3 show the characteristic transitions of the corresponding lanthanide ions with ligand-related emission peaks. Meanwhile, complexes 4 and 7 exhibit ligand-centered fluorescence at room temperature. Magnetic measurements were carried out on complexes 2–6. The magnetic study reveals that 2 displays a magnetocaloric effect, with a maximum −ΔSm value of 16.89 J K−1 kg−1 at 2 K for ΔH = 8 T. Dynamic magnetic studies reveal single-molecule magnet (SMM) behavior for complex 4. Fitting the dynamic magnetic data to the Arrhenius law gives an energy barrier ΔE/kB = 50.33 K and pre-exponential factor τ0 = 1.05 × 10(-8)s.

  1. Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages.

    Directory of Open Access Journals (Sweden)

    Sebastiaan M Bol

    Full Text Available BACKGROUND: HIV-1 infected macrophages play an important role in rendering resting T cells permissive for infection, in spreading HIV-1 to T cells, and in the pathogenesis of AIDS dementia. During highly active anti-retroviral treatment (HAART, macrophages keep producing virus because tissue penetration of antiretrovirals is suboptimal and the efficacy of some is reduced. Thus, to cure HIV-1 infection with antiretrovirals we will also need to efficiently inhibit viral replication in macrophages. The majority of the current drugs block the action of viral enzymes, whereas there is an abundance of yet unidentified host factors that could be targeted. We here present results from a genome-wide association study identifying novel genetic polymorphisms that affect in vitro HIV-1 replication in macrophages. METHODOLOGY/PRINCIPAL FINDINGS: Monocyte-derived macrophages from 393 blood donors were infected with HIV-1 and viral replication was determined using Gag p24 antigen levels. Genomic DNA from individuals with macrophages that had relatively low (n = 96 or high (n = 96 p24 production was used for SNP genotyping with the Illumina 610 Quad beadchip. A total of 494,656 SNPs that passed quality control were tested for association with HIV-1 replication in macrophages, using linear regression. We found a strong association between in vitro HIV-1 replication in monocyte-derived macrophages and SNP rs12483205 in DYRK1A (p = 2.16 × 10(-5. While the association was not genome-wide significant (p<1 × 10(-7, we could replicate this association using monocyte-derived macrophages from an independent group of 31 individuals (p = 0.0034. Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84 × 10(-6. In addition, we found this SNP to be associated with HIV-1 disease progression in vivo in two independent cohort studies (p = 0.035 and p = 0.0048. CONCLUSIONS/SIGNIFICANCE: These findings suggest that the kinase

  2. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2011-01-01

    defense. Antibiotics exhibit a rather limited effect on biofilms. Furthermore, antibiotics have an ‘inherent obsolescence’ because they select for development of resistance. Bacterial infections with origin in bacterial biofilms have become a serious threat in developed countries. Pseudomonas aeruginosa...... that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation......, resistance and QS inhibition as future antimicrobial targets, in particular those that would work to minimize selection pressures for the development of resistant bacteria....

  3. Carbon dioxide corrosion inhibition of N80 carbon steel in single liquid phase and liquid/particle two-phase flow by hydroxyethyl imidazoline derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Liu, X. [State Key Laboratory for Corrosion and Protection, Institute of Metal Research, Chinese Academy of Sciences, 62 Wencui Road, Shenyang 110016, Liaoning Province (China); Department of Applied Chemistry, Shenyang Institute of Chemical Technology, Shenyang 110142 (China); Zheng, Y.G. [State Key Laboratory for Corrosion and Protection, Institute of Metal Research, Chinese Academy of Sciences, 62 Wencui Road, Shenyang 110016, Liaoning Province (China); Okafor, P.C. [State Key Laboratory for Corrosion and Protection, Institute of Metal Research, Chinese Academy of Sciences, 62 Wencui Road, Shenyang 110016, Liaoning Province (China); Department of Pure and Applied Chemistry, University of Calabar, Calabar (Nigeria)

    2009-07-15

    CO{sub 2} corrosion inhibition of N80 steel in liquid single-phase and liquid/particle two-phase flow by 2-undecyl-1-hydroxyethyl imidazoline (HEI-11) and 2-undecyl-1-hydroxyethyl-1-hydroxyethyl quaternary imidazoline (HQI-11) was investigated using weight loss, potentiodynamic polarization, EIS, and scanning electron microscope (SEM) techniques. The results show that the corrosion rate in the absence and presence of the imidazolines is strongly dependent on the flow condition and presence of entrained sand particles. The imidazolines function via a mixed-type corrosion inhibition mechanism. The inhibition efficiencies of the imidazolines followed the trend HQI-11 > HEI-11 in all the systems studied. Inhibition mechanism has been discussed in relation to the polycentric adsorption sites on the imidazoline molecules. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  4. Inhibiting bacterial toxins by channel blockage.

    Science.gov (United States)

    Bezrukov, Sergey M; Nestorovich, Ekaterina M

    2016-03-01

    Emergent rational drug design techniques explore individual properties of target biomolecules, small and macromolecule drug candidates, and the physical forces governing their interactions. In this minireview, we focus on the single-molecule biophysical studies of channel-forming bacterial toxins that suggest new approaches for their inhibition. We discuss several examples of blockage of bacterial pore-forming and AB-type toxins by the tailor-made compounds. In the concluding remarks, the most effective rationally designed pore-blocking antitoxins are compared with the small-molecule inhibitors of ion-selective channels of neurophysiology.

  5. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

  6. Bacterial Wound Culture

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? Bacterial Wound Culture Share this page: Was this page helpful? Also known as: Aerobic Wound Culture; Anaerobic Wound Culture Formal name: Culture, wound Related ...

  7. Bacterial Meningitis in Infants

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-04-01

    Full Text Available A retrospective study of 80 infantile patients (ages 30-365 days; 47 male, 33 female with culture-proven bacterial meningitis seen over a 16 year period (1986-2001 is reported from Taiwan.

  8. Historically aggressive types of follicular cell-derived thyroid cancer often have radioactive avid distant metastases: a study of 314 patients with distant metastases at a single institution

    Energy Technology Data Exchange (ETDEWEB)

    Tala, H.P.; Rondeau, G.; Fagin, J.A.; Tuttle, R.M. [Endocrinology Division, Department of Medicine, Nuclear Medicine Division, Memorial Sloan Kettering Cancer Center, New-York (United States); Ghossein, R.A. [Pathology Department, Nuclear Medecine Division, Memorial Sloan Kettering Cancer Center, New-York (United States); Grewal, R.K.; Larson, S.M. [Radiology Department, Nuclear Medicine Division, Memorial Sloan Kettering Cancer Center, New-York (United States)

    2012-07-01

    Radioactive iodine (RAI) remains one of the primary treatment options for metastatic, follicular cell derived thyroid cancers. The aim of this study was to determine the likelihood that metastatic lesions arising from one of the aggressive thyroid cancer histologies [tall cell variant of papillary thyroid carcinoma (TCV-PTC), poorly differentiated thyroid carcinoma (PDTC) and Hurthle cell carcinoma (HCC)] would demonstrate sufficient RAI avidity for visualization on RAI scanning and therefore could potentially benefit from RAI therapy. The study shows that in patients selected for RAI scanning or therapy at our center, RAI avid lesions can be identified in more than two thirds of the patients with distant metastases arising in the setting of C-PTC, WD-FTC, FV-PTC, TCV-PTC, or PDTC primary tumors. While RAI avidity on a post-therapy scan does not always correlate with clinically significant tumor killing activity, it is likely that some of these patients with RAI avid metastatic disease did obtain a clinical benefit

  9. Skin Antiageing and Systemic Redox Effects of Supplementation with Marine Collagen Peptides and Plant-Derived Antioxidants: A Single-Blind Case-Control Clinical Study.

    Science.gov (United States)

    De Luca, Chiara; Mikhal'chik, Elena V; Suprun, Maxim V; Papacharalambous, Michael; Truhanov, Arseniy I; Korkina, Liudmila G

    2016-01-01

    Recently, development and research of nutraceuticals based on marine collagen peptides (MCPs) have been growing due to their high homology with human collagens, safety, bioavailability through gut, and numerous bioactivities. The major concern regarding safety of MCPs intake relates to increased risk of oxidative stress connected with collagen synthesis (likewise in fibrosis) and to ROS production by MCPs-stimulated phagocytes. In this clinical-laboratory study, fish skin MCPs combined with plant-derived skin-targeting antioxidants (AO) (coenzyme Q10 + grape-skin extract + luteolin + selenium) were administered to volunteers (n = 41). Skin properties (moisture, elasticity, sebum production, and biological age) and ultrasonic markers (epidermal/dermal thickness and acoustic density) were measured thrice (2 months before treatment and before and after cessation of 2-month oral intake). The supplementation remarkably improved skin elasticity, sebum production, and dermal ultrasonic markers. Metabolic data showed significant increase of plasma hydroxyproline and ATP storage in erythrocytes. Redox parameters, GSH/coenzyme Q10 content, and GPx/GST activities were unchanged, while NO and MDA were moderately increased within, however, normal range of values. Conclusions. A combination of MCPs with skin-targeting AOs could be effective and safe supplement to improve skin properties without risk of oxidative damage.

  10. Skin Antiageing and Systemic Redox Effects of Supplementation with Marine Collagen Peptides and Plant-Derived Antioxidants: A Single-Blind Case-Control Clinical Study

    Directory of Open Access Journals (Sweden)

    Chiara De Luca

    2016-01-01

    Full Text Available Recently, development and research of nutraceuticals based on marine collagen peptides (MCPs have been growing due to their high homology with human collagens, safety, bioavailability through gut, and numerous bioactivities. The major concern regarding safety of MCPs intake relates to increased risk of oxidative stress connected with collagen synthesis (likewise in fibrosis and to ROS production by MCPs-stimulated phagocytes. In this clinical-laboratory study, fish skin MCPs combined with plant-derived skin-targeting antioxidants (AO (coenzyme Q10 + grape-skin extract + luteolin + selenium were administered to volunteers (n=41. Skin properties (moisture, elasticity, sebum production, and biological age and ultrasonic markers (epidermal/dermal thickness and acoustic density were measured thrice (2 months before treatment and before and after cessation of 2-month oral intake. The supplementation remarkably improved skin elasticity, sebum production, and dermal ultrasonic markers. Metabolic data showed significant increase of plasma hydroxyproline and ATP storage in erythrocytes. Redox parameters, GSH/coenzyme Q10 content, and GPx/GST activities were unchanged, while NO and MDA were moderately increased within, however, normal range of values. Conclusions. A combination of MCPs with skin-targeting AOs could be effective and safe supplement to improve skin properties without risk of oxidative damage.

  11. Bacterial proteases and virulence

    DEFF Research Database (Denmark)

    Frees, Dorte; Brøndsted, Lone; Ingmer, Hanne

    2013-01-01

    Bacterial pathogens rely on proteolysis for variety of purposes during the infection process. In the cytosol, the main proteolytic players are the conserved Clp and Lon proteases that directly contribute to virulence through the timely degradation of virulence regulators and indirectly by providing....... These extracellular proteases are activated in complex cascades involving auto-processing and proteolytic maturation. Thus, proteolysis has been adopted by bacterial pathogens at multiple levels to ensure the success of the pathogen in contact with the human host....

  12. [Diagnosis of bacterial vaginosis].

    Science.gov (United States)

    Djukić, Slobodanka; Ćirković, Ivana; Arsić, Biljana; Garalejić, Eliana

    2013-01-01

    Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2-producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent's scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up-to-date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short-term and long-term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  13. Microscopic origin of the charge transfer in single crystals based on thiophene derivatives: A combined NEXAFS and density functional theory approach

    Science.gov (United States)

    Chernenkaya, A.; Morherr, A.; Backes, S.; Popp, W.; Witt, S.; Kozina, X.; Nepijko, S. A.; Bolte, M.; Medjanik, K.; Öhrwall, G.; Krellner, C.; Baumgarten, M.; Elmers, H. J.; Schönhense, G.; Jeschke, H. O.; Valentí, R.

    2016-07-01

    We have investigated the charge transfer mechanism in single crystals of DTBDT-TCNQ and DTBDT-F4TCNQ (where DTBDT is dithieno[2,3-d;2',3'-d'] benzo[1,2-b;4,5-b']dithiophene) using a combination of near-edge X-ray absorption spectroscopy (NEXAFS) and density functional theory calculations (DFT) including final state effects beyond the sudden state approximation. In particular, we find that a description that considers the partial screening of the electron-hole Coulomb correlation on a static level as well as the rearrangement of electronic density shows excellent agreement with experiment and allows to uncover the details of the charge transfer mechanism in DTBDT-TCNQ and DTBDT-F4 TCNQ, as well as a reinterpretation of previous NEXAFS data on pure TCNQ. Finally, we further show that almost the same quality of agreement between theoretical results and experiment is obtained by the much faster Z+1/2 approximation, where the core hole effects are simulated by replacing N or F with atomic number Z with the neighboring atom with atomic number Z+1/2.

  14. Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment*

    Science.gov (United States)

    Canul-Tec, Juan Carlos; Riaño-Umbarila, Lidia; Rudiño-Piñera, Enrique; Becerril, Baltazar; Possani, Lourival D.; Torres-Larios, Alfredo

    2011-01-01

    It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 Å resolution. A 15-residue span of the toxin is recognized by the antibody through a cleft formed by residues from five of the complementarity-determining regions of the scFv. Analysis of the interface of the complex reveals three features. First, the epitope of toxin Cn2 overlaps with essential residues for the binding of β-toxins to its Na+ channel receptor site. Second, the putative recognition of Css2 involves mainly residues that are present in both Cn2 and Css2 toxins. Finally, the effect on the increase of affinity of previously reported key residues during the maturation process of different scFvs can be inferred from the structure. Taken together, these results provide the structural basis that explain the mechanism of the 9004G neutralizing activity and give insight into the process of directed evolution that gave rise to this family of neutralizing scFvs. PMID:21489992

  15. Replacement of Fishmeal by Single Cell Protein Derived from Yeast Grown on Date (Phoenix dactylifera) Industry Waste in the Diet of Nile Tilapia (Oreochromis niloticus) Fingerlings

    KAUST Repository

    Al-Hafedh, Yousef S.

    2013-10-02

    Isonitrogenous and isocaloric diets (32% protein, 4.3 Kcal/g) were formulated to replace fishmeal by single cell protein (SCP) from two yeasts, Saccharomyces cerevisiae and Candida utilis, grown on date (Phoenix dactylifera) processing waste in diets for two size groups (avg 15.39 g and 25.14 g) of juvenile Nile tilapia (Oreochromis niloticus). A control diet (T1) with fishmeal and six experimental diets (S1, S2, and S3 with S. cerevisiae, and C1, C2, and C3 with C. utilis) each containing 11.6%, 23.2%, and 34.2% yeast as SCP were prepared to replace 25%, 50%, and 75% of fishmeal, respectively. Tilapia fed on the control and experimental diets (S1, S2, C1, C2) with 25% and 50% replacement of fishmeal showed better growth and feed utilization. Fish fed on diets S3 and C3 (75% fishmeal replacement) had significantly (p < 0.05) poorer growth suggesting that yeast SCP can replace up to 50% of fishmeal in juvenile tilapia diets. © 2013 Copyright Taylor and Francis Group, LLC.

  16. Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment

    Energy Technology Data Exchange (ETDEWEB)

    Canul-Tec, Juan Carlos; Riaño-Umbarila, Lidia; Rudiño-Piñera, Enrique; Becerril, Baltazar; Possani, Lourival D.; Torres-Larios, Alfredo (U. NAM)

    2011-08-09

    It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 {angstrom} resolution. A 15-residue span of the toxin is recognized by the antibody through a cleft formed by residues from five of the complementarity-determining regions of the scFv. Analysis of the interface of the complex reveals three features. First, the epitope of toxin Cn2 overlaps with essential residues for the binding of {beta}-toxins to its Na+ channel receptor site. Second, the putative recognition of Css2 involves mainly residues that are present in both Cn2 and Css2 toxins. Finally, the effect on the increase of affinity of previously reported key residues during the maturation process of different scFvs can be inferred from the structure. Taken together, these results provide the structural basis that explain the mechanism of the 9004G neutralizing activity and give insight into the process of directed evolution that gave rise to this family of neutralizing scFvs.

  17. Microscopic origin of the charge transfer in single crystals based on thiophene derivatives: A combined NEXAFS and density functional theory approach.

    Science.gov (United States)

    Chernenkaya, A; Morherr, A; Backes, S; Popp, W; Witt, S; Kozina, X; Nepijko, S A; Bolte, M; Medjanik, K; Öhrwall, G; Krellner, C; Baumgarten, M; Elmers, H J; Schönhense, G; Jeschke, H O; Valentí, R

    2016-07-21

    We have investigated the charge transfer mechanism in single crystals of DTBDT-TCNQ and DTBDT-F4TCNQ (where DTBDT is dithieno[2,3-d;2',3'-d'] benzo[1,2-b;4,5-b']dithiophene) using a combination of near-edge X-ray absorption spectroscopy (NEXAFS) and density functional theory calculations (DFT) including final state effects beyond the sudden state approximation. In particular, we find that a description that considers the partial screening of the electron-hole Coulomb correlation on a static level as well as the rearrangement of electronic density shows excellent agreement with experiment and allows to uncover the details of the charge transfer mechanism in DTBDT-TCNQ and DTBDT-F4 TCNQ, as well as a reinterpretation of previous NEXAFS data on pure TCNQ. Finally, we further show that almost the same quality of agreement between theoretical results and experiment is obtained by the much faster Z+1/2 approximation, where the core hole effects are simulated by replacing N or F with atomic number Z with the neighboring atom with atomic number Z+1/2.

  18. Local and regional components of aerosol in a heavily trafficked street canyon in central London derived from PMF and cluster analysis of single-particle ATOFMS spectra.

    Science.gov (United States)

    Giorio, Chiara; Tapparo, Andrea; Dall'Osto, Manuel; Beddows, David C S; Esser-Gietl, Johanna K; Healy, Robert M; Harrison, Roy M

    2015-03-17

    Positive matrix factorization (PMF) has been applied to single particle ATOFMS spectra collected on a six lane heavily trafficked road in central London (Marylebone Road), which well represents an urban street canyon. PMF analysis successfully extracted 11 factors from mass spectra of about 700,000 particles as a complement to information on particle types (from K-means cluster analysis). The factors were associated with specific sources and represent the contribution of different traffic related components (i.e., lubricating oils, fresh elemental carbon, organonitrogen and aromatic compounds), secondary aerosol locally produced (i.e., nitrate, oxidized organic aerosol and oxidized organonitrogen compounds), urban background together with regional transport (aged elemental carbon and ammonium) and fresh sea spray. An important result from this study is the evidence that rapid chemical processes occur in the street canyon with production of secondary particles from road traffic emissions. These locally generated particles, together with aging processes, dramatically affected aerosol composition producing internally mixed particles. These processes may become important with stagnant air conditions and in countries where gasoline vehicles are predominant and need to be considered when quantifying the impact of traffic emissions.

  19. Structural basis of neutralization of the major toxic component from the scorpion Centruroides noxius Hoffmann by a human-derived single-chain antibody fragment.

    Science.gov (United States)

    Canul-Tec, Juan Carlos; Riaño-Umbarila, Lidia; Rudiño-Piñera, Enrique; Becerril, Baltazar; Possani, Lourival D; Torres-Larios, Alfredo

    2011-06-10

    It has previously been reported that several single-chain antibody fragments of human origin (scFv) neutralize the effects of two different scorpion venoms through interactions with the primary toxins of Centruroides noxius Hoffmann (Cn2) and Centruroides suffusus suffusus (Css2). Here we present the crystal structure of the complex formed between one scFv (9004G) and the Cn2 toxin, determined in two crystal forms at 2.5 and 1.9 Å resolution. A 15-residue span of the toxin is recognized by the antibody through a cleft formed by residues from five of the complementarity-determining regions of the scFv. Analysis of the interface of the complex reveals three features. First, the epitope of toxin Cn2 overlaps with essential residues for the binding of β-toxins to its Na(+) channel receptor site. Second, the putative recognition of Css2 involves mainly residues that are present in both Cn2 and Css2 toxins. Finally, the effect on the increase of affinity of previously reported key residues during the maturation process of different scFvs can be inferred from the structure. Taken together, these results provide the structural basis that explain the mechanism of the 9004G neutralizing activity and give insight into the process of directed evolution that gave rise to this family of neutralizing scFvs.

  20. Online single particle analysis of ice particle residuals from mountain-top mixed-phase clouds using laboratory derived particle type assignment

    Science.gov (United States)

    Schmidt, Susan; Schneider, Johannes; Klimach, Thomas; Mertes, Stephan; Schenk, Ludwig Paul; Kupiszewski, Piotr; Curtius, Joachim; Borrmann, Stephan

    2017-01-01

    In situ single particle analysis of ice particle residuals (IPRs) and out-of-cloud aerosol particles was conducted by means of laser ablation mass spectrometry during the intensive INUIT-JFJ/CLACE campaign at the high alpine research station Jungfraujoch (3580 m a.s.l.) in January-February 2013. During the 4-week campaign more than 70 000 out-of-cloud aerosol particles and 595 IPRs were analyzed covering a particle size diameter range from 100 nm to 3 µm. The IPRs were sampled during 273 h while the station was covered by mixed-phase clouds at ambient temperatures between -27 and -6 °C. The identification of particle types is based on laboratory studies of different types of biological, mineral and anthropogenic aerosol particles. The outcome of these laboratory studies was characteristic marker peaks for each investigated particle type. These marker peaks were applied to the field data. In the sampled IPRs we identified a larger number fraction of primary aerosol particles, like soil dust (13 ± 5 %) and minerals (11 ± 5 %), in comparison to out-of-cloud aerosol particles (2.4 ± 0.4 and 0.4 ± 0.1 %, respectively). Additionally, anthropogenic aerosol particles, such as particles from industrial emissions and lead-containing particles, were found to be more abundant in the IPRs than in the out-of-cloud aerosol. In the out-of-cloud aerosol we identified a large fraction of aged particles (31 ± 5 %), including organic material and secondary inorganics, whereas this particle type was much less abundant (2.7 ± 1.3 %) in the IPRs. In a selected subset of the data where a direct comparison between out-of-cloud aerosol particles and IPRs in air masses with similar origin was possible, a pronounced enhancement of biological particles was found in the IPRs.

  1. Mesoscopic modeling of bacterial flagellar microhydrodynamics.

    Science.gov (United States)

    Gebremichael, Yeshitila; Ayton, Gary S; Voth, Gregory A

    2006-11-15

    A particle-based hybrid method of elastic network model and smooth-particle hydrodynamics has been employed to describe the propulsion of bacterial flagella in a viscous hydrodynamic environment. The method explicitly models the two aspects of bacterial propulsion that involve flagellar flexibility and long-range hydrodynamic interaction of low-Reynolds-number flow. The model further incorporates the molecular organization of the flagellar filament at a coarse-grained level in terms of the 11 protofilaments. Each of these protofilaments is represented by a collection of material points that represent the flagellin proteins. A computational model of a single flexible helical segment representing the filament of a bacterial flagellum is presented. The propulsive dynamics and the flow fields generated by the motion of the model filament are examined. The nature of flagellar deformation and the influence of hydrodynamics in determining the shape of deformations are examined based on the helical filament.

  2. Assessment of the sensitivity of core/shell parameters derived using the single-particle soot photometer to density and refractive index

    Directory of Open Access Journals (Sweden)

    J. W. Taylor

    2014-06-01

    Full Text Available Black carbon (BC is the dominant absorbing aerosol in the atmosphere, and plays an important role in climate and human health. The optical properties and cloud condensation nuclei (CCN activity of soot depend on the amounts (both relative and absolute of BC and nonrefractory material in the particles. Mixing between these two components is often considered using a core/shell coated sphere morphology. The Single Particle Soot Photometer (SP2 is the premier instrument for reporting distributions of both core size and coating thickness. Most studies combine the SP2's incandescence and scattering data to report coating properties, but there is variation in the assumed density and refractive index of the core that are used in these calculations. In this study we explore the sensitivity of the reported coatings to these parameters. An assessment of the coating properties of freshly-emitted, thermodenuded ambient particles demonstrated that a core density of 1.8 g cm−3 and refractive index n = (2.26-1.26i were the most appropriate to use with ambient soot in the Los Angeles area. Using these parameters generated a distribution of shell/core ratio of 1.04 ± 0.21, corresponding to an absolute coating thickness distribution of 1.7 ± 17.5 nm. This demonstrates that using this technique the SP2 can accurately determine the mixing state (externally or internally mixed of ambient soot, but with limited precision. Using other core parameters resulted in an offset in the coating distribution, but similar precision. For comparison, using the core parameters that resulted in the thickest coatings (on the same particles as before generated a distribution of shell/core ratio of 1.40 ± 0.19, corresponding to an absolute coating thickness distribution of 30.3 ± 14.9 nm. Relative changes in coatings associated with secondary aerosol condensation were captured regardless of the assumed core parameters. These results must be taken into account when comparing BC

  3. Bacterial spores in food : how phenotypic variability complicates prediction of spore properties and bacterial behavior

    NARCIS (Netherlands)

    Eijlander, Robyn T.; Abee, Tjakko; Kuipers, Oscar P.

    2011-01-01

    Bacillus spores are a known cause of food spoilage and their increased resistance poses a major challenge in efficient elimination. Recent studies on bacterial cultures at the single cell level have revealed how minor differences in essential spore properties, such as core water content or germinant

  4. Bacterial spores in food: how phenotypic variability complicates prediction of spore properties and bacterial behavior

    NARCIS (Netherlands)

    Eijlander, R.T.; Abee, T.; Kuipers, O.P.

    2011-01-01

    Bacillus spores are a known cause of food spoilage and their increased resistance poses a major challenge in efficient elimination. Recent studies on bacterial cultures at the single cell level have revealed how minor differences in essential spore properties, such as core water content or germinant

  5. High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation

    DEFF Research Database (Denmark)

    Ren, Dawei; Madsen, Jonas Stenløkke; Sørensen, Søren Johannes;

    2015-01-01

    of single-species biofilms, indicating that all the individual strains benefit from inclusion in the multispecies community. Our results show a high prevalence of synergy in biofilm formation in multispecies consortia isolated from a natural bacterial habitat and suggest that interspecific cooperation...

  6. Digestion, absorption and utilization of single-cell protein by the preruminant calf. The true digestibility of milk and bacterial protein and the apparent digestibility and utilization of their constituent amino acids.

    Science.gov (United States)

    Sedgman, C A; Roy, J H; Thomas, J; Stobo, I J; Ganderton, P

    1985-07-01

    Two experiments of Latin square design were made, each with four Friesian bull calves fitted with re-entrant duodenal and ileal cannulas at 4-10 d of age. The calves were used to study the effect of giving milk-substitutes containing 0, 300, 500 and 700 g bacterial protein (Pruteen)/kg total protein on apparent digestibility of nitrogen fractions and amino acids and true digestibility of 3H-labelled milk protein and 35S-labelled bacterial protein in the small intestine. A third experiment of Latin square design with four intact Friesian calves was used to measure apparent digestibility of nutrients throughout the alimentary tract and retention of N, calcium and phosphorus. At the duodenum, volume of outflow, its pH, and outflow of total-N(TN), protein-N (PN) and non-protein-N (NPN) decreased with time after feeding. At the ileum, volume of outflow and TN outflow were unaffected by time after feeding but PN outflow decreased; NPN outflow at the ileum increased to a maximum 6 h after feeding and then declined. Increased inclusion of Pruteen did not affect the volume of outflow at the duodenum or ileum, but duodenal PN outflow increased. At the ileum, pH values were lower and TN, PN and NPN outflows were higher with increasing concentration of Pruteen in the diet. Apparent digestibility in the small intestine tended to decrease with greater amounts of Pruteen, but was only significant for NPN. Apparent digestibility from mouth to ileum significantly decreased for TN and PN as Pruteen inclusion increased. Amino acid concentration in duodenal outflow, with the exception of that of arginine, reflected intake. The total amount of each amino acid in ileal outflow increased and the apparent digestibility of most amino acids decreased with greater amounts of Pruteen in the diet. Apparent digestibility of nucleic acid-N from Pruteen was very high. True digestibility in the small intestine and between mouth and ileum of 3H-labelled milk protein was high and did not differ

  7. The bacterial lipocalins.

    Science.gov (United States)

    Bishop, R E

    2000-10-18

    The lipocalins were once regarded as a eukaryotic protein family, but new members have been recently discovered in bacteria. The first bacterial lipocalin (Blc) was identified in Escherichia coli as an outer membrane lipoprotein expressed under conditions of environmental stress. Blc is distinguished from most lipocalins by the absence of intramolecular disulfide bonds, but the presence of a membrane anchor is shared with two of its closest homologues, apolipoprotein D and lazarillo. Several common features of the membrane-anchored lipocalins suggest that each may play an important role in membrane biogenesis and repair. Additionally, Blc proteins are implicated in the dissemination of antibiotic resistance genes and in the activation of immunity. Recent genome sequencing efforts reveal the existence of at least 20 bacterial lipocalins. The lipocalins appear to have originated in Gram-negative bacteria and were probably transferred horizontally to eukaryotes from the endosymbiotic alpha-proteobacterial ancestor of the mitochondrion. The genome sequences also reveal that some bacterial lipocalins exhibit disulfide bonds and alternative modes of subcellular localization, which include targeting to the periplasmic space, the cytoplasmic membrane, and the cytosol. The relationships between bacterial lipocalin structure and function further illuminate the common biochemistry of bacterial and eukaryotic cells.

  8. Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

    Directory of Open Access Journals (Sweden)

    E Charlotte E Kvennefors

    invertebrate associates. Finally, the results did not support the contention that a single bacterial pathogen may be the causative agent of WS Acroporids on the GBR.

  9. A hepatitis C virus (HCV) vaccine comprising envelope glycoproteins gpE1/gpE2 derived from a single isolate elicits broad cross-genotype neutralizing antibodies in humans

    DEFF Research Database (Denmark)

    Law, John Lok Man; Chen, Chao; Wong, Jason

    2013-01-01

    , an effective HCV vaccine which could elicit broadly cross-neutralizing antibodies has represented a major challenge. In this study, we tested for the presence of cross-neutralizing antibodies in human volunteers who were immunized with recombinant glycoproteins gpE1/gpE2 derived from a single HCV strain (HCV1...... of genotype 1a). Cross neutralization was tested in Huh-7.5 human hepatoma cell cultures using infectious recombinant HCV (HCVcc) expressing structural proteins of heterologous HCV strains from all known major genotypes, 1-7. Vaccination induced significant neutralizing antibodies against heterologous HCV...... genotype 1a virus which represents the most common genotype in North America. Of the 16 vaccinees tested, 3 were selected on the basis of strong 1a virus neutralization for testing of broad cross-neutralizing responses. At least 1 vaccinee was shown to elicit broad cross-neutralization against all HCV...

  10. Single valproic acid treatment inhibits glycogen and RNA ribose turnover while disrupting glucose-derived cholesterol synthesis in liver as revealed by the [U-C(6)]-d-glucose tracer in mice.

    Science.gov (United States)

    Beger, Richard D; Hansen, Deborah K; Schnackenberg, Laura K; Cross, Brandie M; Fatollahi, Javad J; Lagunero, F Tracy; Sarnyai, Zoltan; Boros, Laszlo G

    2009-09-01

    Previous genetic and proteomic studies identified altered activity of various enzymes such as those of fatty acid metabolism and glycogen synthesis after a single toxic dose of valproic acid (VPA) in rats. In this study, we demonstrate the effect of VPA on metabolite synthesis flux rates and the possible use of abnormal (13)C labeled glucose-derived metabolites in plasma or urine as early markers of toxicity. Female CD-1 mice were injected subcutaneously with saline or 600 mg/kg) VPA. Twelve hours later, the mice were injected with an intraperitoneal load of 1 g/kg [U-(13)C]-d-glucose. (13)C isotopomers of glycogen glucose and RNA ribose in liver, kidney and brain tissue, as well as glucose disposal via cholesterol and glucose in the plasma and urine were determined. The levels of all of the positional (13)C isotopomers of glucose were similar in plasma, suggesting that a single VPA dose does not disturb glucose absorption, uptake or hepatic glucose metabolism. Three-hour urine samples showed an increase in the injected tracer indicating a decreased glucose re-absorption via kidney tubules. (13)C labeled glucose deposited as liver glycogen or as ribose of RNA were decreased by VPA treatment; incorporation of (13)C via acetyl-CoA into plasma cholesterol was significantly lower at 60 min. The severe decreases in glucose-derived carbon flux into plasma and kidney-bound cholesterol, liver glycogen and RNA ribose synthesis, as well as decreased glucose re-absorption and an increased disposal via urine all serve as early flux markers of VPA-induced adverse metabolic effects in the host.

  11. Effects of hydrodynamic interactions in bacterial swimming.

    Science.gov (United States)

    Chattopadhyay, Suddhashil; Lun Wu, Xiao

    2008-03-01

    The lack of precise experimental data has prevented the investigation of the effects of long range hydrodynamic interactions in bacterial swimming. We perform measurements on various strains of bacteria with the aid of optical tweezers to shed light on this aspect of bacterial motility. Geometrical parameters recorded by fluorescence microscopy are used with theories which model flagella propulsion (Resistive force theory & Lighthill's formulation which includes long range interactions). Comparison of the predictions of these theories with experimental data, observed directly from swimming bacterium, led to the conclusion that while long range inetractions were important for single polar flagellated strains (Vibrio Alginolyticus & Caulobacter Crescentus), local force theory was adequate to describe the swimming of multi-flagellated Esherichia Coli. We performed additional measurements on E. Coli minicells (miniature cells with single polar flagellum) to try and determine the cause of this apparent effect of shielding of long range interactions in multiple flagellated bacteria.

  12. Bacterial glycosyltransferase toxins.

    Science.gov (United States)

    Jank, Thomas; Belyi, Yury; Aktories, Klaus

    2015-12-01

    Mono-glycosylation of host proteins is a common mechanism by which bacterial protein toxins manipulate cellular functions of eukaryotic target host cells. Prototypic for this group of glycosyltransferase toxins are Clostridium difficile toxins A and B, which modify guanine nucleotide-binding proteins of the Rho family. However, toxin-induced glycosylation is not restricted to the Clostridia. Various types of bacterial pathogens including Escherichia coli, Yersinia, Photorhabdus and Legionella species produce glycosyltransferase toxins. Recent studies discovered novel unexpected variations in host protein targets and amino acid acceptors of toxin-catalysed glycosylation. These findings open new perspectives in toxin as well as in carbohydrate research.

  13. Host Antimicrobial Peptides in Bacterial Homeostasis and Pathogenesis of Disease

    Directory of Open Access Journals (Sweden)

    Derek R. Heimlich

    2014-11-01

    Full Text Available Innate immune responses function as a first line of host defense against the development of bacterial infection, and in some cases to preserve the sterility of privileged sites in the human host. Bacteria that enter these sites must counter host responses for colonization. From the host’s perspective, the innate immune system works expeditiously to minimize the bacterial threat before colonization and subsequent dysbiosis. The multifactorial nature of disease further challenges predictions of how each independent variable influences bacterial pathogenesis. From bacterial colonization to infection and through disease, the microenvironments of the host are in constant flux as bacterial and host factors contribute to changes at the host-pathogen interface, with the host attempting to eradicate bacteria and the bacteria fighting to maintain residency. A key component of this innate host response towards bacterial infection is the production of antimicrobial peptides (AMPs. As an early component of the host response, AMPs modulate bacterial load and prevent establishment of infection. Under quiescent conditions, some AMPs are constitutively expressed by the epithelium. Bacterial infection can subsequently induce production of other AMPs in an effort to maintain sterility, or to restrict colonization. As demonstrated in various studies, the absence of a single AMP can influence pathogenesis, highlighting the importance of AMP concentration in maintaining homeostasis. Yet, AMPs can increase bacterial virulence through the co-opting of the peptides or alteration of bacterial virulence gene expression. Further, bacterial factors used to subvert AMPs can modify host microenvironments and alter colonization of the residential flora that principally maintain homeostasis. Thus, the dynamic interplay between host defense peptides and bacterial factors produced to quell peptide activity play a critical role in the progression and outcome of disease.

  14. Synthesis, spectral characterization, single crystal X-ray diffraction and DFT studies of 4-((2,4,5-triphenyl-1H-imidazol-1-yl)methyl)pyridine derivatives

    Science.gov (United States)

    Rajkumar, R.; Kamaraj, A.; Bharanidharan, S.; Saleem, H.; Krishnasamy, K.

    2015-03-01

    We have synthesized a series of novel 4-((2,4,5-triphenyl-1H-imidazol-1-yl)methyl)pyridine derivatives. The structures of these compounds were confirmed by IR, HR-MS, 1H and 13C NMR spectra. The compound 5g was also confirmed by single crystal XRD. The geometry of the synthesized compounds 5a-5g were examined by density functional theory (DFT) method at B3LYP/6-31G(d,p) level. The optimized geometrical parameters obtained by DFT calculation are in good agreement with single crystal XRD data. The HOMO-LUMO energies describes charge transfer takes place within the molecule. Furthermore, Mulliken and NBO charges were also calculated. The stability and charge delocalization of the molecule were also studied by natural bond orbital (NBO) analysis. Compound 5g exhibited good non linear optical activity and was 20 times greater than that of urea. In addition, molecular electrostatic potential map (MEP) was studied for predicting the reactive sites.

  15. Genetic parameters and selection for resistance to bacterial spot in recombinant F6 lines of Capsicum annuum

    Directory of Open Access Journals (Sweden)

    Messias Gonzaga Pereira

    2009-01-01

    Full Text Available This study aimed to advance generations and select superior sweet pepper genotypes with resistance tobacterial spot, using the breeding method Single Seed Descent (SSD based on the segregating population derived from thecross between Capsicum annuum L. UENF 1421 (susceptible, non-pungent and UENF 1381 (resistant, pungent. Thesegregating F3 generation was grown in pots in a greenhouse until the F5 generation. The F6 generation was grown in fieldconditions. The reaction to bacterial spot was evaluated by inoculation with isolate ENA 4135 of Xanthomonas campestris pv.vesicatoria, based on a score scale and by calculating the area under the disease progress curve (AUDPC. The presence orabsence of capsaicin was also assessed. Eighteen F6 lines were bacterial leaf spot-resistant. Since no capsaicin was detectedin the F6 lines 032, 316, 399, 434, and 517, these will be used in the next steps of the sweet pepper breeding program.

  16. Seizures Complicating Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-09-01

    Full Text Available The clinical data of 116 patients, 1 month to <5 years of age, admitted for bacterial meningitis, and grouped according to those with and without seizures during hospitalization, were compared in a study at Buddhist Dalin Tzu Chi General Hospital, Chang Gung Memorial Hospital and other centers in Taiwan.

  17. Ribosome-targeting antibiotics and mechanisms of bacterial resistance.

    Science.gov (United States)

    Wilson, Daniel N

    2014-01-01

    The ribosome is one of the main antibiotic targets in the bacterial cell. Crystal structures of naturally produced antibiotics and their semi-synthetic derivatives bound to ribosomal particles have provided unparalleled insight into their mechanisms of action, and they are also facilitating the design of more effective antibiotics for targeting multidrug-resistant bacteria. In this Review, I discuss the recent structural insights into the mechanism of action of ribosome-targeting antibiotics and the molecular mechanisms of bacterial resistance, in addition to the approaches that are being pursued for the production of improved drugs that inhibit bacterial protein synthesis.

  18. Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

    Science.gov (United States)

    Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Guerrero, Leandro; Seely, Mary; Cowan, Don A.

    2017-01-01

    Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations. PMID:28071697

  19. Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment.

    Science.gov (United States)

    Esham; Ye; Moran

    2000-12-01

    Bacterial isolates were obtained from enrichment cultures containing humic substances extracted from estuarine water using an XAD-8 resin. Eighteen isolates were chosen for phylogenetic and physiological characterization based on numerical importance in serial dilutions of the enrichment culture and unique colony morphology. Partial sequences of the 16S rRNA genes indicated that six of the isolates were associated with the alpha subclass of Proteobacteria, three with the gamma-Proteobacteria, and nine with the Gram-positive bacteria. Ten isolates degraded at least one (and up to six) selected aromatic single-ring compounds. Six isolates showed ability to degrade [(14)C]humic substances derived from the dominant salt marsh grass in the estuary from which they were isolated (Spartina alterniflora), mineralizing 0.4-1.1% of the humic substances over 4 weeks. A mixture of all 18 isolates did not degrade humic substances significantly faster than any of the individual strains, however, and no isolate degraded humic substances to the same extent as the natural marine bacterial community (3.0%). Similar studies with a radiolabeled synthetic lignin ([beta-(14)C]dehydropolymerisate) showed measurable levels of degradation by all 18 bacteria (3.0-8.8% in 4 weeks), but mineralization levels were again lower than that observed for the natural marine bacterial community (28.2%). Metabolic capabilities of the 18 isolates were highly variable and generally did not map to phylogenetic affiliation.

  20. Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

    Science.gov (United States)

    Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Guerrero, Leandro; Seely, Mary; Cowan, Don A.

    2017-01-01

    Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.

  1. Preparation, spectroscopic characterization and antimicrobial activities of mixed metal (Sb and Bi) bridged derivatives with mixed sulfur donor ligands

    Science.gov (United States)

    Joshi, Sapana; Chauhan, H. P. S.; Carpenter, Nitin

    2017-01-01

    This article explores the syntheses of six mixed metal derivatives of antimony(III) and bismuth(III) by the reaction of ethane-1,2-dithiol and metal bis derivatives of dithiocarbamates and/or dithiophosphates ligands in 1:1:1 M stoichiometry. These derivatives have been characterized by physicochemical [elemental analysis (C, H, N, S, Sb and Bi), molecular weight and melting point determinations], spectral [UV-Visible, FTIR, NMR (1H, 13C and 31P)], powder X-ray diffraction studies. These derivatives have nano-ranged crystallite size (8.18-18.04 nm) with monoclinic crystal system. All the synthesized derivatives have two metal centers (Sb and Bi) which elevate the zone of inhibition against four bacterial and two fungal species as compared to single metal species (metal precursors) as well as standard drugs.

  2. Bacterial Acclimation Inside an Aqueous Battery.

    Directory of Open Access Journals (Sweden)

    Dexian Dong

    Full Text Available Specific environmental stresses may lead to induced genomic instability in bacteria, generating beneficial mutants and potentially accelerating the breeding of industrial microorganisms. The environmental stresses inside the aqueous battery may be derived from such conditions as ion shuttle, pH gradient, free radical reaction and electric field. In most industrial and medical applications, electric fields and direct currents are used to kill bacteria and yeast. However, the present study focused on increasing bacterial survival inside an operating battery. Using a bacterial acclimation strategy, both Escherichia coli and Bacillus subtilis were acclimated for 10 battery operation cycles and survived in the battery for over 3 days. The acclimated bacteria changed in cell shape, growth rate and colony color. Further analysis indicated that electrolyte concentration could be one of the major factors determining bacterial survival inside an aqueous battery. The acclimation process significantly improved the viability of both bacteria E. coli and B. subtilis. The viability of acclimated strains was not affected under battery cycle conditions of 0.18-0.80 mA cm(-2 and 1.4-2.1 V. Bacterial addition within 1.0×10(10 cells mL(-1 did not significantly affect battery performance. Because the environmental stress inside the aqueous battery is specific, the use of this battery acclimation strategy may be of great potential for the breeding of industrial microorganisms.

  3. Use of single-strand conformation polymorphism of amplified 16S rDNA for grouping of bacteria isolated from foods.

    Science.gov (United States)

    Takahashi, Hajime; Kimura, Bon; Tanaka, Yuichiro; Mori, Mayumi; Yokoi, Asami; Fujii, Tateo

    2008-04-01

    The grouping method for isolated strains from foods using single-strand conformation polymorphism (SSCP) after PCR amplification of a portion of 16S rDNA was developed. This method was able to group the strains from various food samples based on 16S rDNA sequence. As 97.8% of the isolated strains from various foods were grouped correctly, use of the PCR-SSCP method enables the prompt and labor-saving analysis of microbial population of food-derived bacterial strains. Advantages in speed and accuracy of bacterial population identification by the PCR-SSCP method have practical application for food suppliers and testing laboratories.

  4. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem.

    Science.gov (United States)

    Lafortune, Isabelle; Juteau, Pierre; Déziel, Eric; Lépine, François; Beaudet, Réjean; Villemur, Richard

    2009-04-01

    High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. Although several PAH-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all PAHs. A consortium composed of different microorganisms can better achieve this. Two-liquid phase (TLP) culture systems have been developed to increase the bioavailability of poorly soluble substrates for uptake and biodegradation by microorganisms. By combining a silicone oil-water TLP system with a microbial consortium capable of degrading HMW PAHs, we previously developed a highly efficient PAH-degrading system. In this report, we characterized the bacterial diversity of the consortium with a combination of culture-dependent and culture-independent methods. Polymerase chain reaction (PCR) of part of the 16S ribosomal RNA gene (rDNA) sequences combined with denaturing gradient gel electrophoresis was used to monitor the bacterial population changes during PAH degradation of the consortium when pyrene, chrysene, and benzo[a]pyrene were provided together or separately in the TLP cultures. No substantial changes in bacterial profiles occurred during biodegradation of pyrene and chrysene in these cultures. However, the addition of the low-molecular-weight PAHs phenanthrene or naphthalene in the system favored one bacterial species related to Sphingobium yanoikuyae. Eleven bacterial strains were isolated from the consortium but, interestingly, only one-IAFILS9 affiliated to Novosphingobium pentaromativorans-was capable of growing on pyrene and chrysene as sole source of carbon. A 16S rDNA library was derived from the consortium to identify noncultured bacteria. Among 86 clones screened, 20 were affiliated to different bacterial species-genera. Only three strains were represented in the screened clones. Eighty

  5. Facile synthesis of novel benzotriazole derivatives and their antibacterial activities

    Indian Academy of Sciences (India)

    Jun Wan; Peng-Cheng Lv; Na-Na Tian; Hai-Liang Zhu

    2010-07-01

    A series of benzotriazole derivatives (compounds 1-27) were synthesized, and 24 (compounds 1-5, 9-27) of which were first reported. Their chemical structures were confirmed by means of 1H NMR, IR and elemental analyses, coupled with one selected single crystal structure (compound 1). All the compounds were assayed for antibacterial activities against three Gram positive bacterial strains (Bacillus subtilis, Staphylococcus aureus and Streptococcus faecalis) and three Gram negative bacterial strains (Escherichia coli, Pseudomonas aeruginosa and Enterobacter cloacae) by MTT method. Among the compounds tested, most of them exhibited potent antibacterial activity against the six bacterial strains. Most importantly, compound 3-benzotriazol-1-yl-1-(4-bromo-phenyl)-2-[1,2,4]triazol-1-ylpropan-1-one (19) showed the most favourable antibacterial activity against B. subtilis, S. aureus, S. faecalis, P. aeruginosa, E. coli and E. cloacae with MIC of 1.56 g/mL, 1.56 g/mL, 1.56 g/mL, 3.12 g/mL, 6.25 g/mL and 6.25 g/mL, respectively.

  6. Optimising Antibiotic Usage to Treat Bacterial Infections

    Science.gov (United States)

    Paterson, Iona K.; Hoyle, Andy; Ochoa, Gabriela; Baker-Austin, Craig; Taylor, Nick G. H.

    2016-11-01

    The increase in antibiotic resistant bacteria poses a threat to the continued use of antibiotics to treat bacterial infections. The overuse and misuse of antibiotics has been identified as a significant driver in the emergence of resistance. Finding optimal treatment regimens is therefore critical in ensuring the prolonged effectiveness of these antibiotics. This study uses mathematical modelling to analyse the effect traditional treatment regimens have on the dynamics of a bacterial infection. Using a novel approach, a genetic algorithm, the study then identifies improved treatment regimens. Using a single antibiotic the genetic algorithm identifies regimens which minimise the amount of antibiotic used while maximising bacterial eradication. Although exact treatments are highly dependent on parameter values and initial bacterial load, a significant common trend is identified throughout the results. A treatment regimen consisting of a high initial dose followed by an extended tapering of doses is found to optimise the use of antibiotics. This consistently improves the success of eradicating infections, uses less antibiotic than traditional regimens and reduces the time to eradication. The use of genetic algorithms to optimise treatment regimens enables an extensive search of possible regimens, with previous regimens directing the search into regions of better performance.

  7. Forensic identification using skin bacterial communities.

    Science.gov (United States)

    Fierer, Noah; Lauber, Christian L; Zhou, Nick; McDonald, Daniel; Costello, Elizabeth K; Knight, Rob

    2010-04-06

    Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object. Here we describe a series of studies de-monstrating the validity of this approach. We show that skin-associated bacteria can be readily recovered from surfaces (including single computer keys and computer mice) and that the structure of these communities can be used to differentiate objects handled by different individuals, even if those objects have been left untouched for up to 2 weeks at room temperature. Furthermore, we demonstrate that we can use a high-throughput pyrosequencing-based ap-proach to quantitatively compare the bacterial communities on objects and skin to match the object to the individual with a high degree of certainty. Although additional work is needed to further establish the utility of this approach, this series of studies introduces a forensics approach that could eventually be used to independently evaluate results obtained using more traditional forensic practices.

  8. Bacterial community reconstruction using compressed sensing.

    Science.gov (United States)

    Amir, Amnon; Zuk, Or

    2011-11-01

    Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. Our method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of all known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a simple and efficient way for identifying bacterial species compositions in biological samples. All supplementary data and the MATLAB code are available at www.broadinstitute.org/?orzuk/publications/BCS/.

  9. Cooperative Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2009-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  10. Bacterial Colony Optimization

    Directory of Open Access Journals (Sweden)

    Ben Niu

    2012-01-01

    Full Text Available This paper investigates the behaviors at different developmental stages in Escherichia coli (E. coli lifecycle and developing a new biologically inspired optimization algorithm named bacterial colony optimization (BCO. BCO is based on a lifecycle model that simulates some typical behaviors of E. coli bacteria during their whole lifecycle, including chemotaxis, communication, elimination, reproduction, and migration. A newly created chemotaxis strategy combined with communication mechanism is developed to simplify the bacterial optimization, which is spread over the whole optimization process. However, the other behaviors such as elimination, reproduction, and migration are implemented only when the given conditions are satisfied. Two types of interactive communication schemas: individuals exchange schema and group exchange schema are designed to improve the optimization efficiency. In the simulation studies, a set of 12 benchmark functions belonging to three classes (unimodal, multimodal, and rotated problems are performed, and the performances of the proposed algorithms are compared with five recent evolutionary algorithms to demonstrate the superiority of BCO.

  11. Bacterial assays for recombinagens.

    Science.gov (United States)

    Hoffmann, G R

    1992-12-01

    Two principal strategies have been used for studying recombinagenic effects of chemicals and radiation in bacteria: (1) measurement of homologous recombination involving defined alleles in a partially diploid strain, and (2) measurement of the formation and loss of genetic duplications in the bacterial chromosome. In the former category, most methods involve one allele in the bacterial chromosome and another in a plasmid, but it is also possible to detect recombination between two chromosomal alleles or between two extrachromosomal alleles. This review summarizes methods that use each of these approaches for detecting recombination and tabulates data on agents that have been found to be recombinagenic in bacteria. The assays are discussed with respect to their effectiveness in testing for recombinagens and their potential for elucidating mechanisms underlying recombinagenic effects.

  12. The modified extended Hansen method to determine partial solubility parameters of drugs containing a single hydrogen bonding group and their sodium derivatives: benzoic acid/Na and ibuprofen/Na.

    Science.gov (United States)

    Bustamante, P; Pena, M A; Barra, J

    2000-01-20

    Sodium salts are often used in drug formulation but their partial solubility parameters are not available. Sodium alters the physical properties of the drug and the knowledge of these parameters would help to predict adhesion properties that cannot be estimated using the solubility parameters of the parent acid. This work tests the applicability of the modified extended Hansen method to determine partial solubility parameters of sodium salts of acidic drugs containing a single hydrogen bonding group (ibuprofen, sodium ibuprofen, benzoic acid and sodium benzoate). The method uses a regression analysis of the logarithm of the experimental mole fraction solubility of the drug against the partial solubility parameters of the solvents, using models with three and four parameters. The solubility of the drugs was determined in a set of solvents representative of several chemical classes, ranging from low to high solubility parameter values. The best results were obtained with the four parameter model for the acidic drugs and with the three parameter model for the sodium derivatives. The four parameter model includes both a Lewis-acid and a Lewis-base term. Since the Lewis acid properties of the sodium derivatives are blocked by sodium, the three parameter model is recommended for these kind of compounds. Comparison of the parameters obtained shows that sodium greatly changes the polar parameters whereas the dispersion parameter is not much affected. Consequently the total solubility parameters of the salts are larger than for the parent acids in good agreement with the larger hydrophilicity expected from the introduction of sodium. The results indicate that the modified extended Hansen method can be applied to determine the partial solubility parameters of acidic drugs and their sodium salts.

  13. Bacterial contribution to dissolved organic matter in eutrophic Lake Kasumigaura, Japan.

    Science.gov (United States)

    Kawasaki, Nobuyuki; Komatsu, Kazuhiro; Kohzu, Ayato; Tomioka, Noriko; Shinohara, Ryuichiro; Satou, Takayuki; Watanabe, Fumiko Nara; Tada, Yuya; Hamasaki, Koji; Kushairi, M R M; Imai, Akio

    2013-12-01

    Incubation experiments using filtered waters from Lake Kasumigaura were conducted to examine bacterial contribution to a dissolved organic carbon (DOC) pool. Bacterial abundance, bacterial production, concentrations of DOC, total dissolved amino acids (TDAA), and total dissolved neutral sugars (TDNS) were monitored during the experiments. Bacterial production during the first few days was very high (20 to 35 μg C liter(-1) day(-1)), accounting for 40 to 70% of primary production. The total bacterial production accounted for 34 to 55% of the DOC loss during the experiment, indicating high bacterial activities in Lake Kasumigaura. The DOC degradation was only 12 to 15%, whereas the degradation of TDAA and TDNS ranged from 30 to 50%, suggesting the preferential usage of TDAA and TDNS. The contribution of bacterially derived carbon to a DOC pool in Lake Kasumigaura was estimated using d-amino acids as bacterial biomarkers and accounted for 30 to 50% of the lake DOC. These values were much higher than those estimated for the open ocean (20 to 30%). The ratio of bacterially derived carbon to bulk carbon increased slightly with time, suggesting that the bacterially derived carbon is more resistant to microbial degradation than bulk carbon. This is the first study to estimate the bacterial contribution to a DOC pool in freshwater environments. These results indicate that bacteria play even more important roles in carbon cycles in freshwater environments than in open oceans and also suggests that recent increases in recalcitrant DOC in various lakes could be attributed to bacterially derived carbon. The potential differences in bacterial contributions to dissolved organic matter (DOM) between freshwater and marine environments are discussed.

  14. Spontaneous bacterial peritonitis

    OpenAIRE

    Al Amri Saleh

    1995-01-01

    Spontaneous bacterial peritonitis (SBP) is an infection of the ascitic fluid without obvious intra-abdominal source of sepsis; usually complicates advanced liver disease. The pathogenesis of the disease is multifactorial: low ascitic protein-content, which reflects defi-cient ascitic fluid complement and hence, reduced opsonic activity is thought to be the most important pathogenic factor. Frequent and prolonged bacteremia has been considered as another pertinent cause of SBP. This disease is...

  15. Modelling bacterial speciation

    OpenAIRE

    2006-01-01

    A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher–Wright model in which genotypes, defined by the alleles at 140 house-keeping loci, change in each generation by mutation or recombination, and examine conditions in which an initially uniform population gives rise to resolved clusters. Where recombination occurs at equal frequency between all members of the population, we o...

  16. Hemoglobin derivatives

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003371.htm Hemoglobin derivatives To use the sharing features on this page, please enable JavaScript. Hemoglobin derivatives are altered forms of hemoglobin . Hemoglobin is ...

  17. Adaptive Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2011-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  18. Neglected bacterial zoonoses.

    Science.gov (United States)

    Chikeka, I; Dumler, J S

    2015-05-01

    Bacterial zoonoses comprise a group of diseases in humans or animals acquired by direct contact with or by oral consumption of contaminated animal materials, or via arthropod vectors. Among neglected infections, bacterial zoonoses are among the most neglected given emerging data on incidence and prevalence as causes of acute febrile illness, even in areas where recognized neglected tropical diseases occur frequently. Although many other bacterial infections could also be considered in this neglected category, five distinct infections stand out because they are globally distributed, are acute febrile diseases, have high rates of morbidity and case fatality, and are reported as commonly as malaria, typhoid or dengue virus infections in carefully designed studies in which broad-spectrum diagnoses are actively sought. This review will focus attention on leptospirosis, relapsing fever borreliosis and rickettsioses, including scrub typhus, murine typhus and spotted fever group rickettsiosis. Of greatest interest is the lack of distinguishing clinical features among these infections when in humans, which confounds diagnosis where laboratory confirmation is lacking, and in regions where clinical diagnosis is often attributed to one of several perceived more common threats. As diseases such as malaria come under improved control, the real impact of these common and under-recognized infections will become evident, as will the requirement for the strategies and allocation of resources for their control.

  19. 以玉米浆干粉为氮源静态发酵生产细菌纤维素的动力学研究%Study on Static Fermentation Kinetic based on Bacterial Cellulose with Dried Corn Steep Liquor Powder as a Single Nitrogen Source

    Institute of Scientific and Technical Information of China (English)

    鲁敏; 张月明; 关晓辉; 徐小惠

    2013-01-01

    With dried corn steep liquor powder as a single nitrogen source and Gluconacetobacter xylinus as a strain,study on the fermentation kinetic based on bacterial cellulose (BC) was conducted.The kinetic models were proposed based on the Logistic equation,Luedeking-Piret equation and substrate consumption equation for cell growth,BC production and residual sugar consumption,respectively.The above models appeared to provide a reasonable description for the BC fermentation equation.Therefore,the proposed models were applied to predict productivity of the systems and effectively control and optimize fermentation process,as well as offer theoretic foundation for industrial production of bacterial cellulose.%以木葡糖酸醋杆菌为目标菌种,以玉米浆干粉为氮源,进行了静态发酵生产细菌纤维素(BC)的动力学研究.结果表明,菌体生长适合于Logistic方程,BC生成符合Luedeking-Piret方程,还原糖消耗可用基于物料衡算的基质消耗方程描述,且模型计算值与试验值能较好吻合.因此,利用建立的数学模型可以预测系统的生产率,有效控制和优化静态发酵过程,为日后实现工业化规模生产提供理论基础.

  20. Single point mutations in the helicase domain of the NS3 protein enhance dengue virus replicative capacity in human monocyte-derived dendritic cells and circumvent the type I interferon response.

    Science.gov (United States)

    Silveira, G F; Strottmann, D M; de Borba, L; Mansur, D S; Zanchin, N I T; Bordignon, J; dos Santos, C N Duarte

    2016-01-01

    Dengue is the most prevalent arboviral disease worldwide. The outcome of the infection is determined by the interplay of viral and host factors. In the present study, we evaluated the cellular response of human monocyte-derived DCs (mdDCs) infected with recombinant dengue virus type 1 (DV1) strains carrying a single point mutation in the NS3hel protein (L435S or L480S). Both mutated viruses infect and replicate more efficiently and produce more viral progeny in infected mdDCs compared with the parental, non-mutated virus (vBACDV1). Additionally, global gene expression analysis using cDNA microarrays revealed that the mutated DVs induce the up-regulation of the interferon (IFN) signalling and pattern recognition receptor (PRR) canonical pathways in mdDCs. Pronounced production of type I IFN were detected specifically in mdDCs infected with DV1-NS3hel-mutated virus compared with mdDCs infected with the parental virus. In addition, we showed that the type I IFN produced by mdDCs is able to reduce DV1 infection rates, suggesting that cytokine function is effective but not sufficient to mediate viral clearance of DV1-NS3hel-mutated strains. Our results demonstrate that single point mutations in subdomain 2 have important implications for adenosine triphosphatase (ATPase) activity of DV1-NS3hel. Although a direct functional connection between the increased ATPase activity and viral replication still requires further studies, these mutations speed up viral RNA replication and are sufficient to enhance viral replicative capacity in human primary cell infection and circumvent type I IFN activity. This information may have particular relevance for attenuated vaccine protocols designed for DV.

  1. Future of Bacterial Therapy of Cancer.

    Science.gov (United States)

    Hoffman, Robert M

    2016-01-01

    Bacterial therapy of cancer has a centuries-long history and was first-line therapy at the hospital in New York City that would become Memorial Sloan-Kettering Cancer Center, under Dr. William B. Coley. However, after Coley's death in 1936, bacterial therapy of cancer ceased in the clinic until the present century. Clinical trials have been recently carried out for strains of the obligate anaerobe Clostridium novyi with the toxin gene deleted, and on an attenuated strain of Salmonella typhimurium (S. typhimurium), which is a facultative anaerobe that can grow in viable, as well as necrotic, areas of tumors, unlike Clostridium, which can only grow in the hypoxic areas. Our laboratory has developed the novel strain S. typhimurium A1-R that is effective against all tumor types in clinically-relevant mouse models, including patient-derived orthotopic xenograft (PDOX) mouse models. This chapter suggests future clinical applications for S. typhimurium A1-R.

  2. The Bacterial Ghost platform system: production and applications.

    Science.gov (United States)

    Langemann, Timo; Koller, Verena Juliana; Muhammad, Abbas; Kudela, Pavol; Mayr, Ulrike Beate; Lubitz, Werner

    2010-01-01

    The Bacterial Ghost (BG) platform technology is an innovative system for vaccine, drug or active substance delivery and for technical applications in white biotechnology. BGs are cell envelopes derived from Gram-negative bacteria. BGs are devoid of all cytoplasmic content but have a preserved cellular morphology including all cell surface structures. Using BGs as delivery vehicles for subunit or DNA-vaccines the particle structure and surface properties of BGs are targeting the carrier itself to primary antigen-presenting cells. Furthermore, BGs exhibit intrinsic adjuvant properties and trigger an enhanced humoral and cellular immune response to the target antigen. Multiple antigens of the native BG envelope and recombinant protein or DNA antigens can be combined in a single type of BG. Antigens can be presented on the inner or outer membrane of the BG as well as in the periplasm that is sealed during BG formation. Drugs or supplements can also be loaded to the internal lumen or periplasmic space of the carrier. BGs are produced by batch fermentation with subsequent product recovery and purification via tangential flow filtration. For safety reasons all residual bacterial DNA is inactivated during the BG production process by the use of staphylococcal nuclease A and/or the treatment with β-propiolactone. After purification BGs can be stored long-term at ambient room temperature as lyophilized product. The production cycle from the inoculation of the pre-culture to the purified BG concentrate ready for lyophilization does not take longer than a day and thus meets modern criteria of rapid vaccine production rather than keeping large stocks of vaccines. The broad spectrum of possible applications in combination with the comparably low production costs make the BG platform technology a safe and sophisticated product for the targeted delivery of vaccines and active agents as well as carrier of immobilized enzymes for applications in white biotechnology.

  3. Antimicrobial effect against different bacterial strains and bacterial adaptation to essential oils used as feed additives

    OpenAIRE

    Melo, Antonio Diego Brandão; Amaral, Amanda Figueiredo; Schaefer, Gustavo; Luciano, Fernando Bittencourt; Andrade,Carla de; Costa, Leandro Batista; Rostagno, Marcos Horácio

    2015-01-01

    The aim of this study was to evaluate the antimicrobial activity and determine the minimum bactericidal concentration (MBC) of the essential oils derived from Origanum vulgare (oregano), Melaleuca alternifolia (tea tree), Cinnamomum cassia (cassia), and Thymus vulgaris (white thyme) against Salmonella Typhimurium, Salmonella Enteritidis, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. The study also investigated the ability of these different bacterial strains to develop ad...

  4. Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium

    Directory of Open Access Journals (Sweden)

    Santina Santisi

    2015-06-01

    Full Text Available Three bacterial isolates identified as Alcanivorax borkumensis SK2, Rhodococcus erythropolis HS4 and Pseudomonas stutzeri SDM, based on 16S rRNA gene sequences, were isolated from crude oil enrichments of natural seawater. Single strains and four bacterial consortia designed by mixing the single bacterial cultures respectively in the following ratios: (Alcanivorax: Pseudomonas, 1:1, (Alcanivorax: Rhodococcus, 1:1, (Pseudomonas: Rhodococcus, 1:1, and (Alcanivorax: Pseudomonas: Rhodococcus, 1:1:1, were analyzed in order to evaluate their oil degrading capability. All experiments were carried out in microcosms systems containing seawater (with and without addition of inorganic nutrients and crude oil (unique carbon source. Measures of total and live bacterial abundance, Card-FISH and quali-, quantitative analysis of hydrocarbons (GC-FID were carried out in order to elucidate the co-operative action of mixed microbial populations in the process of biodegradation of crude oil. All data obtained confirmed the fundamental role of bacteria belonging to Alcanivorax genus in the degradation of linear hydrocarbons in oil polluted environments.

  5. Thermal desorption-multiphoton ionization time-of-flight mass spectrometry of individual aerosol particles: a simplified approach for online single-particle analysis of polycyclic aromatic hydrocarbons and their derivatives.

    Science.gov (United States)

    Bente, Matthias; Sklorz, Martin; Streibel, Thorsten; Zimmermann, Ralf

    2009-04-01

    Online single-particle (SP) laser mass spectrometry (MS) is an important tool for fundamental and applied aerosol research. Usually laser desorption/ionization (LDI) is applied for ablation and ionization of atoms and molecular fragments from the nanometer- or micrometer-sized air-borne particles and time-of-flight analysers (TOFMS) are used for mass-selective detection of mainly inorganic analytes. The detection of molecular organic compounds is solely possible under very special experimental conditions and extremely dependent on the particle matrix and thus limited to special applications. Very recently it was shown that by implementation of a two-step laser desorption (LD) resonance-enhanced multiphoton ionization (REMPI) postionization approach the single-particulate molecular signature of polycyclic aromatic hydrocarbons (PAH) and their derivatives can be recorded (LD-REMPI-SP-TOFMS). By this, particles from different sources could be differentiated via the patterns of specific molecular source tracers such as retene for soft wood combustion or larger PAH as indicator for gasoline car emissions. One drawback of the LD-REMPI-SP-TOFMS method in particular for field applications is, however, the necessity of operation and adjustment of two lasers. In this paper the successful implementation of a thermal desorption step in single-particle mass spectrometry is described (TD-REMPI-SP-TOFMS). After size determination by particle velocimetry, individual particles are thermally desorbed on a heated surface in the ion source of the TOFMS. Desorbed molecules are ionized subsequently by REMPI, which addresses selectively PAH and molecular trace indicators. The TD-REMPI-SP-TOFMS concept was tested with reference particles and applied for automotive exhaust and ambient monitoring. The comparison of the results with the ones obtained by the two-laser approach (LD-REMPI-SP-TOFMS) indicates that the patented TD-REMPI-SP-TOFMS technology presented here is nearly equally well

  6. Domino Knoevenagel/Michael synthesis of 2,2'-arylmethylenebis(3- hydroxy-5,5-dimethyl-2-cyclohexen-1-one) derivatives catalyzed by silica-diphenic acid and their single crystal X-ray analysis

    Indian Academy of Sciences (India)

    RUPALI VAID; MONIKA GUPTA; RAJNI KANT; VIVEK K GUPTA

    2016-06-01

    An efficient and eco-friendly procedure has been developed for the synthesis of various 2,2'- arylmethylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) derivatives which were isolated and characterizedby melting point, IR,$^{ 1}H-NMR$,$^{ 13}$C-NMR and mass spectrometric techniques. Out of the fourteencompounds synthesized, four compounds yielded crystals suitable for single crystal X-ray analysis whichshowed that 2,2'-phenylmethylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the tetragonalsystem with space group I41/a, 2,2’-(3-nitrophenyl)methylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the monoclinic system with space group P21/n, 2,2’-(4-nitrophenyl)methylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the orthorhombic system with space group Pca21and 2,2’-(4-chlorophenyl)methylenebis(3-hydroxy-5,5-dimethyl-2-cyclohexene-1-one) crystallizes in the monoclinicspace group P21/c.

  7. Hydrolysis/dehydration/aldol-condensation/hydrogenation of lignocellulosic biomass and biomass-derived carbohydrates in the presence of Pd/WO3-ZrO2 in a single reactor.

    Science.gov (United States)

    Dedsuksophon, W; Faungnawakij, K; Champreda, V; Laosiripojana, N

    2011-01-01

    Hydrolysis/dehydration/aldol-condensation/hydrogenation of lignocellulosic-biomass (corncobs) and biomass-derived carbohydrates (tapioca flour) to produce water-soluble C5-C15 compounds was developed in a single reactor system. WO3-ZrO2 efficiently catalyzed the hydrolysis/dehydration of these feedstocks to 5-hydroxymethylfurfural and furfural, while the impregnation of WO3-ZrO2 with Pd allowed sequential aldolcondensation/hydrogenation of these furans to C5-C15 compounds. The highest C5-C15 yields of 14.8-20.3% were observed at a hydrolysis/dehydration temperature of 573 K for 5 min, an aldol-condensation temperature of 353 K for 30 h, and a hydrogenation temperature of 393 K for 6 h. The C5-C15 yield from tapioca flour was higher than that from corncobs (20.3% compared to 14.8%). Tapioca flour produced more C6/C9/C15, whereas corncobs generated more C5/C8/C13 compounds due to the presence of hemicellulose in the corncobs. These water-soluble organic compounds can be further converted to liquid alkanes with high cetane numbers for replacing diesel fuel in transportation applications.

  8. Development of a cost-efficient novel method for rapid, concurrent genotyping of five common single nucleotide polymorphisms of the brain derived neurotrophic factor (BDNF) gene by tetra-primer amplification refractory mutation system.

    Science.gov (United States)

    Wang, Cathy K; Xu, Michael S; Ross, Colin J; Lo, Ryan; Procyshyn, Ric M; Vila-Rodriguez, Fidel; White, Randall F; Honer, William G; Barr, Alasdair M

    2015-09-01

    Brain derived neurotrophic factor (BDNF) is a molecular trophic factor that plays a key role in neuronal survival and plasticity. Single nucleotide polymorphisms (SNPs) of the BDNF gene have been associated with specific phenotypic traits in a large number of neuropsychiatric disorders and the response to psychotherapeutic medications in patient populations. Nevertheless, due to study differences and occasionally contrasting findings, substantial further research is required to understand in better detail the association between specific BDNF SNPs and these psychiatric disorders. While considerable progress has been made recently in developing advanced genotyping platforms of SNPs, many high-throughput probe- or array-based detection methods currently available are limited by high costs, slow processing times or access to advanced instrumentation. The polymerase chain reaction (PCR)-based, tetra-primer amplification refractory mutation system (T-ARMS) method is a potential alternative technique for detecting SNP genotypes efficiently, quickly, easily, and cheaply. As a tool in psychopathology research, T-ARMS was shown to be capable of detecting five common SNPs in the BDNF gene (rs6265, rs988748, rs11030104, 11757G/C and rs7103411), which are all SNPs with previously demonstrated clinical relevance to schizophrenia and depression. The present technique therefore represents a suitable protocol for many research laboratories to study the genetic correlates of BDNF in psychiatric disorders. Copyright Copyright © 2015 John Wiley & Sons, Ltd.

  9. Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks.

    Directory of Open Access Journals (Sweden)

    Giovanna Carpi

    Full Text Available Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors and host-selection behaviors affect their microbiome.Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection

  10. Bacterial foodborne infections after hematopoietic cell transplantation.

    Science.gov (United States)

    Boyle, Nicole M; Podczervinski, Sara; Jordan, Kim; Stednick, Zach; Butler-Wu, Susan; McMillen, Kerry; Pergam, Steven A

    2014-11-01

    Diarrhea, abdominal pain, and fever are common among patients undergoing hematopoietic cell transplantation (HCT), but such symptoms are also typical with foodborne infections. The burden of disease caused by foodborne infections in patients undergoing HCT is unknown. We sought to describe bacterial foodborne infection incidence after transplantation within a single-center population of HCT recipients. All HCT recipients who underwent transplantation from 2001 through 2011 at the Fred Hutchinson Cancer Research Center in Seattle, Washington were followed for 1 year after transplantation. Data were collected retrospectively using center databases, which include information from transplantation, on-site examinations, outside records, and collected laboratory data. Patients were considered to have a bacterial foodborne infection if Campylobacter jejuni/coli, Listeria monocytogenes, E. coli O157:H7, Salmonella species, Shigella species, Vibrio species, or Yersinia species were isolated in culture within 1 year after transplantation. Nonfoodborne infections with these agents and patients with pre-existing bacterial foodborne infection (within 30 days of transplantation) were excluded from analyses. A total of 12 of 4069 (.3%) patients developed a bacterial foodborne infection within 1 year after transplantation. Patients with infections had a median age at transplantation of 50.5 years (interquartile range [IQR], 35 to 57), and the majority were adults ≥18 years of age (9 of 12 [75%]), male gender (8 of 12 [67%]) and had allogeneic transplantation (8 of 12 [67%]). Infectious episodes occurred at an incidence rate of 1.0 per 100,000 patient-days (95% confidence interval, .5 to 1.7) and at a median of 50.5 days after transplantation (IQR, 26 to 58.5). The most frequent pathogen detected was C. jejuni/coli (5 of 12 [42%]) followed by Yersinia (3 of 12 [25%]), although Salmonella (2 of 12 [17%]) and Listeria (2 of 12 [17%]) showed equal frequencies; no cases of Shigella

  11. Bacterial chromosome segregation.

    Science.gov (United States)

    Possoz, Christophe; Junier, Ivan; Espeli, Olivier

    2012-01-01

    Dividing cells have mechanisms to ensure that their genomes are faithfully segregated into daughter cells. In bacteria, the description of these mechanisms has been considerably improved in the recent years. This review focuses on the different aspects of bacterial chromosome segregation that can be understood thanks to the studies performed with model organisms: Escherichia coli, Bacillus subtilis, Caulobacter crescentus and Vibrio cholerae. We describe the global positionning of the nucleoid in the cell and the specific localization and dynamics of different chromosomal loci, kinetic and biophysic aspects of chromosome segregation are presented. Finally, a presentation of the key proteins involved in the chromosome segregation is made.

  12. Bacterial Degradation of Pesticides

    DEFF Research Database (Denmark)

    Knudsen, Berith Elkær

    This PhD project was carried out as part of the Microbial Remediation of Contaminated Soil and Water Resources (MIRESOWA) project, funded by the Danish Council for Strategic Research (grant number 2104-08-0012). The environment is contaminated with various xenobiotic compounds e.g. pesticides......D student, to construct fungal-bacterial consortia in order to potentially stimulate pesticide degradation thereby increasing the chance of successful bioaugmentation. The results of the project are reported in three article manuscripts, included in this thesis. In manuscript I, the mineralization of 2...

  13. Spontaneous bacterial peritonitis

    Directory of Open Access Journals (Sweden)

    Al Amri Saleh

    1995-01-01

    Full Text Available Spontaneous bacterial peritonitis (SBP is an infection of the ascitic fluid without obvious intra-abdominal source of sepsis; usually complicates advanced liver disease. The pathogenesis of the disease is multifactorial: low ascitic protein-content, which reflects defi-cient ascitic fluid complement and hence, reduced opsonic activity is thought to be the most important pathogenic factor. Frequent and prolonged bacteremia has been considered as another pertinent cause of SBP. This disease is associated with high mortality and recurrence. Therefore, orompt recognition and institution of therapy and plan of prophylaxis is vital.

  14. Bacterial mitotic machineries

    DEFF Research Database (Denmark)

    Gerdes, Kenn; Møller-Jensen, Jakob; Ebersbach, Gitte;

    2004-01-01

    Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the Par......M protein of plasmid R1 forms F actin-like filaments that separate and move plasmid DNA from mid-cell to the cell poles. Evidence from three different laboratories indicate that the morphogenetic MreB protein may be involved in segregation of the bacterial chromosome....

  15. Financial Derivatives

    DEFF Research Database (Denmark)

    Wigan, Duncan

    2013-01-01

    Contemporary derivatives mark the development of capital and constitute a novel form of ownership. By reconfiguring the temporal, spatial and legal character of ownership derivatives present a substantive challenge to the tax collecting state. While fiscal systems are nationally bounded and inheren...... and inherently static, capital itself is unprecedentedly mobile, fluid and fungible. As such derivatives raise the specter of ‘financial weapons of mass destruction’....

  16. Bacterial adaptation to the gut environment favors successful colonization

    Science.gov (United States)

    Rezzonico, Enea; Mestdagh, Renaud; Delley, Michèle; Combremont, Séverine; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy; Bibiloni, Rodrigo

    2011-01-01

    Rodent models harboring a simple yet functional human intestinal microbiota provide a valuable tool to study the relationships between mammals and their bacterial inhabitants. In this study, we aimed to develop a simplified gnotobiotic mouse model containing 10 easy-to-grow bacteria, readily available from culture repositories, and of known genome sequence, that overall reflect the dominant commensal bacterial makeup found in adult human feces. We observed that merely inoculating a mix of fresh bacterial cultures into ex-germ free mice did not guarantee a successful intestinal colonization of the entire bacterial set, as mice inoculated simultaneously with all strains only harbored 3 after 21 d. Therefore, several inoculation procedures were tested and levels of individual strains were quantified using molecular tools. Best results were obtained by inoculating single bacterial strains into individual animals followed by an interval of two weeks before allowing the animals to socialize to exchange their commensal microbes. Through this procedure, animals were colonized with almost the complete bacterial set (9/10). Differences in the intestinal composition were also reflected in the urine and plasma metabolic profiles, where changes in lipids, SCFA, and amino acids were observed. We conclude that adaptation of bacterial strains to the host’s gut environment (mono-colonization) may predict a successful establishment of a more complex microbiota in rodents. PMID:22157236

  17. Direct and Auger Electron-Induced, Single- and Double-Strand Breaks on Plasmid DNA Caused by 99mTc-Labeled Pyrene Derivatives and the Effect of Bonding Distance

    Science.gov (United States)

    Reissig, Falco; Mamat, Constantin; Steinbach, Joerg; Pietzsch, Hans-Juergen; Freudenberg, Robert; Navarro-Retamal, Carlos; Caballero, Julio; Kotzerke, Joerg; Wunderlich, Gerd

    2016-01-01

    It is evident that 99mTc causes radical-mediated DNA damage due to Auger electrons, which were emitted simultaneously with the known γ-emission of 99mTc. We have synthesized a series of new 99mTc-labeled pyrene derivatives with varied distances between the pyrene moiety and the radionuclide. The pyrene motif is a common DNA intercalator and allowed us to test the influence of the radionuclide distance on damages of the DNA helix. In general, pUC 19 plasmid DNA enables the investigation of the unprotected interactions between the radiotracers and DNA that results in single-strand breaks (SSB) or double-strand breaks (DSB). The resulting DNA fragments were separated by gel electrophoresis and quantified by fluorescent staining. Direct DNA damage and radical-induced indirect DNA damage by radiolysis products of water were evaluated in the presence or absence of the radical scavenger DMSO. We demonstrated that Auger electrons directly induced both SSB and DSB in high efficiency when 99mTc was tightly bound to the plasmid DNA and this damage could not be completely prevented by DMSO, a free radical scavenger. For the first time, we were able to minimize this effect by increasing the carbon chain lengths between the pyrene moiety and the 99mTc nuclide. However, a critical distance between the 99mTc atom and the DNA helix could not be determined due to the significantly lowered DSB generation resulting from the interaction which is dependent on the type of the 99mTc binding motif. The effect of variable DNA damage caused by the different chain length between the pyrene residue and the Tc-core as well as the possible conformations of the applied Tc-complexes was supplemented with molecular dynamics (MD) calculations. The effectiveness of the DNA-binding 99mTc-labeled pyrene derivatives was demonstrated by comparison to non-DNA-binding 99mTcO4–, since nearly all DNA damage caused by 99mTcO4– was prevented by incubating with DMSO. PMID:27583677

  18. Root bacterial endophytes alter plant phenotype, but not physiology

    DEFF Research Database (Denmark)

    Henning, Jeremiah A.; Weston, David J.; Pelletier, Dale A.

    2016-01-01

    Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant...... phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits...... (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light-Asat, and saturating CO2-Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf...

  19. Antimicrobials for bacterial bioterrorism agents.

    Science.gov (United States)

    Sarkar-Tyson, Mitali; Atkins, Helen S

    2011-06-01

    The limitations of current antimicrobials for highly virulent pathogens considered as potential bioterrorism agents drives the requirement for new antimicrobials that are suitable for use in populations in the event of a deliberate release. Strategies targeting bacterial virulence offer the potential for new countermeasures to combat bacterial bioterrorism agents, including those active against a broad spectrum of pathogens. Although early in the development of antivirulence approaches, inhibitors of bacterial type III secretion systems and cell division mechanisms show promise for the future.

  20. Live bacterial delivery systems for development of mucosal vaccines

    NARCIS (Netherlands)

    Thole, J.E.R.; Dalen, P.J. van; Havenith, C.E.G.; Pouwels, P.H.; Seegers, J.F.M.L.; Tielen, F.D.; Zee, M.D. van der; Zegers, N.D.; Shaw, M.

    2000-01-01

    By expression of foreign antigens in attenuated strains derived from bacterial pathogens and in non-pathogenic commensal bacteria, recombinant vaccines are being developed that aim to stimulate mucosal immunity. Recent advances in the pathogenesis and molecular biology of these bacteria have allowed

  1. 含噻唑烷二酮-3-乙酸结构查尔酮衍生物的合成及抗菌活性的研究%Synthesis and Anti-bacterial Activity of Novel Chalcone Derivatives Containing 2,4-Thiazolidinedione-3-acetic Acid Moiety

    Institute of Scientific and Technical Information of China (English)

    孟凡领; 郑昌吉; 李因晶; 孙良鹏; 刘学坤; 张天一; 朴虎日

    2012-01-01

    A series of novel chalcone derivatives bearing the 2,4-thiazolidinedione-3-acetic acid moieties (8a~8p) were synthesized, and evaluated for their anti-bacterial activity. The results demonstrated that some compounds presented good antimicrobial activities against four multidrug-resistant clinical isolates, among which compounds 8g, 8i, 81 and 8m with minimum inhibitory concentration (MIC) value of 4 ug/mL showed as active as the standard drug, norfloxacin, against methi-cillin-resistant S. Aureus. None of the compounds exhibited obvious activity against the Gram-negative bacteria E. Coli 1356 at 64 μg/mL.%合成了一系列含噻唑烷二酮-3-乙酸结构的新型查尔酮衍生物,并对化合物进行了抗菌活性测定.结果显示,一些化合物对4种多重耐药菌显示出较强的抗菌活性,其中化合物8g,8i,8l和8m在抗耐甲氧西林金黄色葡萄球菌的最小抑制浓度(MIC)达到4 μg/mL,与对照药诺氟沙星(norfloxacin)相当.另外,在64 μg/mL浓度下,所有化合物对大肠杆菌1356均无明显抑制活性.

  2. Ceragenins – a new weapon to fight multidrug resistant bacterial infections

    Directory of Open Access Journals (Sweden)

    Urszula Surel

    2014-09-01

    Full Text Available Growing antibiotic resistance among pathogenic microorganisms is one of the most challenging problems. Often, a single mutation in a bacterial cell leads to the formation of a new drug resistance mechanism. The ceragenins are a novel class of antibiotic, offering great promise in future treatment of infections. These cationic antimicrobial lipids are net positively charged cholic acid derivates that are electrostatically attracted to the negatively charged membranes of bacteria, certain viruses, fungi, and protozoa. After membrane insertion, they interfere with membrane organisation, resulting in membrane dysfunction and cell death. This review focuses on the broad spectrum of antibacterial activity of ceragenins, and their potential to become a new group of antibiotics for prevention and treatment of infections, especially those caused by multidrug-resistant bacteria.

  3. Effects of immune supplementation and immune challenge on bacterial assemblages in the avian cloaca

    NARCIS (Netherlands)

    Matson, K.D.; Versteegh, M.A.; Velde, van der M.; Tieleman, B.I.

    2015-01-01

    Relationships between avian physiology and bacterial assemblages in the cloaca are poorly understood. We used molecular techniques to analyze cloacal swabs from pigeons that were subjected to two immunological manipulations: lysozyme supplementation and endotoxin challenge. From the swabs, we derive

  4. Epigenetics and bacterial infections.

    Science.gov (United States)

    Bierne, Hélène; Hamon, Mélanie; Cossart, Pascale

    2012-12-01

    Epigenetic mechanisms regulate expression of the genome to generate various cell types during development or orchestrate cellular responses to external stimuli. Recent studies highlight that bacteria can affect the chromatin structure and transcriptional program of host cells by influencing diverse epigenetic factors (i.e., histone modifications, DNA methylation, chromatin-associated complexes, noncoding RNAs, and RNA splicing factors). In this article, we first review the molecular bases of the epigenetic language and then describe the current state of research regarding how bacteria can alter epigenetic marks and machineries. Bacterial-induced epigenetic deregulations may affect host cell function either to promote host defense or to allow pathogen persistence. Thus, pathogenic bacteria can be considered as potential epimutagens able to reshape the epigenome. Their effects might generate specific, long-lasting imprints on host cells, leading to a memory of infection that influences immunity and might be at the origin of unexplained diseases.

  5. Bacterial polyhydroxyalkanoates: Still fabulous?

    Science.gov (United States)

    Możejko-Ciesielska, Justyna; Kiewisz, Robert

    2016-11-01

    Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed.

  6. Bacterial diversity in agricultural soils during litter decomposition

    NARCIS (Netherlands)

    Dilly, O.; Bloem, J.; Vos, A.; Munch, J.C.

    2004-01-01

    Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furth

  7. Optically Mapping Multiple Bacterial Genomes Simultaneously in a Single Run

    Science.gov (United States)

    2011-11-21

    but many clinical strains of Acinetobacter baumannii , distinguished by a few insertions, are too closely related to be mapped independently on the...0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing ...instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send

  8. Derivative Chameleons

    CERN Document Server

    Noller, Johannes

    2012-01-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field \\phi, but also of its derivatives via higher order co-ordinate invariants. Specifically we consider the first such non-trivial conformal factor A(\\phi,X), where X is the canonical kinetic term for \\phi. The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for \\phi. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning...

  9. Diagnosis of bacterial hepatic abscess by CT

    Institute of Scientific and Technical Information of China (English)

    Cheng-Lin Wang; Xue-Jun Guo; Shui-Bo Qiu; Yi Lei; Zhi-Dong Yuan; Han-Bin Dong; Hui-An Liu

    2007-01-01

    BACKGROUND: Bacterial hepatic abscess usually is acute and progressive, often resulting in sepsis, impairment of liver function and disseminated intravascular coagulation. The mortality rate was as high as 80%in the past. For the purpose of early diagnosis and differential diagnosis of this disease, we probed the imaging manifestations and their characteristics in bacterial hepatic abscesses by CT scan. METHODS:Twenty-four lesions from 21 patients with bacterial hepatic abscesses that were conifrmed by clinical features, puncture and culture were reviewed for CT manifestations. Fourteen patients were male and 7 were female, with an average age of 56.2 years. All lesions underwent CT plain scan and three-phase enhanced scan and 15 patients underwent delayed-phase imaging. Three senior radiologists read the iflms in accordance with a standard. RESULTS: Among 24 lesions, 18 (75%) were situated in the right liver with diameters of 1.4-9.3 cm (average 4.5 cm). Nineteen (79.2%) lesions were round or sub-round in shape, and 22 (91.7%) had smooth, uninterrupted and sharp edges. All lesions showed low attenuation of less than 20 Hu. Twenty-two enhanced lesions (91.7%) had rim-shaped enhancement in the abscess wall, and 13 (54.2%) showed single or double-ring signs. Eighteen (75%) displayed honeycomb-like, grid-like or strip-like enhancement. Eighteen (75%) were regionally enhanced in the surroundings or upper or lower layers. Only 2 (8.3%) displayed a gas-liquid surface sign. CONCLUSIONS:  The CT ifndings of bacterial hepatic abscess are usually typical, and the diagnosis of the abscess is not dififcult. To precisely diagnose atypical cases, it is necessary to combine CT with clinical observations and follow-up.

  10. Tinidazole in the treatment of bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Nicola R Armstrong

    2009-06-01

    Full Text Available Nicola R Armstrong1, Janet D Wilson21Department of Infectious Diseases and Sexual Health, Trinity Centre, Bradford, UK; 2The Centre for Sexual Health, The General Infirmary at Leeds, Leeds, UKAbstract: Bacterial vaginosis (BV is the commonest cause of vaginal discharge in women of childbearing age. Oral metronidazole has long been established as an effective therapy in the treatment of BV. However, adverse effects due to metronidazole are frequent and this may lead to problems with adherence to a 7-day course of treatment and subsequently result in treatment failure. Oral tinidazole has been used to treat bacterial vaginosis for over 25 years but in a number of different dosage regimens. Placebo controlled trials have consistently shown increases in cure rate with tinidazole. Longer courses of treatment (eg, 1 g daily for 5 days appear to be more effective than a 2 g oral single dose. Comparative studies suggest that oral tinidazole is equivalent to oral metronidazole, intravaginal clindamycin cream, and intravaginal metronidazole tablets, in efficacy in treating BV. However, tinidazole has a more favorable side effect profile than oral metronidazole notably with better gastrointestinal tolerability and less metallic taste. Bacterial vaginosis is associated with high rates of recurrence and appropriate management of such recurrences can prove difficult. Recurrent BV has been linked with persistence of Gardnerella vaginalis after treatment; however the clinical implications of the possible greater activity of tinidazole against G. vaginalis are not yet clear. Repeated courses of oral metronidazole may be poorly tolerated and an alternative but equally effective treatment that is better tolerated may be preferable. In comparison to oral metronidazole, cost is clearly an issue as oral metronidazole is considerably cheaper and available in generic form. However where avoidance of oral metronidazole is necessary because of side effects, oral

  11. Universal quantifier derived from AFM analysis links cellular mechanical properties and cell-surface integration forces with microbial deposition and transport behavior.

    Science.gov (United States)

    Li, Yueyun; Wang, Xin; Onnis-Hayden, Annalisa; Wan, Kai-tak; Gu, April Z

    2014-01-01

    In this study, we employed AFM analysis combined with mathematical modeling for quantifying cell-surface contact mechanics and magnitude and range of cell-surface interaction forces for seven bacterial strains with a wide range of cell morphology, dimension, and surface characteristics. Comprehensive cell-surface characterization including surface charge, extracellular polymeric substance content, hydrophobicity, and cell-cell aggregation analyses were performed. Flow-through column tests were employed to determine the attachment efficiency and deposition-transport behavior of these bacterial strains. No statistically significant correlation between attachment efficiency and any single-cell surface property was identified. Single-cell characterization by atomic force microscopy (AFM) yielded the mechanical deformation and elastic modulus, penetration resistance to AFM probe penetration by cellular surface substances (CSS), range and magnitude of the repulsive-attractive intersurface forces, and geometry of each strain. We proposed and derived a universal dimensionless modified Tabor's parameter to integrate all these properties that account for their collective behavior. Results showed that the Tabor parameter derived from AFM analysis correlated well with experimentally determined attachment efficiency (α), which therefore is able to link microscale cell-surface properties with macroscale bacterial transport behavior. Results suggested that the AFM tests performed between a single cell and a surface captured the key quantities of the interactions between the cell and the surface that dictate overall cell attachment behavior. Tabor's parameter therefore can be potentially incorporated into the microbial transport model.

  12. Performance of resistance gene pyramids to races of rice bacterial blight in Zhejiang Province

    Institute of Scientific and Technical Information of China (English)

    ZHENGKangle; ZHUANGJieyun; WANGHanrong

    1998-01-01

    The effect of gene pyramiding on resistance to bacterial blight (BB) in rice was evahlated among the IR24-based near isogenic lines conraining single resistance gene and gene pyramids containing two, three or lour resistancegenes (see table).

  13. Ontogenetic changes in the bacterial symbiont community of the tropical demosponge Amphimedon queenslandica: metamorphosis is a new beginning

    Directory of Open Access Journals (Sweden)

    Rebecca A Fieth

    2016-11-01

    Full Text Available Vertical transmission of bacterial symbionts, which is known in many species of sponge (Porifera, is expected to promote strong fidelity between the partners. Combining 16S rRNA gene amplicon sequencing and electron microscopy, we have assayed the relative abundance of vertically-inherited bacterial symbionts in several stages of the life cycle of Amphimedon queenslandica, a tropical coral reef sponge. We reveal that adult A. queenslandica house a low diversity microbiome dominated by just three proteobacterial OTUs, with a single gammaprotebacterium clearly dominant through much of the life cycle. This ontogenetic perspective has revealed that, although vertical transmission occurs very early in development, the inherited symbionts do not maintain proportional dominance of the bacterial community at every developmental stage. A reproductive bottleneck in the A. queenslandica life cycle is larval settlement, when a free-swimming pelagic larva settles out of the water column onto the benthos and completes metamorphoses into the sessile body plan within just 3 to 4 days. During this dramatic life cycle transition, an influx of environmentally-derived bacteria leads to a major reorganization of the microbiome, potentially challenging the fidelity and persistence of the vertically-inherited symbiotic relationships. However, dominance of the primary, vertically-inherited symbionts is restored in adult sponges. The mechanisms underlying ontogenetic changes in the bacterial community are unknown, including how the dominance of the primary symbionts is restored in the adult sponge – does the host or symbiont regulate this process? Using high-resolution transcriptional profiling in multiple stages of the A. queenslandica life cycle combined with this natural perturbation of the microbiome immediately following larval settlement, we are beginning to identify candidate host genes associated with animal-bacterial crosstalk. Among the sponge host genes

  14. Bacterial diversity in the oral cavity of 10 healthy individuals.

    Science.gov (United States)

    Bik, Elisabeth M; Long, Clara Davis; Armitage, Gary C; Loomer, Peter; Emerson, Joanne; Mongodin, Emmanuel F; Nelson, Karen E; Gill, Steven R; Fraser-Liggett, Claire M; Relman, David A

    2010-08-01

    The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11,368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.

  15. Derivative chameleons

    Science.gov (United States)

    Noller, Johannes

    2012-07-01

    We consider generalized chameleon models where the conformal coupling between matter and gravitational geometries is not only a function of the chameleon field phi, but also of its derivatives via higher order co-ordinate invariants (such as ∂μphi∂μphi,squphi,...). Specifically we consider the first such non-trivial conformal factor A(phi,∂μphi∂μphi). The associated phenomenology is investigated and we show that such theories have a new generic mass-altering mechanism, potentially assisting the generation of a sufficiently large chameleon mass in dense environments. The most general effective potential is derived for such derivative chameleon setups and explicit examples are given. Interestingly this points us to the existence of a purely derivative chameleon protected by a shift symmetry for phi → phi+c. We also discuss potential ghost-like instabilities associated with mass-lifting mechanisms and find another, mass-lowering and instability-free, branch of solutions. This suggests that, barring fine-tuning, stable derivative models are in fact typically anti-chameleons that suppress the field's mass in dense environments. Furthermore we investigate modifications to the thin-shell regime and prove a no-go theorem for chameleon effects in non-conformal geometries of the disformal type.

  16. Electromagnetism of Bacterial Growth

    Science.gov (United States)

    Ainiwaer, Ailiyasi

    2011-10-01

    There has been increasing concern from the public about personal health due to the significant rise in the daily use of electrical devices such as cell phones, radios, computers, GPS, video games and television. All of these devices create electromagnetic (EM) fields, which are simply magnetic and electric fields surrounding the appliances that simultaneously affect the human bio-system. Although these can affect the human system, obstacles can easily shield or weaken the electrical fields; however, magnetic fields cannot be weakened and can pass through walls, human bodies and most other objects. The present study was conducted to examine the possible effects of bacteria when exposed to magnetic fields. The results indicate that a strong causal relationship is not clear, since different magnetic fields affect the bacteria differently, with some causing an increase in bacterial cells, and others causing a decrease in the same cells. This phenomenon has yet to be explained, but the current study attempts to offer a mathematical explanation for this occurrence. The researchers added cultures to the magnetic fields to examine any effects to ion transportation. Researchers discovered ions such as potassium and sodium are affected by the magnetic field. A formula is presented in the analysis section to explain this effect.

  17. Bacterial endocarditis prophylaxis.

    Science.gov (United States)

    Blanco-Carrión, Andrés

    2004-01-01

    Bacterial endocarditis (BE) is a disease resulting from the association of morphological alterations of the heart and bacteraemia originating from different sources that at times can be indiscernible (infectious endocarditis). It is classified on the basis of the morphological alteration involved, depending on the clinical manifestations and course of illness, which varies according to the causative microorganism and host conditions (for example, it is characteristic in I.V. drug users). The most common microorganisms involved are: Streptococcus viridans (55%), Staphylococcus aureus (30%), Enterococcus (6%) and HACEK bacteria (corresponding to the initials: Haemophilus, Actinobacillus, Cardiobacterium, Eikenella and Kingella), although on occasions it can also be caused by fungi. The oral microbiological flora plays a very important role in the aetiopathogenesis of BE, given that the condition may be of oral or dental origin. This paper will deal with the prevention of said bacteraemia. Prophylaxis will be undertaken using amoxicillin or clindamycin according to action protocols, with special emphasis placed on oral hygiene in patients with structural defects of the heart.

  18. Bacterial degradation of synthetic and kraft lignin by axenic and mixed culture and their metabolic products.

    Science.gov (United States)

    Chandra, Ram; Bharagava, Ram Naresh

    2013-11-01

    Pulp paper mill effluent has high pollution load due to presence of lignin and its derivatives as major colouring and polluting constituents. In this study, two lignin degrading bacteria IITRL1 and IITRSU7 were isolated and identified as Citrobacter freundii (FJ581026) and Citrobacter sp. (FJ581023), respectively. In degradation study by axenic and mixed culture, mixed bacterial culture was found more effective compared to axenic culture as it decolourized 85 and 62% of synthetic and kraft lignin whereas in axenic conditions, bacterium IITRL1 and IITRSU7 decolourized 61 and 64% synthetic and 49 and 54% kraft lignin, respectively. Further, the mixed bacterial culture also showed the removal of 71, 58% TOC; 78, 53% AOX; 70, 58% COD and 74, 58% lignin from synthetic and kraft lignin, respectively. The ligninolytic enzyme was characterized as manganese peroxidase by SDS-PAGE yielding a single band of 43 KDa. The HPLC analysis of degraded samples showed reduction as well as shifting of peaks compared to control indicating the degradation as well as transformation of compounds. Further, in GC-MS analysis of synthetic and kraft lignin degraded samples, hexadecanoic acid was found as recalcitrant compounds while 2,4,6-trichloro-phenol, 2,3,4,5-tetrachloro-phenol and pentachloro-phenol were detected as new metabolites.

  19. Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

    Directory of Open Access Journals (Sweden)

    Huygens Flavia

    2007-08-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species. Results The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH data for Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile. Conclusion Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data.

  20. Profile of oritavancin and its potential in the treatment of acute bacterial skin structure infections

    Science.gov (United States)

    Mitra, Subhashis; Saeed, Usman; Havlichek, Daniel H; Stein, Gary E

    2015-01-01

    Oritavancin, a semisynthetic derivative of the glycopeptide antibiotic chloroeremomycin, received the US Food and Drug Administration approval for the treatment of acute bacterial skin and skin structure infections caused by susceptible Gram-positive bacteria in adults in August 2014. This novel second-generation semisynthetic lipoglycopeptide antibiotic has activity against a broad spectrum of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate S. aureus (VISA), and vancomycin-resistant Enterococcus. Oritavancin inhibits bacterial cell wall synthesis and is rapidly bactericidal against many Gram-positive pathogens. The long half-life of this drug enables a single-dose administration. Oritavancin is not metabolized in the body, and the unchanged drug is slowly excreted by the kidneys. In two large Phase III randomized, double-blind, clinical trials, oritavancin was found to be non-inferior to vancomycin in achieving the primary composite end point in the treatment of acute Gram-positive skin and skin structure infections. Adverse effects noted were mostly mild with nausea, headache, and vomiting being the most common reported side effects. Oritavancin has emerged as another useful antimicrobial agent for treatment of acute Gram-positive skin and skin structure infections, including those caused by MRSA and VISA. PMID:26185459

  1. Profile of oritavancin and its potential in the treatment of acute bacterial skin structure infections

    Directory of Open Access Journals (Sweden)

    Mitra S

    2015-07-01

    Full Text Available Subhashis Mitra, Usman Saeed, Daniel H Havlichek, Gary E Stein Department of Infectious Diseases, Michigan State University, East Lansing, MI, USA Abstract: Oritavancin, a semisynthetic derivative of the glycopeptide antibiotic chloroeremomycin, received the US Food and Drug Administration approval for the treatment of acute bacterial skin and skin structure infections caused by susceptible Gram-positive bacteria in adults in August 2014. This novel second-generation semisynthetic lipoglycopeptide antibiotic has activity against a broad spectrum of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA, vancomycin-intermediate S. aureus (VISA, and vancomycin-resistant Enterococcus. Oritavancin inhibits bacterial cell wall synthesis and is rapidly bactericidal against many Gram-positive pathogens. The long half-life of this drug enables a single-dose administration. Oritavancin is not metabolized in the body, and the unchanged drug is slowly excreted by the kidneys. In two large Phase III randomized, double-blind, clinical trials, oritavancin was found to be non-inferior to vancomycin in achieving the primary composite end point in the treatment of acute Gram-positive skin and skin structure infections. Adverse effects noted were mostly mild with nausea, headache, and vomiting being the most common reported side effects. Oritavancin has emerged as another useful antimicrobial agent for treatment of acute Gram-positive skin and skin structure infections, including those caused by MRSA and VISA. Keywords: antibiotic, Gram-positive bacteria, MRSA, VRSA, vancomycin, MIC

  2. Spatially controlled bacterial adhesion using surface-patterned poly(ethylene glycol) hydrogels.

    Science.gov (United States)

    Krsko, Peter; Kaplan, Jeffrey B; Libera, Matthew

    2009-02-01

    We constructed surface-patterned hydrogels using low-energy focused electron beams to locally crosslink poly(ethylene glycol) (PEG) thin films on silanized glass substrates. Derived from electron-beam lithography, this technique was used to create patterned hydrogels with well-defined spatial positions and degrees of swelling. We found that cells of the bacterium Staphylococcus epidermidis adhered to and grew on the silanized glass substrates. These cells did not, however, adhere to surfaces covered by high-swelling lightly crosslinked PEG hydrogels. This finding is consistent with the cell-repulsiveness generally attributed to PEGylated surfaces. In contrast, S. epidermidis cells did adhere to surfaces covered by low-swelling highly crosslinked hydrogels. By creating precise patterns of repulsive hydrogels combined with adhesive hydrogels or with exposed glass substrate, we were able to spatially control the adhesion of S. epidermidis. Significantly, adhesive areas small enough to trap single bacterial cells could be fabricated. The results suggest that the lateral confinement imposed by cell-repulsive hydrogels hindered the cell proliferation and development into larger bacterial colonies.

  3. Responses of Baltic Sea ice and open-water natural bacterial communities to salinity change.

    Science.gov (United States)

    Kaartokallio, Hermanni; Laamanen, Maria; Sivonen, Kaarina

    2005-08-01

    To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0 degrees C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the alpha- and gamma-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure.

  4. Global Derivatives

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    ." - Steen Parsholt, Chairman and CEO, Aon Nordic Region. "Andersen has done a wonderful job of developing a comprehensive text that deals with risk management in global markets. I would recommend this book to any student or businessman who has a need to better understand the risks and risk management...... management practice. Of particular note is the global and integrated approach chosen in this book which should be of special interest to aspiring managers active in global and international markets." - Dr Jean-Pierre Zigrand, Lecturer in Finance, London School of Economics, UK. More than 90 per cent...... management situations. Its key features include: derivatives are introduced in a global market perspective; describes major derivative pricing models for practical use, extending these principles to valuation of real options; practical applications of derivative instruments are richly illustrated...

  5. Electricity derivatives

    CERN Document Server

    Aïd, René

    2015-01-01

    Offering a concise but complete survey of the common features of the microstructure of electricity markets, this book describes the state of the art in the different proposed electricity price models for pricing derivatives and in the numerical methods used to price and hedge the most prominent derivatives in electricity markets, namely power plants and swings. The mathematical content of the book has intentionally been made light in order to concentrate on the main subject matter, avoiding fastidious computations. Wherever possible, the models are illustrated by diagrams. The book should allow prospective researchers in the field of electricity derivatives to focus on the actual difficulties associated with the subject. It should also offer a brief but exhaustive overview of the latest techniques used by financial engineers in energy utilities and energy trading desks.

  6. Structured attachment of bacterial molecular motors for defined microflow induction

    Directory of Open Access Journals (Sweden)

    Woerdemann Mike

    2014-01-01

    Full Text Available Bacterial rotational motor complexes that propel flagellated bacteria possess unique properties like their size of a few nanometres and the ability of selfreproduction that have led to various exciting applications including biohybrid nano-machines. One mandatory prerequisite to utilize bacterial nano motors in fluid applications is the ability to transfer force and torque to the fluid, which usually can be achieved by attachment of the bacterial cell to adequate surfaces. Additionally, for optimal transfer of force or torque, precise control of the position down to the single cell level is of utmost importance. Based on a PIV (particle image velocimetry evaluation of the induced flow of single bacteria,we propose and demonstrate attachment of arbitrary patterns of motile bacterial cells in a fast light-based two-step process for the first time to our knowledge. First, these cells are pre-structured by holographic optical tweezers and then attached to a homogeneous, polystyrene-coated surface. In contrast to the few approaches that have been implemented up to now and which rely on pre-structured surfaces, our scheme allows for precise control on a single bacterium level, is versatile, interactive and has low requirements with respect to the surface preparation.

  7. Meningitis bacteriana Bacterial meningitis

    Directory of Open Access Journals (Sweden)

    Ana Teresa Alvarado Guevara

    2006-03-01

    causales son virales lo cual conlleva a las diferentes sub-clasificaciones. También en ciertos casos puede ser ocasionada por hongos, bacterias atípicas, micobacterias y parásitos.In Costa Rica the bacterial meningitis had turn into a high-priority subject in which to monitoring epidemiologist. It had been talked about in the last months, to dice an increase in the attention is published of this subject, due to this phenomenon it becomes necessary to make a revision of topic. Meningitis is an inflammation of leptomeninges and colonization of the subarachnoid cerebrospinal fluid (LCR due to different agents, which produces meningeal symptoms (ex. migraine, neck rigidity, and photophobia and pleocytosis in LCR. De pending on the variables to take into account is possible to group it in different classifications, taking into account the time of evolution are possible to be divided in acute or chronic, to first with few hours or days of beginning of the symptoms, whereas the chronicle also presents a silence course but of the disease of approximately 4 weeks of instauration. There is a difference according to its etiologic agent; they can be infectious and non-infectious. Examples of common non-infectious causes include medications (ex, nonsteroidal anti-inflammatory drugs, and antibiotics and carcinomatosis. A classification exists as well according to the causal agent. The acute bacterial meningitis remarks a bacterial origin of the syndrome, which characterizes by the by an acute onset of meningeal symptoms and neutrophilic pleocytosis. Each one of the bacteriological agents, parasitic or fungus finishes by characterizing the different presentations of the clinical features (ex, meningocóccica meningitis, Cryptococcus meningitis. Finally, there is also the aseptic meningitis, denominated in this form because it’s nonpyogenic cellular response caused by many types of agents. The patients show an acute beginning of symptoms, fever and lymphocytic pleocytosis. After

  8. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  9. Bacterial Chromosome Organization and Segregation

    OpenAIRE

    Toro, Esteban; Shapiro, Lucy

    2010-01-01

    Bacterial chromosomes are generally ∼1000 times longer than the cells in which they reside, and concurrent replication, segregation, and transcription/translation of this crowded mass of DNA poses a challenging organizational problem. Recent advances in cell-imaging technology with subdiffraction resolution have revealed that the bacterial nucleoid is reliably oriented and highly organized within the cell. Such organization is transmitted from one generation to the next by progressive segrega...

  10. Bacterial Protein-Tyrosine Kinases

    DEFF Research Database (Denmark)

    Shi, Lei; Kobir, Ahasanul; Jers, Carsten

    2010-01-01

    phosphorylation. Protein-tyrosine phosphorylation in bacteria is particular with respect to very low occupancy of phosphorylation sites in vivo; this has represented a major challenge for detection techniques. Only the recent breakthroughs in gel-free high resolution mass spectrometry allowed the systematic...... and highlighted their importance in bacterial physiology. Having no orthologues in Eukarya, BY-kinases are receiving a growing attention from the biomedical field, since they represent a particularly promising target for anti-bacterial drug design....

  11. Surface micropattern limits bacterial contamination

    OpenAIRE

    Mann, Ethan E.; Manna, Dipankar; Mettetal, Michael R; May, Rhea M.; Dannemiller, Elisa M; Chung, Kenneth K.; Brennan, Anthony B; Reddy, Shravanthi T

    2014-01-01

    Background Bacterial surface contamination contributes to transmission of nosocomial infections. Chemical cleansers used to control surface contamination are often toxic and incorrectly implemented. Additional non-toxic strategies should be combined with regular cleanings to mitigate risks of human error and further decrease rates of nosocomial infections. The Sharklet micropattern (MP), inspired by shark skin, is an effective tool for reducing bacterial load on surfaces without toxic additiv...

  12. Bacterial cellulose/boehmite composites

    Energy Technology Data Exchange (ETDEWEB)

    Salvi, Denise T.B. de; Barud, Hernane S.; Messaddeq, Younes; Ribeiro, Sidney J.L. [Universidade Estadual Paulista Julio de Mesquita Filho. UNESP. Instituto de Quimica de Araraquara, SP (Brazil); Caiut, Jose Mauricio A. [Universidade de Sao Paulo. Departamento de Quimica - FFCLRP/USP, Ribeirao Preto, SP (Brazil)

    2011-07-01

    Composites based on bacterial cellulose membranes and boehmite were obtained. SEM results indicate that the bacterial cellulose (BC) membranes are totally covered by boehmite and obtained XRD patterns suggest structural changes due to this boehmite addition. Thermal stability is accessed through TG curves and is dependent on boehmite content. Transparency is high comparing to pure BC as can be seen through UV-vis absorption spectroscopy. (author)

  13. The bacterial elicitor flagellin activates its receptor in tomato cells according to the address-message concept.

    Science.gov (United States)

    Meindl, T; Boller, T; Felix, G

    2000-09-01

    flg22, a peptide corresponding to the most conserved domain of bacterial flagellin, acts as a potent elicitor in plants. Here, we have used an iodinated derivative of flg22 ((125)I-labeled Tyr-flg22) as a molecular probe for the flagellin receptor in tomato cells. This radioligand showed rapid binding to a single class of specific, saturable, high-affinity receptor sites in intact cells and membrane preparations. Binding, although essentially nonreversible under physiological conditions, was not covalent, and chemical cross-linking was required to specifically label a single polypeptide of 115 kD. Intact flagellin and elicitor-active flagellin peptides but not biologically inactive analogs efficiently competed for binding of radioligand. Peptides lacking the C terminus of the conserved domain, previously found to act as competitive antagonists of elicitor action in tomato cells, also competed for binding of radioligand. Thus, this novel, high-affinity binding site exhibited all the characteristics expected of a functional receptor of bacterial flagellin. For a model of receptor activation, we propose a two-step mechanism according to the address-message concept, in which binding of the N terminus (address) is the first step and activation of responses with the C terminus (message) is the second step.

  14. Studying bacterial multispecies biofilms

    DEFF Research Database (Denmark)

    Røder, Henriette Lyng; Sørensen, Søren Johannes; Burmølle, Mette

    2016-01-01

    and drawbacks of varying the degree of complexity. This review aims to facilitate multispecies biofilm research in order to expand the current limited knowledge on interspecies interactions. Recent technological advances have enabled total diversity analysis of highly complex and diverse microbial communities...... at the microscale of complex communities, including biofilms.Studies of multispecies biofilms and the interactions shaping these are conducted in traditional approaches used for single-species biofilms with some adjustments; but a crucial point for consideration is which strains to combine and where these should...

  15. 单电感电流连续型推挽类拓扑的推衍和特性研究%Derivation and Characterization of Single-inductor Push-pull Based Topologies With Continuous Currents

    Institute of Scientific and Technical Information of China (English)

    陈骞; 郑琼林; 李艳

    2013-01-01

    In view of the widely applications of push-pull based converters in aircraft power supply and the superiority of the topology with continuous input and output currents, this paper proposed a concept of single-inductor push-pull based topologies with continuous input and output currents. Four new kinds of non-isolated push-pull cells are deduced from traditional push-pull cells. The circuit configurations based on these four kinds of push-pull cells are also derived, three of them are firstly proposed. These topologies can be divided into the Smart type and the Weinberg type according to topology structures and control methods. Sags exist in the low ripple current of the Smart topology and spikes exist in that of the Weinberg topology, while the problem isn't exist in proposed topologies. The push-pull-based topologies can be used for battery discharge regulators (BDR) or battery charge regulators (BCR) based on the condition that the bus current should be of low-ripple. The advantages and disadvantages of topologies are achieved by comparing characteristics, which can provide a theoretical support for DC-DC converters used in PCU. In addition, the experimental results based on one of the proposed topologies are given to verify the validity of theoretical analysis.%鉴于电流连续型拓扑的优越性,结合推挽类拓扑在卫星电源系统中应用广泛的现状,提出单电感电流连续型推挽类拓扑的概念.通过对传统推挽单元进行推导得到4种新的非隔离型推挽单元.以此为基础,分别推衍得到4类推挽单元的单电感电流连续型拓扑族,其中有3种拓扑为首次提出的新型拓扑.根据拓扑结构以及控制方式的不同,可将这些拓扑分成Smart和Weinberg两类,其中Smart类拓扑低纹波侧电流存在凹陷,已提出的Weinberg类拓扑低纹波侧电流存在尖峰,而该文提出的3种新型拓扑不存在此问题.由母线侧电流低纹波的条件,还可将所有拓扑分成适用作蓄

  16. Single-cell bioluminescence and GFP in biofilm research

    Energy Technology Data Exchange (ETDEWEB)

    Palmer, R.J. Jr, Sayler, G., White, D.C. [Tennessee Univ., Knoxville, TN (United States), Ctr. Env. Biotech; Phiefer, C. [Oak Ridge National Lab., TN (United States), Environmental Sciences Div.

    1996-12-31

    Using flow cells and a combination of microscopy techniques, we can unequivocally identify single bacterial cells that express bioluminescent and fluorescent bioreporters. We have shown that, for attached cells, bioluminescence output within a bacterial strain can vary greatly from cell to cell.

  17. Single chain Fab (scFab fragment

    Directory of Open Access Journals (Sweden)

    Brenneis Mariam

    2007-03-01

    Full Text Available Abstract Background The connection of the variable part of the heavy chain (VH and and the variable part of the light chain (VL by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv was a breakthrough for the functional production of antibody fragments in Escherichia coli. Being double the size of fragment variable (Fv fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields in E. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody in E. coli and antibody phage display. Results Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd and the light chain (LC, resulting in the formation of a single chain Fab fragment (scFab, can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC connecting the constant part 1 of the heavy chain (CH1 and the constant part of the light chain (CL were best suited for phage display and production of soluble antibody fragments. Beside the expression system E. coli, the new antibody format was also expressed in Pichia pastoris. Monovalent and divalent fragments (DiFabodies as well as multimers were characterised. Conclusion A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of

  18. Bacterial invasion reconstructed molecule by molecule

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the

  19. PRODUCTION AND CHARACTERIZATION OF ECONOMICAL BACTERIAL CELLULOSE

    Directory of Open Access Journals (Sweden)

    Houssni El-Saied

    2008-11-01

    Full Text Available The present study investigates the economical production of bacterial cellulose (BC by Gluconacetobacter subsp. Xylinus (ATCC 10245 in 250 ml Erlenmeyer flasks cultivated under static conditions. The fermentation media used contained food industrial by-product liquors, such as black strap molasses solution and corn steep liquor (CSL, which represents some of the most economical carbon and nitrogen sources. However, because of the presence of undesirable components in molasses (such as coloring substances, heavy metals, and other compounds that may act as inhibitors, and in order to eliminate them, crude molasses has been treated with an acid, as an attempt to increase BC productivity. The amount of BC produced using these carbon and nitrogen sources was determined and compared to that produced using previously reported fermentation media. The characterizations of the bacterial cellulose (BC pellicles obtained using either conventional or by-product media were studied by thermal and spectral techniques and compared to those of plant-derived cellulose such as cotton linter, viscose pulp, and microcrystalline cellulose.

  20. Osmotic pressure in a bacterial swarm.

    Science.gov (United States)

    Ping, Liyan; Wu, Yilin; Hosu, Basarab G; Tang, Jay X; Berg, Howard C

    2014-08-19

    Using Escherichia coli as a model organism, we studied how water is recruited by a bacterial swarm. A previous analysis of trajectories of small air bubbles revealed a stream of fluid flowing in a clockwise direction ahead of the swarm. A companion study suggested that water moves out of the agar into the swarm in a narrow region centered ∼ 30 μm from the leading edge of the swarm and then back into the agar (at a smaller rate) in a region centered ∼ 120 μm back from the leading edge. Presumably, these flows are driven by changes in osmolarity. Here, we utilized green/red fluorescent liposomes as reporters of osmolarity to verify this hypothesis. The stream of fluid that flows in front of the swarm contains osmolytes. Two distinct regions are observed inside the swarm near its leading edge: an outer high-osmolarity band (∼ 30 mOsm higher than the agar baseline) and an inner low-osmolarity band (isotonic or slightly hypotonic to the agar baseline). This profile supports the fluid-flow model derived from the drift of air bubbles and provides new (to our knowledge) insights into water maintenance in bacterial swarms. High osmotic pressure at the leading edge of the swarm extracts water from the underlying agar and promotes motility. The osmolyte is of high molecular weight and probably is lipopolysaccharide.

  1. 考虑桩体剪切变形的分数导数黏弹性土层中单桩水平振动%Lateral Vibration of Single Pile in Viscoelastic Soil Described by Fractional Derivative Model Considering Shear Deformation

    Institute of Scientific and Technical Information of China (English)

    杨文领; 傅敏

    2011-01-01

    The lateral vibration equations of the soil described by fractional derivative viscoelastic model are established. The lateral dynamic equivalent stiffness and damping of viscoelastic soil described by fractional derivative viscoelastic model are obtained on the basis of assumed surface strain of Novak. The dynamic interaction between pile and soil is described by equivalent Winkler dynamic spring - damping model, and the pile is simplified as Timoshenko model. The formula of lateral vibration of single pile is established by considering bending and shear deformation. The lateral dynamic impedance of single pile in soil is obtained by considering shear deformation. The influences of fractional derivative order, soil constitutive model parameters and shear shape factor of pile on lateral dynamic impedance are then investigated. It is indicated through the research that the results of Euler beam model and Timoshenko beam model have great difference for the pile in viscoelastic soil. The fractional derivative order has influence on the peaks of curves of dynamic impedance versus frequency. The dynamic impedance of pile increases with the decrease of constitutive model parameters of the soil. The shear shape factor of pile has great effect on the dynamic impedance.

  2. Synthesis of antimicrobial cyclodextrins bearing polyarylamino and polyalkylamino groups via click chemistry for bacterial membrane disruption.

    Science.gov (United States)

    Yamamura, Hatsuo; Sugiyama, Yuuki; Murata, Kensuke; Yokoi, Takanori; Kurata, Ryuji; Miyagawa, Atsushi; Sakamoto, Kenji; Komagoe, Keiko; Inoue, Tsuyoshi; Katsu, Takashi

    2014-05-28

    Cyclodextrin derivatives are synthesized as membrane-disrupting agents via a microwave-assisted Huisgen reaction. Their ability to permeabilize bacterial membranes depends on the amino substituents and an appropriate balance of hydrophobicity and hydrophilicity, thus enabling the preparation of derivatives with selective toxicity against bacteria.

  3. Flows around bacterial swarms

    Science.gov (United States)

    Dauparas, Justas; Lauga, Eric

    2015-11-01

    Flagellated bacteria on nutrient-rich substrates can differentiate into a swarming state and move in dense swarms across surfaces. A recent experiment (HC Berg, Harvard University) measured the flow in the fluid around the swarm. A systematic chiral flow was observed in the clockwise direction (when viewed from above) ahead of a E.coli swarm with flow speeds of about 10 μm/s, about 3 times greater than the radial velocity at the edge of the swarm. The working hypothesis is that this flow is due to the flagella of cells stalled at the edge of a colony which extend their flagellar filaments outwards, moving fluid over the virgin agar. In this talk we quantitatively test his hypothesis. We first build an analytical model of the flow induced by a single flagellum in a thin film and then use the model, and its extension to multiple flagella, to compare with experimental measurements.

  4. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Ahrenfeldt, Johanne; Bellod Cisneros, Jose Luis;

    2016-01-01

    web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates. The pipeline will automatically identify the bacterial species and, if applicable, assemble the genome, identify the multilocus sequence type, plasmids, virulence genes...... and made publicly available, providing easy-to-use automated analysis of bacterial whole genome sequencing data. The platform may be of immediate relevance as a guide for investigators using whole genome sequencing for clinical diagnostics and surveillance. The platform is freely available at: https......Recent advances in whole genome sequencing have made the technology available for routine use in microbiological laboratories. However, a major obstacle for using this technology is the availability of simple and automatic bioinformatics tools. Based on previously published and already available...

  5. Effective Rheological Properties in Semidilute Bacterial Suspensions

    CERN Document Server

    Potomkin, Mykhailo; Berlyand, Leonid

    2015-01-01

    Interactions between swimming bacteria have led to remarkable experimentally observable macroscopic properties such as the reduction of the effective viscosity, enhanced mixing, and diffusion. In this work, we study an individual based model for a suspension of interacting point dipoles representing bacteria in order to gain greater insight into the physical mechanisms responsible for the drastic reduction in the effective viscosity. In particular, asymptotic analysis is carried out on the corresponding kinetic equation governing the distribution of bacteria orientations. This allows one to derive an explicit asymptotic formula for the effective viscosity of the bacterial suspension in the limit of bacterium non-sphericity. The results show good qualitative agreement with numerical simulations and previous experimental observations. Finally, we justify our approach by proving existence, uniqueness, and regularity properties for this kinetic PDE model.

  6. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

    Full Text Available The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV. PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition.

  7. Functional Insights into Sponge Microbiology by Single Cell Genomics

    KAUST Repository

    Hentschel, Ute

    2011-04-09

    Marine Sponges (Porifera) are known to harbor enormous amounts of microorganisms with members belonging to at least 30 different bacterial phyla including several candidate phyla and both archaeal lineages. Here, we applied single cell genomics to the mic

  8. Selection of bacterial wilt-resistant tomato through tissue culture.

    Science.gov (United States)

    Toyoda, H; Shimizu, K; Chatani, K; Kita, N; Matsuda, Y; Ouchi, S

    1989-06-01

    Bacterial wilt-resistant plants were obtained using a tomato tissue culture system. A virulent strain ofPseudomonas solanacearum secreted some toxic substances into the culture medium. Leaf explant-derived callus tissues which were resistant to these toxic substances in the culture filtrate were selectedin vitro and regenerated into plants. These plants expressed bacterial wilt resistance at the early infection stage to suppress or delay the growth of the inoculated bacteria. On the other hand, complete resistance was obtained in self-pollinated progeny of regenerants derived from non-selected callus tissues. These plants showed a high resistance when inoculated with this strain, and were also resistant when planted in a field infested with a different strain of the pathogen.

  9. Root bacterial endophytes alter plant phenotype, but not physiology

    Directory of Open Access Journals (Sweden)

    Jeremiah A. Henning

    2016-11-01

    Full Text Available Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light–Asat, and saturating CO2–Amax. Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content. In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.

  10. Measurement of Behavioral Evolution in Bacterial Populations

    Science.gov (United States)

    Austin, Robert

    2013-03-01

    A curious aspect of bacterial behavior under stress is the induction of filamentation: the anomalous growth of certain bacteria in which cells continue to elongate but do not divide into progeny. We show that E.coli under the influence of the genotoxic antibiotic ciprofloxacin have robust filamentous growth, which provides individual bacteria a mesoscopic niche for evolution until resistant progeny can bud off and propagate. Hence, filamentation is a form of genomic amplification where even a single, isolated bacteria can have access to multiple genomes. We propose a model that predicts that the first arrival time of the normal sized progeny should follow a Gompertz distribution with the mean first arrival time proportional to the elongation rate of filament. These predictions agree with our experimental measurements. Finally, we suggest bacterial filament growth and budding has many similarities to tumor growth and metastasis and can serve as a simpler model to study those complicated processes. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

  11. New Treatments for Bacterial Keratitis

    Directory of Open Access Journals (Sweden)

    Raymond L. M. Wong

    2012-01-01

    Full Text Available Purpose. To review the newer treatments for bacterial keratitis. Data Sources. PubMed literature search up to April 2012. Study Selection. Key words used for literature search: “infectious keratitis”, “microbial keratitis”, “infective keratitis”, “new treatments for infectious keratitis”, “fourth generation fluoroquinolones”, “moxifloxacin”, “gatifloxacin”, “collagen cross-linking”, and “photodynamic therapy”. Data Extraction. Over 2400 articles were retrieved. Large scale studies or publications at more recent dates were selected. Data Synthesis. Broad spectrum antibiotics have been the main stay of treatment for bacterial keratitis but with the emergence of bacterial resistance; there is a need for newer antimicrobial agents and treatment methods. Fourth-generation fluoroquinolones and corneal collagen cross-linking are amongst the new treatments. In vitro studies and prospective clinical trials have shown that fourth-generation fluoroquinolones are better than the older generation fluoroquinolones and are as potent as combined fortified antibiotics against common pathogens that cause bacterial keratitis. Collagen cross-linking was shown to improve healing of infectious corneal ulcer in treatment-resistant cases or as an adjunct to antibiotics treatment. Conclusion. Fourth-generation fluoroquinolones are good alternatives to standard treatment of bacterial keratitis using combined fortified topical antibiotics. Collagen cross-linking may be considered in treatment-resistant infectious keratitis or as an adjunct to antibiotics therapy.

  12. Bacterial carbonatogenesis; La carbonatogenese bacterienne

    Energy Technology Data Exchange (ETDEWEB)

    Castanier, S. [Angers Univ., 49 (France). Faculte des Sciences; Le Metayer-Levrel, G.; Perthuisot, J.P. [Nantes Univ., 44 (France). Laboratoire de Biogeologie, Faculte des Sciences et des Techniques

    1998-12-31

    Several series of experiments in the laboratory as well as in natural conditions teach that the production of carbonate particles by heterotrophic bacteria follows different ways. The `passive` carbonatogenesis is generated by modifications of the medium that lead to the accumulation of carbonate and bicarbonate ions and to the precipitation of solid particles. The `active` carbonatogenesis is independent of the metabolic pathways. The carbonate particles are produced by ionic exchanges through the cell membrane following still poorly known mechanisms. Carbonatogenesis appears to be the response of heterotrophic bacterial communities to an enrichment of the milieu in organic matter. The active carbonatogenesis seems to start first. It is followed by the passive one which induces the growth of initially produced particles. The yield of heterotrophic bacterial carbonatogenesis and the amounts of solid carbonates production by bacteria are potentially very high as compared to autotrophic or chemical sedimentation from marine, paralic or continental waters. Furthermore, the bacterial processes are environmentally very ubiquitous; they just require organic matter enrichment. Thus, apart from purely evaporite and autotrophic ones, all Ca and/or Mg carbonates must be considered as from heterotrophic bacterial origin. By the way, the carbon of carbonates comes from primary organic matter. Such considerations ask questions about some interpretations from isotopic data on carbonates. Finally, bacterial heterotrophic carbonatogenesis appears as a fundamental phase in the relationships between atmosphere and lithosphere and in the geo-biological evolution of Earth. (author) 43 refs.

  13. Same, same but different: symbiotic bacterial associations in GBR sponges

    Directory of Open Access Journals (Sweden)

    Nicole S Webster

    2013-01-01

    Full Text Available Symbioses in marine sponges involve diverse consortia of microorganisms that contribute to the health and ecology of their hosts. The microbial communities of 13 taxonomically diverse Great Barrier Reef (GBR sponge species were assessed by DGGE and 16S rRNA gene sequencing to determine intra and inter species variation in bacterial symbiont composition. Microbial profiling revealed communities that were largely conserved within different individuals of each species with intra species similarity ranging from 65-100%. 16S rRNA gene sequencing revealed that the communities were dominated by Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Nitrospira and Cyanobacteria. Sponge-associated microbes were also highly host-specific with no operational taxonomic units (OTUs common to all species and the most ubiquitous OTU found in only 5 of the 13 sponge species. In total, 91% of the OTUs were restricted to a single sponge species. However, GBR sponge microbes were more closely related to other sponge-derived bacteria than they were to environmental communities with sequences falling within 50 of the 173 previously defined sponge-(or sponge-coral specific sequence clusters. These sequence clusters spanned the Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Gemmatimonadetes, Nitrospira and the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. The number of sequences assigned to these sponge-specific clusters across all species ranged from 0% to 92%. No relationship between host phylogeny and symbiont communities were observed across the different sponge orders, although the highest level of similarity was detected in two closely related Xestospongia species. This study identifies the core microbial inhabitants in a range of GBR sponges thereby providing the basis for future studies on sponge symbiotic function and research aiming to predict how sponge holobionts will respond to environmental

  14. Detection and identification of bacterial DNA in serum from patients with acute pancreatitis

    Science.gov (United States)

    de Madaria, E; Martínez, J; Lozano, B; Sempere, L; Benlloch, S; Such, J; Uceda, F; Francés, R; Pérez-Mateo, M

    2005-01-01

    Background and aims: Bacterial infections are common complications in patients with acute pancreatitis, and translocation of bacteria from the intestinal lumen is probably the first step in the pathogenesis of these infections. As blood cultures in afebrile patients are usually negative, more sensitive methods to investigate this hypothesis in patients are needed. Our group has recently developed a method to detect the presence of bacterial DNA in biological fluids, and we aimed to detect bacterial DNA in patients with acute pancreatitis, as molecular evidences of bacterial translocation. Methods: Samples of blood were obtained on three consecutive days within the first six days after admission. Bacterial DNA was detected using a polymerase chain reaction based method, and an automated DNA nucleotide sequencing process allowed identification of bacteria species. Results: Thirty one consecutively admitted patients with acute pancreatitis were studied. Bacterial DNA was detected in six patients (19.3%), and the sequencing process allowed identification of Citrobacter freundii and Pseudomonas aeruginosa. In two patients the same bacteria detected at admission was detected 24 hours later (above 99.9% homology of nucleotide sequence). Basic clinical and biochemical characteristics were similar among patients with or without the presence of bacterial DNA. Conclusion: Detection of gram negative bacteria derived bacterial DNA in our series supports the contention that bacterial translocation is a systemic process in approximately 20% of patients with acute pancreatitis that does not seem to be related to the severity of the episode or immediate development of infection. PMID:16099797

  15. Building bridges within the bacterial chromosome.

    Science.gov (United States)

    Song, Dan; Loparo, Joseph J

    2015-03-01

    All organisms must dramatically compact their genomes to accommodate DNA within the cell. Bacteria use a set of DNA-binding proteins with low sequence specificity called nucleoid-associated proteins (NAPs) to assist in chromosome condensation and organization. By bending or bridging DNA, NAPs also facilitate chromosome segregation and regulate gene expression. Over the past decade, emerging single-molecule and chromosome conformation capture techniques have investigated the molecular mechanisms by which NAPs remodel and organize the bacterial chromosome. In this review we describe how such approaches reveal the biochemical mechanisms of three NAPs that are believed to facilitate DNA bridging: histone-like nucleoid structuring protein (H-NS), ParB, and structural maintenance of chromosomes (SMC). These three proteins form qualitatively different DNA bridges, leading to varied effects on transcription and chromosome segregation.

  16. Transforming clinical microbiology with bacterial genome sequencing.

    Science.gov (United States)

    Didelot, Xavier; Bowden, Rory; Wilson, Daniel J; Peto, Tim E A; Crook, Derrick W

    2012-09-01

    Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

  17. Vaccination against bacterial kidney disease: Chapter 22

    Science.gov (United States)

    Elliott, Diane G.; Wiens, Gregory D.; Hammell, K. Larry; Rhodes, Linda D.; Edited by Gudding, Roar; Lillehaug, Atle; Evensen, Øystein

    2014-01-01

    Bacterial kidney disease (BKD) of salmonid fishes, caused by Renibacterium salmoninarum, has been recognized as a serious disease in salmonid fishes since the 1930s. This chapter discusses the occurrence and significance, etiology, and pathogenesis of BKD. It then describes the different vaccination procedures and the effects and side-effects of vaccination. Despite years of research, however, only a single vaccine has been licensed for prevention of BKD, and has demonstrated variable efficacy. Therefore, in addition to a presentation of the current status of BKD vaccination, a discussion of potential future directions for BKD vaccine development is included in the chapter. This discussion is focused on the unique characteristics of R. salmoninarum and its biology, as well as aspects of the salmonid immune system that might be explored specifically to develop more effective vaccines for BKD prevention.

  18. Synthesis and biodistribution of a novel (⁹⁹m)TcN complex of norfloxacin dithiocarbamate as a potential agent for bacterial infection imaging.

    Science.gov (United States)

    Zhang, Shijian; Zhang, Weifang; Wang, Yue; Jin, Zhonghui; Wang, Xuebin; Zhang, Junbo; Zhang, Yanyan

    2011-03-16

    Achieving a (⁹⁹m)Tc-labeled fluoroquinolone derivative as a single photon emission computed tomography (SPECT) tracer is considered to be of great interest. The norfloxacin dithiocarbamate (NFXDTC) was synthesized and radiolabeled with a [(⁹⁹m)TcN]²(+) intermediate to form the (⁹⁹m)TcN-NFXDTC complex in high yield. The radiochemical purity of (⁹⁹m)TcN-NFXDTC was over 90%, as measured by thin layer chromatography (TLC) and high performance liquid chromatography (HPLC), without any notable decomposition at room temperature over a period of 6 h. The partition coefficient and electrophoresis results indicated that (⁹⁹m)TcN-NFXDTC was lipophilic and neutral. The bacterial binding assay studies showed tht (⁹⁹m)TcN-NFXDTC had a good binding affinity. Biodistribution results in bacterial infected mice showed that (⁹⁹m)TcN-NFXDTC had a higher uptake at the sites of infection and better abscess/blood and abscess/muscle ratios than those of (⁹⁹m)Tc-ciprofloxacin and (⁹⁹m)TcN-CPFXDTC (CPFXDTC = ciprofloxacin dithiocarbamate). The biodistribution results of (⁹⁹m)TcN-NFXDTC in bacterially infected mice and in mice with turpentine-induced abscesses indicated that (⁹⁹m)TcN-NFXDTC was suited to be a bacteria-specific infection imaging agent. Single photon emission computed tomography (SPECT) image studies showed there was a visible accumulation in infection sites, suggesting that it would be a promising candidate for bacterial infection imaging.

  19. Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

    DEFF Research Database (Denmark)

    Logue, J.B.; Stedmon, Colin; Kellerman, A.M.

    2016-01-01

    Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition...... and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover......, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single...

  20. Clinical prediction model to aid emergency doctors managing febrile children at risk of serious bacterial infections: Diagnostic study

    NARCIS (Netherlands)

    R.G. Nijman (Ruud); Y. Vergouwe (Yvonne); M.J. Thompson (Matthew); M.V. Veen (Mirjam Van); A.H.J. van Meurs (Alfred); J. van der Lei (Johan); E.W. Steyerberg (Ewout); H.A. Moll (Henriëtte); R. Oostenbrink (Rianne)

    2013-01-01

    textabstractObjective: To derive, cross validate, and externally validate a clinical prediction model that assesses the risks of different serious bacterial infections in children with fever at the emergency department. Design: Prospective observational diagnostic study. Setting: Three paediatric em

  1. Chiral lactic hydrazone derivatives as potential bioactive antibacterial agents: Synthesis, spectroscopic, structural and molecular docking studies

    Science.gov (United States)

    Noshiranzadeh, Nader; Heidari, Azam; Haghi, Fakhri; Bikas, Rahman; Lis, Tadeusz

    2017-01-01

    A series of novel chiral lactic-hydrazone derivatives were synthesized by condensation of (S)-lactic acid hydrazide with salicylaldehyde derivatives and characterized by elemental analysis and spectroscopic studies (FT-IR, 1H NMR and 13C NMR spectroscopy). The structure of one compound was determined by single crystal X-ray analysis. Antibacterial activity of the synthesized compounds was studied against Staphylococcus aureus, Streptococcus pneumonia, Escherichia coli and Pseudomonas aeruginosa as bacterial cultures by broth microdilution method. All of the synthesized compounds showed good antibacterial activity with MIC range of 64-512 μg/mL. Compounds (S,E)-2-hydroxy-N-(2-hydroxy-5-nitrobenzylidene)propanehydrazide (5) and (S,E)-2-hydroxy-N-((3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl)propanehydrazide (7) were the most effective antibacterial derivatives against S. aureus and E. coli respectively with a MIC value of 64 μg/mL. Bacterial biofilm formation assay showed that these compounds significantly inhibited biofilm formation of P. aeruginosa. Also, in silico molecular docking studies were performed to show lipoteichoic acid synthase (LtaS) inhibitory effect of lactic hydrazone derivatives. The association between electronic and structural effects of some substituents on the benzylidene moiety and the biological activity of these chiral compounds were studied. Structural studies show that compound with higher hydrogen bonding interactions show higher antibacterial activity. The results show chiral hydrazone derivatives based on lactic acid hydrazide could be used as potential lead compounds for developing novel antibacterial agents.

  2. Mechanisms of Bacterial Spore Germination and Its Heterogeneity

    Science.gov (United States)

    2015-01-10

    Clostridium difficile ribotype 027 in Chile , Emerging Infectious isease, (08 2012): 1370. doi: Arturo Ramirez-Peralta, Srishti Gupta, Xuan Yi Butzin...Molecular Biology, (09 2010): . doi: Lingbo Kong, Peter Setlow, Yong-qing Li. Direct analysis of water content and movement in single dormant bacterial... Students Received Book TOTAL: Received Book Chapter TOTAL: PERCENT_SUPPORTEDNAME FTE Equivalent: Total Number: Discipline John Sekar 1.00 Robert Sheehan

  3. Bacterial genome reengineering.

    Science.gov (United States)

    Zhou, Jindan; Rudd, Kenneth E

    2011-01-01

    The web application PrimerPair at ecogene.org generates large sets of paired DNA sequences surrounding- all protein and RNA genes of Escherichia coli K-12. Many DNA fragments, which these primers amplify, can be used to implement a genome reengineering strategy using complementary in vitro cloning and in vivo recombineering. The integration of a primer design tool with a model organism database increases the level of quality control. Computer-assisted design of gene primer pairs relies upon having highly accurate genomic DNA sequence information that exactly matches the DNA of the cells being used in the laboratory to ensure predictable DNA hybridizations. It is equally crucial to have confidence that the predicted start codons define the locations of genes accurately. Annotations in the EcoGene database are queried by PrimerPair to eliminate pseudogenes, IS elements, and other problematic genes before the design process starts. These projects progressively familiarize users with the EcoGene content, scope, and application interfaces that are useful for genome reengineering projects. The first protocol leads to the design of a pair of primer sequences that were used to clone and express a single gene. The N-terminal protein sequence was experimentally verified and the protein was detected in the periplasm. This is followed by instructions to design PCR primer pairs for cloning gene fragments encoding 50 periplasmic proteins without their signal peptides. The design process begins with the user simply designating one pair of forward and reverse primer endpoint positions relative to all start and stop codon positions. The gene name, genomic coordinates, and primer DNA sequences are reported to the user. When making chromosomal deletions, the integrity of the provisional primer design is checked to see whether it will generate any unwanted double deletions with adjacent genes. The bad designs are recalculated and replacement primers are provided alongside the

  4. Behind the lines–actions of bacterial type III effector proteins in plant cells

    OpenAIRE

    Büttner, Daniela

    2016-01-01

    Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Ty...

  5. Validation of the extension of the range of application and of the single system of injection for the determination of total nitrogen in petroleum and its derivatives by chemiluminescence; Validacao da ampliacao da faixa de aplicacao e do sistema unico de injecao para a determinacao de nitrogenio total em petroleos e derivados por quimiluminescencia

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Maria de Fatima Pereira dos [Fundacao Gorceix, Ouro Preto, MG(Brazil)]. E-mail: santos@cenpes.petrobras.com.br; Tamanqueira, Juliana Boechat [Universidade Federal Fluminense, Niteroi, RJ (Brazil); Magalhaes, Julio Cesar Dias [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas. Avaliacao de Petroleo; Oliveira, Elcio Cruz de [Transpetro, Rio de Janeiro, RJ (Brazil). Logistica e Planejamento; Vaitsman, Delmo Santiago [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Quimica. Dept. de Quimica Analitica

    2003-12-01

    With the objectives of using a single system of injection and of extending the range of application for the method ASTM D4629/02 'Total Nitrogen in Petroleum Derivatives by the System of Injection with a Syringe and Detection by Chemo- Luminescence', it was studied a procedure by statistical validation with the objective of guaranteeing the analytical reliability of the assay and allowing the inclusion of samples of petroleum and heavy derivatives in one single methodology. The determination of total nitrogen for petroleum and derivatives is traditionally assayed using the method of Kjeldahl - a time-consuming methodology that requires a large amount of time for giving the final result, at the same time that is not recommended for concentrations below 0.1%w/w, which does not meet the requirements for the specifications of the product, in the petroleum industry. An alternative for the method of Kjeldahl is the pyro-chemo luminescence, which allows the achievement of more repetitive results for total nitrogen. In the detection of nitrogen, the technique combines the reliability of oxidative combustion with the sensitivity of chemiluminescence. Therefore, it was developed a protocol of validation in the methodology ASTM D4629/02 for the validation of the extension of the range of application and for the evaluation of the performance of the equipment in analytical conditions, according to the calibration curve. (author)

  6. Molecular mechanisms underlying bacterial persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

    All bacteria form persisters, cells that are multidrug tolerant and therefore able to survive antibiotic treatment. Due to the low frequencies of persisters in growing bacterial cultures and the complex underlying molecular mechanisms, the phenomenon has been challenging to study. However, recent...

  7. Bacterial Cytotoxins Target Rho GTPases

    Science.gov (United States)

    Schmidt, Gudula; Aktories, Klaus

    1998-06-01

    Low molecular mass GTPases of the Rho family, which are involved in the regulation of the actin cytoskeleton and in various signal transduction processes, are the eukaryotic targets of bacterial protein toxins. The toxins covalently modify Rho proteins by ADP ribosylation, glucosylation, and deamidation, thereby inactivating and activating the GTPases.

  8. Disease notes - Bacterial root rot

    Science.gov (United States)

    Bacterial root rot initiated by lactic acid bacteria, particularly Leuconostoc, occurs every year in Idaho sugarbeet fields. Hot fall weather seems to make the problem worse. Although Leuconostoc initiates the rot, other bacteria and yeast frequently invade the tissue as well. The acetic acid bac...

  9. Bacterial canker resistance in tomato

    NARCIS (Netherlands)

    Sen, Y.

    2014-01-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) is the pathogen causing bacterial  canker in tomato. The disease was described for the first time in 1910 in Michigan, USA. Cmmis considered the most harmful bacteria threatening tomato. Disease transmission occurs via seed and symptoms becom

  10. Biotechnological applications of bacterial cellulases

    Directory of Open Access Journals (Sweden)

    Esther Menendez

    2015-08-01

    Full Text Available Cellulases have numerous applications in several industries, including biofuel production, food and feed industry, brewing, pulp and paper, textile, laundry, and agriculture.Cellulose-degrading bacteria are widely spread in nature, being isolated from quite different environments. Cellulose degradation is the result of a synergic process between an endoglucanase, an exoglucanase and a,β-glucosidase. Bacterial endoglucanases degrade ß-1,4-glucan linkages of cellulose amorphous zones, meanwhile exoglucanases cleave the remaining oligosaccharide chains, originating cellobiose, which is hydrolyzed by ß-glucanases. Bacterial cellulases (EC 3.2.1.4 are comprised in fourteen Glycosil Hydrolase families. Several advantages, such as higher growth rates and genetic versatility, emphasize the suitability and advantages of bacterial cellulases over other sources for this group of enzymes. This review summarizes the main known cellulolytic bacteria and the best strategies to optimize their cellulase production, focusing on endoglucanases, as well as it reviews the main biotechnological applications of bacterial cellulases in several industries, medicine and agriculture.

  11. Food irradiation and bacterial toxins

    Energy Technology Data Exchange (ETDEWEB)

    Tranter, H.S.; Modi, N.K.; Hambleton, P.; Melling, J.; Rose, S.; Stringer, M.F.

    1987-07-04

    The authors' findings indicate that irradiation confers no advantage over heat processing in respect of bacterial toxins (clostridium botulinum, neurotoxin A and staphylococcal enterotoxin A). It follows that irradiation at doses less than the ACINF recommended upper limit of 10 kGy could not be used to improve the ambient temperature shelf life on non-acid foods.

  12. Extracardiac manifestations of bacterial endocarditis.

    Science.gov (United States)

    Heffner, J E

    1979-08-01

    Bacterial endocarditis is an elusive disease that challenges clinicians' diagnostic capabilities. Because it can present with various combinations of extravalvular signs and symptoms, the underlying primary disease can go unnoticed.A review of the various extracardiac manifestations of bacterial endocarditis suggests three main patterns by which the valvular infection can be obscured. (1) A major clinical event may be so dramatic that subtle evidence of endocarditis is overlooked. The rupture of a mycotic aneurysm may simulate a subarachnoid hemorrhage from a congenital aneurysm. (2) The symptoms of bacterial endocarditis may be constitutional complaints easily attributable to a routine, trivial illness. Symptoms of low-grade fever, myalgias, back pain and anorexia may mimic a viral syndrome. (3) Endocarditis poses a difficult diagnostic dilemma when it generates constellations of findings that are classic for other disorders. Complaints of arthritis and arthralgias accompanied by hematuria and antinuclear antibody may suggest systemic lupus erythematosus; a renal biopsy study showing diffuse proliferative glomerulonephritis may support this diagnosis. The combination of fever, petechiae, altered mental status, thrombocytopenia, azotemia and anemia may promote the diagnosis of thrombotic thrombocytopenic purpura. When the protean guises of bacterial endocarditis create these clinical difficulties, errors in diagnosis occur and appropriate therapy is delayed. Keen awareness of the varied disease presentations will improve success in managing endocarditis by fostering rapid diagnosis and prompt therapy.

  13. What bacteria leave behind: bacterial organic matter quality and biomarker signals

    DEFF Research Database (Denmark)

    Piil, Kristoffer; Schramm, Andreas; Niggemann, Jutta;

    WHAT BACTERIA LEAVE BEHIND: BACTERIAL ORGANIC MATTER QUALITY AND BIOMARKER SIGNALS Knowledge of the cellular content of bacterial biomarkers (D-amino acids and muramic acid) provides us with a powerful tool to trace production and fate of bacterially derived organic matter. The biochemical...... composition of prokaryotic cells was studied by re-growing a mixed community of native sediment bacteria in anoxic sediment pore water. Cellular concentrations of L- and D-amino acids and amino sugars were determined by high performance liquid chromatography (HPLC). The proportion of Archaea, Gram positive...

  14. Pyrazole derivatives as antitumor, anti-inflammatory and antibacterial agents.

    Science.gov (United States)

    Liu, Jia-Jia; Zhao, Meng-Yue; Zhang, Xin; Zhao, Xin; Zhu, Hai-Liang

    2013-11-01

    Within the past years, many researches on the synthesis, structure-activity relationships (SAR), antitumor, antiinflammatory and anti-bacterial activities of the pyrazole derivatives have been reported. Several pyrazole derivatives possess important pharmacological activities and they have been proved useful materials in drug research. Pyrazole derivatives play an important role in antitumor agents because of their good inhibitory activity against BRAF(V600E), EGFR, telomerase, ROS Receptor Tyrosine Kinase and Aurora-A kinase. In addition, pyrazole derivatives also show good antiinflammatory and anti-bacterial activities. In this review, the bioactivities of the pyrazole derivatives mentioned above will be summarized in detail. We sincerely hope that increasing knowledge of the SAR and cellular processes underlying the bioactivity of pyrazole derivatives will be beneficial to the rational design of new generation of small molecule drugs.

  15. Identification and characterization of a bacterial glutamic peptidase

    Directory of Open Access Journals (Sweden)

    Jensen Kenneth

    2010-12-01

    Full Text Available Abstract Background Glutamic peptidases, from the MEROPS family G1, are a distinct group of peptidases characterized by a catalytic dyad consisting of a glutamate and a glutamine residue, optimal activity at acidic pH and insensitivity towards the microbial derived protease inhibitor, pepstatin. Previously, only glutamic peptidases derived from filamentous fungi have been characterized. Results We report the first characterization of a bacterial glutamic peptidase (pepG1, derived from the thermoacidophilic bacteria Alicyclobacillus sp. DSM 15716. The amino acid sequence identity between pepG1 and known fungal glutamic peptidases is only 24-30% but homology modeling, the presence of the glutamate/glutamine catalytic dyad and a number of highly conserved motifs strongly support the inclusion of pepG1 as a glutamic peptidase. Phylogenetic analysis places pepG1 and other putative bacterial and archaeal glutamic peptidases in a cluster separate from the fungal glutamic peptidases, indicating a divergent and independent evolution of bacterial and fungal glutamic peptidases. Purification of pepG1, heterologously expressed in Bacillus subtilis, was performed using hydrophobic interaction chromatography and ion exchange chromatography. The purified peptidase was characterized with respect to its physical properties. Temperature and pH optimums were found to be 60°C and pH 3-4, in agreement with the values observed for the fungal members of family G1. In addition, pepG1 was found to be pepstatin-insensitive, a characteristic signature of glutamic peptidases. Conclusions Based on the obtained results, we suggest that pepG1 can be added to the MEROPS family G1 as the first characterized bacterial member.

  16. Temporal relationships exist between cecum, ileum and litter bacterial microbiomes in a commercial turkey flock, and subtherapeutic penicillin treatment impacts ileum bacterial community establishment

    Directory of Open Access Journals (Sweden)

    Jessica L Danzeisen

    2015-11-01

    Full Text Available Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the developing host immune system. In this study, a single flock of commercial turkeys was followed over the course of twelve weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of turkeys were distinct, yet shifted in parallel to one another over time during bird maturation. Corresponding poultry litter was also distinct yet more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low dose in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study identified the dynamics of the turkey gastrointestinal microbiome during development, correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on modulation of bacterial communities in the ileum. Such modulations provide a target for alternatives to low-dose antibiotics.

  17. The bacterial community of entomophilic nematodes and host beetles.

    Science.gov (United States)

    Koneru, Sneha L; Salinas, Heilly; Flores, Gilberto E; Hong, Ray L

    2016-05-01

    Insects form the most species-rich lineage of Eukaryotes and each is a potential host for organisms from multiple phyla, including fungi, protozoa, mites, bacteria and nematodes. In particular, beetles are known to be associated with distinct bacterial communities and entomophilic nematodes. While entomopathogenic nematodes require symbiotic bacteria to kill and reproduce inside their insect hosts, the microbial ecology that facilitates other types of nematode-insect associations is largely unknown. To illuminate detailed patterns of the tritrophic beetle-nematode-bacteria relationship, we surveyed the nematode infestation profiles of scarab beetles in the greater Los Angeles area over a five-year period and found distinct nematode infestation patterns for certain beetle hosts. Over a single season, we characterized the bacterial communities of beetles and their associated nematodes using high-throughput sequencing of the 16S rRNA gene. We found significant differences in bacterial community composition among the five prevalent beetle host species, independent of geographical origin. Anaerobes Synergistaceae and sulphate-reducing Desulfovibrionaceae were most abundant in Amblonoxia beetles, while Enterobacteriaceae and Lachnospiraceae were common in Cyclocephala beetles. Unlike entomopathogenic nematodes that carry bacterial symbionts, insect-associated nematodes do not alter the beetles' native bacterial communities, nor do their microbiomes differ according to nematode or beetle host species. The conservation of Diplogastrid nematodes associations with Melolonthinae beetles and sulphate-reducing bacteria suggests a possible link between beetle-bacterial communities and their associated nematodes. Our results establish a starting point towards understanding the dynamic interactions between soil macroinvertebrates and their microbiota in a highly accessible urban environment.

  18. Caracterização de cepas de Schistosoma mansoni por morfometria de vermes adultos provenientes de infecção unissexual Characterization of Schistosoma mansoni strains by morphometry of adult worms derived from single-sex infection

    Directory of Open Access Journals (Sweden)

    José Roberto Machado-Silva

    2003-12-01

    Full Text Available Camundongos foram infectados com cercárias, de um único sexo, de cepas simpátricas do Schistosoma mansoni. Nos vermes adultos, foram encontradas diferenças significativas (pMice were infected with only one sex cercaria derived from sympatric strains of Schistosoma mansoni. Adult worms presented significative differences (p<0.05 regarding suckers, testicular lobes, ovary and thickness of the tegument. Data show that morphometric study of unisexual infection worms can be also used for characterization of Schistosoma mansoni strains.

  19. Prostatitis-bacterial - self-care

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000395.htm Prostatitis- bacterial - self-care To use the sharing features ... enable JavaScript. You have been diagnosed with bacterial prostatitis . This is an infection of the prostate gland. ...

  20. Cognitive outcome in adults after bacterial meningitis.

    NARCIS (Netherlands)

    Hoogman, M.; Beek, D. van de; Weisfelt, M.; Gans, J. de; Schmand, B.

    2007-01-01

    OBJECTIVE: To evaluate cognitive outcome in adult survivors of bacterial meningitis. METHODS: Data from three prospective multicentre studies were pooled and reanalysed, involving 155 adults surviving bacterial meningitis (79 after pneumococcal and 76 after meningococcal meningitis) and 72 healthy c

  1. Factors influencing neurological outcome of children with bacterial meningitis at the emergency department.

    Science.gov (United States)

    Bargui, Fatiha; D'Agostino, Irene; Mariani-Kurkdjian, Patricia; Alberti, Corinne; Doit, Catherine; Bellier, Nathalie; Morin, Laurence; Galli Gibertini, Giuliano; Smail, Assia; Zanin, Anna; Lorrot, Mathie; Dauger, Stéphane; Neve, Mathieu; Faye, Albert; Armoogum, Priscilla; Bourrillon, Antoine; Bingen, Edouard; Mercier, Jean-Christophe; Bonacorsi, Stéphane; Nigrovic, Lise E; Titomanlio, Luigi

    2012-09-01

    We performed a cohort study of children who survived bacterial meningitis after the neonatal period at a single pediatric center in France over a 10-year period (1995-2004) to identify predictors of death and long-term neurological deficits in children with bacterial meningitis. We performed multivariate regression to determine independent predictors of death and neurologic deficits. We identified 101 children with bacterial meningitis of which 19 died during initial hospitalization. Need for mechanical ventilation [hazard ratio (HR) 11.5, 95 % confidence interval (CI) 2.4-55.5)] and thrombocytopenia defined as a platelet count highest risk.

  2. Demodex-associated bacterial proteins induce neutrophil activation.

    LENUS (Irish Health Repository)

    2012-02-01

    Background: Patients with rosacea demonstrate a higher density of Demodex mites in their skin than controls. A bacterium isolated from a Demodex mite from a patient with papulopustular rosacea (PPR) was previously shown to provoke an immune response in patients with PPR or ocular rosacea thus suggesting a possible role for bacterial proteins in the etiology of this condition. Objectives: To examine the response of neutrophils to proteins derived from a bacterium isolated from a Demodex mite. Methods: Bacterial cells were lysed and proteins were partially purified by AKTA-FPLC. Isolated neutrophils were exposed to bacterial proteins and monitored for alterations in migration, degranulation and cytokine production. Results: Neutrophils exposed to proteins from Bacillus cells demonstrated increased levels of migration and elevated release of MMP-9, an enzyme known to degrade collagen and cathelicidin, an antimicrobial peptide. In addition neutrophils exposed to the bacterial proteins demonstrated elevated rates of Il-8 and TNF-alpha production. Conclusions: Proteins produced by a bacterium isolated from a Demodex mite have the ability to increase the migration, degranulation and cytokine production abilities of neutrophils. These results suggest that bacteria may play a role in the inflammatory erythema associated with rosacea.

  3. Single-chain antibody-based gene therapy: Inhibition of tumor growth by in situ production of phage-derived antibodies blocking functionally active sites of cell-associated matrices

    DEFF Research Database (Denmark)

    Sanz, Laura; Kristensen, Peter; Blanco, Belén

    2002-01-01

    . This scFv inhibits angiogenesis in vivo in the chick embryo chorioallantoic membrane assay and prevents the establishment and growth of subcutaneous tumors in mice, either when administered as bolus protein therapy or when produced locally by gene-modified tumor cells. Our work represents the first...... demonstration of a direct in vivo therapeutic effect of a single-chain antibody secreted by gene-modified mammalian cells. These results open the way for a new antibody-based gene therapy strategy of cancer....

  4. On $n$-derivations

    Directory of Open Access Journals (Sweden)

    Mohammad Hossein Sattari

    2016-06-01

    Full Text Available In this article, the notion of $n-$derivation is introduced for all integers $ngeq 2$. Although all derivations are $n-$derivations,  in general these notions are not equivalent. Some properties of ordinary derivations are  investigated for $n-$derivations. Also, we show that under certain mild condition  $n-$derivations are derivations.

  5. RNA-stable-isotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel.

    Science.gov (United States)

    Tannock, Gerald W; Lawley, Blair; Munro, Karen; Sims, Ian M; Lee, Julian; Butts, Christine A; Roy, Nicole

    2014-04-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope ((13)C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [(13)C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect (13)C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the (13)C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA-stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.

  6. Possible implication of bacterial infection in acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation

    Directory of Open Access Journals (Sweden)

    Shigeo eFuji

    2014-04-01

    Full Text Available Graft-versus-host disease (GVHD is still one of the major causes of morbidity and mortality in allogeneic hematopoietic stem cell transplantation (HSCT. In the pathogenesis of acute GVHD, it has been established that donor-derived T cells activated in the recipient play a major role in GVHD in initiation and maintenance within an inflammatory cascade. To reduce the risk of GVHD, intensification of GVHD prophylaxis like T cell depletion is effective, but it inevitably increases the risk of infectious diseases and abrogates beneficial graft-versus-leukemia effects. Although various cytokines are considered to play an important role in the pathogenesis of GVHD, GVHD initiation is such a complex process that cannot be prevented by means of single inflammatory cytokine inhibition. Thus, efficient methods to control the whole inflammatory milieu both on cellular and humoral view are needed. In this context, infectious diseases can theoretically contribute to an elevation of inflammatory cytokines after allogeneic HSCT and activation of various subtypes of immune effector cells, which might in summary lead to an aggravation of acute GVHD. The appropriate treatments or prophylaxis of bacterial infection during the early phase after allogeneic HSCT might be beneficial to reduce not only infectious-related but also GVHD-related mortality. Here, we aim to review the literature addressing the interactions of bacterial infections and GVHD after allogeneic HSCT.

  7. Possible Implication of Bacterial Infection in Acute Graft-Versus-Host Disease after Allogeneic Hematopoietic Stem Cell Transplantation

    Science.gov (United States)

    Fuji, Shigeo; Kapp, Markus; Einsele, Hermann

    2014-01-01

    Graft-versus-host disease (GVHD) is still one of the major causes of morbidity and mortality in allogeneic hematopoietic stem cell transplantation (HSCT). In the pathogenesis of acute GVHD, it has been established that donor-derived T-cells activated in the recipient play a major role in GVHD in initiation and maintenance within an inflammatory cascade. To reduce the risk of GVHD, intensification of GVHD prophylaxis like T-cell depletion is effective, but it inevitably increases the risk of infectious diseases and abrogates beneficial graft-versus-leukemia effects. Although various cytokines are considered to play an important role in the pathogenesis of GVHD, GVHD initiation is such a complex process that cannot be prevented by means of single inflammatory cytokine inhibition. Thus, efficient methods to control the whole inflammatory milieu both on cellular and humoral view are needed. In this context, infectious diseases can theoretically contribute to an elevation of inflammatory cytokines after allogeneic HSCT and activation of various subtypes of immune effector cells, which might in summary lead to an aggravation of acute GVHD. The appropriate treatments or prophylaxis of bacterial infection during the early phase after allogeneic HSCT might be beneficial to reduce not only infectious-related but also GVHD-related mortality. Here, we aim to review the literature addressing the interactions of bacterial infections and GVHD after allogeneic HSCT. PMID:24795865

  8. The ATRX cDNA is prone to bacterial IS10 element insertions that alter its structure.

    Science.gov (United States)

    Valle-García, David; Griffiths, Lyra M; Dyer, Michael A; Bernstein, Emily; Recillas-Targa, Félix

    2014-01-01

    The SWI/SNF-like chromatin-remodeling protein ATRX has emerged as a key factor in the regulation of α-globin gene expression, incorporation of histone variants into the chromatin template and, more recently, as a frequently mutated gene across a wide spectrum of cancers. Therefore, the availability of a functional ATRX cDNA for expression studies is a valuable tool for the scientific community. We have identified two independent transposon insertions of a bacterial IS10 element into exon 8 of ATRX isoform 2 coding sequence in two different plasmids derived from a single source. We demonstrate that these insertion events are common and there is an insertion hotspot within the ATRX cDNA. Such IS10 insertions produce a truncated form of ATRX, which significantly compromises its nuclear localization. In turn, we describe ways to prevent IS10 insertion during propagation and cloning of ATRX-containing vectors, including optimal growth conditions, bacterial strains, and suggested sequencing strategies. Finally, we have generated an insertion-free plasmid that is available to the community for expression studies of ATRX.

  9. Control of intestinal bacterial proliferation in regulation of lifespan in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Portal-Celhay Cynthia

    2012-03-01

    Full Text Available Abstract Background A powerful approach to understanding complex processes such as aging is to use model organisms amenable to genetic manipulation, and to seek relevant phenotypes to measure. Caenorhabditis elegans is particularly suited to studies of aging, since numerous single-gene mutations have been identified that affect its lifespan; it possesses an innate immune system employing evolutionarily conserved signaling pathways affecting longevity. As worms age, bacteria accumulate in the intestinal tract. However, quantitative relationships between worm genotype, lifespan, and intestinal lumen bacterial load have not been examined. We hypothesized that gut immunity is less efficient in older animals, leading to enhanced bacterial accumulation, reducing longevity. To address this question, we evaluated the ability of worms to control bacterial accumulation as a functional marker of intestinal immunity. Results We show that as adult worms age, several C. elegans genotypes show diminished capacity to control intestinal bacterial accumulation. We provide evidence that intestinal bacterial load, regulated by gut immunity, is an important causative factor of lifespan determination; the effects are specified by bacterial strain, worm genotype, and biologic age, all acting in concert. Conclusions In total, these studies focus attention on the worm intestine as a locus that influences longevity in the presence of an accumulating bacterial population. Further studies defining the interplay between bacterial species and host immunity in C. elegans may provide insights into the general mechanisms of aging and age-related diseases.

  10. Aerosol optical properties derived from the DRAGON-NE Asia campaign, and implications for a single-channel algorithm to retrieve aerosol optical depth in spring from Meteorological Imager (MI) on-board the Communication, Ocean, and Meteorological Satellite (COMS)

    Science.gov (United States)

    Kim, M.; Kim, J.; Jeong, U.; Kim, W.; Hong, H.; Holben, B.; Eck, T. F.; Lim, J. H.; Song, C. K.; Lee, S.; Chung, C.-Y.

    2016-02-01

    An aerosol model optimized for northeast Asia is updated with the inversion data from the Distributed Regional Aerosol Gridded Observation Networks (DRAGON)-northeast (NE) Asia campaign which was conducted during spring from March to May 2012. This updated aerosol model was then applied to a single visible channel algorithm to retrieve aerosol optical depth (AOD) from a Meteorological Imager (MI) on-board the geostationary meteorological satellite, Communication, Ocean, and Meteorological Satellite (COMS). This model plays an important role in retrieving accurate AOD from a single visible channel measurement. For the single-channel retrieval, sensitivity tests showed that perturbations by 4 % (0.926 ± 0.04) in the assumed single scattering albedo (SSA) can result in the retrieval error in AOD by over 20 %. Since the measured reflectance at the top of the atmosphere depends on both AOD and SSA, the overestimation of assumed SSA in the aerosol model leads to an underestimation of AOD. Based on the AErosol RObotic NETwork (AERONET) inversion data sets obtained over East Asia before 2011, seasonally analyzed aerosol optical properties (AOPs) were categorized by SSAs at 675 nm of 0.92 ± 0.035 for spring (March, April, and May). After the DRAGON-NE Asia campaign in 2012, the SSA during spring showed a slight increase to 0.93 ± 0.035. In terms of the volume size distribution, the mode radius of coarse particles was increased from 2.08 ± 0.40 to 2.14 ± 0.40. While the original aerosol model consists of volume size distribution and refractive indices obtained before 2011, the new model is constructed by using a total data set after the DRAGON-NE Asia campaign. The large volume of data in high spatial resolution from this intensive campaign can be used to improve the representative aerosol model for East Asia. Accordingly, the new AOD data sets retrieved from a single-channel algorithm, which uses a precalculated look-up table (LUT) with the new aerosol model, show an

  11. A model capturing novel strand symmetries in bacterial DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sobottka, Marcelo, E-mail: sobottka@mtm.ufsc.br [Departamento de Matematica, Universidade Federal de Santa Catarina (Brazil); Hart, Andrew G., E-mail: ahart@dim.uchile.cl [Departamento de Ingenieria Matematica and Centro de Modelamiento Matematico, Universidad de Chile (Chile)

    2011-07-15

    Highlights: {yields} We propose a simple stochastic model to construct primitive DNA sequences. {yields} The model provide an explanation for Chargaff's second parity rule in primitive DNA sequences. {yields} The model is also used to predict a novel type of strand symmetry in primitive DNA sequences. {yields} We extend the results for bacterial DNA sequences and compare distributional properties intrinsic to the model to statistical estimates from 1049 bacterial genomes. {yields} We find out statistical evidences that the novel type of strand symmetry holds for bacterial DNA sequences. -- Abstract: Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown that, with the exception of organellar DNA, this parity rule generally holds for double-stranded DNA genomes and fails to hold for single-stranded genomes. While Chargaff's first parity rule is fully explained by the Watson-Crick pairing in the DNA double helix, a definitive explanation for the second parity rule has not yet been determined. In this work, we propose a model based on a hidden Markov process for approximating the distributional structure of primitive DNA sequences. Then, we use the model to provide another possible theoretical explanation for Chargaff's second parity rule, and to predict novel distributional aspects of bacterial DNA sequences.

  12. Channel-Forming Bacterial Toxins in Biosensing and Macromolecule Delivery

    Directory of Open Access Journals (Sweden)

    Philip A. Gurnev

    2014-08-01

    Full Text Available To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on “Intracellular Traffic and Transport of Bacterial Protein Toxins”, reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their “second life” in a variety of developing medical and technological applications.

  13. Channel-forming bacterial toxins in biosensing and macromolecule delivery.

    Science.gov (United States)

    Gurnev, Philip A; Nestorovich, Ekaterina M

    2014-08-21

    To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.

  14. Exploring anti-bacterial compounds against intracellular Legionella.

    Directory of Open Access Journals (Sweden)

    Christopher F Harrison

    Full Text Available Legionella pneumophila is a ubiquitous fresh-water bacterium which reproduces within its erstwhile predators, environmental amoeba, by subverting the normal pathway of phagocytosis and degradation. The molecular mechanisms which confer resistance to amoeba are apparently conserved and also allow replication within macrophages. Thus, L. pneumophila can act as an 'accidental' human pathogen and cause a severe pneumonia known as Legionnaires' disease. The intracellular localisation of L. pneumophila protects it from some antibiotics, and this fact must be taken into account to develop new anti-bacterial compounds. In addition, the intracellular lifestyle of L. pneumophila may render the bacteria susceptible to compounds diminishing bacterial virulence and decreasing intracellular survival and replication of this pathogen. The development of a single infection cycle intracellular replication assay using GFP-producing L. pneumophila and Acanthamoebacastellanii amoeba is reported here. This fluorescence-based assay allows for continuous monitoring of intracellular replication rates, revealing the effect of bacterial gene deletions or drug treatment. To examine how perturbations of the host cell affect L. pneumophila replication, several known host-targeting compounds were tested, including modulators of cytoskeletal dynamics, vesicle scission and Ras GTPase localisation. Our results reveal a hitherto unrealized potential antibiotic property of the β-lactone-based Ras depalmitoylation inhibitor palmostatin M, but not the closely related inhibitor palmostatin B. Further characterisation indicated that this compound caused specific growth inhibition of Legionella and Mycobacterium species, suggesting that it may act on a common bacterial target.

  15. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  16. Antibiotic drugs targeting bacterial RNAs

    Directory of Open Access Journals (Sweden)

    Weiling Hong

    2014-08-01

    Full Text Available RNAs have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. The recent increase in structural and functional information related to RNAs has put them in the limelight as a drug target for small molecule therapy. In addition, the recognition of the marked difference between prokaryotic and eukaryotic rRNA has led to the development of antibiotics that specifically target bacterial rRNA, reduce protein translation and thereby inhibit bacterial growth. To facilitate the development of new antibiotics targeting RNA, we here review the literature concerning such antibiotics, mRNA, riboswitch and tRNA and the key methodologies used for their screening.

  17. Electromagnetic Signals from Bacterial DNA

    CERN Document Server

    Widom, A; Srivastava, Y N; Sivasubramanian, S

    2011-01-01

    Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although is is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals hold true for muck lower frequencies. In E. coli bacteria such electromagnetic signals can be generated by electric transitions between energy levels describing electrons moving around DNA loops. The electromagnetic signals between different bacteria within a community is a "wireless" version of intercellular communication found in bacterial communities connected by "nanowires". The wireless broadcasts can in principle be of both the AM and FM variety due to the magnetic flux periodicity in electron energy spectra in bacterial DNA orbital motions.

  18. Bacterial survival in Martian conditions

    CERN Document Server

    D'Alessandro, Giuseppe Galletta; Giulio Bertoloni; Maurizio

    2010-01-01

    We shortly discuss the observable consequences of the two hypotheses about the origin of life on Earth and Mars: the Lithopanspermia (Mars to Earth or viceversa) and the origin from a unique progenitor, that for Earth is called LUCA (the LUCA hypothesis). To test the possibility that some lifeforms similar to the terrestrial ones may survive on Mars, we designed and built two simulators of Martian environments where to perform experiments with different bacterial strains: LISA and mini-LISA. Our LISA environmental chambers can reproduce the conditions of many Martian locations near the surface trough changes of temperature, pressure, UV fluence and atmospheric composition. Both simulators are open to collaboration with other laboratories interested in performing experiments on many kind of samples (biological, minerals, electronic) in situations similar to that of the red planet. Inside LISA we have studied the survival of several bacterial strains and endospores. We verified that the UV light is the major re...

  19. Bacterial streamers in curved microchannels

    Science.gov (United States)

    Rusconi, Roberto; Lecuyer, Sigolene; Guglielmini, Laura; Stone, Howard

    2009-11-01

    Biofilms, generally identified as microbial communities embedded in a self-produced matrix of extracellular polymeric substances, are involved in a wide variety of health-related problems ranging from implant-associated infections to disease transmissions and dental plaque. The usual picture of these bacterial films is that they grow and develop on surfaces. However, suspended biofilm structures, or streamers, have been found in natural environments (e.g., rivers, acid mines, hydrothermal hot springs) and are always suggested to stem from a turbulent flow. We report the formation of bacterial streamers in curved microfluidic channels. By using confocal laser microscopy we are able to directly image and characterize the spatial and temporal evolution of these filamentous structures. Such streamers, which always connect the inner corners of opposite sides of the channel, are always located in the middle plane. Numerical simulations of the flow provide evidences for an underlying hydrodynamic mechanism behind the formation of the streamers.

  20. Bacterial chromosome organization and segregation.

    Science.gov (United States)

    Badrinarayanan, Anjana; Le, Tung B K; Laub, Michael T

    2015-01-01

    If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation.