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Sample records for bacteria structure mode

  1. Nitrogen-removal performance and community structure of nitrifying bacteria under different aeration modes in an oxidation ditch.

    Science.gov (United States)

    Guo, Chang-Zi; Fu, Wei; Chen, Xue-Mei; Peng, Dang-Cong; Jin, Peng-Kang

    2013-07-01

    Oxidation-ditch operation modes were simulated using sequencing batch reactors (SBRs) with alternate stirring and aerating. The nitrogen-removal efficiencies and nitrifying characteristics of two aeration modes, point aeration and step aeration, were investigated. Under the same air-supply capacity, oxygen dissolved more efficiently in the system with point aeration, forming a larger aerobic zone. The nitrifying effects were similar in point aeration and step aeration, where the average removal efficiencies of NH4(+) N were 98% and 96%, respectively. When the proportion of anoxic and oxic zones was 1, the average removal efficiencies of total nitrogen (TN) were 45% and 66% under point aeration and step aeration, respectively. Step aeration was more beneficial to both anoxic denitrification and simultaneous nitrification and denitrification (SND). The maximum specific ammonia-uptake rates (AUR) of point aeration and step aeration were 4.7 and 4.9 mg NH4(+)/(gMLVSS h), respectively, while the maximum specific nitrite-uptake rates (NUR) of the two systems were 7.4 and 5.3 mg NO2(-)-N/(gMLVSS h), respectively. The proportions of ammonia-oxidizing bacteria (AOB) to all bacteria were 5.1% under point aeration and 7.0% under step aeration, and the proportions of nitrite-oxidizing bacteria (NOB) reached 6.5% and 9.0% under point and step aeration, respectively. The dominant genera of AOB and NOB were Nitrosococcus and Nitrospira, which accounted for 90% and 91%, respectively, under point aeration, and the diversity of nitrifying bacteria was lower than under step aeration. Point aeration was selective of nitrifying bacteria. The abundance of NOB was greater than that of AOB in both of the operation modes, and complete transformation of NH4(+) N to NO3(-)-N was observed without NO2(-)-N accumulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Physical mode of bacteria and virus coevolution

    Science.gov (United States)

    Han, Pu; Niestemski, Liang; Deem, Michael

    2013-03-01

    Single-cell hosts such as bacteria or archaea possess an adaptive, heritable immune system that protects them from viral invasion. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences from viruses or plasmids. The sequences form what are called ``spacers'' in the CRISPR. Spacers in the CRISPR loci provide a record of the host and predator coevolution history. We develop a physical model to study the dynamics of this coevolution due to immune pressure. Hosts and viruses reproduce, die, and evolve due to viral infection pressure, host immune pressure, and mutation. We will discuss the differing effects of point mutation and recombination on CRISPR evolution. We will also discuss the effect of different spacer deletion mechanisms. We will describe population structure of hosts and viruses, how spacer diversity depends on position within CRISPR, and match of the CRISPR spacers to the virus population.

  3. 17α-Ethynylestradiol biodegradation in different river-based groundwater recharge modes with reclaimed water and degradation-associated community structure of bacteria and archaea.

    Science.gov (United States)

    Ma, Weifang; Sun, Jiaji; Li, Yangyao; Lun, Xiaoxiu; Shan, Dan; Nie, Chao; Liu, Miaomiao

    2018-02-01

    This study investigated 17α-ethynylestradiol (EE2) biodegradation process and primary metabolic pathways associated with community structures of microorganism during groundwater recharge using reclaimed water. The attenuation rate is 1.58 times higher in wetting and drying alternative recharge (WDAR) than in continual recharge (CR). The primary biotransformation pathways of EE2 in WDAR system began with the oxidation of C-17 on ring D to form a ketone group, and D-ring was subsequently hydroxylated and cleaved. In the CR system, the metabolic pathway changed from the oxidation of C-17 on ring D to hydroxylation of C-4 on ring A, and ring A or B subsequently cleaved; this transition was related to DO, and the microbial community structure. Four hundred fifty four pyrosequencing of 16s rRNA genes indicated that the bacterial communities in the upper layer of the WDAR system were more diverse than those found in the bottom layer of the CR system; this result was reversed for archaea. Unweighted UniFrac and taxonomic analyses were conducted to relate the change in bacterial community structure to the metabolic pathway. Microorganism community diversity and structure were related to the concentrations of dissolved oxygen, EE2 and its intermediates in the system. Five known bacterial classes and one known archaeal class, five major bacterial genera and one major archaeal genus might be involved in EE2 degradation. The findings of this study provide an understanding of EE2 biodegradation in groundwater recharge areas under different recharging modes and can facilitate the prediction of the fate of EE2 in underground aquifers. Copyright © 2017. Published by Elsevier B.V.

  4. Mode structure of active resonators

    NARCIS (Netherlands)

    Ernst, G.J.; Witteman, W.J.

    1973-01-01

    An analysis is made of the mode structure of lasers when the interaction with the active medium is taken into account. We consider the combined effect of gain and refractive-index variations for arbitrary mirror configurations. Using a dimensionless round-trip matrix for a medium with a quadratic

  5. Resonant modes in Josephson structures

    International Nuclear Information System (INIS)

    Paterno, G.

    1985-01-01

    It is well-know that a Josephson junction held at finite voltage V generates an alternating current at a frequency *o=(2e/h)V. When the junction is coupled to an external resonator self-induced dc current modes occur in the structure. The nonlinear interaction with the ac Josephson radiation gives rise to current singularities at voltages corresponding to the resonance frequencies of the resonator. These resonances appear in the dc current voltage characteristics as current singularities. They are due to a conversion of dc power to ac power that in turn is internally dissipated. In a tunneling junction the resonator is formed of the two superconducting electrodes separated by the oxide layer. In a two junctions interferometer the resonant structure is formed of the loop inductance and the junction capacitances. A good knowledge of the behaviour of these singularities is very important when switching properties are considered or ac power has to be extracted from the structure. In this paper we review the behaviour of resonant modes in Josephson junctions coupled to a resonant structure. A comparison between experimental data and the theoretical description at present available is reported

  6. Extremophile bacteria glycolipids: structure and biological activity

    OpenAIRE

    Carillo, Sara

    2013-01-01

    Extremophile bacteria are able to survive in harsh life conditions, such as high or low temperatures (thermophiles and psychrophiles, respectively), high pressure (barophiles), high or low pH values (acidophiles or alkalophiles), environments characterized by high salt concentrations (halophiles). Structural features of the macromolecules belonging to the external layer are fundamental in adaptation mechanisms, e.g. it is well known that halophiles membrane phospholipids showed an increase...

  7. Multi-Mode Cavity Accelerator Structure

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yong [Yale Univ., New Haven, CT (United States); Hirshfield, Jay Leonard [Omega-P R& D, Inc., New Haven, CT (United States)

    2016-11-10

    This project aimed to develop a prototype for a novel accelerator structure comprising coupled cavities that are tuned to support modes with harmonically-related eigenfrequencies, with the goal of reaching an acceleration gradient >200 MeV/m and a breakdown rate <10-7/pulse/meter. Phase I involved computations, design, and preliminary engineering of a prototype multi-harmonic cavity accelerator structure; plus tests of a bimodal cavity. A computational procedure was used to design an optimized profile for a bimodal cavity with high shunt impedance and low surface fields to maximize the reduction in temperature rise ΔT. This cavity supports the TM010 mode and its 2nd harmonic TM011 mode. Its fundamental frequency is at 12 GHz, to benchmark against the empirical criteria proposed within the worldwide High Gradient collaboration for X-band copper structures; namely, a surface electric field Esurmax< 260 MV/m and pulsed surface heating ΔTmax< 56 °K. With optimized geometry, amplitude and relative phase of the two modes, reductions are found in surface pulsed heating, modified Poynting vector, and total RF power—as compared with operation at the same acceleration gradient using only the fundamental mode.

  8. Comment on radial structure of high-mode-number toroidal modes in general equilibrium profiles

    International Nuclear Information System (INIS)

    Zhang, Y.Z.; Mahajan, S.M.

    1995-01-01

    The comment express the disagreement of the authors with the results claimed in the paper 'Radial Structure of High-Mode-Number Toroidal Modes in General Equilibrium Profiles' by J-Y.Kim and M.Wakatani, Phys.Rev.Lett.73, 2200 (1994) concerning the 2D structure (ballooning theory) of the modes in an axisymmetric torus. 5 refs

  9. Modes of action for biological control of Botrytis cinerea by antagonistic bacteria

    Directory of Open Access Journals (Sweden)

    Rana HAIDAR

    2017-01-01

    Full Text Available The role of beneficial bacteria in biocontrol of plant diseases, particularly those caused by the necrotrophic fungus Botrytis cinerea, has been investigated by testing many bacteria under laboratory and field conditions. Bacteria may protect plants against B. cinerea by direct antagonistic interactions between biocontrol agents and this pathogen, as well as indirect effects through the induction of host resistance. This review focuses on various bacteria that act as biological control agents (BCAs of B. cinerea and their associated mechanisms. The modes of action (MoAs include: i synthesis of anti-fungal metabolites, such as antibiotics, cell wall-degrading enzymes and volatile organic compounds (VOCs; ii competition for nutrients and/or a niche; and iii induction of host resistance. The challenge for development of BCAs is to reduce the variability of efficiency and to prove persistence under a large range of conditions. We discuss the advantages and drawbacks of MoA for future applications of bacteria in the field and in post-harvest storage, as well as combination of different MoAs as a strategy to achieve a more regular efficacy.

  10. Polarization Characterization of a Multi-Moded Feed Structure

    Data.gov (United States)

    National Aeronautics and Space Administration — The Polarization Characterization of a Multi-Moded Feed Structure projects characterize the polarization response of a multi-moded feed horn as an innovative...

  11. Effect of tetracycline dose and treatment mode on selection of resistant coliform bacteria in nursery pigs

    DEFF Research Database (Denmark)

    Græsbøll, Kaare; Damborg, Peter; Mellerup, Anders

    2017-01-01

    This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig...... by the time that the pigs left the nursery unit. The counts and proportions of tetracyclineresistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated...

  12. Synergistic interaction and mode of action of Citrus hystrix essential oil against bacteria causing periodontal diseases.

    Science.gov (United States)

    Wongsariya, Karn; Phanthong, Phanida; Bunyapraphatsara, Nuntavan; Srisukh, Vimol; Chomnawang, Mullika Traidej

    2014-03-01

    Citrus hystrix de Candolle (Rutaceae), an edible plant regularly used as a food ingredient, possesses antibacterial activity, but there is no current data on the activity against bacteria causing periodontal diseases. C. hystrix essential oil from leaves and peel were investigated for antibiofilm formation and mode of action against bacteria causing periodontal diseases. In vitro antibacterial and antibiofilm formation activities were determined by broth microdilution and time kill assay. Mode of action of essential oil was observed by SEM and the active component was identified by bioautography and GC/MS. C. hystrix leaves oil exhibited antibacterial activity at the MICs of 1.06 mg/mL for P. gingivalis and S. mutans and 2.12 mg/mL for S. sanguinis. Leaf oil at 4.25 mg/mL showed antibiofilm formation activity with 99% inhibition. The lethal effects on P. gingivalis were observed within 2 and 4 h after treated with 4 × MIC and 2 × MIC, respectively. S. sanguinis and S. mutans were completely killed within 4 and 8 h after exposed to 4 × MIC and 2 × MIC of oil. MICs of tested strains showed 4 times reduction suggesting synergistic interaction of oil and chlorhexidine. Bacterial outer membrane was disrupted after treatment with leaves oil. Additionally, citronellal was identified as the major active compound of C. hystrix oil. C. hystrix leaf oil could be used as a natural active compound or in combination with chlorhexidine in mouthwash preparations to prevent the growth of bacteria associated with periodontal diseases and biofilm formation.

  13. A Bloch mode expansion approach for analyzing quasi-normal modes in open nanophotonic structures

    DEFF Research Database (Denmark)

    de Lasson, Jakob Rosenkrantz; Kristensen, Philip Trøst; Mørk, Jesper

    2014-01-01

    We present a new method for determining quasi-normal modes in open nanophotonic structures using a modal ex- pansion technique. The outgoing wave boundary condition of the quasi-normal modes is satisfied automatically without absorbing boundaries, representing a significant advantage compared...... to conventional techniques. The quasi-normal modes are determined by constructing a cavity roundtrip matrix and iterating the complex mode wavelength towards a unity eigenvalue. We demonstrate the method by deter- mining quasi-normal modes of cavities in two-dimensional photonic crystals side-coupled to W1...

  14. Edge-localized mode avoidance and pedestal structure in I-mode plasmasa)

    Science.gov (United States)

    Walk, J. R.; Hughes, J. W.; Hubbard, A. E.; Terry, J. L.; Whyte, D. G.; White, A. E.; Baek, S. G.; Reinke, M. L.; Theiler, C.; Churchill, R. M.; Rice, J. E.; Snyder, P. B.; Osborne, T.; Dominguez, A.; Cziegler, I.

    2014-05-01

    I-mode is a high-performance tokamak regime characterized by the formation of a temperature pedestal and enhanced energy confinement, without an accompanying density pedestal or drop in particle and impurity transport. I-mode operation appears to have naturally occurring suppression of large Edge-Localized Modes (ELMs) in addition to its highly favorable scalings of pedestal structure and overall performance. Extensive study of the ELMy H-mode has led to the development of the EPED model, which utilizes calculations of coupled peeling-ballooning MHD modes and kinetic-ballooning mode (KBM) stability limits to predict the pedestal structure preceding an ELM crash. We apply similar tools to the structure and ELM stability of I-mode pedestals. Analysis of I-mode discharges prepared with high-resolution pedestal data from the most recent C-Mod campaign reveals favorable pedestal scalings for extrapolation to large machines—pedestal temperature scales strongly with power per particle Pnet/n ¯e, and likewise pedestal pressure scales as the net heating power (consistent with weak degradation of confinement with heating power). Matched discharges in current, field, and shaping demonstrate the decoupling of energy and particle transport in I-mode, increasing fueling to span nearly a factor of two in density while maintaining matched temperature pedestals with consistent levels of Pnet/n ¯e. This is consistent with targets for increased performance in I-mode, elevating pedestal βp and global performance with matched increases in density and heating power. MHD calculations using the ELITE code indicate that I-mode pedestals are strongly stable to edge peeling-ballooning instabilities. Likewise, numerical modeling of the KBM turbulence onset, as well as scalings of the pedestal width with poloidal beta, indicates that I-mode pedestals are not limited by KBM turbulence—both features identified with the trigger for large ELMs, consistent with the observed suppression of

  15. Chemotaxonomy of bacteria by comprehensive GC and GC-MS in electron impact and chemical ionisation mode.

    Science.gov (United States)

    David, Frank; Tienpont, Bart; Sandra, Pat

    2008-10-01

    The analysis of the cellular lipidic fraction of bacteria is described. After hydrolysis and methylation, the fatty acid methyl esters (FAMEs) are determined by 1-D GC using the Sherlock MIDI bacteria identification system, by comprehensive GC (GC x GC) and by GC-MS in electron impact (EI) and positive chemical ionisation (PCI) mode. With GC x GC, the enhanced selectivity and group type separation provides a more complete elucidation of the fatty acids in microorganisms. GC-EI-MS and GC-PCI-MS were helpful for confirmation. The bacteria selected in this study are Brevundimonas diminuta, Chryseobacterium gleum and Stenotrophomonas maltophilia.

  16. Direct characterization of states and modes in defect grating structures

    NARCIS (Netherlands)

    van Groesen, Embrecht W.C.; Sopaheluwakan, A.; Andonowati, A.

    2004-01-01

    For one-dimensional optical structures consisting of gratings surrounding a defect region, optical field solutions inside the bandgap are investigated that are steady states or fully transmitted modes. The observation that a mode is a suitable combination of two states, and that each state is a

  17. Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs.

    Science.gov (United States)

    Græsbøll, Kaare; Damborg, Peter; Mellerup, Anders; Herrero-Fresno, Ana; Larsen, Inge; Holm, Anders; Nielsen, Jens Peter; Christiansen, Lasse Engbo; Angen, Øystein; Ahmed, Shahana; Folkesson, Anders; Olsen, John Elmerdahl

    2017-06-15

    This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig herds were treated with oxytetracycline for Lawsonia intracellularis -induced diarrhea. Each group was randomly allocated to one of five treatment groups: oral flock treatment with a (i) high (20 mg/kg of body weight), (ii) medium (10 mg/kg), or (iii) low (5 mg/kg) dose, (iv) oral pen-wise (small-group) treatment (10 mg/kg), and (v) individual intramuscular injection treatment (10 mg/kg). All groups were treated once a day for 5 days. In all groups, treatment caused a rise in the numbers and proportions of tetracycline-resistant coliform bacteria right after treatment, followed by a significant drop by the time that the pigs left the nursery unit. The counts and proportions of tetracycline-resistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated with tiamulin did not show significant changes in the numbers or proportions of tetracycline-resistant coliforms. Selection for tetracycline-resistant coliforms was significantly correlated to selection for ampicillin- and sulfonamide-resistant strains but not to selection for cefotaxime-resistant strains. In conclusion, the difference in the dose of oxytetracycline and the way in which the drug was applied did not cause significantly different levels of selection of tetracycline-resistant coliform bacteria under the conditions tested. IMPORTANCE Antimicrobial resistance is a global threat to human health. Treatment of livestock with antimicrobials has a direct impact on this problem, and there is a need to improve the ways that we use antimicrobials in livestock

  18. Filtering of higher-order laser modes using plasma structures

    Science.gov (United States)

    Djordjevic, Blagoje; Benedetti, Carlo; Schroeder, Carl; Esarey, Eric; Leemans, Wim

    2017-10-01

    Plasma structures based on leaky channels are proposed to filter higher-order laser mode content. The evolution and propagation of non-Gaussian laser pulses in leaky channels is studied, and it is shown that, for appropriate laser-plasma parameters, the higher-order laser mode content may be removed while the fundamental mode remains well-guided. The behavior of the multi-mode laser pulse is described analytically, including the derivation of the leakage coefficients, and compared to numerical calculations. Gaussian laser pulse propagation, without higher-order mode content, improves guiding in parabolic plasma channels, enabling extended interaction lengths for laser-plasma accelerator applications. This work was supported by the Director, Office of Science, Office of High Energy Physics, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

  19. Dual-Mode Patch Filter with Metal Wall Structures

    Directory of Open Access Journals (Sweden)

    D. Kang

    2013-01-01

    Full Text Available A dual-mode patch filter with metal wall structures is presented. The proposed structure consists of substrate 1 with metal wall structures and substrate 2 with a patch resonator. Because the symmetry of the structure can be perturbed by both long and short strips of the metal wall structures, the dual mode is achieved. The inductive element is introduced to the patch resonator through vias of the metal wall structures. The capacitive element is introduced through a gap between the patch resonator and the metal strips. The measured 3 dB fractional bandwidth for the passband is 10.4%, and the measured minimum insertion loss is 1.3 dB.

  20. Structural diversity and biological significance of lipoteichoic acid in Gram-positive bacteria: focusing on beneficial probiotic lactic acid bacteria.

    Science.gov (United States)

    Shiraishi, Tsukasa; Yokota, Shinichi; Fukiya, Satoru; Yokota, Atsushi

    2016-01-01

    Bacterial cell surface molecules are at the forefront of host-bacterium interactions. Teichoic acids are observed only in Gram-positive bacteria, and they are one of the main cell surface components. Teichoic acids play important physiological roles and contribute to the bacterial interaction with their host. In particular, lipoteichoic acid (LTA) anchored to the cell membrane has attracted attention as a host immunomodulator. Chemical and biological characteristics of LTA from various bacteria have been described. However, most of the information concerns pathogenic bacteria, and information on beneficial bacteria, including probiotic lactic acid bacteria, is insufficient. LTA is structurally diverse. Strain-level structural diversity of LTA is suggested to underpin its immunomodulatory activities. Thus, the structural information on LTA in probiotics, in particular strain-associated diversity, is important for understanding its beneficial roles associated with the modulation of immune response. Continued accumulation of structural information is necessary to elucidate the detailed physiological roles and significance of LTA. In this review article, we summarize the current state of knowledge on LTA structure, in particular the structure of LTA from lactic acid bacteria. We also describe the significance of structural diversity and biological roles of LTA.

  1. The split coaxial linac structure and its RF modes

    International Nuclear Information System (INIS)

    Mueller, R.W.

    1989-01-01

    The Split Coaxial Cavity structure has been invented and applied for the first time in the heavy-ion RFQ linac MAXILAC of GSI. It has an ideally flat RF voltage distribution and a good power economy. From another standpoint, it is a member of the small family of linac structures where the two modes, the wanted one and the unflatness mode, are clearly and strictly separable. The unflatness or ''Q Line'' mode is analyzed in more detail in this paper. It is necessary for the understanding of the interaction of the beam with the cavity, possible beam instabilities resulting from it, and for curing these instabilities with the chance of obtaining improved beams. (orig.)

  2. Structural system identification based on variational mode decomposition

    Science.gov (United States)

    Bagheri, Abdollah; Ozbulut, Osman E.; Harris, Devin K.

    2018-03-01

    In this paper, a new structural identification method is proposed to identify the modal properties of engineering structures based on dynamic response decomposition using the variational mode decomposition (VMD). The VMD approach is a decomposition algorithm that has been developed as a means to overcome some of the drawbacks and limitations of the empirical mode decomposition method. The VMD-based modal identification algorithm decomposes the acceleration signal into a series of distinct modal responses and their respective center frequencies, such that when combined their cumulative modal responses reproduce the original acceleration response. The decaying amplitude of the extracted modal responses is then used to identify the modal damping ratios using a linear fitting function on modal response data. Finally, after extracting modal responses from available sensors, the mode shape vector for each of the decomposed modes in the system is identified from all obtained modal response data. To demonstrate the efficiency of the algorithm, a series of numerical, laboratory, and field case studies were evaluated. The laboratory case study utilized the vibration response of a three-story shear frame, whereas the field study leveraged the ambient vibration response of a pedestrian bridge to characterize the modal properties of the structure. The modal properties of the shear frame were computed using analytical approach for a comparison with the experimental modal frequencies. Results from these case studies demonstrated that the proposed method is efficient and accurate in identifying modal data of the structures.

  3. Coupled mode theory for resonant excitation of waveguiding structures

    NARCIS (Netherlands)

    Hoekstra, Hugo

    2000-01-01

    Resonant coupling of light beams via high-index media or gratings to planar waveguiding structures are of interest for both applications and from a theoretical point of view. Coupled Mode theory (CMT) can give an accurate description of the coupling process in terms of relatively simple expressions

  4. TE-polarized graphene modes sustained by photonic crystal structures.

    Science.gov (United States)

    Degli-Eredi, I; Sipe, J E; Vermeulen, N

    2015-05-01

    We present the design of a supporting photonic crystal structure that would allow for the excitation of the predicted transverse electric (TE) polarized excitation in a single layer of graphene. We show that it is possible to measure this excitation at room temperature, and that adding an extra layer of dielectric material on top of the structure would further facilitate the experimental observation of the graphene mode.

  5. Oviduct structure and function and reproductive modes in amphibians.

    Science.gov (United States)

    Wake, M H; Dickie, R

    The structure and function of the oviducts of members of the three Orders of the Class Amphibia (Anura, frogs and toads; Urodela, salamanders and newts; Gymnophiona, caecilians) are well described for only a few species. Further, the majority of such descriptions relate only to temperate species that breed in water, lay their eggs there, and have free-living larvae, the presumed ancestral condition of oviparity. Many species of amphibians have derived reproductive modes. Such modes include breeding terrestrially and arboreally, making foam nests, parental transport of eggs and/or tadpoles, direct development (copulating on land, laying the eggs in terrestrial sites, fully metamorphosed juveniles hatching, obviating the free-living larval stage). Other derived modes are ovoviviparity (developing embryos retained in the oviducts, born at a diversity stages of development, no maternal nutrition in addition to yolk) and viviparity (oviductal retention of developing young, maternal nutrition after yolk is resorbed, young born as fully metamorphosed juveniles). The amphibian oviduct is regionally differentiated to secrete varying numbers of layers of material around each egg, which function in fertilization, etc.; it is responsive to endocrine output and environmental mediation during the reproductive cycle; and it maintains developing embryos in some members of all three orders, some with oviductal epithelial secretion of nutrients. However, little is known of the structure-function relationships of the oviduct in species with derived reproductive modes. A comparison of oviduct morphology, function, endocrinology, ecology and phylogeny in amphibians with diverse reproductive modes suggests a number of highly productive avenues of investigation.

  6. Genotyping Oral Commensal Bacteria to Predict Social Contact and Structure.

    Directory of Open Access Journals (Sweden)

    Stephen Starko Francis

    Full Text Available Social network structure is a fundamental determinant of human health, from infectious to chronic diseases. However, quantitative and unbiased approaches to measuring social network structure are lacking. We hypothesized that genetic relatedness of oral commensal bacteria could be used to infer social contact between humans, just as genetic relatedness of pathogens can be used to determine transmission chains of pathogens. We used a traditional, questionnaire survey-based method to characterize the contact network of the School of Public Health at a large research university. We then collected saliva from a subset of individuals to analyze their oral microflora using a modified deep sequencing multilocus sequence typing (MLST procedure. We examined micro-evolutionary changes in the S. viridans group to uncover transmission patterns reflecting social network structure. We amplified seven housekeeping gene loci from the Streptococcus viridans group, a group of ubiquitous commensal bacteria, and sequenced the PCR products using next-generation sequencing. By comparing the generated S. viridans reads between pairs of individuals, we reconstructed the social network of the sampled individuals and compared it to the network derived from the questionnaire survey-based method. The genetic relatedness significantly (p-value < 0.001 correlated with social distance in the questionnaire-based network, and the reconstructed network closely matched the network derived from the questionnaire survey-based method. Oral commensal bacterial are thus likely transmitted through routine physical contact or shared environment. Their genetic relatedness can be used to represent a combination of social contact and shared physical space, therefore reconstructing networks of contact. This study provides the first step in developing a method to measure direct social contact based on commensal organism genotyping, potentially capable of unmasking hidden social networks that

  7. Deflecting modes of the side-coupled cavity structure

    International Nuclear Information System (INIS)

    Inagaki, Shigemi.

    1990-11-01

    The deflecting modes of the 805 MHz side-coupled cavity structure with the relativistic factor 0.566 are studied. Our main concern is the dispersion properties among different configurations of side-coupling cells and their interpretations. It is shown that the ninety degree side-coupling cell configuration, so to speak, the Mickey Mouse configuration has a merit in reducing the HEM 1 passband. Another concern is the magnitude of the transverse coupling impedance around the synchronization condition. It is shown that the existence of the coupling cell introduces the nonuniformity of the deflecting mode and gives different impedance relative to the beam axis and that the coupling impedance at π/10 exceeds 50 MΩ/m if the quality value of the mode is around 12000

  8. Structural mode significance using INCA. [Interactive Controls Analysis computer program

    Science.gov (United States)

    Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

    1990-01-01

    Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

  9. Effect of tetracycline dose and treatment-mode on selection of resistant coliform bacteria in nursery pigs

    DEFF Research Database (Denmark)

    Græsbøll, Kaare; Damborg, Peter; Mellerup, Anders

    2017-01-01

    , and there is a need to improve the ways that we use antimicrobial in livestock production. We hypothesized that antibiotic resistance development following treatment of diarrhea in nursery pigs could be reduced by either lowering the dose of oxytetracycline or by replacing the commonly used practice of flock......This study describes results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on selection of antibiotic resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4-7 weeks of age) were treated....../kg), and (v) individual intramuscular injection treatment (10mg/kg). All groups were treated once a day for five days. In all groups, treatment caused a rise in numbers and proportion of tetracycline resistant coliform bacteria right after treatment, followed by a significant drop by the time where pigs left...

  10. Failure modes and materials design for biomechanical layer structures

    Science.gov (United States)

    Deng, Yan

    Ceramic materials are finding increasing usage in the area of biomechanical replacements---dental crowns, hip and bone implants, etc.---where strength, wear resistance, biocompatibility, chemical durability and even aesthetics are critical issues. Aesthetic ceramic crowns have been widely used in dentistry to replace damaged or missing teeth. However, the failure rates of ceramic crowns, especially all-ceramic crowns, can be 1%˜6% per year, which is not satisfactory to patients. The materials limitations and underlying fracture mechanisms of these prostheses are not well understood. In this thesis, fundamental fracture and damage mechanisms in model dental bilayer and trilayer structures are studied. Principle failure modes are identified from in situ experimentation and confirmed by fracture mechanics analysis. In bilayer structures of ceramic/polycarbonate (representative of ceramic crown/dentin structure), three major damage sources are identified: (i) top-surface cone cracks or (ii) quasiplasticity, dominating in thick ceramic bilayers; (iii) bottom-surface radial cracks, dominating in thin ceramic bilayers. Critical load P for each damage mode are measured in six dental ceramics: Y-TZP zirconia, glass-infiltrated zirconia and alumina (InCeram), glass-ceramic (Empress II), Porcelain (Mark II and Empress) bonded to polymer substrates, as a function of ceramic thickness d in the range of 100 mum to 10 mm. P is found independent of d for mode (i) and (ii), but has a d 2 relations for mode (iii)---bottom surface radial cracking. In trilayer structures of glass/core-ceramic/polycarbonate (representing veneer porcelain/core/dentin structures), three inner fracture origins are identified: radial cracks from the bottom surface in the (i) first and (ii) second layers; and (iii) quasiplasticity in core-ceramic layer. The role of relative veneer/core thickness, d1/d 2 and materials properties is investigated for three core materials with different modulus (114--270GPa

  11. Exopolysaccharides from Marine and Marine Extremophilic Bacteria: Structures, Properties, Ecological Roles and Applications

    Directory of Open Access Journals (Sweden)

    Angela Casillo

    2018-02-01

    Full Text Available The marine environment is the largest aquatic ecosystem on Earth and it harbours microorganisms responsible for more than 50% of total biomass of prokaryotes in the world. All these microorganisms produce extracellular polymers that constitute a substantial part of the dissolved organic carbon, often in the form of exopolysaccharides (EPS. In addition, the production of these polymers is often correlated to the establishment of the biofilm growth mode, during which they are important matrix components. Their functions include adhesion and colonization of surfaces, protection of the bacterial cells and support for biochemical interactions between the bacteria and the surrounding environment. The aim of this review is to present a summary of the status of the research about the structures of exopolysaccharides from marine bacteria, including capsular, medium released and biofilm embedded polysaccharides. Moreover, ecological roles of these polymers, especially for those isolated from extreme ecological niches (deep-sea hydrothermal vents, polar regions, hypersaline ponds, etc., are reported. Finally, relationships between the structure and the function of the exopolysaccharides are discussed.

  12. RNA tertiary structure prediction with ModeRNA.

    Science.gov (United States)

    Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M

    2011-11-01

    Noncoding RNAs perform important roles in the cell. As their function is tightly connected with structure, and as experimental methods are time-consuming and expensive, the field of RNA structure prediction is developing rapidly. Here, we present a detailed study on using the ModeRNA software. The tool uses the comparative modeling approach and can be applied when a structural template is available and an alignment of reasonable quality can be performed. We guide the reader through the entire process of modeling Escherichia coli tRNA(Thr) in a conformation corresponding to the complex with an aminoacyl-tRNA synthetase (aaRS). We describe the choice of a template structure, preparation of input files, and explore three possible modeling strategies. In the end, we evaluate the resulting models using six alternative benchmarks. The ModeRNA software can be freely downloaded from http://iimcb.genesilico.pl/moderna/ under the conditions of the General Public License. It runs under LINUX, Windows and Mac OS. It is also available as a server at http://iimcb.genesilico.pl/modernaserver/. The models and the script to reproduce the study from this article are available at http://www.genesilico.pl/moderna/examples/.

  13. Antimicrobial compounds targeting Gram-negative bacteria in food: Their mode of action and combinational effects

    DEFF Research Database (Denmark)

    Hyldgaard, Morten

    2015-01-01

    they interact with bacterial cells to exert their mechanism of inhibition or killing. Furthermore, natural antimicrobials are often not potent enough as single compounds, and may cause unwanted sensory side-effects, which limit the quantities that can be applied to food. These problems might be circumvented......Gram-negative bacteria are a major cause of food spoilage and foodborne illnesses. However, finding effective solutions against Gram-negative bacteria are complicated because of increasing consumer demands for more natural, minimally processed, and fresh high quality food products without...... that isoeugenol permeabilized the cytoplasmic membrane, and probably inhibited intracellular esterases. We proposed that isoeugenol interacted with cytoplasmic membranes of E. coli in a reversible fashion, which destabilized membranes to become leaky in a non-disruptive detergent-like mechanism. In the third...

  14. Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture.

    Science.gov (United States)

    Turner, Robert D; Hurd, Alexander F; Cadby, Ashley; Hobbs, Jamie K; Foster, Simon J

    2013-01-01

    Cellular integrity and morphology of most bacteria is maintained by cell wall peptidoglycan, the target of antibiotics essential in modern healthcare. It consists of glycan strands, cross-linked by peptides, whose arrangement determines cell shape, prevents lysis due to turgor pressure and yet remains dynamic to allow insertion of new material, and hence growth. The cellular architecture and insertion pattern of peptidoglycan have remained elusive. Here we determine the peptidoglycan architecture and dynamics during growth in rod-shaped Gram-negative bacteria. Peptidoglycan is made up of circumferentially oriented bands of material interspersed with a more porous network. Super-resolution fluorescence microscopy reveals an unexpected discontinuous, patchy synthesis pattern. We present a consolidated model of growth via architecture-regulated insertion, where we propose only the more porous regions of the peptidoglycan network that are permissive for synthesis.

  15. Cold atmospheric-pressure plasma and bacteria: understanding the mode of action using vibrational microspectroscopy

    International Nuclear Information System (INIS)

    Kartaschew, Konstantin; Mischo, Meike; Bründermann, Erik; Havenith, Martina; Baldus, Sabrina; Awakowicz, Peter

    2016-01-01

    Cold atmospheric-pressure plasma show promising antimicrobial effects, however the detailed biochemical mechanism of the bacterial inactivation is still unknown. We investigated, for the first time, plasma-treated Gram-positive Bacillus subtilis and Gram-negative Escherichia coli bacteria with Raman and infrared microspectroscopy. A dielectric barrier discharge was used as a plasma source. We were able to detect several plasma-induced chemical modifications, which suggest a pronounced oxidative effect on the cell envelope, cellular proteins and nucleotides as well as a generation of organic nitrates in the treated bacteria. Vibrational microspectroscopy is used as a comprehensive and a powerful tool for the analysis of plasma interactions with whole organisms such as bacteria. Analysis of reaction kinetics of chemical modifications allow a time-dependent insight into the plasma-mediated impact. Investigating possible synergistic effects between the plasma-produced components, our observations strongly indicate that the detected plasma-mediated chemical alterations can be mainly explained by the particle effect of the generated reactive species. By changing the polarity of the applied voltage pulse, and hence the propagation mechanisms of streamers, no significant effect on the spectral results could be detected. This method allows the analysis of the individual impact of each plasma constituent for particular chemical modifications. Our approach shows great potential to contribute to a better understanding of plasma-cell interactions. (paper)

  16. Structural basis for mannose recognition by a lectin from opportunistic bacteria Burkholderia cenocepacia.

    Science.gov (United States)

    Lameignere, Emilie; Malinovská, Lenka; Sláviková, Margita; Duchaud, Eric; Mitchell, Edward P; Varrot, Annabelle; Sedo, Ondrej; Imberty, Anne; Wimmerová, Michaela

    2008-04-15

    Chronic colonization of the lungs by opportunist bacteria such as Pseudomonas aeruginosa and members of the Bcc (Burkholderia cepacia complex) is the major cause of morbidity and mortality among CF (cystic fibrosis) patients. PA-IIL (lecB gene), a soluble lectin from Ps. aeruginosa, has been the subject of much interest because of its very strong affinity for fucose. Orthologues have been identified in the opportunist bacteria Ralstonia solanacearum, Chromobacterium violaceum and Burkholderia of Bcc. The genome of the J2315 strain of B. cenocepacia, responsible for epidemia in CF centres, contains three genes that code for proteins with PA-IIL domains. The shortest gene was cloned in Escherichia coli and pure recombinant protein, BclA (B. cenocepacia lectin A), was obtained. The presence of native BclA in B. cenocepacia extracts was checked using a proteomic approach. The specificity of recombinant BclA was characterized using surface plasmon resonance showing a preference for mannosides and supported with glycan array experiments demonstrating a strict specificity for oligomannose-type N-glycan structures. The interaction thermodynamics of BclA with methyl alpha-D-mannoside demonstrates a dissociation constant (K(d)) of 2.75 x 10(-6) M. The X-ray crystal structure of the complex with methyl alpha-D-mannoside was determined at 1.7 A (1 A=0.1 nm) resolution. The lectin forms homodimers with one binding site per monomer, acting co-operatively with the second dimer site. Each monomer contains two Ca2+ ions and one sugar ligand. Despite strong sequence similarity, the differences between BclA and PA-IIL in their specificity, binding site and oligomerization mode indicate that the proteins should have different roles in the bacteria.

  17. UV-A photocatalytic treatment of Legionella pneumophila bacteria contaminated airflows through three-dimensional solid foam structured photocatalytic reactors

    Energy Technology Data Exchange (ETDEWEB)

    Josset, Sebastien; Hajiesmaili, Shabnam; Begin, Dominique; Edouard, David; Pham-Huu, Cuong [Laboratoire des Materiaux, Surfaces et Procedes pour la Catalyse (LMSPC), European Laboratory for Catalysis and Surface Sciences (ELCASS), CNRS, Strasbourg University, 25 rue Becquerel 67087 Strasbourg (France); Lett, Marie-Claire [Laboratoire de Genetique Moleculaire, Genomique, Microbiologie, CNRS, Strasbourg University, 28, rue Goethe 67083 Strasbourg Cedex (France); Keller, Nicolas, E-mail: nkeller@chimie.u-strasbg.fr [Laboratoire des Materiaux, Surfaces et Procedes pour la Catalyse (LMSPC), European Laboratory for Catalysis and Surface Sciences (ELCASS), CNRS, Strasbourg University, 25 rue Becquerel 67087 Strasbourg (France); Keller, Valerie [Laboratoire des Materiaux, Surfaces et Procedes pour la Catalyse (LMSPC), European Laboratory for Catalysis and Surface Sciences (ELCASS), CNRS, Strasbourg University, 25 rue Becquerel 67087 Strasbourg (France)

    2010-03-15

    A 3D-structured photocatalytic media was designed for allowing a tubular reactor to work in a traversing-flow mode at low pressure drops with a strong increase in the surface area-to-volume ratio inside the reactor. A protective polysiloxane coating was performed for protecting a structured polyurethane foam and anchoring the active TiO{sub 2} particles. Filled with the 3D-structured solid foam supporting TiO{sub 2} photocatalyst, the reactor could thus take advantages from the static mixer effect and from the low pressure drop resulting from the reticulated foam support. Very efficient decontamination levels towards airborne Legionella pneumophila bacteria were reached in a single-pass test mode.

  18. UV-A photocatalytic treatment of Legionella pneumophila bacteria contaminated airflows through three-dimensional solid foam structured photocatalytic reactors.

    Science.gov (United States)

    Josset, Sébastien; Hajiesmaili, Shabnam; Begin, Dominique; Edouard, David; Pham-Huu, Cuong; Lett, Marie-Claire; Keller, Nicolas; Keller, Valérie

    2010-03-15

    A 3D-structured photocatalytic media was designed for allowing a tubular reactor to work in a traversing-flow mode at low pressure drops with a strong increase in the surface area-to-volume ratio inside the reactor. A protective polysiloxane coating was performed for protecting a structured polyurethane foam and anchoring the active TiO(2) particles. Filled with the 3D-structured solid foam supporting TiO(2) photocatalyst, the reactor could thus take advantages from the static mixer effect and from the low pressure drop resulting from the reticulated foam support. Very efficient decontamination levels towards airborne Legionella pneumophila bacteria were reached in a single-pass test mode. (c) 2009 Elsevier B.V. All rights reserved.

  19. Identification of multiple modes of axisymmetric or circularly repetitive structures

    International Nuclear Information System (INIS)

    Kopff, P.

    1983-01-01

    The axisymmetric structures, or those composed with circularly repetitive elements, often display multiple modes, which are not easy to separate by modal identification of experimental responses. To be able to solve in situ some problems related to the vibrational behaviour of reactor vessels or other such huge structures, ELECTRICITY DE FRANCE developed a few years ago, experimental capabilities providing heavy harmonic driving forces, and elaborate data acquisition, signal processing and modal identification software, self-contained in an integrated mobile test facility. The modal analysis techniques we have developed with the LABORATOIRE DE MECANIQUE Appliquee of University of BESANCON (FRANCE) were especially suited for identification of multiple or separation of quasi-multiple modes, i.e. very close and strongly coupled resonances. Besides, the curve fitting methods involved, compute the same complex eigen-frequencies for all the vibration pick-ups, for better accuracy of the related eigen-vector components. Moreover, the latest extensions of these algorithms give us the means to deal with non-linear behaviour. The performances of these programs are drawn from some experimental results on axisymmetric or circularly repetitive structure, we tested in our laboratory to validate the computational hypothesis used in models for seismic responses of breeder reactor vessels. (orig.)

  20. Detecting Bacteria by Direct Counting of Structural Protein Units by IVDS and Mass Spectrometry.

    Science.gov (United States)

    Wick, Charles H; Jabbour, Rabih E; McCubbin, Patrick E; Deshpande, Samir V

    2006-01-01

    This report explores the direct counting of "hair-like" struc-tures specific for Gram-positive bacteria. Indications show that these structures are intact after removal from the cell and are sufficiently different from species to species of bacteria to give an indication of bacteria type if not actual identification. Their detection would represent a new approach to bacteria detection and identification. This report documents the detection of the bacterial structures using the physical nanometer counting methodology in the Integrated Virus Detection System (IVDS) and electrospray ionization-mass spectrometry.

  1. Structure and application of antifreeze proteins from Antarctic bacteria.

    Science.gov (United States)

    Muñoz, Patricio A; Márquez, Sebastián L; González-Nilo, Fernando D; Márquez-Miranda, Valeria; Blamey, Jenny M

    2017-08-07

    Antifreeze proteins (AFPs) production is a survival strategy of psychrophiles in ice. These proteins have potential in frozen food industry avoiding the damage in the structure of animal or vegetal foods. Moreover, there is not much information regarding the interaction of Antarctic bacterial AFPs with ice, and new determinations are needed to understand the behaviour of these proteins at the water/ice interface. Different Antarctic places were screened for antifreeze activity and microorganisms were selected for the presence of thermal hysteresis in their crude extracts. Isolates GU1.7.1, GU3.1.1, and AFP5.1 showed higher thermal hysteresis and were characterized using a polyphasic approach. Studies using cucumber and zucchini samples showed cellular protection when samples were treated with partially purified AFPs or a commercial AFP as was determined using toluidine blue O and neutral red staining. Additionally, genome analysis of these isolates revealed the presence of genes that encode for putative AFPs. Deduced amino acids sequences from GU3.1.1 (gu3A and gu3B) and AFP5.1 (afp5A) showed high similarity to reported AFPs which crystal structures are solved, allowing then generating homology models. Modelled proteins showed a triangular prism form similar to β-helix AFPs with a linear distribution of threonine residues at one side of the prism that could correspond to the putative ice binding side. The statistically best models were used to build a protein-water system. Molecular dynamics simulations were then performed to compare the antifreezing behaviour of these AFPs at the ice/water interface. Docking and molecular dynamics simulations revealed that gu3B could have the most efficient antifreezing behavior, but gu3A could have a higher affinity for ice. AFPs from Antarctic microorganisms GU1.7.1, GU3.1.1 and AFP5.1 protect cellular structures of frozen food showing a potential for frozen food industry. Modeled proteins possess a β-helix structure, and

  2. Quantification of Structural Isomers via Mode-Selective Irmpd

    Science.gov (United States)

    Polfer, Nicolas C.

    2016-06-01

    Mixtures of structural isomers can pose a challenge for vibrational ion spectroscopy. In cases where particular structures display diagnostic vibrations, these structures can be selectively "burned away". In ion traps, the ion population can be subjected to multiple laser shots, in order to fully deplete a particular structure, in effect allowing a quantification of this structure. Protonated para-amino benzoic acid (PABA) serves as an illustrative example. PABA is known to preferentially exist in the N-protonated (N-prot) form in solution, but in the gas phase it is energetically favorable in the O-protonated (O-prot) form. As shown in Figure 1, the N-prot structure can be kinetically trapped in the gas phase when sprayed from non-protic solvent, whereas the O-prot structure is obtained when sprayed from protic solvents, analogous to results by others [1,2]. y parking the light source on the diagnostic 3440 wn mode, the percentage of the O-prot structure can be determined, and by default the remainder is assumed to adopt the N-prot structure. It will be shown that the relative percentages of O-prot vs N-prot are highly dependent on the solvent mixture, going from close to 0% O-prot in non-protic solvents, to 99% in protic solvents. Surprisingly, water behaves much more like a non-protic solvent than methanol. It is observed that the capillary temperature, which aids droplet desolvation by black-body radiation in the ESI source, is critical to promote the appearance of O-prot structures. These results are consistent with the picture that a protic bridge mechanism is at play to facilitate proton transfer, and thus allow conversion from N-prot to O-prot, but that this mechanism is subject to appreciable kinetic barriers on the timescale of solvent evaporation. 1. J. Phys. Chem. A 2011, 115, 7625. 2. Anal. Chem. 2012, 84, 7857.

  3. The specificationof nano-structure superficial layers in some of the pathogen bacteria

    Directory of Open Access Journals (Sweden)

    Shilla Jalalpoor

    2010-11-01

    Full Text Available Background: The superficial layer is a part of the cellular envelop that is seen in bacteria and archaea. This superficial layer is a single layer structure composed of subordinate proteins or glycoproteins. The superficial layer is the outer most cellular structure that is in the exchange and reaction around environment with bacteria. This structure has very diversity in bacteria different types.Materials and Method: The related articles to superficial layer were extracted of these articles: Pubmed, Elsevier Science, and Yahoo, from 1995 to 2010 years. For this purpose keywords were searched including superficial layer, pathogenesis, pathogen bacteria,Results: There is consensus in the case of the superficial layer and about the existence of this superficial structure lead to increased pathogenesis in bacteria, in all of the research articles.Conclusion: S-layers in pathogen bacteria with bacteria protection against bacteriophages and phagocytosis, resistance against low pH, adhesion, stabilisation of the membrane and providing adhesion sites for exoproteins caused pathogenesis, infection resistant and antibiotic resistant in host.The result of this study shows the prevalence of considerable S-layer in pathogen bacteria and this matter identified the bacteria generator importance of this structure in the laboratory

  4. Nonlinear eigen-mode structures in complex astroclouds

    International Nuclear Information System (INIS)

    Karmakar, P K; Haloi, A

    2017-01-01

    The evolutionary dynamics of strongly nonlinear waves (of arbitrary amplitude) in an inhomogeneous complex astrophysical viscous cloud is investigated without recourse to any kind of swindle. It consists of warm lighter electrons and ions (Boltzmanian); and cold massive bi-polar dust grains (inertial fluids) alongside vigorous neutral dynamics in quasi-neural hydrodynamic equilibrium. Application of the Sagdeev pseudo-potential method transforms the analytic model into a conjugated pair of intermixed non-integrable energy integral laws. A natural excitation of electrostatic quasi-monotonic compressive dispersive shock-like eigen-modes is numerically demonstrated. In contrast, the self-gravitational waves grow purely as non-monotonic compressive oscillatory shock-like structures. The unique features of both the distinct classes are depicted. Their non-trivial significance in the astro-context is emphasized. (paper)

  5. Nonlinear eigen-mode structures in complex astroclouds

    Science.gov (United States)

    Karmakar, P. K.; Haloi, A.

    2017-05-01

    The evolutionary dynamics of strongly nonlinear waves (of arbitrary amplitude) in an inhomogeneous complex astrophysical viscous cloud is investigated without recourse to any kind of swindle. It consists of warm lighter electrons and ions (Boltzmanian); and cold massive bi-polar dust grains (inertial fluids) alongside vigorous neutral dynamics in quasi-neural hydrodynamic equilibrium. Application of the Sagdeev pseudo-potential method transforms the analytic model into a conjugated pair of intermixed non-integrable energy integral laws. A natural excitation of electrostatic quasi-monotonic compressive dispersive shock-like eigen-modes is numerically demonstrated. In contrast, the self-gravitational waves grow purely as non-monotonic compressive oscillatory shock-like structures. The unique features of both the distinct classes are depicted. Their non-trivial significance in the astro-context is emphasized.

  6. The Very Model of a Modern PI-Mode Structure

    CERN Multimedia

    Katarina Anthony

    2014-01-01

    Linac4's PI-Mode Structures (PIMS) are the first structures of their kind to accelerate protons. Now, over three years after work began on production, over 180 PIMS elements have been rough-machined and the first new PIMS cavity is being assembled at CERN.   The newly assembled PIMS cavity undergoes testing in CERN's Main Workshop. As the final accelerating structures of Linac4, located 53 m to 74 m downstream of the source, the state-of-the-art PIMS cavities will take protons from 100 to 160 MeV. While the first cavity was built entirely at CERN, construction of the remaining cavities has become a larger, multi-national operation. The newest PIMS cavity is being assembled and validated at CERN's Main Workshop. Built in collaboration with the National Centre for Nuclear Research (NCBJ, Poland) and the Jülich Research Centre (Germany), it is the first of its kind to be produced outside the Organization. Sharing all the required know...

  7. Choke-Mode Damped Structure Design for the CLIC Main Linac

    CERN Document Server

    Zha, Hao; Tang, Chuanxiang; Huang, Wenhui; Shi, Jiaru; Grudiev, Alexej; Wuensch, Walter

    2012-01-01

    Choke-mode damped structures are being studied as an alternative design for the accelerating structures of main linacs of the compact linear collider (CLIC). Choke-mode structures have the potential for much lower pulsed temperature rise, and lower cost of manufacture and fabrication. A new kind of choke-mode structure was proposed and simulated by Gdfidl. This structures has comparable wakefield damping effect as the baseline design of CLIC main linacs.

  8. Multidrug transporters from bacteria to man : similarities in structure and function

    NARCIS (Netherlands)

    van Veen, HW; Konings, WN

    Organisms ranging from bacteria to man possess transmembrane transporters which confer resistance to toxic corn pounds. Underlining their biological significance, prokaryotic and eukaryotic multidrug transport proteins are very similar in structure and function. Therefore, a study of the factors

  9. MEMS Reliability: Infrastructure, Test Structures, Experiments, and Failure Modes

    Energy Technology Data Exchange (ETDEWEB)

    TANNER,DANELLE M.; SMITH,NORMAN F.; IRWIN,LLOYD W.; EATON,WILLIAM P.; HELGESEN,KAREN SUE; CLEMENT,J. JOSEPH; MILLER,WILLIAM M.; MILLER,SAMUEL L.; DUGGER,MICHAEL T.; WALRAVEN,JEREMY A.; PETERSON,KENNETH A.

    2000-01-01

    The burgeoning new technology of Micro-Electro-Mechanical Systems (MEMS) shows great promise in the weapons arena. We can now conceive of micro-gyros, micro-surety systems, and micro-navigators that are extremely small and inexpensive. Do we want to use this new technology in critical applications such as nuclear weapons? This question drove us to understand the reliability and failure mechanisms of silicon surface-micromachined MEMS. Development of a testing infrastructure was a crucial step to perform reliability experiments on MEMS devices and will be reported here. In addition, reliability test structures have been designed and characterized. Many experiments were performed to investigate failure modes and specifically those in different environments (humidity, temperature, shock, vibration, and storage). A predictive reliability model for wear of rubbing surfaces in microengines was developed. The root causes of failure for operating and non-operating MEMS are discussed. The major failure mechanism for operating MEMS was wear of the polysilicon rubbing surfaces. Reliability design rules for future MEMS devices are established.

  10. Design of a choke-mode damped accelerating structure for CLIC Main LINAC

    CERN Document Server

    Shi, J; Grudiev, A; Wuensch, W; Tang, C; Chen, H; Huang, W

    2011-01-01

    Choke-mode damped accelerating structures are being studied as an alternative to the baseline structure of the compact linear collider (CLIC) by a CERN-Tsinghua collaboration. Choke-mode structures hold the potential for much lower levels of pulsed surface heating and, since milling is not needed, reduced cost. Structures with radial choke attached are simulated in GdfidL to investigate the damping of the transverse wake. The first pass-band of the dipole modes is well damped, while the higher order dipole modes are possibly reflected by the choke. Therefore, the geometry of the choke is tuned to minimize the reflection of these higher order dipole modes. Based on this damping scheme, an accelerating structure with the same iris dimensions as the nominal CLIC design but with choke-mode damping has been designed. A prototype structure will be manufactured and high power tested in the near future.

  11. On Kinetic Slow Modes, Fluid Slow Modes, and Pressure-balanced Structures in the Solar Wind

    International Nuclear Information System (INIS)

    Verscharen, Daniel; Chen, Christopher H. K.; Wicks, Robert T.

    2017-01-01

    Observations in the solar wind suggest that the compressive component of inertial-range solar-wind turbulence is dominated by slow modes. The low collisionality of the solar wind allows for nonthermal features to survive, which suggests the requirement of a kinetic plasma description. The least-damped kinetic slow mode is associated with the ion-acoustic (IA) wave and a nonpropagating (NP) mode. We derive analytical expressions for the IA-wave dispersion relation in an anisotropic plasma in the framework of gyrokinetics and then compare them to fully kinetic numerical calculations, results from two-fluid theory, and magnetohydrodynamics (MHD). This comparison shows major discrepancies in the predicted wave phase speeds from MHD and kinetic theory at moderate to high β . MHD and kinetic theory also dictate that all plasma normal modes exhibit a unique signature in terms of their polarization. We quantify the relative amplitude of fluctuations in the three lowest particle velocity moments associated with IA and NP modes in the gyrokinetic limit and compare these predictions with MHD results and in situ observations of the solar-wind turbulence. The agreement between the observations of the wave polarization and our MHD predictions is better than the kinetic predictions, which suggests that the plasma behaves more like a fluid in the solar wind than expected.

  12. Competition between modes with different axial structures in gyrotrons

    International Nuclear Information System (INIS)

    Khutoryan, Eduard M.; Nusinovich, Gregory S.; Sinitsyn, Oleksandr V.

    2014-01-01

    This study was motivated by some experiments in which it was found that during the voltage rise, instead of expected excitation of a high-frequency parasitic mode, the excitation of a lower-frequency parasitic mode takes place in a certain range of voltages. For explaining this fact, the dependence of start currents of possible competing modes on the beam voltage was carried out in the cold-cavity approximation and by using the self-consistent approach. It was found that in the case of cavities, which consist of the combination of a section of constant radius waveguide and a slightly uptapered waveguide, these two approaches yield completely different results. Thus, experimentally observed excitation of the low-frequency parasitic mode can be explained by the self-consistent modification of the axial profile of the excited field, which has strong influence on the diffractive quality factor of competing modes. This modification is especially pronounced in the case of excitation of modes with many axial variations which can be excited in the region of beam interaction with the backward-wave component of such modes

  13. Effect of boundary conditions on radial mode structure of whistlers

    International Nuclear Information System (INIS)

    Boswell, R.W.

    1983-01-01

    The dispersion of the radical eigen modes of a cylindrical m=1 whistler wave with Ωsub(i) << ω << Ωsub(e) << ωsub(pe) are investigated for both conducting and insulating boundaries, where Ωsub(e) and Ωsub(i) are the electron and ion gyro frequencies, Ωsub(pe) is the electron plasma frequency. The effects of electron inertia and resistivity on the modes are discussed

  14. Higher‐order mode absorption measurement of X-band choke-mode cavities in a radial line structure

    Energy Technology Data Exchange (ETDEWEB)

    Zha, Hao [Department of Engineering Physics, Tsinghua University, Beijing CN-100086 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing (China); The European Organization for Nuclear Research, Geneva CH-1211 (Switzerland); Shi, Jiaru, E-mail: shij@mail.tsinghua.edu.cn [Department of Engineering Physics, Tsinghua University, Beijing CN-100086 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing (China); The European Organization for Nuclear Research, Geneva CH-1211 (Switzerland); Wu, Xiaowei; Chen, Huaibi [Department of Engineering Physics, Tsinghua University, Beijing CN-100086 (China); Key Laboratory of Particle and Radiation Imaging, Tsinghua University, Ministry of Education, Beijing (China)

    2016-04-01

    An experiment is presented to study the higher-order mode (HOM) suppression of X-band choke-mode structures with a vector network analyzer (VNA). Specific radial line disks were built to test the reflection from the corresponding damping load and different choke geometries. The mismatch between the radial lines and the VNA was calibrated through a special multi-short-load calibration method. The measured reflections of different choke geometries showed good agreement with the theoretical calculations and verified the HOM absorption feature of each geometric design.

  15. Higher-order mode absorption measurement of X-band choke-mode cavities in a radial line structure

    Science.gov (United States)

    Zha, Hao; Shi, Jiaru; Wu, Xiaowei; Chen, Huaibi

    2016-04-01

    An experiment is presented to study the higher-order mode (HOM) suppression of X-band choke-mode structures with a vector network analyzer (VNA). Specific radial line disks were built to test the reflection from the corresponding damping load and different choke geometries. The mismatch between the radial lines and the VNA was calibrated through a special multi-short-load calibration method. The measured reflections of different choke geometries showed good agreement with the theoretical calculations and verified the HOM absorption feature of each geometric design.

  16. Molecular Structure of Endotoxins from Gram-negative Marine Bacteria: An Update

    Directory of Open Access Journals (Sweden)

    Antonio Molinaro

    2007-09-01

    Full Text Available Marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. The main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. Nonetheless, lipopolysaccharides (LPSs, or their portions, from Gram-negative marine bacteria, have often shown low virulence, and represent potential candidates in the development of drugs to prevent septic shock. Besides, the molecular architecture of such molecules is related to the possibility of thriving in marine habitats, shielding the cell from the disrupting action of natural stress factors. Over the last few years, the depiction of a variety of structures of lipids A, core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been given. In particular, here we will examine the most recently encountered structures for bacteria belonging to the genera Shewanella, Pseudoalteromonas and Alteromonas, of the γ-Proteobacteria phylum, and to the genera Flavobacterium, Cellulophaga, Arenibacter and Chryseobacterium, of the Cytophaga- Flavobacterium-Bacteroides phylum. Particular attention will be paid to the chemical features expressed by these structures (characteristic monosaccharides, non-glycidic appendages, phosphate groups, to the typifying traits of LPSs from marine bacteria and to the possible correlation existing between such features and the adaptation, over years, of bacteria to marine environments.

  17. Molecular structure of endotoxins from Gram-negative marine bacteria: an update.

    Science.gov (United States)

    Leone, Serena; Silipo, Alba; L Nazarenko, Evgeny; Lanzetta, Rosa; Parrilli, Michelangelo; Molinaro, Antonio

    2007-09-19

    Marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. The main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. Nonetheless, lipopolysaccharides (LPSs), or their portions, from Gram-negative marine bacteria, have often shown low virulence, and represent potential candidates in the development of drugs to prevent septic shock. Besides, the molecular architecture of such molecules is related to the possibility of thriving in marine habitats, shielding the cell from the disrupting action of natural stress factors. Over the last few years, the depiction of a variety of structures of lipids A, core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been given. In particular, here we will examine the most recently encountered structures for bacteria belonging to the genera Shewanella, Pseudoalteromonas and Alteromonas, of the gamma-Proteobacteria phylum, and to the genera Flavobacterium, Cellulophaga, Arenibacter and Chryseobacterium, of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention will be paid to the chemical features expressed by these structures (characteristic monosaccharides, non-glycidic appendages, phosphate groups), to the typifying traits of LPSs from marine bacteria and to the possible correlation existing between such features and the adaptation, over years, of bacteria to marine environments.

  18. Global structure of mirror modes in the magnetosheath

    International Nuclear Information System (INIS)

    Johnson, J.R.; Cheng, C.Z.

    1996-01-01

    A global stability analysis of mirror modes in the magnetosheath is presented. The analysis is based upon the kinetic-MHD formulation which includes relevant kinetic effects such as Landau resonance and gradient drift effects related to inhomogeneities in the background density, temperature, pressure and its anisotropy, magnetic field, and plasma flow velocity. Pressure anisotropy provides the free energy for the global mirror mode. The local theory of mirror modes predicts purely growing modes confined in the unstable magnetosheath region; however, the nonlocal theory that includes the effects of gradients and plasma flow predicts modes with real frequencies which propagate with the flow from the magnetosheath toward the magnetopause boundary. The real frequency is on the order of a combination of the diamagnetic drift frequency and the Doppler shift frequency associated with plasma flow. The diamagnetic drift frequency provides a wave phase velocity in the direction of the magnetopause so that wave energy accumulates against the magnetopause boundary, and the amplitude is skewed in that direction. On the other hand, plasma flow also gives rise to a real phase velocity, but the phase velocity is smaller than the flow velocity. As a result, the wave amplitude is increased in the wake of the plasma flow and piles up against the bow shock boundary

  19. Spatial mode structures of electrostatic drift waves in a collisional cylindrical helicon plasma

    DEFF Research Database (Denmark)

    Schröder, C.; Grulke, O.; Klinger, T.

    2004-01-01

    In a cylindrical helicon plasma, mode structures of coherent drift waves are studied in the poloidal plane, the plane perpendicular to the ambient magnetic field. The mode structures rotate with a constant angular velocity in the direction of the electron diamagnetic drift and show significant...

  20. An Innovative Structural Mode Selection Methodology: Application for the X-33 Launch Vehicle Finite Element Model

    Science.gov (United States)

    Hidalgo, Homero, Jr.

    2000-01-01

    An innovative methodology for determining structural target mode selection and mode selection based on a specific criterion is presented. An effective approach to single out modes which interact with specific locations on a structure has been developed for the X-33 Launch Vehicle Finite Element Model (FEM). We presented Root-Sum-Square (RSS) displacement method computes resultant modal displacement for each mode at selected degrees of freedom (DOF) and sorts to locate modes with highest values. This method was used to determine modes, which most influenced specific locations/points on the X-33 flight vehicle such as avionics control components, aero-surface control actuators, propellant valve and engine points for use in flight control stability analysis and for flight POGO stability analysis. Additionally, the modal RSS method allows for primary or global target vehicle modes to also be identified in an accurate and efficient manner.

  1. Mode structure analysis of a Bessel-Gauss resonator

    CSIR Research Space (South Africa)

    Litvin, IA

    2006-08-01

    Full Text Available each other (F – focal length of mirrors). The core zone of mirror L1 is blinded by diaphragm with radius R1. As a whole this scheme is similar to scheme of resonator which was investigated by work [23]. Figure 1: Illustration... (circle with gauss field distribution of cross section) for all mode numbers23, then increasing or decreasing of diaphragm R1 or mirror L1 itself, we can expect an increasing or decreasing losses for each modes simultaneous only. We have another...

  2. Failure mode maps of a hierarchical sandwich structure made of self-reinforced PET

    Science.gov (United States)

    Velea, Marian N.; Lache, Simona

    2018-02-01

    In previous published works, poly-ethylene terephthalate fiber reinforced poly-ethylene terephthalate (SrPET) combined with poly-ethylene terephthalate foam material have been used to develop novel core topologies for sandwich structures. In this study, failure mode maps are created for a hierarchical sandwich structure made of the SrPET material and PET foam, based on analytical estimates, under quasi-static out of plane compression loading conditions. It is shown that four dominant collapse modes may occur: local buckling, general buckling, shear buckling and core shear failure. Each failure mode has an associated weight that varies with the structure load carrying capacity. Based on the developed failure mode maps, the geometric parameters of the structure under study can be chosen such as the structure has the minimum possible weight by ensuring that the failure modes occur simultaneously. The analytical results are compared with experimental tests previously published.

  3. Observation of Protein Structural Vibrational Mode Sensitivity to Ligand Binding

    Science.gov (United States)

    Niessen, Katherine; Xu, Mengyang; Snell, Edward; Markelz, Andrea

    2014-03-01

    We report the first measurements of the dependence of large-scale protein intramolecular vibrational modes on ligand binding. These collective vibrational modes in the terahertz (THz) frequency range (5-100 cm-1) are of great interest due to their predicted relation to protein function. Our technique, Crystals Anisotropy Terahertz Microscopy (CATM), allows for room temperature, table-top measurements of the optically active intramolecular modes. CATM measurements have revealed surprisingly narrowband features. CATM measurements are performed on single crystals of chicken egg-white lysozyme (CEWL) as well as CEWL bound to tri-N-acetylglucosamine (CEWL-3NAG) inhibitor. We find narrow band resonances that dramatically shift with binding. Quasiharmonic calculations are performed on CEWL and CEWL-3NAG proteins with CHARMM using normal mode analysis. The expected CATM response of the crystals is then calculated by summing over all protein orientations within the unit cell. We will compare the CATM measurements with the calculated results and discuss the changes which arise with protein-ligand binding. This work is supported by NSF grant MRI 2 grant DBI2959989.

  4. On the Theory of Coupled Modes in Optical Cavity-Waveguide Structures

    DEFF Research Database (Denmark)

    Kristensen, Philip Trøst; de Lasson, Jakob Rosenkrantz; Heuck, Mikkel

    2017-01-01

    Light propagation in systems of optical cavities coupled to waveguides can be conveniently described by a general rate equation model known as (temporal) coupled mode theory (CMT). We present an alternative derivation of the CMT for optical cavitywaveguide structures, which explicitly relies...... on the treatment of the cavity modes as quasi-normal modes with properties that are distinctly different from those of the modes in the waveguides. The two families of modes are coupled via the field equivalence principle to provide a physically appealing yet surprisingly accurate description of light propagation...... in the coupled systems. Practical application of the theory is illustrated using example calculations in one and two dimensions....

  5. Isolation, structural elucidation and in vitro activity of 2-acetyl-2-decarboxamido-oxytetracycline against environmental relevant bacteria, including tetracycline-resistant bacteria

    DEFF Research Database (Denmark)

    Lykkeberg, Anne Kruse; Sengeløv, Gitte; Cornett, Claus

    2004-01-01

    i.d., 5 microm), and the mobile phase contained methanol-water (27:73 (v/v)) with 0.08 M formic acid added. The flow rate was 9.0 ml/min. It was possible to isolate few milligram ADOTC in a day. The compound was unambiguously identified using NMR and MS-MS. The anti-microbial activity against...... activated sludge bacteria was determined giving a potency of only 3% of that of OTC. With tetracycline-resistant bacteria, no anti-microbial activity was observed, indicating a mode of action similar to that of OTC....

  6. Design, fabrication and high-gradient tests of X-band choke-mode structures

    OpenAIRE

    Wu, Xiaowei; Shi, Jiaru; Chen, Huaibi; Zha, Hao; Abe, Tetsuo; Higo, Toshiyasu; Matsumoto, Shuji

    2017-01-01

    Two standing-wave single-cell choke-mode damped structures with different choke dimensions which worked at 11.424 GHz were designed, manufactured and tuned by accelerator group in Tsinghua University. High power test was carried out to study choke-mode structure's properties in high gradient and related breakdown phenomenon. A single-cell structure without choke which almost has the same inner dimension as choke-mode structure was also tested as a comparison to study how the choke affects hig...

  7. Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria

    KAUST Repository

    Ross, Avena C.

    2013-01-23

    Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus. © 2012 American Chemical Society.

  8. Sensitivity analysis of the stiffness between the frame structure and the frequency and vibration mode

    Science.gov (United States)

    Chen, Wenyuan

    2018-03-01

    The modal parameters such as natural frequency and vibration mode of the frame structure of the layer stiffness sensitivity is inconsistent. This article focuses on the theoretical derivation of the frequency and mode of the frame structure layer stiffness of the first-order sensitivity. The numerical examples show that the frame structure of layer stiffness higher than with the first order sensitivity vibration frequency.

  9. True photonic band-gap mode-control in VCSEL structures

    DEFF Research Database (Denmark)

    Romstad, F.; Madsen, M.; Birkedal, Dan

    2003-01-01

    Photonic band-gap mode confinement in novel nano-structured large area VCSEL structures is confirmed by the amplified spontaneous emission spectrum. Both guide and anti-guide VCSEL structures are experimentally characterised to verify the photonic band-gap effect.......Photonic band-gap mode confinement in novel nano-structured large area VCSEL structures is confirmed by the amplified spontaneous emission spectrum. Both guide and anti-guide VCSEL structures are experimentally characterised to verify the photonic band-gap effect....

  10. Simple countermeasures against the TM110-beam-blowup-mode in biperiodic structures

    International Nuclear Information System (INIS)

    Euteneuer, H.; Herminghaus, H.; Schoeler, H.

    1984-01-01

    The two fundamental methods of fighting beam blow-up in rf-accelerating-structures are staggered detuning and selective Q-spoiling of their higher order modes. Biperiodic structures offer a very simple way of applying the latter technique of the most dangerous TM 110 -like blowup mode at 1.7 times the accelerating frequency: letting this mode propagate but giving a large gap to the TM 110 -passband. This gap must be positive for electric coupling (f(phi=0) =1.7c. With asymmetric coupling elements between the cavities of a structure, one has a simple tool for staggered detuning: a change of the relative orientation of these elements spreads the resonance frequencies not only of the TM 110 -mode, but of at least all dipole modes. (orig.)

  11. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Stienstra, A.W.; Heilig, G.H.J.; Stephen, J.R.; Woldendorp, J.W.

    2000-01-01

    The community structure of beta-subclass Proteobacteria ammonia-oxidizing bacteria was determined in semi-natural chalk grassland soils at different stages of secondary succession. Both culture-mediated (most probable number; MPN) and direct nucleic acid-based approaches targeting genes encoding 16S

  12. Structure, diversity and evolution of protein toxins from spore-forming entomopathogenic bacteria

    NARCIS (Netherlands)

    Maagd, de R.A.; Bravo, A.; Berry, C.; Crickmore, N.; Schnepf, H.E.

    2003-01-01

    Gram-positive spore-forming entomopathogenic bacteria can utilize a large variety of protein toxins to help them invade, infect, and finally kill their hosts, through their action on the insect midgut. These toxins belong to a number of homology groups containing a diversity of protein structures

  13. Measurement of fluid dynamic loading on staphylococci bacteria bio-film structures using μPIV

    Science.gov (United States)

    Sherman, Erica; Moormeier, Derek; Bayles, Kenneth; Davidson, John; Ryu, Sangjin; Wei, Timothy

    2013-11-01

    Staphylococci bacteria are recognized as the most frequent cause of biofilm-associated infections. Although humans are regularly exposed to these bacteria without consequence, a localized infection can enter the bloodstream and lead to serious infections such as endocarditis, pneumonia, or toxic shock syndrome. The mechanics of staphylococci biofilm formation and dispersion through the bloodstream are not well known. It has recently been observed that under certain flow conditions, bacteria organize in tower-like structures which break and are transported downstream by the flow. The fundamental questions of interest are i) whether or not fluid mechanics plays a role in differentiating between film or tower formation and ii) whether or not the faulty towers are a bio-film propagation mechanism. This talk focuses on the application of μPIV to study this problem. Staphylococcus aureus bacteria were cultured in the Bioflux Fluxion square microchannel of a 65 by 65 um cross section, and subjected to a steady shear rate of 0.5 dynes. μPIV measurements were made to map the flow over and around a biofilm tower structure which occluded approximately 66% of the channel width. Data were recorded around the structure at a series of two dimensional planes, which when stacked vertically show a two dimensional flow field as a function of tower height. Measurements and control volume analysis will be presented quantifying forces acting on these structures.

  14. Canonical structure and extra mode of generalized unimodular gravity

    Science.gov (United States)

    Bufalo, Rodrigo; Oksanen, Markku

    2018-02-01

    We consider a recently proposed generalization of unimodular gravity, where the lapse function is constrained to be equal to a function of the determinant of the spatial metric f (h ), as a potential origin of a dark fluid with a generally h -dependent equation of state parameter. We establish the Hamiltonian analysis and the canonical path integral for the theory. All the special cases that do not match unimodular gravity involve the violation of general covariance, and consequently the physical content of the theory is changed significantly. Particularly, the case of a constant function f is shown to contain an extra physical degree of freedom in each point of space. Physical consequences of the extra degree of freedom are studied in a linearized theory, where the extra mode is carried by the trace of the metric perturbation. The trace mode does not propagate as a wave, since it satisfies an elliptic partial differential equation in spacetime. Consequently, the trace perturbation is shown to grow exponentially with time, which implies instability. The case of a general f (h ) involves additional second-class constraints, which implies the presence of an extra global degree of freedom that depends only on time (instead of the extra local degree of freedom in the case of a constant f ).

  15. Transverse kick in misaligned traveling wave structures driven at the fundamental mode

    International Nuclear Information System (INIS)

    Whittum, D.H.

    1998-04-01

    Fabrication errors in traveling wave structures result in non-axisymmetric RF fields that couple to the rf drive at the fundamental mode frequency. The authors calculate the excitation of the dipole mode and the integrated effect on the beam, using the thin iris and small hole approximation

  16. The Structural Diversity of Carbohydrate Antigens of Selected Gram-Negative Marine Bacteria

    Directory of Open Access Journals (Sweden)

    Elena P. Ivanova

    2011-10-01

    Full Text Available Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens found in cell walls of Gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.

  17. The structural diversity of carbohydrate antigens of selected gram-negative marine bacteria.

    Science.gov (United States)

    Nazarenko, Evgeny L; Crawford, Russell J; Ivanova, Elena P

    2011-01-01

    Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.

  18. Biological and structure-activity evaluation of chalcone derivatives against bacteria and fungi

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Wender A.; Andrade, Carlos Kleber Z.; Napolitano, Hamilton B., E-mail: wender@unb.br, E-mail: ckleber@unb.br [Universidade de Brasilia (LaQMOS/UnB), DF (Brazil). Inst. de Quimica; Vencato, Ivo; Castro, Miriam R.C. de; Camargo, Ademir J. [Universidade Estadual de Goias (UEG), Anapolis, GO (Brazil). Ciencias Exatas e Tecnologicas; Lariucci, Carlito [Universidade Estadual de Goias (UEG), Goiania, GO (Brazil). Inst. de Fisica

    2013-01-15

    The present work describes the antibacterial and antifungal activities of several chalcones obtained by a straight Claisen-Schmidt aldol condensation determined by the minimal inhibitory concentration against different microorganisms (Gram-positive and Gram-negative bacteria and fungi). Solid state crystal structures of seven chalcones were determined by X-ray diffraction (XRD) analysis. Chemometric studies were carried out in order to identify a potential structure activity relationship. (author)

  19. Biological and structure-activity evaluation of chalcone derivatives against bacteria and fungi

    OpenAIRE

    Silva, Wender A.; Andrade, Carlos Kleber Z.; Napolitano, Hamilton B.; Vencato, Ivo; Lariucci, Carlito; Castro, Miriam. R. C. de; Camargo, Ademir J.

    2013-01-01

    The present work describes the antibacterial and antifungal activities of several chalcones obtained by a straight Claisen-Schmidt aldol condensation determined by the minimal inhibitory concentration against different microorganisms (Gram-positive and Gram-negative bacteria and fungi). Solid state crystal structures of seven chalcones were determined by X-ray diffraction (XRD) analysis. Chemometric studies were carried out in order to identify a potential structure-activity relationship. ...

  20. Structural Damage Localization by Outlier Analysis of Signal-processed Mode Shapes

    DEFF Research Database (Denmark)

    Ulriksen, Martin Dalgaard; Damkilde, Lars

    2016-01-01

    Contrary to global modal parameters such as eigenfrequencies, mode shapes inherently provide structural information on a local level. Therefore, this particular modal parameter and its derivatives are utilized extensively for damage identification. Typically, more or less advanced mathematical...

  1. Reduction of Flight Control System/Structural Mode Interaction, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — A novel approach is proposed for reducing the degree of interaction of a high gain flight control system with the airframe structural vibration modes, representing a...

  2. Inverse boundary element calculations based on structural modes

    DEFF Research Database (Denmark)

    Juhl, Peter Møller

    2007-01-01

    The inverse problem of calculating the flexural velocity of a radiating structure of a general shape from measurements in the field is often solved by combining a Boundary Element Method with the Singular Value Decomposition and a regularization technique. In their standard form these methods solve...... for the unknown normal velocities of the structure at the relatively large number of nodes in the numerical model. Efficiently the regularization technique smoothes the solution spatially, since a fast spatial variation is associated with high index singular values, which is filtered out or damped...... in the regularization. Hence, the effective number of degrees of freedom in the model is often much lower than the number of nodes in the model. The present paper deals with an alternative formulation possible for the subset of radiation problems in which a (structural) modal expansion is known for the structure...

  3. Metacommunity structuring in stream networks: roles of dispersal mode, distance type, and regional environmental context

    OpenAIRE

    Gronroos, Mira; Heino, Jani; Siqueira, Tadeu [UNESP; Landeiro, Victor L.; Kotanen, Juho; Bini, Luis M.

    2013-01-01

    Within a metacommunity, both environmental and spatial processes regulate variation in local community structure. The strength of these processes may vary depending on species traits (e.g., dispersal mode) or the characteristics of the regions studied (e.g., spatial extent, environmental heterogeneity). We studied the metacommunity structuring of three groups of stream macroinvertebrates differing in their overland dispersal mode (passive dispersers with aquatic adults; passive dispersers wit...

  4. Investigating the Effectiveness of Centaureacyanus Extracts on Planktonic Growth and Biofilm Structures of Six Pathogenic Bacteria

    Directory of Open Access Journals (Sweden)

    Z Mohsenipour

    2014-10-01

    Full Text Available Introduction: Nowadays, the treatments of infectious disease are regarded difficult due to increasing antibiotic resistance among pathogenic bacteria, which the reason may be placing of microorganisms in a structure named biofilm. Biofilms are complex structures consisting of surface-attached bacteria. Therefore, it is essential to find new compounds in order to remove and inhibit biofilms. This study aimed to examine the antibacterial activities of alcoholic extracts of Centaurea cyanus on the biofilm structures and planktonic form of six pathogen bacteria(Staphylococcusaureus, Bacilluscereus, Streptococcuspneumoniae, Pseudomonasaeruginosa, Escherichiacoli and Klebsiellapneumonia. Methods: Antimicrobial activities of the alcoholic plant extracts against the planktonic form of bacteria were assessed via using the disc diffusion method. MIC and MBC values were determined by a macrobroth dilution technique and anti-biofilm effects were scrutinized by microtiter plate method. Results: The results of this study confirmed high ability of C.cyanus extracts against the biofilm of the tested bacteria as well as their free-living forms. To inhibit bacterial growth, ethanolic extracts proved to be more effective than methanolic extracts. Anti-biofilm effects of plant extracts were associated with the solvent type and extract concentration. C.cyanus extracts were reported to be most efficient to inhibit biofilm formation of E. coli (84/26% and S. pneumoniae(83/14%. The greatest eradication of biofilm structures were observed on S. pneumonia biofilm (75.66%, and the highest decrease in metabolic activity was reported in S.aureus biofilms (71/85%. Conclusion: In this study the high capacity of C. cyanus extracts to encounter with whit biofilm was emphasized. Moreover, it was demonstrated that these extracts possess an appropriate potential to become active principles of new drugs.

  5. Soft x-ray measurement of internal tearing mode structure in a reversed-field pinch

    International Nuclear Information System (INIS)

    Chartas, G.; Hokin, S.

    1991-01-01

    The structure of internally resonant tearing modes has been studied in the Madison Symmetric Torus reversed-field pinch with a soft x-ray detector system consisting of an imaging array at one toroidal location and several detectors at different toroidal locations. The toroidal mode numbers of m = 1 structures are in the range n = -5, -6, -7. The modes propagate with phase velocity v = 1--6 x 10 6 cm/s, larger than the diamagnetic drift velocity v d ∼ 5 x 10 5 cm/s. Phase locking between modes with different n in manifested as a beating of soft x-ray signals which is found to be strongest near the resonant surfaces of the modes (r/a = 0.1 -- 0.5). 15 refs., 5 figs

  6. Topology optimization of continuum structure with dynamic constraints using mode identification

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jianhongyu; Chen, Shenyan; Huang, Hai [Beihang University, Beijing (China)

    2015-04-15

    For the problems such as mode exchange and localized modes in topology optimization of continuum structure with dynamic constraints, it is difficult to apply the traditional optimization model which considers fixed order mode frequencies as constraints in optimization calculation. A new optimization model is established, in which the dynamical constraints are changed as frequencies of structural principal vibrations. The order of the principal vibrations is recognized through modal identification in the optimization process, and the constraints are updated to make the optimization calculation execute smoothly. Localized mode elimination techniques are introduced to reduce the localized modes induced by the low density elements, which could improve the optimization efficiency. A new optimization process is designed, which achieves the purpose of overcoming mode exchange problem and localized mode problem at the cost of increasing several structural analyses. Optimization system is developed by using Nastran to perform structural analysis and sensitivity analysis and two-level multipoint approximation algorithm as optimizer. Numerical results verified that the presented method is effective and reasonable.

  7. Zero-mode waveguide nanophotonic structures for single molecule characterization

    Science.gov (United States)

    Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.

    2018-05-01

    Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (µM–mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer, and fluorescence correlation spectroscopy for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs. In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.

  8. Inverse boundary element calculations based on structural modes

    DEFF Research Database (Denmark)

    Juhl, Peter Møller

    2007-01-01

    The inverse problem of calculating the flexural velocity of a radiating structure of a general shape from measurements in the field is often solved by combining a Boundary Element Method with the Singular Value Decomposition and a regularization technique. In their standard form these methods sol...

  9. Complex modes and frequencies in damped structural vibrations

    DEFF Research Database (Denmark)

    Krenk, Steen

    2004-01-01

    It is demonstrated that the state space formulation of the equation of motion of damped structural elements like cables and beams leads to a symmetric eigenvalue problem if the stiffness and damping operators are self-adjoint, and that this is typically the case in the absence of gyroscopic forces...

  10. Choke-mode damped structure design for the Compact Linear Collider main linac

    Directory of Open Access Journals (Sweden)

    Hao Zha

    2012-12-01

    Full Text Available Choke-mode damped structures are being studied as an alternative design to waveguide damped structures for the main linac of the Compact Linear Collider (CLIC. Choke-mode structures have the potential for lower pulsed temperature rise and simpler and less expensive fabrication. An equivalent circuit model based on transmission line theory for higher-order-mode damping is presented. Using this model, a new choke geometry is proposed and the wakefield performance is verified using Gdfidl. This structure has a comparable wakefield damping effect to the baseline design which uses waveguide damping. A prototype structure with the same iris dimensions and accelerating gradient as the nominal CLIC design, but with the new choke geometry, has been designed for high-power tests.

  11. Choke-mode damped structure design for the Compact Linear Collider main linac

    CERN Document Server

    Zha, Hao; Grudiev, Alexej; Huang, Wenhui; Shi, Jiaru; Tang, Chuanxiang; Wuensch, Walter

    2012-01-01

    Choke-mode damped structures are being studied as an alternative design to waveguide damped structures for the main linac of the Compact Linear Collider (CLIC). Choke-mode structures have the potential for lower pulsed temperature rise and simpler and less expensive fabrication. An equivalent circuit model based on transmission line theory for higher-order-mode damping is presented. Using this model, a new choke geometry is proposed and the wakefield performance is verified using GDFIDL. This structure has a comparable wakefield damping effect to the baseline design which uses waveguide damping. A prototype structure with the same iris dimensions and accelerating gradient as the nominal CLIC design, but with the new choke geometry, has been designed for high-power tests. DOI: 10.1103/PhysRevSTAB.15.122003

  12. Higher order mode damping for a detuned structure

    International Nuclear Information System (INIS)

    Kroll, N.; Gluckstern, R.

    1994-08-01

    We report in this paper the current status of our investigation of the possibility of suppressing the wake reappearance by providing relatively weak damping via the vacuum manifolds. The four vacuum manifolds running the length of the structure also function as multimode waveguides which serve to drain power from the HOM's through the large coupling slots located in each cell, except, as discussed later, for a few at each end of the manifolds

  13. Genetics, Biosynthesis, Structure, and Mode of Action of Lantibiotics

    Science.gov (United States)

    Kuipers, Anneke; Rink, Rick; Moll, Gert N.

    Lantibiotics are lanthionine-containing peptide antibiotics. They are characterized by having meso-lanthionine(s) and/or β-methyllanthionine(s) or both. These intramolecular monosulfide cross-links render the peptide resistant against breakdown by peptidases. Moreover, in several cases, the (methyl)lanthionines are essential for interaction with the so-called docking molecule lipid II. The best known lantibiotic, nisin, highly effectively inhibits growth of target cells via two mechanisms: (1) abduction of the cell wall precursor lipid II from the septum and (2) formation of pores composed of lipid II and nisin. (Methyl)lanthionines result from two enzyme-catalyzed posttranslational modifications: dehydration of serines/threonines and coupling of the resulting dehydro amino acids to cysteines. Besides the localization of the thioether bridges and dehydro amino acids in the lantibiotics, also the three-dimensional structure of some lantibiotics has been resolved by NMR. Genes encoding proteins involved in the biosynthesis of lantibiotics are present in clusters and may comprise combinations of the following genes in varying order: a structural gene that encodes a leader peptide and the lantibiotic propeptide, modification enzyme(s), a transporter responsible for the export of the lantibiotic and in some cases for cleavage of the leader peptide, a leader peptidase, a so-called immunity protein involved in self-protection of the host cell, components of a transporter also involved in self-protection, and two components of an autoinduction system.

  14. Effect of Buckling Modes on the Fatigue Life and Damage Tolerance of Stiffened Structures

    Science.gov (United States)

    Davila, Carlos G.; Bisagni, Chiara; Rose, Cheryl A.

    2015-01-01

    The postbuckling response and the collapse of composite specimens with a co-cured hat stringer are investigated experimentally and numerically. These specimens are designed to evaluate the postbuckling response and the effect of an embedded defect on the collapse load and the mode of failure. Tests performed using controlled conditions and detailed instrumentation demonstrate that the damage tolerance, fatigue life, and collapse loads are closely tied with the mode of the postbuckling deformation, which can be different between two nominally identical specimens. Modes that tend to open skin/stringer defects are the most damaging to the structure. However, skin/stringer bond defects can also propagate under shearing modes. In the proposed paper, the effects of initial shape imperfections on the postbuckling modes and the interaction between different postbuckling deformations and the propagation of skin/stringer bond defects under quasi-static or fatigue loads will be examined.

  15. ModeRNA server: an online tool for modeling RNA 3D structures.

    Science.gov (United States)

    Rother, Magdalena; Milanowska, Kaja; Puton, Tomasz; Jeleniewicz, Jaroslaw; Rother, Kristian; Bujnicki, Janusz M

    2011-09-01

    The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program. ModeRNA server was implemented using the Python language and the Django web framework. It is freely available at http://iimcb.genesilico.pl/modernaserver. iamb@genesilico.pl.

  16. Isolation, structural elucidation and in vitro activity of 2-acetyl-2-decarboxamido-oxytetracycline against environmental relevant bacteria, including tetracycline-resistant bacteria

    DEFF Research Database (Denmark)

    Lykkeberg, Anne Kruse; Sengeløv, Gitte; Cornett, Claus

    2004-01-01

    2-Acetyl-2-decarboxamido-oxytetracycline (ADOTC) is a major impurity of oxytetracycline (OTC) produced as a side product during fermentation. ADOTC was isolated from OTC and other impurities using preparative HPLC. The preparative column was an Xterra MS. C-18 chromatographic column (100 mm x 19...... turn W., 5 mum), and the mobile phase contained methanol-water (27:73 (v/v)) with 0.08 M formic acid added. The flow rate was 9.0 ml/min. It was possible to isolate few milligram ADOTC in a day. The compound was unambiguously identified using NMR and MS-MS. The anti-microbial activity against activated...... sludge bacteria was deter-mined giving a potency of only 3% of that of OTC. With tetracycline-resistant bacteria, no anti-microbial activity was observed, indicating a mode of action similar to that of OTC....

  17. Development of structure design program for venturi scrubber working at self-priming mode

    International Nuclear Information System (INIS)

    Wang Meng; Sun Zhongning; Gu Haifeng

    2012-01-01

    A structure design program was developed for Venturi scrubber working at the self-priming mode. This program proposed a complete logic for thermal parameters calculation and structure design of the throat. A revised calculation for resistance relationship was carried out based on experimental study. The relative error between revised results and experimental values is within 8.6%. (authors)

  18. Roundtrip matrix method for calculating the leaky resonant modes of open nanophotonic structures

    DEFF Research Database (Denmark)

    de Lasson, Jakob Rosenkrantz; Kristensen, Philip Trøst; Mørk, Jesper

    2014-01-01

    We present a numerical method for calculating quasi-normal modes of open nanophotonic structures. The method is based on scattering matrices and a unity eigenvalue of the roundtrip matrix of an internal cavity, and we develop it in detail with electromagnetic fields expanded on Bloch modes...... cavities are side-coupled and in-line-coupled to an infinite W1 waveguide and show that the scattering spectrum of these types of cavities can be reconstructed from the complex quasi-normal mode frequency....

  19. Fractal Dimension Analysis of Higher-Order Mode Shapes for Damage Identification of Beam Structures

    OpenAIRE

    Bai, Runbo; Cao, Maosen; Su, Zhongqing; Ostachowicz, Wieslaw; Xu, Hao

    2012-01-01

    Fractal dimension analysis is an emerging method for vibration-based structural damage identification. An unresolved problem in this method is its incapability of identifying damage by higher-order mode shapes. The natural inflexions of higher-order mode shapes may cause false peaks of high-magnitude estimates of fractal dimension, largely masking any signature of damage. In the situation of a scanning laser vibrometer (SLV) providing a chance to reliably acquire higher-order (around tenth-or...

  20. Connecting structural relaxation with the low frequency modes in a hard-sphere colloidal glass.

    Science.gov (United States)

    Ghosh, Antina; Chikkadi, Vijayakumar; Schall, Peter; Bonn, Daniel

    2011-10-28

    Structural relaxation in hard-sphere colloidal glasses has been studied using confocal microscopy. The motion of individual particles is followed over long time scales to detect the rearranging regions in the system. We have used normal mode analysis to understand the origin of the rearranging regions. The low-frequency modes, obtained over short time scales, show strong spatial correlation with the rearrangements that happen on long time scales.

  1. Choice of Measurement Locations of Nonlinear Structures Using Proper Orthogonal Modes and Effective Independence Distribution Vector

    Directory of Open Access Journals (Sweden)

    T. G. Ritto

    2014-01-01

    Full Text Available This paper proposes a methodology to automatically choose the measurement locations of a nonlinear structure/equipment that needs to be monitored while operating. The response of the computational model (or experimental data is used to construct the proper orthogonal modes applying the proper orthogonal decomposition (POD, and the effective independence distribution vector (EIDV procedure is employed to eliminate, iteratively, locations that contribute less for the independence of the target proper orthogonal modes.

  2. Introduction to structural failure modes for nuclear power facilities

    International Nuclear Information System (INIS)

    Reed, J.W.; Gurbuz, O.

    1993-01-01

    This introduction provides a background of the evaluation methods for earthquakes larger than design basis. Seismic probabilistic risk assessment (SPRA) and seismic margin assessment (SMA) methods are introduced to the reader. The basic parameters used to define seismic capacity for each method are explained. The objectives of both evaluation methods and how they can be used to evaluate the adequacy of a seismic design are discussed. General issues related to computing seismic capacity are reviewed relative to SPRA and SMA. Four companion papers presented in the journal following this introduction discuss the types of information (i.e., dynamic tests, earthquake experience, and analytical data) that are used to determine the real capacity of structures and equipment in nuclear power plants to resist earthquakes. The motivation for discussing these three types of information is presented as an introduction to these papers that following in this journal edition. The purpose of the present paper is to lay the groundwork and provide motivation for these papers

  3. Optimal sensor configuration for flexible structures with multi-dimensional mode shapes

    International Nuclear Information System (INIS)

    Chang, Minwoo; Pakzad, Shamim N

    2015-01-01

    A framework for deciding the optimal sensor configuration is implemented for civil structures with multi-dimensional mode shapes, which enhances the applicability of structural health monitoring for existing structures. Optimal sensor placement (OSP) algorithms are used to determine the best sensor configuration for structures with a priori knowledge of modal information. The signal strength at each node is evaluated by effective independence and modified variance methods. Euclidean norm of signal strength indices associated with each node is used to expand OSP applicability into flexible structures. The number of sensors for each method is determined using the threshold for modal assurance criterion (MAC) between estimated (from a set of observations) and target mode shapes. Kriging is utilized to infer the modal estimates for unobserved locations with a weighted sum of known neighbors. A Kriging model can be expressed as a sum of linear regression and random error which is assumed as the realization of a stochastic process. This study presents the effects of Kriging parameters for the accurate estimation of mode shapes and the minimum number of sensors. The feasible ranges to satisfy MAC criteria are investigated and used to suggest the adequate searching bounds for associated parameters. The finite element model of a tall building is used to demonstrate the application of optimal sensor configuration. The dynamic modes of flexible structure at centroid are appropriately interpreted into the outermost sensor locations when OSP methods are implemented. Kriging is successfully used to interpolate the mode shapes from a set of sensors and to monitor structures associated with multi-dimensional mode shapes. (paper)

  4. Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria

    Directory of Open Access Journals (Sweden)

    Kiwamu eMinamisawa

    2015-02-01

    Full Text Available A number of studies have shown that elevated atmospheric CO2 ([CO2] affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE experiment (ambient + 200 μmol⋅mol−1 using three rice cultivars (Akita 63, Takanari, and Koshihikari and two experimental lines of Koshihikari (chromosome segment substitution and near-isogenic lines to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA gene and increased methyl coenzyme M reductase (mcrA in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields.

  5. Online channel operation mode: Game theoretical analysis from the supply chain power structure

    Directory of Open Access Journals (Sweden)

    Song Huang

    2015-11-01

    Full Text Available Purpose: Dual-channels have been widely used in practice, and the pricing decisions and the online channel operation mode choice have been the core problems in dual-channel supply chain management. This paper focuses on the online channel operation mode choice from the supply chain power structures based on game theoretical analysis. Design/methodology/approach: This paper utilizes three kinds of game theoretical models to analyze the impact of supply chain power structures on the optimal pricing and online channel operation mode choice. Findings: Results derived in this paper indicate that when the self-price elasticity is large, the power structures have no direct impact on the decisions. However, when the self-price elasticity is small and customers’ preference for the online channel is low, then in the MS market, it is better for the retailer to operate the online channel, while in the RS market or in the VN market, it is better for the manufacturer to operate the online channel. Research limitations/implications: In this paper, we do not consider stochastic demand and asymmetric information, which may not well suit the reality. Originality/value: This paper provides a different perspective to analyze the impact of supply chain power structures on the pricing decisions and online channel operation mode choice. The comparison of these two online channel operation modes in this paper is also a unique point.

  6. Structural modifications of bacterial lipopolysaccharide that facilitate Gram-negative bacteria evasion of host innate immunity

    Directory of Open Access Journals (Sweden)

    Motohiro eMatsuura

    2013-05-01

    Full Text Available Bacterial lipopolysaccharide (LPS, a cell wall component characteristic of Gram-negative bacteria, is a representative pathogen-associated molecular pattern that allows mammalian cells to recognize bacterial invasion and trigger innate immune responses. The polysaccharide moiety of LPS primary plays protective roles for bacteria such as prevention from complement attacks or camouflage with common host carbohydrate residues. The lipid moiety, termed lipid A, is recognized by the Toll-like receptor 4 (TLR4/MD-2 complex, which transduces signals for activation of host innate immunity. The basic structure of lipid A is a glucosamine disaccharide substituted by phosphate groups and acyl groups. Lipid A with 6 acyl groups (hexa-acylated form has been indicated to be a strong stimulator of the TLR4/MD-2 complex. This type of lipid A is conserved among a wide variety of Gram-negative bacteria, and those bacteria are easily recognized by host cells for activation of defensive innate immune responses. Modifications of the lipid A structure to less-acylated forms have been observed in some bacterial species, and those forms are poor stimulators of the TLR4/MD-2 complex. Such modifications are thought to facilitate bacterial evasion of host innate immunity, thereby enhancing pathogenicity. This hypothesis is supported by studies of Yersinia pestis LPS, which contains hexa-acylated lipid A when the bacterium grows at 27ºC (the temperature of the vector flea, and shifts to contain less-acylated forms when grown at the human body temperature of 37ºC. This alteration of lipid A forms following transmission of Y. pestis from fleas to humans contributes predominantly to the virulence of this bacterium over other virulence factors. A similar role for less-acylated lipid A forms has been indicated in some other bacterial species, such as Francisella tularensis, Helicobacter pylori, and Porphyromonas gingivalis, and further studies to explore this concept are

  7. Fractal Dimension Analysis of Higher-Order Mode Shapes for Damage Identification of Beam Structures

    Directory of Open Access Journals (Sweden)

    Runbo Bai

    2012-01-01

    Full Text Available Fractal dimension analysis is an emerging method for vibration-based structural damage identification. An unresolved problem in this method is its incapability of identifying damage by higher-order mode shapes. The natural inflexions of higher-order mode shapes may cause false peaks of high-magnitude estimates of fractal dimension, largely masking any signature of damage. In the situation of a scanning laser vibrometer (SLV providing a chance to reliably acquire higher-order (around tenth-order mode shapes, an improved fractal dimension method that is capable of treating higher-order mode shapes for damage detection is of important significance. This study proposes a sophisticated fractal dimension method with the aid of a specially designed affine transformation that is able to obviate natural inflexions of a higher-order mode shape while preserving its substantial damage information. The affine transformed mode shape facilitates the fractal dimension analysis to yield an effective damage feature: fractal dimension trajectory, in which an abruptly risking peak clearly characterizes the location and severity of the damage. This new fractal dimension method is demonstrated on multiple cracks identification in numerically simulated damage scenarios. The effectiveness of the method is experimentally validated by using a SLV to acquire higher-order mode shapes of a cracked cantilever beam.

  8. Efficacy of removal of cariogenic bacteria and carious dentin by ablation using different modes of Er:YAG lasers

    Directory of Open Access Journals (Sweden)

    A. Baraba

    2018-01-01

    Full Text Available The primary objective of this in vitro study was to evaluate the efficiency of removal of cariogenic bacteria and carious dentin by ablation using two lasers: fluorescence-feedback controlled (FFC Er:YAG laser and different pulses of Er:YAG laser based on variable square pulse technology (VSPt. The secondary objective was to measure the temperature during laser ablation of carious tissue. Seventy-two extracted human molars were used in this study. Sixty teeth with carious dentin were randomly divided into four experimental groups according to the treatment for caries removal: group 1: 400 µs (FFC group; group 2: super short pulse (SSP group, 50 µs pulse; group 3: medium short pulse (MSP group, 100 µs pulse; group 4: short pulse (SP group, 300 µs pulse and one positive control group with no treatment. Twelve teeth without carious lesion were used as a negative control group. After caries removal, swabs were taken with cotton pellets and real-time PCR analysis was performed. During caries ablation, a thermal infrared camera was used to measure the temperature changes. In all experimental groups, specimens were free of bacterial contamination after the treatment. In the SSP, MSP and SP groups, temperatures measured during caries ablation were significantly higher compared to temperatures in the FFC group (P<0.001. In this in vitro study, laser treatment for removal of carious dentin and cariogenic bacteria was an efficient treatment modality without causing excessive temperatures that might adversely affect pulp vitality.

  9. Matching of the coupler cavity to travelling wave structures at any operating mode

    International Nuclear Information System (INIS)

    Chanudet, M.

    1993-06-01

    For the realization of an accelerating travelling wave structure, it is important to adjust the coupler so that the rf power arriving through a rectangular waveguide is coupled to the structure without reflection from the input aperture of the first cavity, the coupler cavity. The problem consists in carefully determining the dimensions of the coupling aperture. A method is proposed to measure this coupling in the case of monoperiodic forward and backward wave structures. The theory is based on the possibility of representing the properties of electromagnetic modes in periodic structures by coupled RLC circuits. The study of current I and voltage V versus frequency ω allows the simulation of H and E fields, respectively, for the different modes appearing in a travelling wave structure. (K.A.) 4 refs.; 14 figs

  10. Factorial Structure and Preliminary Validation of the Schema Mode Inventory for Eating Disorders (SMI-ED

    Directory of Open Access Journals (Sweden)

    Susan G. Simpson

    2018-04-01

    Full Text Available Objective: The aim of this study was to examine the psychometric properties and factorial structure of the Schema Mode Inventory for Eating Disorders (SMI-ED in a disordered eating population.Method: 573 participants with disordered eating patterns as measured by the Eating Disorder Examination Questionnaire (EDE-Q completed the 190-item adapted version of the Schema Mode Inventory (SMI. The new SMI-ED was developed by clinicians/researchers specializing in the treatment of eating disorders, through combining items from the original SMI with a set of additional questions specifically representative of the eating disorder population. Psychometric testing included Confirmatory Factor Analysis (CFA and internal consistency (Cronbach's α. Multivariate Analyses of Covariance (MANCOVA was also run to test statistical differences between the EDE-Q subscales on the SMI-ED modes, while controlling for possible confounding variables.Results: Factorial analysis confirmed an acceptable 16-related-factors solution for the SMI-ED, thus providing preliminary evidence for the adequate validity of the new measure based on internal structure. Concurrent validity was also established through moderate to high correlations on the modes most relevant to eating disorders with EDE-Q subscales. This study represents the first step in creating a psychometrically sound instrument for measuring schema modes in eating disorders, and provides greater insight into the relevant schema modes within this population.Conclusion: This research represents an important preliminary step toward understanding and labeling the schema mode model for this clinical group. Findings from the psychometric evaluation of SMI-ED suggest that this is a useful tool which may further assist in the measurement and conceptualization of schema modes in this population.

  11. Structural Context for Protein N-glycosylation in Bacteria: The Structure of PEB3, an Adhesin from Campylobacter Jejuni

    Energy Technology Data Exchange (ETDEWEB)

    Rangarajan,E.; Bhatia, S.; Watson, D.; Munger, C.; Cygler, M.; Matte, A.; Young, N.

    2007-01-01

    Campylobacter jejuni is unusual among bacteria in possessing a eukaryotic-like system for N-linked protein glycosylation at Asn residues in sequons of the type Asp/Glu-Xaa-Asn-Xaa-Ser/Thr. However, little is known about the structural context of the glycosylated sequons, limiting the design of novel recombinant glycoproteins. To obtain more information on sequon structure, we have determined the crystal structure of the PEB3 (Cj0289c) dimer. PEB3 has the class II periplasmic-binding protein fold, with each monomer having two domains with a ligand-binding site containing citrate located between them, and overall resembles molybdate- and sulfate-binding proteins. The sequon around Asn90 is located within a surface-exposed loop joining two structural elements. The three key residues are well exposed on the surface; hence, they may be accessible to the PglB oligosaccharyltransferase in the folded state.

  12. Linking microbial community structure and function to characterize antibiotic resistant bacteria and antibiotic resistant genes from cattle feces

    Science.gov (United States)

    There is widespread interest in monitoring the development of antibiotic resistant bacteria and antibiotic resistance genes in agriculturally impacted environments, however little is known about the relationships between bacterial community structure, and antibiotic resistance gene profiles. Cattl...

  13. Identification of dominant flow structures in rapidly rotating convection of liquid metals using Dynamic Mode Decomposition

    Science.gov (United States)

    Horn, S.; Schmid, P. J.; Aurnou, J. M.

    2016-12-01

    The Earth's metal core acts as a dynamo whose efficiency in generating and maintaining the magnetic field is essentially determined by the rotation rate and the convective motions occurring in its outer liquid part. For the description of the primary physics in the outer core the idealized system of rotating Rayleigh-Bénard convection is often invoked, with the majority of studies considering only working fluids with Prandtl numbers of Pr ≳ 1. However, liquid metals are characterized by distinctly smaller Prandtl numbers which in turn result in an inherently different type of convection. Here, we will present results from direct numerical simulations of rapidly rotating convection in a fluid with Pr ≈ 0.025 in cylindrical containers and Ekman numbers as low as 5 × 10-6. In this system, the Coriolis force is the source of two types of inertial modes, the so-called wall modes, that also exist at moderate Prandtl numbers, and cylinder-filling oscillatory modes, that are a unique feature of small Prandtl number convection. The obtained flow fields were analyzed using the Dynamic Mode Decomposition (DMD). This technique allows to extract and identify the structures that govern the dynamics of the system as well as their corresponding frequencies. We have investigated both the regime where the flow is purely oscillatory and the regime where wall modes and oscillatory modes co-exist. In the purely oscillatory regime, high and low frequency oscillatory modes characterize the flow. When both types of modes are present, the DMD reveals that the wall-attached modes dominate the flow dynamics. They precess with a relatively low frequency in retrograde direction. Nonetheless, also in this case, high frequency oscillations have a significant contribution.

  14. Internal Mode Structure of Resonant Field Amplification in DIII-D

    Science.gov (United States)

    Lanctot, M. J.; Navratil, G.; Reimerdes, H.; Bogatu, I. N.; in, Y.; Chu, M. S.; Garofalo, A. M.; Jackson, G. L.; La Haye, R. J.; Strait, E. J.; Turnbull, A. D.; Liu, Y. Q.; Okabayashi, M.; Solomon, W. M.

    2008-11-01

    The sensitivity of high-β plasmas to error fields is caused by a paramagnetic plasma response to error fields with a topology that is resonant with the structure of weakly-damped resistive wall modes (RWM), a phenomenon referred to as resonant field amplification (RFA) [1]. The RFA has been driven in DIII-D H-mode plasmas by applying slowly-rotating, low-n magnetic fields with a set of 12 coils located inside the vacuum vessel. Measurements of the RFA mode structure have been obtained using a pair of soft x-ray photodiode cameras. A virtual diagnostic has been developed to compare the measurements to the eigenfunctions for the free boundary external kink and the RWM, which were calculated using the stability codes GATO and MARS-F. Details of the analysis will be presented. 6pt [1] A.H. Boozer, Phys. Rev. Lett. 86, 5059 (2001).

  15. A Comparison of pi/2-mode standing wave structures for Linac4

    CERN Document Server

    Wegner, R; CERN. Geneva. AB Department

    2006-01-01

    Cell coupled structures at twice the basic frequency provide a higher shunt impedance for proton energies above 90 MeV for Linac4 when compared to drift tube based geometries. For this reason the nominal accelerating structure for the energy range of 90-160 MeV in Linac4 was chosen to be a Side Coupled Structure at 704.4 MHz. High power klystrons will feed this structure, with the consequence that a large number of cells are coupled together in one module. To provide field stability in a long chain of resonators, a pi/2-mode structure will be used. In this report, the three best known and most widely used ones - the Annular Ring Coupled Structure (ACS), the On Axis Coupled Structure (OCS) and the Side Coupled Structure (SCS) - are compared in terms of the electrical parameters Q-value and shunt impedance as well as structure dimensions.

  16. Damage detection and quantification using mode curvature variation on framed structures: analysis of the preliminary results

    Science.gov (United States)

    Iacovino, Chiara; Ditommaso, Rocco; Auletta, Gianluca; Ponzo, Felice C.

    2017-04-01

    Continuous monitoring based on vibrational identification methods is increasingly employed for the evaluation of the state of health of existing buildings after strong motion earthquake. Different damage identification methods are based on the variations of damage indices defined in terms modal (eigenfrequencies, mode shapes, and modal damping) and/or non-modal parameters. Most of simplified methods for structural health monitoring and damage detection are based on the evaluation of the dynamic characteristics evolution associated to the fundamental mode of vibration of a monitored structure. Aim of this work is the upgrade of an existing method for damage localization on framed structures during a moderate/destructive earthquake. The existing version of the method is based on the comparison of the geometric characteristics (with particular reference to the mode curvature) exhibited by the structures, related to fundamental mode of vibration, before and during an earthquake. The approach is based on the use of a nonlinear filter, the band-variable filter, based on the Stockwell Transform able to extract the nonlinear response of each mode of vibration. The new version of the method provides the possibility to quantify a possible damage occurred on the monitored structure linking the mode curvature variation with the maximum inter-story drift. This paper shows the preliminary results obtained from several simulations on nonlinear numerical models of reinforced concrete framed structures, designed for only gravity loads, without and with the presence of infill panels. Furthermore, a correlation between maximum mode curvature difference and maximum inter-story drift has been defined for the different numerical models in order to quantify the structural damage. Acknowledgements This study was partially funded by the Italian Department of Civil Protection within the project DPC-RELUIS 2016 - RS4 ''Seismic observatory of structures and health monitoring'' and by the

  17. Structural studies of the O-specific polysaccharide from detergent degrading bacteria Pseudomonas putida TSh-18.

    Science.gov (United States)

    Sigida, Elena N; Fedonenko, Yuliya P; Shashkov, Alexander S; Zdorovenko, Evelina L; Ignatov, Vladimir V; Knirel, Yuriy A

    2017-08-07

    An O-specific polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of bacteria Pseudomonas putida TSh-18, capable of degrading non-ionogenic technical detergents. The polysaccharide was found to contain a rarely occurring sugar derivative 4,6-dideoxy-4-[(R)-3-hydroxybutanoylamino]-d-galactose [d-Fucp4N(RHb)]. Sugar and methylation analyses, Smith degradation, solvolysis with CF 3 CO 2 H, and 1 H and 13 C NMR spectroscopy enabled elucidation of the following structure of the branched trisaccharide repeating units of the polysaccharide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Comparative research on the transmission-mode GaAs photocathodes of exponential-doping structures

    International Nuclear Information System (INIS)

    Chen Liang; Qian Yun-Sheng; Zhang Yi-Jun; Chang Ben-Kang

    2012-01-01

    Early research has shown that the varied doping structures of the active layer of GaAs photocathodes have been proven to have a higher quantum efficiency than uniform doping structures. On the basis of our early research on the surface photovoltage of GaAs photocathodes, and comparative research before and after activation of reflection-mode GaAs photocathodes, we further the comparative research on transmission-mode GaAs photocathodes. An exponential doping structure is the typical varied doping structure that can form a uniform electric field in the active layer. By solving the one-dimensional diffusion equation for no equilibrium minority carriers of transmission-mode GaAs photocathodes of the exponential doping structure, we can obtain the equations for the surface photovoltage (SPV) curve before activation and the spectral response curve (SRC) after activation. Through experiments and fitting calculations for the designed material, the body-material parameters can be well fitted by the SPV before activation, and proven by the fitting calculation for SRC after activation. Through the comparative research before and after activation, the average surface escape probability (SEP) can also be well fitted. This comparative research method can measure the body parameters and the value of SEP for the transmission-mode GaAs photocathode more exactly than the early method, which only measures the body parameters by SRC after activation. It can also help us to deeply study and exactly measure the parameters of the varied doping structures for transmission-mode GaAs photocathodes, and optimize the Cs-O activation technique in the future. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  20. A versatile stereo photogrammetry based technique for measuring fracture mode displacements in structures

    DEFF Research Database (Denmark)

    Alvarado, Jonathan Shmueli; Eder, Martin Alexander; Tesauro, Angelo

    2015-01-01

    The measurement of fracture mode displacements in structures which are susceptible to cracking such as adhesive joints in composite components – is becoming increasingly important. Such measurements are essential for the understanding of the root causes for specific fracture damage types. Further...

  1. LALAGE - a computer program to calculate the TM01 modes of cylindrically symmetrical multicell resonant structures

    International Nuclear Information System (INIS)

    Fernandes, P.

    1982-01-01

    An improvement has been made to the LALA program to compute resonant frequencies and fields for all the modes of the lowest TM 01 band-pass of multicell structures. The results are compared with those calculated by another popular rf cavity code and with experimentally measured quantities. (author)

  2. An Indicator for Separation of Structural and Harmonic Modes in Output-Only Modal Testing

    DEFF Research Database (Denmark)

    Brincker, Rune; Andersen, P.; Møller, N.

    2000-01-01

    . The indicator is demonstrated on an example where a plate is loaded by an engine rotating with quasi-stationary speed. An output-only modal identification is performed using a technique based on Frequency Domain Decomposition (FDD), and what appears to be three harmonic components and five structural modes were...

  3. An Indicator for Separation of Structural and Harmonic Modes in Output-Only Modal Testing

    DEFF Research Database (Denmark)

    Brincker, Rune; Andersen, P.; Møller, N.

    2000-01-01

    . The indicator is demonstrated on an example where a plate is loaded by an engine rotating with quasi-stationary speed. An output-only modal identification is performed using a technique based on Frequency Domain Decomposition (FDD), and what appeared to be three harmonic components and five structural modes...

  4. Indicator for Separation of Structural and Harmonic Modes in Output-only Modal Testing

    DEFF Research Database (Denmark)

    Brincker, Rune; Andersen, Palle; Møller, Nis

    2000-01-01

    . The indicator is demonstrated on an example where a plate is loaded by an engine rotating with quasi-stationary speed. An output-only modal identification is performed using a technique based on Frequency Domain Decomposition (FDD), and what appears to be three harmonic components and five structural modes were...

  5. Connecting structural relaxation with the low frequency modes in a hard-sphere colloidal glass

    NARCIS (Netherlands)

    Ghosh, A.; Chikkadi, V.; Schall, P.; Bonn, D.

    2011-01-01

    Structural relaxation in hard-sphere colloidal glasses has been studied using confocal microscopy. The motion of individual particles is followed over long time scales to detect the rearranging regions in the system. We have used normal mode analysis to understand the origin of the rearranging

  6. The Relative Effects of Explicit Correction and Recasts on Two Target Structures via Two Communication Modes

    Science.gov (United States)

    Yilmaz, Yucel

    2012-01-01

    This study investigated the effects of negative feedback type (i.e., explicit correction vs. recasts), communication mode (i.e., face-to-face communication vs. synchronous computer-mediated communication), and target structure salience (i.e., salient vs. nonsalient) on the acquisition of two Turkish morphemes. Forty-eight native speakers of…

  7. Active power filter for harmonic compensation using a digital dual-mode-structure repetitive control approach

    DEFF Research Database (Denmark)

    Zou, Zhixiang; Wang, Zheng; Cheng, Ming

    2012-01-01

    This paper presents an digital dual-mode-structure repetitive control approach for the single-phase shunt active power filter (APF), which aims to enhance the tracking ability and eliminate arbitrary order harmonic. The proposed repetitive control scheme blends the characteristics of both odd-har...

  8. Optimization of hardening/softening behavior of plane frame structures using nonlinear normal modes

    DEFF Research Database (Denmark)

    Dou, Suguang; Jensen, Jakob Søndergaard

    2016-01-01

    Devices that exploit essential nonlinear behavior such as hardening/softening and inter-modal coupling effects are increasingly used in engineering and fundamental studies. Based on nonlinear normal modes, we present a gradient-based structural optimization method for tailoring the hardening....../softening behavior of nonlinear mechanical systems. The iterative optimization procedure consists of calculation of nonlinear normal modes, solving an adjoint equation system for sensitivity analysis and an update of design variables using a mathematical programming tool. We demonstrate the method with examples...

  9. Factors influencing the survival and leaching of tetracycline-resistant bacteria and Escherichia coli through structured agricultural fields

    DEFF Research Database (Denmark)

    Bech, Tina Bundgaard; Rosenbom, Annette E.; Kjær, Jeanne

    2014-01-01

    Intense use of antibiotics in agricultural production may lead to the contamination of surface and groundwater by antibiotic-resistant bacteria. In the present study, the survival and leaching of E. coli and tetracycline-resistant bacteria were monitored at two well-structured agricultural fields....... Non-spiked pig slurry was injected in accordance with agricultural practice in the area. In both fields, the concentration of E. coli and tetracycline-resistant bacteria in the injected part of the plough layer decreased to the detection limit within 46–49 days. At Silstrup the decay was initiated...... with a lag phase and a decimal reduction time of 16 days for E. coli and 18 days for tetracycline-resistant bacteria. At Estrup the decay was immediate and the decimal reduction time was 22 days for E .coli and 26 days for tetracycline-resistant bacteria. Despite the two fields being prone to rapid...

  10. Data on correlation between Aβ42 structural aggregation propensity and toxicity in bacteria

    Directory of Open Access Journals (Sweden)

    Anita Carija

    2016-06-01

    Full Text Available Protein aggregation and amyloid formation is a hallmark of an increasing number of human disorders. Because protein aggregation is deleterious for the cell physiology and results in a decrease in overall cell fitness, it is thought that natural selection acts to purify aggregating proteins during evolution. This data article contains complementary figures and results related to the research article entitled “Selection against toxic aggregation-prone protein sequences in bacteria” (Navarro et al., 2014 [1]. Here, we used the AGGRESCAN3D (A3D server, a novel in house predictor that forecasts protein aggregation properties in protein structures to illustrate a striking correlation between the structure-based predictions of aggregation propensities for Alzheimer’s Aβ42 peptide variants and their previously reported deleterious effects in bacteria.

  11. Structural aspects of the interaction of dairy phages with their host bacteria.

    Science.gov (United States)

    Mahony, Jennifer; van Sinderen, Douwe

    2012-09-01

    Knowledge of phage-host interactions at a fundamental level is central to the design of rational strategies for the development of phage-resistant strains that may be applied in industrial settings. Phages infecting lactic acid bacteria, in particular Lactococcus lactis and Streptococcus thermophilus, negatively impact on dairy fermentation processes with serious economic implications. In recent years a wealth of information on structural protein assembly and topology has become available relating to phages infecting Escherichia coli, Bacillus subtilis and Lactococcus lactis, which act as models for structural analyses of dairy phages. In this review, we explore the role of model tailed phages, such as T4 and SPP1, in advancing our knowledge regarding interactions between dairy phages and their hosts. Furthermore, the potential of currently investigated dairy phages to in turn serve as model systems for this particular group of phages is discussed.

  12. Microwave measurements of energy lost to longitudinal modes by single electron bunches traversing periodic structures

    International Nuclear Information System (INIS)

    Wang, J.W.; Loew, G.A.; Weaver, J.N.; Wilson, P.B.

    1981-10-01

    In the design of future linear colliders, it will be important to minimize the loss of beam energy due to the excitation of higher-order modes in the accelerator structure by single bunches of electrons or positrons. This loss is not only detrimental in itself but also gives rise to energy spectrum widening and transverse emittance growth. Microwave measurements made on disk-loaded and alternating-spoke structures to determine the loss to the longitudinal modes are described. In these measurements the Gaussian bunch is simulated by a current pulse of the same shape transmitted through the structure on an axial center conductor. Results to date are presented for the total longitudinal loss parameter per period K in volts per picocoulomb

  13. Flutter Analysis of RX-420 Balistic Rocket Fin Involving Rigid Body Modes of Rocket Structures

    Directory of Open Access Journals (Sweden)

    Novi Andria

    2013-03-01

    Full Text Available Flutter is a phenomenon that has brought a catastrophic failure to the flight vehicle structure. In this experiment, flutter was analyzed for its symmetric and antisymmetric configuration to understand the effect of rocket rigid modes to the fin flutter characteristic. This research was also expected to find out the safety level of RX-420 structure design. The analysis was performed using half rocket model. Fin structure used in this research was a fin which has semispan 600 mm, thickness 12 mm, chord root 700 mm, chord tip 400 mm, made by Al 6061-T651, double spar configuration with skin thickness of 2 mm. Structural dynamics and flutter stability were analyzed using finite element software implemented on MSC. Nastran. The analysis shows that the antisymmetric flutter mode is more critical than symmetric flutter mode. At sea level altitude, antisymmetric flutter occurs at 6.4 Mach, and symmetric flutter occurs at 10.15 Mach. Compared to maximum speed of RX-420 which is 4.5 Mach at altitude 11 km or equivalent to 2.1 Mach at sea level, it can be concluded that the RX-420 structure design is safe, and flutter will not occur during flight.

  14. New structural and functional defects in polyphosphate deficient bacteria: A cellular and proteomic study

    Directory of Open Access Journals (Sweden)

    Chávez Francisco P

    2010-01-01

    Full Text Available Abstract Background Inorganic polyphosphate (polyP, a polymer of tens or hundreds of phosphate residues linked by ATP-like bonds, is found in all organisms and performs a wide variety of functions. PolyP is synthesized in bacterial cells by the actions of polyphosphate kinases (PPK1 and PPK2 and degraded by exopolyphosphatase (PPX. Bacterial cells with polyP deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence among others. The cause of this pleiotropy is not entirely understood. Results The overexpression of exopolyphosphatase in bacteria mimicked some pleitropic defects found in ppk1 mutants. By using this approach we found new structural and functional defects in the polyP-accumulating bacteria Pseudomonas sp. B4, which are most likely due to differences in the polyP-removal strategy. Colony morphology phenotype, lipopolysaccharide (LPS structure changes and cellular division malfunction were observed. Finally, we used comparative proteomics in order to elucidate the cellular adjustments that occurred during polyP deficiency in this bacterium and found some clues that helped to understand the structural and functional defects observed. Conclusions The results obtained suggest that during polyP deficiency energy metabolism and particularly nucleoside triphosphate (NTP formation were affected and that bacterial cells overcame this problem by increasing the flux of energy-generating metabolic pathways such as tricarboxilic acid (TCA cycle, β-oxidation and oxidative phosphorylation and by reducing energy-consuming ones such as active transporters and amino acid biosynthesis. Furthermore, our results suggest that a general stress response also took place in the cell during polyP deficiency.

  15. Study of Higher Order Modes in Superconducting Accelerating Structures for Linac Applications

    CERN Document Server

    Schuh, Marcel; Welsch, C P

    2011-01-01

    Higher Order Modes (HOMs) can severely limit the operation of superconducting cavities in a linear accelerator with high beam current, high duty factor and complex pulse structure. Therefore, the full HOM spectrum has to be analysed in detail to identify potentially dangerous modes already during the design phase and to define their damping requirements. For this purpose a dedicated beam dynamics simulation code, Simulation of higher order Mode Dynamics (SMD), focusing on beam-HOM interaction, has been developed in the frame of this project. SMD allows to analyse the beam behaviour under the presence of HOMs, taking into account many important effects, such as for example the HOM frequency spread, beam input jitter, different chopping patterns, as well as klystron and alignment errors. SMD is used to investigate in detail into the effects of HOMs in the Superconducting Proton Linac (SPL) at CERN and in particular their potential to drive beam instabili- ties in the longitudinal and transverse direction. Based...

  16. Mode decomposition and Lagrangian structures of the flow dynamics in orbitally shaken bioreactors

    Science.gov (United States)

    Weheliye, Weheliye Hashi; Cagney, Neil; Rodriguez, Gregorio; Micheletti, Martina; Ducci, Andrea

    2018-03-01

    In this study, two mode decomposition techniques were applied and compared to assess the flow dynamics in an orbital shaken bioreactor (OSB) of cylindrical geometry and flat bottom: proper orthogonal decomposition and dynamic mode decomposition. Particle Image Velocimetry (PIV) experiments were carried out for different operating conditions including fluid height, h, and shaker rotational speed, N. A detailed flow analysis is provided for conditions when the fluid and vessel motions are in-phase (Fr = 0.23) and out-of-phase (Fr = 0.47). PIV measurements in vertical and horizontal planes were combined to reconstruct low order models of the full 3D flow and to determine its Finite-Time Lyapunov Exponent (FTLE) within OSBs. The combined results from the mode decomposition and the FTLE fields provide a useful insight into the flow dynamics and Lagrangian coherent structures in OSBs and offer a valuable tool to optimise bioprocess design in terms of mixing and cell suspension.

  17. Peculiarities of the fundamental mode structure in stable-resonator lasers upon spatially inhomogeneous amplification

    International Nuclear Information System (INIS)

    Gorbunkov, Mikhail V; Kostryukov, P V; Telegin, L S; Tunkin, V G; Yakovlev, D V

    2007-01-01

    The structure of the fundamental mode of a laser is calculated by the iteration Fox-Li method in the case of inhomogeneous unsaturated amplification produced by axially symmetric longitudinal pumping. The calculation is performed for different parameters g 1 and g 2 of the resonator within the entire stability region. It is shown that in the case of inhomogeneous amplification, the fundamental mode considerably deviates from the Gaussian mode of an empty resonator only in the so-called critical configurations of the resonator, when the quantity [arccos(g 1 g 2 ) 1/2 ]/π is zero or takes a number of values expressed by irreducible fractions m/n. For the Fresnel number N F = 9, configurations with m/n = 1/2, 2/5, 3/8, 1/3, 3/10, 1/4, 1/5, 1/6, 1/8, and 1/10 are pronounced. As N F increases, the number of critical configurations increases. The expansion in a system of Laguerre-Gaussian beams shows that the fundamental mode in critical configurations is formed by a set of beams with certain radial indices p phased in the active medium. (resonators. modes)

  18. The structure and binding mode of citrate in the stabilization of gold nanoparticles

    KAUST Repository

    Al-Johani, Hind

    2017-03-27

    Elucidating the binding mode of carboxylate-containing ligands to gold nanoparticles (AuNPs) is crucial to understand their stabilizing role. A detailed picture of the three-dimensional structure and coordination modes of citrate, acetate, succinate and glutarate to AuNPs is obtained by 13C and 23Na solid-state NMR in combination with computational modelling and electron microscopy. The binding between the carboxylates and the AuNP surface is found to occur in three different modes. These three modes are simultaneously present at low citrate to gold ratios, while a monocarboxylate monodentate (1κO1) mode is favoured at high citrate:gold ratios. The surface AuNP atoms are found to be predominantly in the zero oxidation state after citrate coordination, although trace amounts of Auδ+ are observed. 23Na NMR experiments show that Na+ ions are present near the gold surface, indicating that carboxylate binding occurs as a 2e− L-type interaction for each oxygen atom involved. This approach has broad potential to probe the binding of a variety of ligands to metal nanoparticles.

  19. The inhibitory effect of Thymus vulgaris extracts on the planktonic form and biofilm structures of six human pathogenic bacteria

    OpenAIRE

    Mohsenipour, Zeinab; Hassanshahian, Mehdi

    2015-01-01

    Objective: Microorganisms are responsible for many problems in industry and medicine because of biofilm formation. Therefore, this study was aimed to examine the effect of Thymus vulgaris (T. vulgaris) extracts on the planktonic form and biofilm structures of six pathogenic bacteria. Materials and methods: Antimicrobial activities of the plant extracts against the planktonic form of the bacteria were determined using the disc diffusion method. MIC and MBC values were evaluated using macrobrot...

  20. Phase space interrogation of the empirical response modes for seismically excited structures

    Science.gov (United States)

    Paul, Bibhas; George, Riya C.; Mishra, Sudib K.

    2017-07-01

    Conventional Phase Space Interrogation (PSI) for structural damage assessment relies on exciting the structure with low dimensional chaotic waveform, thereby, significantly limiting their applicability to large structures. The PSI technique is presently extended for structure subjected to seismic excitations. The high dimensionality of the phase space for seismic response(s) are overcome by the Empirical Mode Decomposition (EMD), decomposing the responses to a number of intrinsic low dimensional oscillatory modes, referred as Intrinsic Mode Functions (IMFs). Along with their low dimensionality, a few IMFs, retain sufficient information of the system dynamics to reflect the damage induced changes. The mutually conflicting nature of low-dimensionality and the sufficiency of dynamic information are taken care by the optimal choice of the IMF(s), which is shown to be the third/fourth IMFs. The optimal IMF(s) are employed for the reconstruction of the Phase space attractor following Taken's embedding theorem. The widely referred Changes in Phase Space Topology (CPST) feature is then employed on these Phase portrait(s) to derive the damage sensitive feature, referred as the CPST of the IMFs (CPST-IMF). The legitimacy of the CPST-IMF is established as a damage sensitive feature by assessing its variation with a number of damage scenarios benchmarked in the IASC-ASCE building. The damage localization capability, remarkable tolerance to noise contamination and the robustness under different seismic excitations of the feature are demonstrated.

  1. Recent Advances In Structural Vibration And Failure Mode Control In Mainland China: Theory, Experiments And Applications

    International Nuclear Information System (INIS)

    Li Hui; Ou Jinping

    2008-01-01

    A number of researchers have been focused on structural vibration control in the past three decades over the world and fruit achievements have been made. This paper introduces the recent advances in structural vibration control including passive, active and semiactive control in mainland China. Additionally, the co-author extends the structural vibration control to failure mode control. The research on the failure mode control is also involved in this paper. For passive control, this paper introduces full scale tests of buckling-restrained braces conducted to investigate the performance of the dampers and the second-editor of the Code of Seismic Design for Buildings. For active control, this paper introduces the HMD system for wind-induced vibration control of the Guangzhou TV tower. For semiactive control, the smart damping devices, algorithms for semi-active control, design methods and applications of semi-active control for structures are introduced in this paper. The failure mode control for bridges is also introduced

  2. A Multi-Mode Blade Damping Control using Shunted Piezoelectric Transducers with Active Feedback Structure

    Science.gov (United States)

    Choi, Benjamin; Morrison, Carlos; Min, James

    2009-01-01

    The Structural Dynamics and. Mechanics branch (RXS) is developing smart adaptive structures to improve fan blade damping at resonances using piezoelectric (PE) transducers. In this presentation, only one shunted PE transducer was used to demonstrate active control of multi-mode blade resonance damping on a titanium alloy (Ti-6A1-4V) flat plate model, regardless of bending, torsion, and 2-stripe modes. This work would have a significant impact on the conventional passive shunt damping world because the standard feedback control design tools can now be used to design and implement electric shunt for vibration control. In other words, the passive shunt circuit components using massive inductors and. resistors for multi-mode resonance control can be replaced with digital codes. Furthermore, this active approach with multi patches can simultaneously control several modes in the engine operating range. Dr. Benjamin Choi presented the analytical and experimental results from this work at the Propulsion-Safety and. Affordable Readiness (P-SAR) Conference in March, 2009.

  3. The Orbital Angular Momentum Modes Supporting Fibers Based on the Photonic Crystal Fiber Structure

    Directory of Open Access Journals (Sweden)

    Hu Zhang

    2017-10-01

    Full Text Available The orbital angular momentum (OAM of light can be another physical dimension that we exploit to make multiplexing in the spatial domain. The design of the OAM mode supporting fiber attracts many attentions in the field of the space division multiplexing (SDM system. This paper reviews the recent progresses in photonic crystal fiber (PCF supporting OAM modes, and summarizes why a PCF structure can be used to support stable OAM transmission modes. The emphasis is on the circular PCFs, which possess many excellent features of transmission performance, such as good-quality OAM modes, enough separation of the effective indices, low confinement loss, flat dispersion, a large effective area, and a low nonlinear coefficient. We also compare the transmission properties between the circular PCF and the ring core fiber, as well as the properties between the OAM EDFA based on circular PCF and the OAM EDFA based on the ring core fiber. At last, the challenges and prospects of OAM fibers based on the PCF structure are also discussed.

  4. Finite element normal mode analysis of resistance welding jointed of dissimilar plate hat structure

    Science.gov (United States)

    Nazri, N. A.; Sani, M. S. M.

    2017-10-01

    Structural joints offer connection between structural element (beam, plate, solid etc.) in order to build a whole assembled structure. The complex behaviour of connecting elements plays a valuable role in characteristics of dynamic such as natural frequencies and mode shapes. In automotive structures, the trustworthiness arrangement of the structure extremely depends on joints. In this paper, top hat structure is modelled and designed with spot welding joint using dissimilar materials which is mild steel 1010 and stainless steel 304, using finite element software. Different types of connector elements such as rigid body element (RBE2), welding joint element (CWELD), and bar element (CBAR) are applied to represent real connection between two dissimilar plates. Normal mode analysis is simulated with different types of joining element in order to determine modal properties. Natural frequencies using RBE2, CBAR and CWELD are compared to equivalent rigid body method. Connection that gives the lowest percentage error among these three will be selected as the most reliable joining for resistance spot weld. From the analysis, it is shown that CWELD is better compared to others in term of weld joining among dissimilar plate materials. It is expected that joint modelling of finite element plays significant role in structural dynamics.

  5. Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment.

    Science.gov (United States)

    Lipsewers, Yvonne A; Vasquez-Cardenas, Diana; Seitaj, Dorina; Schauer, Regina; Hidalgo-Martinez, Silvia; Sinninghe Damsté, Jaap S; Meysman, Filip J R; Villanueva, Laura; Boschker, Henricus T S

    2017-05-15

    Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria ( Thiotrichales ) and Epsilonproteobacteria ( Campylobacterales ) were prevalent during spring, whereas Deltaproteobacteria ( Desulfobacterales ) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H 2 S, S 0 , and S 2 O 3 2- ) and electron acceptors (O 2 and NO 3 - ) regulated by seasonal hypoxia. IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A

  6. A Novel Triple-Mode Bandpass Filter Based on a Dual-Mode Defected Ground Structure Resonator and a Microstrip Resonator

    Directory of Open Access Journals (Sweden)

    Xuehui Guan

    2013-01-01

    Full Text Available A novel triple-mode bandpass filter (BPF using a dual-mode defected ground structure (DGS resonator and a microstrip resonator is proposed in this paper. The dual-mode characteristic is achieved by loading a defected T-shaped stub to a uniform impedance DGS resonator. A uniform impedance microstrip resonator is designed on the top layer of the DGS resonator and a compact bandpass filter with three resonant modes in the passband can be achieved. A coupling scheme for the structure is given and the coupling matrix is synthesized. Based on the structure, a triple-mode BPF with central frequency of 2.57 GHz and equal ripple bandwidth of 15% is designed for the Wireless Local Area Network. Three transmission zeros are achieved at 1.48 GHz, 2.17 GHz, and 4.18 GHz, respectively, which improve the stopband characteristics of the filter. The proposed filter is fabricated and measured. Good agreements between measured results and simulated results verify the proposed structure well.

  7. Thermal expansion in 2D honeycomb structures: Role of transverse phonon modes

    OpenAIRE

    Mann, Sarita; Jindal, V. K.

    2016-01-01

    Graphene and its derivatives including hexagonal BN are notorious for their large negative thermal expansion over a wide range of temperature which is quite unusual. We attempt to analyze this unusual behavior on the basis of character of the phonon modes. The linear thermal expansion coefficients (LTEC) of two-dimensional honeycomb structured pure graphene, h-BN and B/N doped graphene are studied using density functional perturbation theory (DFPT) under quasi harmonic approximation. The dyna...

  8. Structure and activity of lacustrine sediment bacteria involved in nutrient and iron cycles

    DEFF Research Database (Denmark)

    da Silva Martins, Gilberto Jorge; Terada, Akihiko; Ribeiro, Daniel C

    2011-01-01

    lakes with distinct trophic states (Verde, Azul, Furnas and Fogo). Inferred from quantitative PCR, bacteria performing anaerobic ammonia oxidation were the most abundant in the eutrophic lakes Verde, Azul and Furnas (4.5-16.6%), followed by nitrifying bacteria (0.8-13.0%), denitrifying bacteria (DNB) (0...

  9. Modified Adaptive Control for Region 3 Operation in the Presence of Wind Turbine Structural Modes

    Science.gov (United States)

    Frost, Susan Alane; Balas, Mark J.; Wright, Alan D.

    2010-01-01

    Many challenges exist for the operation of wind turbines in an efficient manner that is reliable and avoids component fatigue and failure. Turbines operate in highly turbulent environments resulting in aerodynamic loads that can easily excite turbine structural modes, possibly causing component fatigue and failure. Wind turbine manufacturers are highly motivated to reduce component fatigue and failure that can lead to loss of revenue due to turbine down time and maintenance costs. The trend in wind turbine design is toward larger, more flexible turbines that are ideally suited to adaptive control methods due to the complexity and expense required to create accurate models of their dynamic characteristics. In this paper, we design an adaptive collective pitch controller for a high-fidelity simulation of a utility-scale, variable-speed horizontal axis wind turbine operating in Region 3. The objective of the adaptive pitch controller is to regulate generator speed, accommodate wind gusts, and reduce the excitation of structural modes in the wind turbine. The control objective is accomplished by collectively pitching the turbine blades. The adaptive collective pitch controller for Region 3 was compared in simulations with a baseline classical Proportional Integrator (PI) collective pitch controller. The adaptive controller will demonstrate the ability to regulate generator speed in Region 3, while accommodating gusts, and reducing the excitation of certain structural modes in the wind turbine.

  10. Separation and identification of structural modes in largely underdetermined scenarios using frequency banding

    Science.gov (United States)

    Castiglione, Roberto; Antoni, Jerome; Garibaldi, Luigi

    2018-02-01

    In recent years, blind source separation (BSS) has gained significant interest in the context of operational modal analysis, as a non-parametric alternative to the identification of mechanical structures from output-only measurements. One persisting limitation of most BSS methods, however, is to they cannot identify more active modes than the number of simultaneously measured outputs. The aim of this work is to propose a solution to the largely underdetermined case - where many more modes are to be identified than the number of available measurements - by dividing the frequency axis in subbands, such that each band provides an (over)determined problem where BSS can be applied separately. The approach comes with the proposal of a new second-order BSS that operates directly in the frequency domain and takes as an input the cross-spectral matrix of the data. A data augmentation technique is also devised to artificially increase the dimension of the measurements in severely undetermined scenarios. Finally, an identification algorithm is introduced that estimates the modal parameters of the separated structural modes. A remarkable aspect of these algorithms is that they are all based on the unified use of multi-filters designed in the frequency domain, yet with different frequency bandwidths. Another particularity of the present paper is to demonstrate the validity of the proposed approach on several benchmark databases with various degrees of difficulty including complex modes, high modal overlap, singular modes, and the presence of engine harmonics. In all cases, the proposed methodology was efficient and, above all, easy to deal with even in largely undetermined cases.

  11. Using Acoustic Structure Quantification During B-Mode Sonography for Evaluation of Hashimoto Thyroiditis.

    Science.gov (United States)

    Rhee, Sun Jung; Hong, Hyun Sook; Kim, Chul-Hee; Lee, Eun Hye; Cha, Jang Gyu; Jeong, Sun Hye

    2015-12-01

    This study aimed to evaluate the usefulness of Acoustic Structure Quantification (ASQ; Toshiba Medical Systems Corporation, Nasushiobara, Japan) values in the diagnosis of Hashimoto thyroiditis using B-mode sonography and to identify a cutoff ASQ level that differentiates Hashimoto thyroiditis from normal thyroid tissue. A total of 186 thyroid lobes with Hashimoto thyroiditis and normal thyroid glands underwent sonography with ASQ imaging. The quantitative results were reported in an echo amplitude analysis (Cm(2)) histogram with average, mode, ratio, standard deviation, blue mode, and blue average values. Receiver operating characteristic curve analysis was performed to assess the diagnostic ability of the ASQ values in differentiating Hashimoto thyroiditis from normal thyroid tissue. Intraclass correlation coefficients of the ASQ values were obtained between 2 observers. Of the 186 thyroid lobes, 103 (55%) had Hashimoto thyroiditis, and 83 (45%) were normal. There was a significant difference between the ASQ values of Hashimoto thyroiditis glands and those of normal glands (P Hashimoto thyroiditis were significantly greater than those in patients with normal thyroid glands. The areas under the receiver operating characteristic curves for the ratio, blue average, average, blue mode, mode, and standard deviation were: 0.936, 0.902, 0.893, 0.855, 0.846, and 0.842, respectively. The ratio cutoff value of 0.27 offered the best diagnostic performance, with sensitivity of 87.38% and specificity of 95.18%. The intraclass correlation coefficients ranged from 0.86 to 0.94, which indicated substantial agreement between the observers. Acoustic Structure Quantification is a useful and promising sonographic method for diagnosing Hashimoto thyroiditis. Not only could it be a helpful tool for quantifying thyroid echogenicity, but it also would be useful for diagnosis of Hashimoto thyroiditis. © 2015 by the American Institute of Ultrasound in Medicine.

  12. The structural bases of long-term anabiosis in non-spore-forming bacteria

    Science.gov (United States)

    Suzina, Natalia E.; Mulyukin, Andrey L.; Dmitriev, Vladimir V.; Nikolaev, Yury A.; Shorokhova, Anna P.; Bobkova, Yulia S.; Barinova, Ekaterina S.; Plakunov, Vladimir K.; El-Registan, Galina I.; Duda, Vitalii I.

    2006-01-01

    Peculiarities of the structural organization in non-spore-forming bacteria associated with long-term anabiosis were revealed both in laboratory cultures and in natural populations isolated from 1 3-Myr-old Eastern Siberian permafrost and tundra soil. Different advanced methods were used, including (a) high-resolution electron microscopy; (b) simulation of in situ conditions in the laboratory by varying the composition of growth medium and cultivation conditions; (c) low-temperature fractionation to isolate and concentrate microbial cells from natural soils; (d) comparative morphological analysis of microbial cells in model cultures and natural soils (in situ). Under laboratory conditions, the intense formation of resting cells by representatives of various taxa of eubacteria and halophilic archaea occurred in 2 9-month-old cultures grown in carbon-, nitrogen-, or phosphorus-limited media, in starved cell suspensions in the presence of sodium silicate, or on soil agar. Among resting cells, we revealed cystlike forms having a complicated structure and common features. These included a thick capsule; a thickened and multiprofile cell wall; the presence of large intramembrane particles on PF- and EF-fracture surfaces; fine-grained or lumpy cytoplasm; and a condensed nucleoid. The general morphological properties, ultrastructural organization, physiological features of cystlike cells, and their ability to germinate under the appropriate conditions suggest the existence of constitutive dormancy in non-spore-forming bacteria. It was found that the majority of microorganisms in permafrost and tundra soil are cystlike cells, very similar to those in laboratory cultures. Anabiotic (resting) cystlike cells are responsible for the survival of non-spore-formers in extreme Earth habitats and may be regarded as possible analogs of extraterrestrial forms of microbial life.

  13. Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

    Directory of Open Access Journals (Sweden)

    Diallo, MD.

    2015-01-01

    Full Text Available Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB community composition and nitrogen (N availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. The aim of this study was to determine the influence of leaf litter decomposition on N mineralization. The specific objectives of this study were to evaluate the influence of the litter biochemistry of five plants species (Faidherbia albida A.Chev., Azadirachta indica A.Juss., Casuarina equisetifolia L., Andropogon gayanus Kunth and Eragrostis tremula Hochst. ex Steud. on N mineralization in a tropical ferrous soil (Lixisol, nitrification, and genetic diversity of ammonia-oxidizing bacteria. 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 leaf litter in soils. Method. Community structure of AOB was determined at two time periods: day 0 and day 140. Ten strains were tested and each of these strains produced a single band. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. Plant secondary compounds such as polyphenols are purported to influence nutrient cycling by affecting organic matter degradation, mineralization rates, N availability and humus formation. In a laboratory study, we investigated the influence of six phenolic acids (ferulic, gallic, vanillic, syringic, p-coumaric and p-HBA acids commonly found in the plant residues on N mineralization and NH4+ and NO3- production in soils. Results. The results showed that litter type did affect soil nitrification. Faidherbia albida litter was associated with

  14. Bacteriophages with potential for inactivation of fish pathogenic bacteria: survival, host specificity and effect on bacterial community structure.

    Science.gov (United States)

    Pereira, Carla; Silva, Yolanda J; Santos, Ana L; Cunha, Angela; Gomes, Newton C M; Almeida, Adelaide

    2011-01-01

    Phage therapy may represent a viable alternative to antibiotics to inactivate fish pathogenic bacteria. Its use, however, requires the awareness of novel kinetics phenomena not applied to conventional drug treatments. The main objective of this work was to isolate bacteriophages with potential to inactivate fish pathogenic bacteria, without major effects on the structure of natural bacterial communities of aquaculture waters. The survival was determined in marine water, through quantification by the soft agar overlay technique. The host specificity was evaluated by cross infection. The ecological impact of phage addition on the structure of the bacterial community was evaluated by DGGE of PCR amplified 16S rRNA gene fragments. The survival period varied between 12 and 91 days, with a higher viability for Aeromonas salmonicida phages. The phages of Vibrio parahaemolyticus and of A. salmonicida infected bacteria of different families with a high efficacy of plating. The specific phages of pathogenic bacteria had no detectable impact on the structure of the bacterial community. In conclusion, V. parahaemolyticus and A. salmonicida phages show good survival time in marine water, have only a moderated impact on the overall bacterial community structure and the desired specificity for host pathogenic bacteria, being potential candidates for therapy of fish infectious diseases in marine aquaculture systems.

  15. Bacteriophages with Potential for Inactivation of Fish Pathogenic Bacteria: Survival, Host Specificity and Effect on Bacterial Community Structure

    Directory of Open Access Journals (Sweden)

    Yolanda J. Silva

    2011-11-01

    Full Text Available Phage therapy may represent a viable alternative to antibiotics to inactivate fish pathogenic bacteria. Its use, however, requires the awareness of novel kinetics phenomena not applied to conventional drug treatments. The main objective of this work was to isolate bacteriophages with potential to inactivate fish pathogenic bacteria, without major effects on the structure of natural bacterial communities of aquaculture waters. The survival was determined in marine water, through quantification by the soft agar overlay technique. The host specificity was evaluated by cross infection. The ecological impact of phage addition on the structure of the bacterial community was evaluated by DGGE of PCR amplified 16S rRNA gene fragments. The survival period varied between 12 and 91 days, with a higher viability for Aeromonas salmonicida phages. The phages of Vibrio parahaemolyticus and of A. salmonicida infected bacteria of different families with a high efficacy of plating. The specific phages of pathogenic bacteria had no detectable impact on the structure of the bacterial community. In conclusion, V. parahaemolyticus and A. salmonicida phages show good survival time in marine water, have only a moderated impact on the overall bacterial community structure and the desired specificity for host pathogenic bacteria, being potential candidates for therapy of fish infectious diseases in marine aquaculture systems.

  16. DC Voltage Droop Control Structures and its Impact on the Interaction Modes in Interconnected AC-HVDC Systems

    DEFF Research Database (Denmark)

    Thams, Florian; Chatzivasileiadis, Spyros; Eriksson, Robert

    2017-01-01

    Different dc voltage droop control structures for future multi-terminal HVDC systems have been proposed in literature. This paper contributes to the evaluation of those structures by an analysis of their impact on the coupling of the interconnected subsystems. In particular, the modes of the syst......Different dc voltage droop control structures for future multi-terminal HVDC systems have been proposed in literature. This paper contributes to the evaluation of those structures by an analysis of their impact on the coupling of the interconnected subsystems. In particular, the modes...... respectively the different HVDC converters. The lowest damped interaction modes of the different subsets are analyzed in more detail....

  17. A class of k-modes algorithms for extracting knowledge structures from data.

    Science.gov (United States)

    de Chiusole, Debora; Stefanutti, Luca; Spoto, Andrea

    2017-08-01

    One of the most crucial issues in knowledge space theory is the construction of the so-called knowledge structures. In the present paper, a new data-driven procedure for large data sets is described, which overcomes some of the drawbacks of the already existing methods. The procedure, called k-states, is an incremental extension of the k-modes algorithm, which generates a sequence of locally optimal knowledge structures of increasing size, among which a "best" model is selected. The performance of k-states is compared to other two procedures in both a simulation study and an empirical application. In the former, k-states displays a better accuracy in reconstructing knowledge structures; in the latter, the structure extracted by k-states obtained a better fit.

  18. Residual mode correction in calibrating nonlinear damper for vibration control of flexible structures

    Science.gov (United States)

    Sun, Limin; Chen, Lin

    2017-10-01

    Residual mode correction is found crucial in calibrating linear resonant absorbers for flexible structures. The classic modal representation augmented with stiffness and inertia correction terms accounting for non-resonant modes improves the calibration accuracy and meanwhile avoids complex modal analysis of the full system. This paper explores the augmented modal representation in calibrating control devices with nonlinearity, by studying a taut cable attached with a general viscous damper and its Equivalent Dynamic Systems (EDSs), i.e. the augmented modal representations connected to the same damper. As nonlinearity is concerned, Frequency Response Functions (FRFs) of the EDSs are investigated in detail for parameter calibration, using the harmonic balance method in combination with numerical continuation. The FRFs of the EDSs and corresponding calibration results are then compared with those of the full system documented in the literature for varied structural modes, damper locations and nonlinearity. General agreement is found and in particular the EDS with both stiffness and inertia corrections (quasi-dynamic correction) performs best among available approximate methods. This indicates that the augmented modal representation although derived from linear cases is applicable to a relatively wide range of damper nonlinearity. Calibration of nonlinear devices by this means still requires numerical analysis while the efficiency is largely improved owing to the system order reduction.

  19. Frustration-induced internal stresses are responsible for quasilocalized modes in structural glasses

    Science.gov (United States)

    Lerner, Edan; Bouchbinder, Eran

    2018-03-01

    It has been recently shown [E. Lerner, G. Düring, and E. Bouchbinder, Phys. Rev. Lett. 117, 035501 (2016), 10.1103/PhysRevLett.117.035501] that the nonphononic vibrational modes of structural glasses at low frequencies ω are quasilocalized and follow a universal density of states D (ω ) ˜ω4 . Here we show that the gapless nature of the observed density of states depends on the existence of internal stresses that generically emerge in glasses due to frustration, thus elucidating a basic element underlying this universal behavior. Similarly to jammed particulate packings, low-frequency modes in structural glasses emerge from a balance between a local elasticity term and an internal stress term in the dynamical matrix, where the difference between them is orders of magnitude smaller than their typical magnitude. By artificially reducing the magnitude of internal stresses in a computer glass former in three dimensions, we show that a gap is formed in the density of states below which no vibrational modes exist, thus demonstrating the crucial importance of internal stresses. Finally, we show that while better annealing the glass upon cooling from the liquid state significantly reduces its internal stresses, the self-organizational processes during cooling render the gapless D (ω ) ˜ω4 density of state unaffected.

  20. Analysis of vibrating structures with localized nonlinearities using nonlinear normal modes

    International Nuclear Information System (INIS)

    Moussi, E.H.

    2013-01-01

    This work is a collaboration between EDF R and D and the Laboratory of Mechanics and Acoustics. The objective is to develop theoretical and numerical tools to compute nonlinear normal modes (NNMs) of structures with localized nonlinearities. We use an approach combining the harmonic balance and the asymptotic numerical methods, known for its robustness principally for smooth systems. Regularization techniques are used to apply this approach for the study of non-smooth problems. Moreover, several aspects of the method are improved to allow the computation of NNMs for systems with a high number of degrees of freedom (DOF). Finally, the method is implemented in Code-Aster, an open-source finite element solver developed by EDF R and D. The nonlinear normal modes of a two degrees-of-freedom system are studied and some original characteristics are observed. These observations are then used to develop a methodology for the study of systems with a high number of DOFs. The developed method is finally used to compute the NNMs for a model U-tube of a nuclear plant steam generator. The analysis of the NNMs reveals the presence of an interaction between an out-of-plane (low frequency) and an in-plane (high frequency) modes, a result also confirmed by the experiment. This modal interaction is not possible using linear modal analysis and confirms the interest of NNMs as a diagnostic tool in structural dynamics. (author) [fr

  1. Musical Creativity "Revealed" in Brain Structure: Interplay between Motor, Default Mode, and Limbic Networks.

    Science.gov (United States)

    Bashwiner, David M; Wertz, Christopher J; Flores, Ranee A; Jung, Rex E

    2016-02-18

    Creative behaviors are among the most complex that humans engage in, involving not only highly intricate, domain-specific knowledge and skill, but also domain-general processing styles and the affective drive to create. This study presents structural imaging data indicating that musically creative people (as indicated by self-report) have greater cortical surface area or volume in a) regions associated with domain-specific higher-cognitive motor activity and sound processing (dorsal premotor cortex, supplementary and pre-supplementary motor areas, and planum temporale), b) domain-general creative-ideation regions associated with the default mode network (dorsomedial prefrontal cortex, middle temporal gyrus, and temporal pole), and c) emotion-related regions (orbitofrontal cortex, temporal pole, and amygdala). These findings suggest that domain-specific musical expertise, default-mode cognitive processing style, and intensity of emotional experience might all coordinate to motivate and facilitate the drive to create music.

  2. Temporal coupled mode analysis of one-dimensional magneto-photonic crystals with cavity structures

    Energy Technology Data Exchange (ETDEWEB)

    Saghirzadeh Darki, Behnam, E-mail: b.saghirzadeh@ec.iut.ac.ir; Zeidaabadi Nezhad, Abolghasem; Firouzeh, Zaker Hossein

    2016-12-01

    In this paper, we propose the time-dependent coupled mode analysis of one-dimensional magneto-photonic crystals including one, two or multiple defect layers. The performance of the structures, namely the total transmission, Faraday rotation and ellipticity, is obtained using the proposed method. The results of the developed analytic approach are verified by comparing them to the results of the exact numerical transfer matrix method. Unlike the widely used numerical method, our proposed analytic method seems promising for the synthesis as well as the analysis purposes. Moreover, the proposed method has not the restrictions of the previously examined analytic methods. - Highlights: • A time-dependent coupled mode analysis is proposed for the cavity-type 1D MPCs. • Analytical formalism is presented for the single, double and multiple-defect MPCs. • Transmission, Faraday rotation and ellipticity are gained using the proposed method. • The proposed analytic method has advantages over the previously examined methods.

  3. Structure of the human macrophage MARCO receptor and characterization of its bacteria-binding region.

    Science.gov (United States)

    Elomaa, O; Sankala, M; Pikkarainen, T; Bergmann, U; Tuuttila, A; Raatikainen-Ahokas, A; Sariola, H; Tryggvason, K

    1998-02-20

    The primary structure of human macrophage receptor with collagenous structure (MARCO) was determined from cDNA clones and shown to be highly similar to that of mouse (Elomaa, O., Kangas, M., Sahlberg, C. , Tuukkanen, J., Sormunen, R., Liakka, A., Thesleff, I., Kraal, G., and Tryggvason, K. (1995) Cell 80, 603-609). Features such as potential carbohydrate attachment sites in the extracellular spacer domain III and the interruption of Gly-Xaa-Yaa repeats in the collagenous domain IV were conserved between the two species. However, the human MARCO polypeptide chain lacked the intracellular cysteine present in mouse, as well as two extracellular cysteines that form interchain disulfide bonds in the murine protein. In situ hybridization showed MARCO to be strongly expressed in macrophages of several tissues of human individuals with sepsis. No expression was observed in other cell types. The bacteria-binding region of MARCO was determined in binding studies with full-length and truncated variants of MARCO, and localized to a region proximal to the cysteine-rich part of the COOH-terminal domain V. The intrachain disulfide bond pattern of domain V was established showing that these bonds are between cysteine pairs C1-C5, C2-C6, and C3-C4.

  4. Structural Aspects of the Interaction of Dairy Phages with Their Host Bacteria

    Directory of Open Access Journals (Sweden)

    Jennifer Mahony

    2012-08-01

    Full Text Available Knowledge of phage-host interactions at a fundamental level is central to the design of rational strategies for the development of phage-resistant strains that may be applied in industrial settings. Phages infecting lactic acid bacteria, in particular Lactococcus lactis and Streptococcus thermophilus, negatively impact on dairy fermentation processes with serious economic implications. In recent years a wealth of information on structural protein assembly and topology has become available relating to phages infecting Escherichia coli, Bacillus subtilis and Lactococcus lactis, which act as models for structural analyses of dairy phages. In this review, we explore the role of model tailed phages, such as T4 and SPP1, in advancing our knowledge regarding interactions between dairy phages and their hosts. Furthermore, the potential of currently investigated dairy phages to in turn serve as model systems for this particular group of phages is discussed.

  5. Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity.

    Directory of Open Access Journals (Sweden)

    Anna Popinako

    Full Text Available Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na+. Octaheme nitrite reductases (ONRs from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11 and salinity (up to 1 M NaCl. To establish adaptation mechanisms of ONRs from haloalkaliphilic bacteria a comparative analysis of amino acid sequences and structures of ONRs from haloalkaliphilic bacteria and their homologues from non-halophilic neutrophilic bacteria was performed. The following adaptation strategies were observed: (1 strategies specific for halophilic and alkaliphilic proteins (an increase in the number of aspartate and glutamate residues and a decrease in the number of lysine residues on the protein surface, (2 strategies specific for halophilic proteins (an increase in the arginine content and a decrease in the number of hydrophobic residues on the solvent-accessible protein surface, (3 strategies specific for alkaliphilic proteins (an increase in the area of intersubunit hydrophobic contacts. Unique adaptation mechanism inherent in the ONRs from bacteria of genus Thioalkalivibrio was revealed (an increase in the core in the number of tryptophan and phenylalanine residues, and an increase in the number of small side chain residues, such as alanine and valine, in the core.

  6. Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data

    Directory of Open Access Journals (Sweden)

    Christian Gorba

    2010-06-01

    Full Text Available We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures. This method uses a linear combination of low-frequency normal modes from an elastic network description of the molecule in an iterative manner to deform the structure to conform optimally to the target pair distribution function derived from SAXS data. For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained. In this paper, we demonstrate the validity of our coarse- graining approach to study SAXS data. Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.

  7. The structural connectivity pattern of the default mode network and its association with memory and anxiety

    Directory of Open Access Journals (Sweden)

    Yan eTao

    2015-11-01

    Full Text Available The default mode network (DMN is one of the most widely studied resting state functional networks. The structural basis for the DMN is of particular interest and has been studied by several researchers using diffusion tensor imaging (DTI. Most of these previous studies focused on a few regions or white matter tracts of the DMN so that the global structural connectivity pattern and network properties of the DMN remain unclear. Moreover, evidences indicate that the DMN is involved in both memory and emotion, but how the DMN regulates memory and anxiety from the perspective of the whole DMN structural network remains unknown. We used multimodal neuroimaging methods to investigate the structural connectivity pattern of the DMN and the association of its network properties with memory and anxiety in 205 young healthy subjects. Using a probabilistic fiber tractography technique based on DTI data and graph theory methods, we constructed the global structural connectivity pattern of the DMN and found that memory quotient (MQ score was significantly positively correlated with the global and local efficiency of the DMN whereas anxiety was found to be negatively correlated with the efficiency. The strong structural connectivity between multiple brain regions within DMN may reflect that the DMN has certain structural basis. Meanwhile, we found the network efficiency of the DMN were related to memory and anxiety measures, which indicated that the DMN may play a role in the memory and anxiety.

  8. The glassy and supercooled state of elemental sulfur: Vibrational modes, structure metastability, and polymer content

    Science.gov (United States)

    Andrikopoulos, K. S.; Kalampounias, A. G.; Falagara, O.; Yannopoulos, S. N.

    2013-09-01

    We report a detailed investigation of vibrational modes, structure, and dynamics of elemental sulfur in the glassy and the supercooled state, using Raman scattering and ab initio calculations. Polarized Raman spectra are recorded - for sulfur quenched from 473 K - over a broad temperature range from 93 K to 273 K where the supercooled liquid crystallized. The temperature induced shifts of the majority of the vibrational modes are determined and compared with the corresponding ones of crystalline sulfur. Analysis of the reduced isotropic spectra showed that the structure of the quenched product is composed of eight member rings (S8) and polymeric chains (Sμ) with a relative fraction comparable to that of the parent liquid at 473 K. Low temperature spectra, where spectral line broadening due to thermal effects is limited, revealed that two different polymeric species are present in the glass with distinct vibrational frequencies. Their interpretation was assisted by ab initio calculations used to simulate the vibrational frequencies of polymeric chains S8k (k = 1, …, 7). Theoretical results exhibit an increasing breathing mode frequency for sulfur chains up to k = 2, although it remains constant beyond the above value. The polymeric content is metastable; heating the glass above its glass transition temperature, Tg, destabilizes the chains and drives them back to the more thermodynamically stable rings. This bond interchange mechanism provides the structural origin of a secondary relaxation process in supercooled sulfur reported long ago, which has been also considered as a complication in the correct fragility estimation of this material. Finally, the Boson peak of the glass was found to exhibit strong temperature dependence even at temperatures below Tg.

  9. The inhibitory effect of Thymus vulgaris extracts on the planktonic form and biofilm structures of six human pathogenic bacteria.

    Science.gov (United States)

    Mohsenipour, Zeinab; Hassanshahian, Mehdi

    2015-01-01

    Microorganisms are responsible for many problems in industry and medicine because of biofilm formation. Therefore, this study was aimed to examine the effect of Thymus vulgaris (T. vulgaris) extracts on the planktonic form and biofilm structures of six pathogenic bacteria. Antimicrobial activities of the plant extracts against the planktonic form of the bacteria were determined using the disc diffusion method. MIC and MBC values were evaluated using macrobroth dilution technique. Anti-biofilm effects were assessed by microtiter plate method. According to disc diffusion test (MIC and MBC), the ability of Thymus vulgaris (T. vulgaris ) extracts for inhibition of bacteria in planktonic form was confirmed. In dealing with biofilm structures, the inhibitory effect of the extracts was directly correlated to their concentration. Except for the inhibition of biofilm formation, efficacy of each extract was independent from type of solvent. According to the potential of Thymus vulgaris (T. vulgaris) extracts to inhibit the test bacteria in planktonic and biofilm form, it can be suggested that Thymus vulgaris (T. vulgaris) extracts can be applied as antimicrobial agents against the pathogenic bacteria particularly in biofilm forms.

  10. Adaptive Sliding Mode Control of Dynamic Systems Using Double Loop Recurrent Neural Network Structure.

    Science.gov (United States)

    Fei, Juntao; Lu, Cheng

    2018-04-01

    In this paper, an adaptive sliding mode control system using a double loop recurrent neural network (DLRNN) structure is proposed for a class of nonlinear dynamic systems. A new three-layer RNN is proposed to approximate unknown dynamics with two different kinds of feedback loops where the firing weights and output signal calculated in the last step are stored and used as the feedback signals in each feedback loop. Since the new structure has combined the advantages of internal feedback NN and external feedback NN, it can acquire the internal state information while the output signal is also captured, thus the new designed DLRNN can achieve better approximation performance compared with the regular NNs without feedback loops or the regular RNNs with a single feedback loop. The new proposed DLRNN structure is employed in an equivalent controller to approximate the unknown nonlinear system dynamics, and the parameters of the DLRNN are updated online by adaptive laws to get favorable approximation performance. To investigate the effectiveness of the proposed controller, the designed adaptive sliding mode controller with the DLRNN is applied to a -axis microelectromechanical system gyroscope to control the vibrating dynamics of the proof mass. Simulation results demonstrate that the proposed methodology can achieve good tracking property, and the comparisons of the approximation performance between radial basis function NN, RNN, and DLRNN show that the DLRNN can accurately estimate the unknown dynamics with a fast speed while the internal states of DLRNN are more stable.

  11. Nitrogen cycling and community structure of proteobacterial ß-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments

    NARCIS (Netherlands)

    McCaig, A.E.; Phillips, C.B.; Stephen, J.R.; Kowalchuk, G.A.; Harvey, S.M.; Herbert, R.A.; Embley, T.M.; Prosser, J.I.

    1999-01-01

    A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer

  12. Multiplet structure of the defect modes in 1D helical photonic crystals with twist defects

    Energy Technology Data Exchange (ETDEWEB)

    Avendano, C G [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo. P 20-364 01000, Mexico DF (Mexico); Ponti, S [Dipartimento di Fisica Politecnico di Torino and INFM, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Reyes, J A [Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Apdo. P 20-364 01000, Mexico DF (Mexico); Oldano, C [Dipartimento di Fisica Politecnico di Torino and INFM, Corso Duca degli Abruzzi 24, 10129 Torino (Italy)

    2005-10-14

    We theoretically analyse the defect modes generated by equispaced twist defects in 1D helical (cholesteric-like) structures within their frequency gap which is such that only the first two of the four eigenwaves 1{sup {+-}}, 2{sup {+-}} are exponentially attenuated. n{sub 0} identical defects generate n{sub 0} different defect modes, each one represented by a linear combination of the four eigenwaves. The components 1{sup +} and 1{sup -} are by far the dominant ones and they are localized near the defect planes. We give exact analytic expressions for the elements of the transfer and scattering matrices of the defect planes, for the functions defining the defect mode when n{sub 0} = 1, and for the defect frequencies when n{sub 0} = 1, 2, 3. In the particular case n{sub 0} = 2 and twist angle {theta} = {pi}/2, the difference between the two defect wavelengths {lambda}{sub d2}, {lambda}{sub d1} depends exponentially on the distance z{sub 1} between the defect planes, going to zero for z{sub 1} {yields} {infinity} and becoming as large as the entire frequency gap for z{sub 1} {yields} 0.

  13. Manufacturing the LINAC4 PI-Mode Structure Prototype at CERN

    CERN Document Server

    Favre, A; Dallocchio, A; Geisser, J M; Gentini, L; Gerigk, L; Mathot, S; Polini, M; Sgobba, S; Tardy, T; Wegner, R

    2011-01-01

    The PI-Mode Structure (PIMS) of Linac4 consists of 7-cell cavities made from alternating OFE copper discs and rings welded together with electron beam (EB) welding. A full-scale prototype cavity of almost 1.5 m in length has been manufactured, assembled, and tested at CERN to prepare the series production of 12 PIMS cavities as part of an international collaboration. This paper reports on the construction experience including machining operations, EB welding, vacuum brazing, and metrological measurements results.

  14. Analysis of Higher Order Modes in Large Superconducting Radio Frequency Accelerating Structures

    CERN Document Server

    Galek, Tomasz; Brackebusch, Korinna; Van Rienen, Ursula

    2015-01-01

    Superconducting radio frequency cavities used for accelerating charged particle beams are commonly used in accelerator facilities around the world. The design and optimization of modern superconducting RF cavities requires intensive numerical simulations. Vast number of operational parameters must be calculated to ensure appropriate functioning of the accelerating structures. In this study, we primarily focus on estimation and behavior of higher order modes in superconducting RF cavities connected in chains. To calculate large RF models the state-space concatenation scheme, an efficient hybrid method, is employed.

  15. Electron temperature structures associated with magnetic tearing modes in the Madison Symmetric Torus

    Science.gov (United States)

    Stephens, Hillary Dianne

    Tearing mode induced magnetic islands have a significant impact on the thermal characteristics of magnetically confined plasmas such as those in the reversed-field-pinch. Using a state-of-the-art Thomson scattering (TS) diagnostic, electron temperature fluctuations correlated with magnetic tearing modes have been observed on the Madison Symmetric Torus reversed-field-pinch. The TS diagnostic consists of two independently triggerable Nd:YAG lasers that can each pulse up to 15 times each plasma discharge and 21 General Atomics polchromators equipped with avalanche photodiode modules. Detailed calibrations focusing on accuracy, ease of use and repeatability and in-situ measurements have been performed on the system. Electron temperature (Te) profiles are acquired at 25 kHz with 2 cm or less resolution along the minor radius, sufficient to measure the effect of an island on the profile as the island rotates by the measurement point. Bayesian data analysis techniques are developed and used to detect fluctuations over an ensemble of shots. Four cases are studied; standard plasmas in quiescent periods, through sawteeth, through core reconnection events and in plasmas where the tearing mode activity is decreased. With a spectrum of unstable tearing modes, remnant islands that tend to flatten the temperature profile are present in the core between sawtooth-like reconnection events. This flattening is characteristic of rapid parallel heat conduction along helical magnetic field lines. The spatial structure of the temperature fluctuations show that the location of the rational surface of the m/n = 1/6 tearing mode is significantly further in than equilibrium suggestions predict. The fluctuations also provide a measurement of the remnant island width which is significantly smaller than the predicted full island width. These correlated fluctuations disappear during both global and core reconnection events. In striking contrast to temperature flattening, a temperature gradient

  16. Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen

    NARCIS (Netherlands)

    Do, Huyen Thi; Dao, Khoa Trong; Nguyen, Viet Khanh Hoang; Le Ngoc, Giang; Nguyen, Phuong Thi Mai; Le, Lam Tung; Phung, Nguyet Thu; M. van Straalen, Nico; Roelofs, Dick; Truong, Hai Nam

    2017-01-01

    Objective: In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen

  17. Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode.

    Science.gov (United States)

    Bae, Ji-Eun; Kim, In Jung; Nam, Ki Hyun

    2017-11-04

    Glucose isomerase (GI) is an intramolecular oxidoreductase that interconverts aldoses and ketoses. These characteristics are widely used in the food, detergent, and pharmaceutical industries. In order to obtain an efficient GI, identification of novel GI genes and substrate binding/inhibition have been studied. Xylitol is a well-known inhibitor of GI. In Streptomyces rubiginosus, two crystal structures have been reported for GI in complex with xylitol inhibitor. However, a structural comparison showed that xylitol can have variable conformation at the substrate binding site, e.g., a nonspecific binding mode. In this study, we report the crystal structure of S. rubiginosus GI in a complex with xylitol and glycerol. Our crystal structure showed one metal binding mode in GI, which we presumed to represent the inactive form of the GI. The metal ion was found only at the M1 site, which was involved in substrate binding, and was not present at the M2 site, which was involved in catalytic function. The O 2 and O 4 atoms of xylitol molecules contributed to the stable octahedral coordination of the metal in M1. Although there was no metal at the M2 site, no large conformational change was observed for the conserved residues coordinating M2. Our structural analysis showed that the metal at the M2 site was not important when a xylitol inhibitor was bound to the M1 site in GI. Thus, these findings provided important information for elucidation or engineering of GI functions. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Sulfate-reducing bacteria inhabiting natural corrosion deposits from marine steel structures.

    Science.gov (United States)

    Païssé, Sandrine; Ghiglione, Jean-François; Marty, Florence; Abbas, Ben; Gueuné, Hervé; Amaya, José Maria Sanchez; Muyzer, Gerard; Quillet, Laurent

    2013-08-01

    In the present study, investigations were conducted on natural corrosion deposits to better understand the role of sulfate-reducing bacteria (SRB) in the accelerated corrosion process of carbon steel sheet piles in port environments. We describe the abundance and diversity of total and metabolically active SRB within five natural corrosion deposits located within tidal or low water zone and showing either normal or accelerated corrosion. By using molecular techniques, such as quantitative real-time polymerase chain reaction, denaturing gel gradient electrophoresis, and sequence cloning based on 16S rRNA, dsrB genes, and their transcripts, we demonstrated a clear distinction between SRB population structure inhabiting normal or accelerated low-water corrosion deposits. Although SRB were present in both normal and accelerated low-water corrosion deposits, they dominated and were exclusively active in the inner and intermediate layers of accelerated corrosion deposits. We also highlighted that some of these SRB populations are specific to the accelerated low-water corrosion deposit environment in which they probably play a dominant role in the sulfured corrosion product enrichment.

  19. Rice root-associated bacteria: insights into community structures across 10 cultivars.

    Science.gov (United States)

    Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

    2011-07-01

    In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined, to a large extent, the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa ssp. indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of 'improved' and 'traditional' plants was noted for all communities analyzed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae, were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed among rice replicates. These findings suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  20. Rice root-associated bacteria – insights in community structures across ten cultivars

    Science.gov (United States)

    Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

    2015-01-01

    In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

  1. A new fuzzy sliding mode controller for vibration control systems using integrated-structure smart dampers

    Science.gov (United States)

    Dzung Nguyen, Sy; Kim, Wanho; Park, Jhinha; Choi, Seung-Bok

    2017-04-01

    Vibration control systems using smart dampers (SmDs) such as magnetorheological and electrorheological dampers (MRD and ERD), which are classified as the integrated structure-SmD control systems (ISSmDCSs), have been actively researched and widely used. This work proposes a new controller for a class of ISSmDCSs in which high accuracy of SmD models as well as increment of control ability to deal with uncertainty and time delay are to be expected. In order to achieve this goal, two formualtion steps are required; a non-parametric SmD model based on an adaptive neuro-fuzzy inference system (ANFIS) and a novel fuzzy sliding mode controller (FSMC) which can weaken the model error of the ISSmDCSs and hence provide enhanced vibration control performances. As for the formulation of the proposed controller, first, an ANFIS controller is desgned to identify SmDs using the improved control algorithm named improved establishing neuro-fuzzy system (establishing neuro-fuzzy system). Second, a new control law for the FSMC is designed via Lyapunov stability analysis. An application to a semi-active MRD vehicle suspension system is then undertaken to illustrate and evaluate the effectiveness of the proposed control method. It is demonstrated through an experimental realization that the FSMC proposed in this work shows superior vibration control performance of the vehicle suspension compared to other surveyed controller which have similar structures to the FSMC, such as fuzzy logic and sliding mode control.

  2. Propagation of whistler mode chorus to low altitudes: Spacecraft observations of structured ELF hiss

    Science.gov (United States)

    SantolíK, O.; Chum, J.; Parrot, M.; Gurnett, D. A.; Pickett, J. S.; Cornilleau-Wehrlin, N.

    2006-10-01

    We interpret observations of low-altitude electromagnetic ELF hiss observed on the dayside at subauroral latitudes. A divergent propagation pattern has been reported between 50° and 75° of geomagnetic latitude. The waves propagate with downward directed wave vectors which are slightly equatorward inclined at lower magnetic latitudes and slightly poleward inclined at higher latitudes. Reverse ray tracing using different plasma density models indicates a possible source region near the geomagnetic equator at a radial distance between 5 and 7 Earth radii by a mechanism acting on highly oblique wave vectors near the local Gendrin angle. We analyze waveforms received at altitudes of 700-1200 km by the Freja and DEMETER spacecraft and we find that low-altitude ELF hiss contains discrete time-frequency structures resembling wave packets of whistler mode chorus. Emissions of chorus also predominantly occur on the dawnside and dayside and have recently been considered as a possible source of highly accelerated electrons in the outer Van Allen radiation belt. Detailed measurements of the Cluster spacecraft at radial distances of 4-5 Earth radii show chorus propagating downward from the source region localized close to the equator. The time-frequency structure and frequencies of chorus observed by Cluster along the reverse raypaths of ELF hiss are consistent with the hypothesis that the frequently observed dayside ELF hiss is just the low-altitude manifestation of natural magnetospheric emissions of whistler mode chorus.

  3. On the structure and the antisymmetric ν3 IR mode of covalent azide group

    Science.gov (United States)

    Rozenberg, Mark; Tibika-Apfelbaum, Francoise

    2013-03-01

    A new correlation ν3 = 1997 + 1.17 × 103 Δr between the stretching mode ν3 of the IR band frequency and the bond length asymmetry expressed as Δr ≡ r(Nα - Nβ) - r(Nβ - Nγ) is established in molecular azides Rsbnd Nαsbnd Nβsbnd Nγ with the correlation coefficient R = 0.972. The database represents recent spectral and structural information for more than fifty organic molecules and inorganic metal complexes. Because the absolute term practically coincides with the ν3 frequency value for the free azide group, this correlation shows that the blue shift Δν3 (in cm-1) of the ν3 from the free azide value varies in direct proportion with the N3 group asymmetry Δr (in Å) (Δν3 = 1.17 × 103 Δr) at formation of different azide structures.

  4. Computation of coupling elements between waveguides and modes for large launching structures

    International Nuclear Information System (INIS)

    Hurtak, O.; Preinhaelter, J.

    1989-05-01

    Optimization of large launching structures - grills and multijunction grills which are intended for lower hybrid current drive in big tokamaks - calls for quick and sufficiently precise computation of the coupling elements between waveguides and modes. The original method of computation is described which is efficient for small structures only and is based on integration along the real axis. For computation of coupling elements between more distant waveguides another method of integration is developed which uses a shift of the integration path. For this purpose, the analytical continuation of the plasma surface impedance into the complex N z -plane is calculated and a new numerical code developed. Some numerical results are given to compare both methods. A combination of both methods speeds up the computation needed for the grill design. (author). 2 figs., 2 tabs., 2 refs

  5. Application of Dynamic Mode Decomposition: Temporal Evolution of Flow Structures in an Aneurysm

    Science.gov (United States)

    Conlin, William; Yu, Paulo; Durgesh, Vibhav

    2017-11-01

    An aneurysm is an enlargement of a weakened arterial wall that can be fatal or debilitating on rupture. Aneurysm hemodynamics is integral to developing an understanding of aneurysm formation, growth, and rupture. The flow in an aneurysm exhibits complex fluid dynamics behavior due to an inherent unsteady inflow condition and its interactions with large-scale flow structures present in the aneurysm. The objective of this study is to identify the large-scale structures in the aneurysm, study temporal behavior, and quantify their interaction with the inflow condition. For this purpose, detailed Particle Image Velocimetry (PIV) measurements were performed at the center plane of an idealized aneurysm model for a range of inflow conditions. Inflow conditions were precisely controlled using a ViVitro SuperPump system. Dynamic Modal Decomposition (DMD) of the velocity field was used to identify coherent structures and their temporal behavior. DMD was successful in capturing the large-scale flow structures and their temporal behavior. A low dimensional approximation to the flow field was obtained with the most relevant dynamic modes and was used to obtain temporal information about the coherent structures and their interaction with the inflow, formation, evolution, and growth.

  6. The Structural Connectivity Pattern of the Default Mode Network and Its Association with Memory and Anxiety.

    Science.gov (United States)

    Tao, Yan; Liu, Bing; Zhang, Xiaolong; Li, Jin; Qin, Wen; Yu, Chunshui; Jiang, Tianzi

    2015-01-01

    The default mode network (DMN) is one of the most widely studied resting state functional networks. The structural basis for the DMN is of particular interest and has been studied by several researchers using diffusion tensor imaging (DTI). Most of these previous studies focused on a few regions or white matter tracts of the DMN so that the global structural connectivity pattern and network properties of the DMN remain unclear. Moreover, evidences indicate that the DMN is involved in both memory and emotion, but how the DMN regulates memory and anxiety from the perspective of the whole DMN structural network remains unknown. We used multimodal neuroimaging methods to investigate the structural connectivity pattern of the DMN and the association of its network properties with memory and anxiety in 205 young healthy subjects with age ranging from 18 to 29 years old. The Group ICA method was used to extract the DMN component from functional magnetic resonance imaging (fMRI) data and a probabilistic fiber tractography technique based on DTI data was applied to construct the global structural connectivity pattern of the DMN. Then we used the graph theory method to analyze the DMN structural network and found that memory quotient (MQ) score was significantly positively correlated with the global and local efficiency of the DMN whereas anxiety was found to be negatively correlated with the efficiency. The strong structural connectivity between multiple brain regions within DMN may reflect that the DMN has certain structural basis. Meanwhile, the results we found that the network efficiency of the DMN were related to memory and anxiety measures, indicated that the DMN may play a role in the memory and anxiety.

  7. Strain sensor based on gourd-shaped single-mode-multimode-single-mode hybrid optical fibre structure.

    Science.gov (United States)

    Tian, Ke; Farrell, Gerald; Wang, Xianfan; Yang, Wenlei; Xin, Yifan; Liang, Haidong; Lewis, Elfed; Wang, Pengfei

    2017-08-07

    A fibre-optic strain sensor based on a gourd-shaped joint multimode fibre (MMF) sandwiched between two single-mode fibres (SMFs) is described both theoretically and experimentally. The cladding layers of the two MMFs are reshaped to form a hemisphere using an electrical arc method and spliced together, yielding the required gourd shape. The gourd-shaped section forms a Fabry-Perot cavity between the ends of two adjacent but non-contacting multimode fibres' core. The effectiveness of the multimode interference based on the Fabry-Perot interferometer (FPI) formed within the multimode inter-fibre section is greatly improved resulting in an experimentally determined strain sensitivity of -2.60 pm/με over the range 0-1000 με. The sensing characteristics for temperature and humidity of this optical fibre strain sensor are also investigated.

  8. Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria

    NARCIS (Netherlands)

    Hijum, S.A.F.T. van; Kralj, S.; Ozimek, L.K.; Dijkhuizen, L.; Geel-Schutten, G.H. van

    2006-01-01

    Lactic acid bacteria (LAB) employ sucrase-type enzymes to convert sucrose into homopolysaccharides consisting of either glucosyl units (glucans) or fructosyl units (fructans). The enzymes involved are labeled glucansucrases (GS) and fructansucrases (FS), respectively. The available molecular,

  9. Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community

    Directory of Open Access Journals (Sweden)

    Parro Víctor

    2010-06-01

    Full Text Available Abstract Background Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy. Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers. In the Río Tinto (Spain, brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum spp. (L. ferrooxidans and L. ferriphilum and Acidithiobacillus ferrooxidans are abundant. These microorganisms play a critical role in bioleaching processes for industrial (biominery and environmental applications (acid mine drainage, bioremediation. The aim of this study was to investigate the physiological differences between the free living (planktonic and the sessile (biofilm associated lifestyles of Leptospirillum spp. as part of its natural extremely acidophilic community. Results Total RNA extracted from environmental samples was used to determine the composition of the metabolically active members of the microbial community and then to compare the biofilm and planktonic environmental transcriptomes by hybridizing to a genomic microarray of L. ferrooxidans. Genes up-regulated in the filamentous biofilm are involved in cellular functions related to biofilm formation and maintenance, such as: motility and quorum sensing (mqsR, cheAY, fliA, motAB, synthesis of cell wall structures (lnt, murA, murB, specific proteases (clpX/clpP, stress response chaperons (clpB, clpC, grpE-dnaKJ, groESL, etc. Additionally, genes involved in mixed acid fermentation (poxB, ackA were up-regulated in the biofilm. This result, together with the presence of small organic acids like acetate and formate (1.36 mM and 0.06 mM respectively in the acidic (pH 1.8 water stream, suggests that either L. ferrooxidans or other member of the microbial community are producing acetate in the acidophilic biofilm under microaerophilic conditions. Conclusions Our results indicate that the

  10. Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season.

    Science.gov (United States)

    Yamaguchi, Nobuyasu; Baba, Takashi; Ichijo, Tomoaki; Himezawa, Yuka; Enoki, Kanami; Saraya, Makoto; Li, Pin-Fang; Nasu, Masao

    2016-01-01

    Approximately 180 t/km(2) of Asian dust particles are estimated to fall annually on Beijing, China, and there is significant concern about the influence of microbes transported by Asian dust events on human health and downwind ecosystems. In this study, we collected Asian dust particles in Beijing, and analyzed the bacterial communities on these particles by culture-independent methods. Bacterial cells on Asian dust particles were visualized first by laser scanning microscopy, which demonstrated that Asian dust particles carry bacterial cells to Beijing. Bacterial abundance, as determined by quantitative polymerase chain reaction (PCR), was 10(8) to 10(9) cells/g, a value about 10 times higher than that in Asian dust source soils. Inter-seasonal variability of bacterial community structures among Asian dust samples, as compared by terminal restriction fragment length polymorphism (T-RFLP), was low during the Asian dust season. Several viable bacteria, including intestinal bacteria, were found in Asian dust samples by denaturing gradient gel electrophoresis (DGGE). Clone library analysis targeting 16S ribosomal RNA (rRNA) gene sequences demonstrated that bacterial phylogenetic diversity was high in the dust samples, and most of these were environmental bacteria distributed in soil and air. The dominant species in the clone library was Segetibacter aerophilus (Bacteroidetes), which was first isolated from an Asian dust sample collected in Korea. Our results also indicate the possibility of a change in the bacterial community structure during transportation and increases in desiccation-tolerant bacteria such as Firmicutes.

  11. The three-dimensional structure of CFA/I adhesion pili: traveler's diarrhea bacteria hang on by a spring.

    Science.gov (United States)

    Mu, Xiang-Qi; Savarino, Stephen J; Bullitt, Esther

    2008-02-22

    To survive the harsh environment of a churning intestinal tract, bacteria attach to the host epithelium via thin fibers called pili (or fimbriae). Enterotoxigenic Escherichia coli bacteria expressing colonization factor antigen I (CFA/I) pili and related pili are the most common known bacterial cause of diarrheal disease, including traveler's diarrhea. CFA/I pili, assembled via the alternate chaperone pathway, are essential for binding and colonization of the small bowel by these pathogenic bacteria. Herein, we elucidate unique structural features of CFA/I pili that appear to optimize their function as bacterial tethers in the intestinal tract. Using transmission electron microscopy of negatively stained samples in combination with iterative three-dimensional helical reconstruction methods for image processing, we determined the structure of the CFA/I pilus filament. Our results indicate that strong end-to-end protein interactions and weak interactions between the coils of a sturdy spring-like helix provide the combination of strength, stability, and flexibility required to sustain bacterial adhesion and incite intestinal disease. We propose that CFA/I pili behave like a spring to maintain attachment to the gut lining during vortex mixing and downward flow of the intestinal contents, thereby persisting long enough for these bacteria to colonize the host epithelium and cause enteric disease.

  12. Analysis of complex elastic structures by a Rayleigh-Ritz component modes method using Lagrange multipliers. Ph.D. Thesis

    Science.gov (United States)

    Klein, L. R.

    1974-01-01

    The free vibrations of elastic structures of arbitrary complexity were analyzed in terms of their component modes. The method was based upon the use of the normal unconstrained modes of the components in a Rayleigh-Ritz analysis. The continuity conditions were enforced by means of Lagrange Multipliers. Examples of the structures considered are: (1) beams with nonuniform properties; (2) airplane structures with high or low aspect ratio lifting surface components; (3) the oblique wing airplane; and (4) plate structures. The method was also applied to the analysis of modal damping of linear elastic structures. Convergence of the method versus the number of modes per component and/or the number of components is discussed and compared to more conventional approaches, ad-hoc methods, and experimental results.

  13. Characterizing structure connectivity correlation with the default mode network in Alzheimer's patients and normal controls

    Science.gov (United States)

    Guo, Jia; Xu, Peng; Song, Chao; Yao, Li; Zhao, Xiaojie

    2012-03-01

    Magnetic resonance diffusion tensor imaging (DTI) is a kind of effective measure to do non-invasive investigation on brain fiber structure at present. Studies of fiber tracking based on DTI showed that there was structural connection of white matter fiber among the nodes of resting-state functional network, denoting that the connection of white matter was the basis of gray matter regions in functional network. Nevertheless, relationship between these structure connectivity regions and functional network has not been clearly indicated. Moreover, research of fMRI found that activation of default mode network (DMN) in Alzheimer's disease (AD) was significantly descended, especially in hippocampus and posterior cingulated cortex (PCC). The relationship between this change of DMN activity and structural connection among functional networks needs further research. In this study, fast marching tractography (FMT) algorithm was adopted to quantitative calculate fiber connectivity value between regions, and hippocampus and PCC which were two important regions in DMN related with AD were selected to compute white matter connection region between them in elderly normal control (NC) and AD patient. The fiber connectivity value was extracted to do the correlation analysis with activity intensity of DMN. Results showed that, between PCC and hippocampus of NC, there exited region with significant high connectivity value of white matter fiber whose performance has relatively strong correlation with the activity of DMN, while there was no significant white matter connection region between them for AD patient which might be related with reduced network activation in these two regions of AD.

  14. Bound acoustic modes in the radiation continuum in isotropic layered systems without periodic structures

    Science.gov (United States)

    Maznev, A. A.; Every, A. G.

    2018-01-01

    We study the existence of guided acoustic modes in layered structures whose phase velocity is higher than that of bulk waves in a solid substrate or an adjacent fluid half space, which belong to the class of bound states in the radiation continuum (BICs). We demonstrate that in contrast to the electromagnetic case, non-symmetry-protected BICs exist in isotropic layered systems without periodic structures. Two systems supporting non-symmetry-protected sagittally polarized BICs have been identified: (i) a supported solid layer yields BICs whose phase velocity is higher than the transverse velocity of the substrate but lower than the longitudinal velocity; (ii) a supported solid layer loaded by a fluid half space supports BICs whose velocity is higher that the bulk velocity of the fluid but lower than acoustic velocities of the substrate. The latter case is a unique example of BICs in the sense that it does not involve an evanescent field in the fluid half space providing the radiation continuum. In either case, BICs are represented by isolated points in the dispersion relations located within "leaky" branches. We show that these BICs are robust with respect to small perturbations of the system parameters. Numerical results are provided for realistic materials combinations. We also show that no BICs exist in all-fluid layered structures, whereas in solid layered structures there are no shear horizontal BICs and no sagittally polarized BICs whose velocity exceeds the longitudinal velocity of the substrate.

  15. Aging influence on grey matter structural associations within the default mode network utilizing Bayesian network modeling

    Directory of Open Access Journals (Sweden)

    Yan eWang

    2014-05-01

    Full Text Available Recent neuroimaging studies have revealed normal aging-related alterations in functional and structural brain networks such as the default mode network (DMN. However, less is understood about specific brain structural dependencies or interactions between brain regions within the DMN in the normal aging process. In this study, using Bayesian network (BN modeling, we analyzed grey matter volume data from 109 young and 82 old subjects to characterize the influence of aging on associations between core brain regions within the DMN. Furthermore, we investigated the discriminability of the aging-associated BN models for the young and old groups. Compared to their young counterparts, the old subjects showed significant reductions in connections from right inferior temporal cortex (ITC to medial prefrontal cortex (mPFC, right hippocampus (HP to right ITC, and mPFC to posterior cingulate cortex (PCC and increases in connections from left HP to mPFC and right inferior parietal cortex (IPC to right ITC. Moreover, the classification results showed that the aging-related BN models could predict group membership with 88.48% accuracy, 88.07% sensitivity and 89.02% specificity. Our findings suggest that structural associations within the DMN may be affected by normal aging and provide crucial information about aging effects on brain structural networks.

  16. THE IMMUNOLOGICAL STRUCTURE OF POPULATION OF KARAKUL LAMBS BUCCINATED AGAINST CONDITIONALLY AND ACUTE PATHOGENOUS BACTERIA

    Directory of Open Access Journals (Sweden)

    Rachmatullo Ruzikulov

    2014-12-01

    Full Text Available Antibodies, developing in animal and human organisms against antigens of external and internal origin are not limited with opsonization functions, lying on the base of formation of humoral immunity. Being the product of somatic mutations of plasmatic cells, according to clonal selection theory of immunity, they themselves are also alien proteins for organisms. Thus, they themselves also begin to display antigen pressure on the immune competent system. So, they will start themselves the elaboration of antibodies against them, which are called anti–idiotypic ones. Anti–idiotypic antibodies, imitating the corresponding bacterial and virus antigens are able to initiate the immune response of animal organism against them, which play great immune modulating role. The immunological structure of populations of Karakul sheep lambs vaccinated against E. coli bacteria, salmonellosis and anthrax antigen from the age of 2–3 days till 2–3 weeks was studied. Experiments were carried out in the 1–2, 3–4, 5–6, 7–8, 9–10 and 11–12 weeks old Karakul lambs. Experimental lambs during appraisal were vaccinated once by associated hydroxide aluminum form vaccine against paratyphoid and coli bacteriosis of calves, pigs and lambs. In another experiment, the lambs were immunized by rare naturally occurring bacterial antigen. As such an immunogenic was selected sterile soluble anthrax antigen. Developed and tested in the application of Ascoli reaction the role of anti–idiotype antibodies in the formation of natural immunity against opportunistic pathogens identified the nature of normal antibodies was studied. The nature of wavelike character of the immune reaction of an organism of newborn animals of vaccination was revealed. Also the immunomodulation role of anti–idiotypic antibodies was determined.

  17. The hot prototype of the Pi-mode structure for LINAC4

    CERN Document Server

    Gerigk, F; Bourquin, P; Dallocchio, A; Favre, G; Geisser, J M; Gentini, L; Giguet, J M; Mathot, S; Polini, M; Pugnat, D; Riffaud, B; Sgobba, S; Tardy, T; Ugena Tirado, P; Vretenar, M

    2010-01-01

    The PIMS (Pi-Mode-Structure) cavities for Linac4 are made of 7 coupled cells operating in !-mode at a frequency of 352 MHz. The mechanical concept is derived from the 5-cell cavities used in the LEP machine, whereas cell length and coupling are adapted for proton acceleration in the range from 50 to 160 MeV. Linac4 will be the first machine to employ this type of cavities for low-beta protons. During the first years of operation the PIMS will be used at low duty cycle (0.1%) as part of the consolidated LHC proton injector complex. It is designed, however, to operate eventually in a high duty cycle (10%) proton injector, which could be used as proton front-end for neutrino or RIB applications. To prepare for the series construction of the 12 PIMS units the first cavity (102 MeV beam energy) has been designed and constructed at CERN, to be used as a hot prototype for RF tests and as a pre-series mechanical unit. In this paper we report on some of the design features, the construction experience, and first measu...

  18. Tuning procedure for the Linac4 PI Mode Structure(PIMS)

    CERN Document Server

    Ugena Tirado, P

    2012-01-01

    PI-Mode-Structure (PIMS) cavities will be used in the high energy section of LINAC4 (102-160 MeV). Each cavity is made of 7 coupled cells, operated in the π-mode at a resonant frequency of 352.2 MHz. The cell length remains constant for each of the 12 cavities but changes from cavity to cavity to synchronise with the increased beam energy. This paper reports on the tuning process required to get a constant voltage in each cell at the resonant frequency which consists of re-machining to the required level the tuning rings located on each cell-wall. An algorithm based on single cell detuning, equivalent circuit simulations and precise 3D simulations for the 3 different cell types of each cavity has been developed and successfully applied to the tuning of the first PIMS cavity. In order to reduce the simulation effort for the remaining 11 cavities, an interpolation algorithm based on 3 cavities has been developed and validated. In a second tuning step, after the electron beam welding of all elements, the final ...

  19. Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists.

    Directory of Open Access Journals (Sweden)

    Sehan Lee

    Full Text Available The flexible hydrophobic ligand binding pocket (LBP of estrogen receptor α (ERα allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicable to other nuclear receptors.

  20. An optimized variational mode decomposition for extracting weak feature of viscoelastic sandwich cylindrical structures

    Science.gov (United States)

    Guo, Yanfei; Zhang, Zhousuo; Cao, Jianbin; Gong, Teng; Yang, Wenzhan

    2018-03-01

    Variational mode decomposition (VMD), which is an alternative to empirical mode decomposition (EMD), has been widely used to extract the feature components of nonstationary signals. However, as a parameterized method, the performance of VMD is heavily influenced by its parameters. Meanwhile, it cannot efficiently extract weak feature components submerged in powerful ones. To address these problems, a novel method based on an optimized VMD is developed for precisely extracting the weak feature of viscoelastic sandwich cylindrical structures (VSCSs). In this method, a parameter optimization algorithm first is proposed to simultaneously select the crucial parameters in the VMD, and to reveal the characteristics of the influence of these parameters on the decomposition performance. Then, the weak feature components submerged in low-frequency strong ones are extracted twice by using the VMD with the optimized parameters. The effectiveness of the proposed method is verified by simulation signals and the experiment vibration signal collected from the VSCS. Its robustness to noise is also discussed. The results indicate that the parameter optimization algorithm can adaptively obtain optimal parameters, and compared with the optimized complementary ensemble EMD (CEEMD) and the original VMD, the proposed method can precisely extract the weak feature components submerged in strong ones.

  1. Structure, stability and ELM dynamics of the H-mode pedestal in DIII-D

    International Nuclear Information System (INIS)

    Fenstermacher, M.E.; Leonard, A.W.; Osborne, T.H.

    2005-01-01

    Experiments are described that have increased understanding of the transport and stability physics that set the H-mode edge pedestal width and height, determine the onset of Type-I edge localized modes (ELMs), and produce the nonlinear dynamics of the ELM perturbation in the pedestal and scrape-off layer (SOL). Predictive models now exist for the n e pedestal profile and the p e height at the onset of Type-I ELMs, and progress has been made toward predictive models of the T e pedestal width and nonlinear ELM evolution. Similarity experiments between DIII-D and JET suggested that neutral penetration physics dominates in the relationship between the width and height of the n e pedestal while plasma physics dominates in setting the T e pedestal width. Measured pedestal conditions including edge current at ELM onset agree with intermediate-n peeling-ballooning (P-B) stability predictions. Midplane ELM dynamics data show the predicted (P-B) structure at ELM onset, large rapid variations of the SOL parameters, and fast radial propagation in later phases, similar to features in nonlinear ELM simulations. (author)

  2. Enhancement of Fracture Resistance by Multiple Cracks in Layered Structures under Mode I and Mix Mode Loading

    DEFF Research Database (Denmark)

    Goutianos, Stergios; Sørensen, Bent F.

    beams bonded together with a thermoset adhesive, more delamination cracks could be developed next to the main/primary adhesive/laminate crack. An analytical model, based on the J integral, was developed for multiple delaminations [3]. It is shown that the maximum possible increase (upper limit......Layered structures are susceptible to delamination because they often exhibit low interlaminar fracture resistance. Through-thickness stresses e.g. due to manufacturing defects or geometric discontinuities, can result in growing interlaminar cracks which may lead to loss of structural integrity [1...

  3. Structure and mode of action of cyclic lipopeptide pseudofactin II with divalent metal ions.

    Science.gov (United States)

    Janek, Tomasz; Rodrigues, Lígia R; Gudiña, Eduardo J; Czyżnikowska, Żaneta

    2016-10-01

    The interaction of natural lipopeptide pseudofactin II with a series of doubly charged metal cations was examined by matrix-assisted laser-desorption ionization-time of flight (MALDI-TOF) mass spectrometry and molecular modelling. The molecular modelling for metal-pseudofactin II provides information on the metal-peptide binding sites. Overall, Mg(2+), Ca(2+) and Zn(2+) favor the association with oxygen atoms spanning the peptide backbone, whereas Cu(2+) is coordinated by three nitrogens. Circular dichroism (CD) results confirmed that Zn(2+) and Cu(2+) can disrupt the secondary structure of pseudofactin II at high concentrations, while Ca(2+) and Mg(2+) did not essentially affect the structure of the lipopeptide. Interestingly, our results showed that the addition of Zn(2+) and Cu(2+) helped smaller micelles to form larger micellar aggregates. Since pseudofactin II binds metals, we tested whether this phenomena was somehow related to its antimicrobial activity against Staphylococcus epidermidis and Proteus mirabilis. We found that the antimicrobial effect of pseudofactin II was increased by supplementation of culture media with all tested divalent metal ions. Finally, by using Gram-positive and Gram-negative bacteria we showed that the higher antimicrobial activity of metal complexes of pseudofactin II is attributed to the disruption of the cytoplasmic membrane. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Nonlinear control system for optical interferometry based on variable structure control and sliding modes.

    Science.gov (United States)

    Martin, Roberta I; Sakamoto, João M S; Teixeira, Marcelo C M; Martinez, Guilherme A; Pereira, Fernando C; Kitano, Cláudio

    2017-03-20

    This work presents a novel nonlinear control system designed for interferometry based on variable structure control and sliding modes. This approach can fully compensate the nonlinear behavior of the interferometer and lead to high accuracy control for large disturbances, featuring low cost, ease of implementation and high robustness, without a reset circuit (when compared with a linear control system). A deep stability analysis was accomplished and the global asymptotic stability of the system was proved. The results showed that the nonlinear control is able to keep the interferometer in the quadrature point and suppress signal fading for arbitrary signals, sinusoidal signals, or zero input signal, even under strong external disturbances. The system showed itself suitable to characterize a multi-axis piezoelectric flextentional actuator, which displacements that are much smaller than half wavelength. The high robustness allows the system to be embedded and to operate in harsh environments as factories, bringing the interferometry outside the laboratory.

  5. The study of antilock braking system based on sliding mode variable structure control

    Science.gov (United States)

    Liu, GuoFu; Zhang, Qi; Wang, Yueke; Liu, Bo

    2006-11-01

    The friction characteristic between road surface and tire makes the anti-lock braking system (ABS) take on the properties of nonlinearity, time variation and uncertainties. The sliding mode variable structure controller (SMVSC) has strong robust ability in dealing with uncertainties including the model error and unknown interference, so SMVSC is used in ABS extensively. In order to achieve expected performance, SMVSC has to identify the road characteristics in real time. The mathematical model of ABS is established, and the application of SMVSC in ABS is realized. One kind of estimation algorithm of optimal slip ratio based on the shape of μ-λ curve is proposed. By computer simulation, the feasibility and validity of SMVSC based on optimal slip ratio is verified.

  6. Spinor-electron wave guided modes in coupled quantum wells structures by solving the Dirac equation

    Energy Technology Data Exchange (ETDEWEB)

    Linares, Jesus [Area de Optica, Departamento de Fisica Aplicada, Facultade de Fisica, Escola Universitaria de Optica e Optometria, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Galicia (Spain)], E-mail: suso.linares.beiras@usc.es; Nistal, Maria C. [Area de Optica, Departamento de Fisica Aplicada, Facultade de Fisica, Escola Universitaria de Optica e Optometria, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Galicia (Spain)

    2009-05-04

    A quantum analysis based on the Dirac equation of the propagation of spinor-electron waves in coupled quantum wells, or equivalently coupled electron waveguides, is presented. The complete optical wave equations for Spin-Up (SU) and Spin-Down (SD) spinor-electron waves in these electron guides couplers are derived from the Dirac equation. The relativistic amplitudes and dispersion equations of the spinor-electron wave-guided modes in a planar quantum coupler formed by two coupled quantum wells, or equivalently by two coupled slab electron waveguides, are exactly derived. The main outcomes related to the spinor modal structure, such as the breaking of the non-relativistic degenerate spin states, the appearance of phase shifts associated with the spin polarization and so on, are shown.

  7. Molecular microbiology of gut bacteria: genetic diversity and community structure analysis.

    Science.gov (United States)

    Peterka, M; Tepsic, Katarina; Accetto, T; Kostanjsek, R; Ramsak, Andreja; Lipoglavsek, L; Avgustin, G

    2003-01-01

    Recently developed molecular biology approaches make possible the detailed genetic, taxonomic and ecological examination of microorganisms from various habitats. Animal gut represents one of the most complex microbial ecosystems with a large degree of microbial biodiversity present. Bacteria inhabiting the gut usually play important roles in metabolic transformations of substrates and sometimes, e.g. in ruminants, they make the basis for an obligate symbiosis with the host. Here we discuss molecular microbiology as a strategy for examination of gut bacteria, concentrating on a typical and in such environment dominant group of strictly anaerobic Gram-negative bacteria from the phylogenetic group Cytophaga/Flexibacter/Bacteroides. The bacteria from the genus Prevotella are the most abundant Gram-negative bacteria in the rumen and form a distinctive phylogenetic cluster, clearly separated from prevotellas isolated from other ecological niches. They may represent a good choice for a model organism in genetic manipulation experiments and for studies of gene transfer mechanisms taking place in the gut. The molecular tools for detection and monitoring of ruminal prevotellas are discussed.

  8. One-step sol-gel imprint lithography for guided-mode resonance structures.

    Science.gov (United States)

    Huang, Yin; Liu, Longju; Johnson, Michael; C Hillier, Andrew; Lu, Meng

    2016-03-04

    Guided-mode resonance (GMR) structures consisting of sub-wavelength periodic gratings are capable of producing narrow-linewidth optical resonances. This paper describes a sol-gel-based imprint lithography method for the fabrication of submicron 1D and 2D GMR structures. This method utilizes a patterned polydimethylsiloxane (PDMS) mold to fabricate the grating coupler and waveguide for a GMR device using a sol-gel thin film in a single step. An organic-inorganic hybrid sol-gel film was selected as the imprint material because of its relatively high refractive index. The optical responses of several sol-gel GMR devices were characterized, and the experimental results were in good agreement with the results of electromagnetic simulations. The influence of processing parameters was investigated in order to determine how finely the spectral response and resonant wavelength of the GMR devices could be tuned. As an example potential application, refractometric sensing experiments were performed using a 1D sol-gel device. The results demonstrated a refractive index sensitivity of 50 nm/refractive index unit. This one-step fabrication process offers a simple, rapid, and low-cost means of fabricating GMR structures. We anticipate that this method can be valuable in the development of various GMR-based devices as it can readily enable the fabrication of complex shapes and allow the doping of optically active materials into sol-gel thin film.

  9. Measurement of deforming mode of lattice truss structures under impact loading

    Directory of Open Access Journals (Sweden)

    Zhao H.

    2012-08-01

    Full Text Available Lattice truss structures, which are used as a core material in sandwich panels, were widely investigated experimentally and theoretically. However, explanation of the deforming mechanism using reliable experimental results is almost rarely reported, particularly for the dynamic deforming mechanism. The present work aimed at the measurement of the deforming mode of lattice truss structures. Indeed, quasi-static and Split Hopkinson Pressure Bar (SHPB tests have been performed on the tetrahedral truss cores structures made of Aluminum 3003-O. Global values such as crushing forces and displacements between the loading platens are obtained. However, in order to understand the deforming mechanism and to explain the observed impact strength enhancement observed in the experiments, images of the truss core element during the tests are recorded. A method based on the edge detection algorithm is developed and applied to these images. The deforming profiles of one beam are extracted and it allows for calculating the length of beam. It is found that these lengths diminish to a critical value (due to compression and remain constant afterwards (because of significant bending. The comparison between quasi-static and impact tests shows that the beam were much more compressed under impact loading, which could be understood as the lateral inertia effect in dynamic bucking. Therefore, the impact strength enhancement of tetrahedral truss core sandwich panel can be explained by the delayed buckling of beam under impact (more compression reached, together with the strain hardening of base material.

  10. Electromagnetic-thermal-structural coupling analysis of the ITER edge localized mode coil with flexible supports

    Science.gov (United States)

    Zhang, Shanwen; Song, Yuntao; Tang, Linlin; Wang, Zhongwei; Ji, Xiang; Du, Shuangsong

    2017-05-01

    In a fusion reactor, the edge localized mode (ELM) coil has a mitigating effect on the ELMs of the plasma. The coil is placed close to the plasma between the vacuum vessel and the blanket to reduce its design power and improve its mitigating ability. The coil works in a high-temperature, high-nuclear-heat and high-magnetic-field environment. Due to the existence of outer superconducting coils, the coil is subjected to an alternating electromagnetic force induced by its own alternating current and the outer magnetic field. The design goal for the ELM coil is to maintain its structural integrity in the multi-physical field. Taking as an example the middle ELM coil (with flexible supports) of ITER (the International Thermonuclear Fusion Reactor), an electromagnetic-thermal-structural coupling analysis is carried out using ANSYS. The results show that the flexible supports help the three-layer casing meet the static and fatigue design requirements. The structural design of the middle ELM coil is reasonable and feasible. The work described in this paper provides the theoretical basis and method for ELM coil design.

  11. Fine structure of the stimulated Raman spectrum in compressed hydrogen. The relaxation-oscillation mode of backscattered Stokes emission

    International Nuclear Information System (INIS)

    Bespalov, V.G.; Efimov, Yu.N.; Staselko, D.I.

    1992-01-01

    This paper studies the emission spectra of backscattered stimulated Raman scattering (SRS) in compressed hydrogen in the relaxation-oscillation mode and the compression SRS mode for the minimum width of the spontaneous scattering spectrum (in the region of the Dicke dip). It is shown that the generation of a train of Stokes-emission subpulses results in the appearance of fine structure in the backscattered SRS spectrum. The influence of the temporal structure of reflected Stokes pulses on this spectrum and on the appearance of fine structure in it is analyzed. The conditions for generating spectrally limited (without phase modulation), extremely coherent Stokes pulses are explained. 18 refs., 3 figs

  12. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.

    Science.gov (United States)

    Lindahl, Erik; Azuara, Cyril; Koehl, Patrice; Delarue, Marc

    2006-07-01

    Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitations associated with full dynamics simulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions. The server can be accessed at the URL http://lorentz.immstr.pasteur.fr/nomad-ref.php.

  13. Generating high-peak-power structured lights in selectively pumped passively Q-switched lasers with astigmatic mode transformations

    Science.gov (United States)

    Chang, C. C.; Hsieh, Y. H.; Lee, C. Y.; Sung, C. L.; Tuan, P. H.; Tung, J. C.; Liang, H. C.; Chen, Y. F.

    2017-12-01

    Various high-order Hermite–Gaussian (HG) modes with high repetition rates and high peak powers are systematically generated by designing the cavity configuration to satisfy the criterion of the passive Q-switching. For the HG m,0 modes with the order m  =  1–9, the pulse repetition rate can exceed 100 kHz with peak power higher than 0.3 kW. For the HG m,m modes with the order m  =  1–10, the pulse repetition rate can be up to 37 kHz with peak power higher than 0.35 kW. Furthermore, the high-order HG beams is transformed by using an astigmatic mode converter to generate various structured lights with optical vortices. Experimental patterns of the transformed high-order HG beams in the propagation are theoretically analyzed and the phase structures are numerically manifested.

  14. A novel beta-defensin structure: a potential strategy of big defensin for overcoming resistance by Gram-positive bacteria.

    Science.gov (United States)

    Kouno, Takahide; Fujitani, Naoki; Mizuguchi, Mineyuki; Osaki, Tsukasa; Nishimura, Shin-ichiro; Kawabata, Shun-ichiro; Aizawa, Tomoyasu; Demura, Makoto; Nitta, Katsutoshi; Kawano, Keiichi

    2008-10-07

    Big defensin is a 79-residue peptide derived from hemocytes of the Japanese horseshoe crab. It has antimicrobial activities against Gram-positive and -negative bacteria. The amino acid sequence of big defensin can be divided into an N-terminal hydrophobic half and a C-terminal cationic half. Interestingly, the trypsin cleaves big defensin into two fragments, the N-terminal and C-terminal fragments, which are responsible for antimicrobial activity against Gram-positive and -negative bacteria, respectively. To explore the antimicrobial mechanism of big defensin, we determined the solution structure of mature big defensin and performed a titration experiment with DPC micelles. Big defensin has a novel defensin structure; the C-terminal domain adopts a beta-defensin structure, and the N-terminal domain forms a unique globular conformation. It is noteworthy that the hydrophobic N-terminal domain undergoes a conformational change in micelle solution, while the C-terminal domain remains unchanged. Here, we propose that the N-terminal domain achieves its antimicrobial activity in a novel fashion and explain that big defensin has developed a strategy different from those of other beta-defensins to suppress the growth of Gram-positive bacteria.

  15. ROLE OF NEUTRALS IN CORE FUELING AND PEDESTAL STRUCTURE IN H-MODE DIII-D DISCHARGES

    International Nuclear Information System (INIS)

    WOLF, NS; PETRIE, TW; PORTER, GD; ROGNLIEN, TD; GROEBNER, RJ; MAKOWSKI, MA

    2002-01-01

    OAK A271 ROLE OF NEUTRALS IN CORE FUELING AND PEDESTAL STRUCTURE IN H-MODE DIII-D DISCHARGES. The 2-D fluid code UEDGE was used to analyze DIII-D experiments to determine the role of neutrals in core fueling, core impurities, and also the H-mode pedestal structure. The authors compared the effects of divertor closure on the fueling rate and impurity density of high-triangularity, H-mode plasmas. UEDGE simulations indicate that the decrease in both deuterium core fueling (∼ 15%-20%) and core carbon density (∼ 15%-30%) with the closed divertor compared to the open divertor configuration is due to greater divertor screening of neutrals. They also compared UEDGE results with a simple analytic model of the H-mode pedestal structure. The model predicts both the width and gradient of the transport barrier in n e as a function of the pedestal density. The more sophisticated UEDGE simulations of H-mode discharges corroborate the simple analytic model, which is consistent with the hypothesis that fueling processes play a role in H-mode transport barrier formation

  16. Aberrant default-mode functional and structural connectivity in heroin-dependent individuals.

    Directory of Open Access Journals (Sweden)

    Xiaofen Ma

    Full Text Available Little is known about connectivity within the default mode network (DMN in heroin-dependent individuals (HDIs. In the current study, diffusion-tensor imaging (DTI and resting-state functional MRI (rs-fMRI were combined to investigate both structural and functional connectivity within the DMN in HDIs.Fourteen HDIs and 14 controls participated in the study. Structural (path length, tracts count, (fractional anisotropy FA and (mean diffusivity MD derived from DTI tractographyand functional (temporal correlation coefficient derived from rs-fMRI DMN connectivity changes were examined in HDIs. Pearson correlation analysis was performed to compare the structural/functional indices and duration of heroin use/Iowa gambling task(IGT performance in HDIs.HDIs had lower FA and higher MD in the tract connecting the posterior cingulate cortex/precuneus (PCC/PCUN to right parahippocampal gyrus (PHG, compared to the controls. HDIs also had decreased FA and track count in the tract connecting the PCC/PCUN and medial prefrontal cortex (MPFC, as well as decreased functional connectivity between the PCC/PCUN and bilateral PHG and MPFC, compared to controls. FA values for the tract connecting PCC/PCUN to the right PHG and connecting PCC/PCUN to the MPFC were negatively correlated to the duration of heroin use. The temporal correlation coefficients between the PCC/PCUN and the MPFC, and the FA values for the tract connecting the PCC/PCUN to the MPFC were positively correlated to IGT performance in HDIs.Structural and functional connectivity within the DMN are both disturbed in HDIs. This disturbance progresses as duration of heroin use increases and is related to deficits in decision making in HDIs.

  17. Different shades of default mode disturbance in schizophrenia: Subnodal covariance estimation in structure and function.

    Science.gov (United States)

    Lefort-Besnard, Jérémy; Bassett, Danielle S; Smallwood, Jonathan; Margulies, Daniel S; Derntl, Birgit; Gruber, Oliver; Aleman, Andre; Jardri, Renaud; Varoquaux, Gaël; Thirion, Bertrand; Eickhoff, Simon B; Bzdok, Danilo

    2018-02-01

    Schizophrenia is a devastating mental disease with an apparent disruption in the highly associative default mode network (DMN). Interplay between this canonical network and others probably contributes to goal-directed behavior so its disturbance is a candidate neural fingerprint underlying schizophrenia psychopathology. Previous research has reported both hyperconnectivity and hypoconnectivity within the DMN, and both increased and decreased DMN coupling with the multimodal saliency network (SN) and dorsal attention network (DAN). This study systematically revisited network disruption in patients with schizophrenia using data-derived network atlases and multivariate pattern-learning algorithms in a multisite dataset (n = 325). Resting-state fluctuations in unconstrained brain states were used to estimate functional connectivity, and local volume differences between individuals were used to estimate structural co-occurrence within and between the DMN, SN, and DAN. In brain structure and function, sparse inverse covariance estimates of network coupling were used to characterize healthy participants and patients with schizophrenia, and to identify statistically significant group differences. Evidence did not confirm that the backbone of the DMN was the primary driver of brain dysfunction in schizophrenia. Instead, functional and structural aberrations were frequently located outside of the DMN core, such as in the anterior temporoparietal junction and precuneus. Additionally, functional covariation analyses highlighted dysfunctional DMN-DAN coupling, while structural covariation results highlighted aberrant DMN-SN coupling. Our findings reframe the role of the DMN core and its relation to canonical networks in schizophrenia. We thus underline the importance of large-scale neural interactions as effective biomarkers and indicators of how to tailor psychiatric care to single patients. © 2017 Wiley Periodicals, Inc.

  18. Fatigue Debond Growth in Sandwich Structures Loaded in Mixed Mode Bending (MMB)

    DEFF Research Database (Denmark)

    Quispitupa, Amilcar; Berggreen, Christian; Carlsson, Leif A.

    2008-01-01

    Static and cyclic debond growth in sandwich specimens loaded in mixed mode bending (MMB) is examined. The MMB sandwich specimens were manufactured using H100 PVC foam core and E-glass/polyester non-crimp quadro-axial [0/45/90/-45]s DBLT-850 face sheets. Static test were performed to determine...... the fracture toughness of the debonded sandwich specimens at different mixed mode loadings. The mixed mode ratio (mode I to mode II) was controlled by changing the lever arm distance of the MMB test rig. Compliance technique and visual inspection was employed to measure the crack length during fatigue. Fatigue...

  19. The Period Ratio for Standing Kink and Sausage Modes in Solar Structures with Siphon Flow. I. Magnetized Slabs

    Science.gov (United States)

    Li, Bo; Habbal, Shadia Rifai; Chen, Yanjun

    2013-04-01

    In the applications of solar magneto-seismology, the ratio of the period of the fundamental mode to twice the period of its first overtone, P 1/2P 2, plays an important role. We examine how field-aligned flows affect the dispersion properties, and hence the period ratios, of standing modes supported by magnetic slabs in the solar atmosphere. We numerically solve the dispersion relations and devise a graphic means to construct standing modes. For coronal slabs, we find that the flow effects are significant for the fast kink and sausage modes alike. For the kink ones, they may reduce P 1/2P 2 by up to 23% compared with the static case, and the minimum allowed P 1/2P 2 can fall below the lower limit analytically derived for static slabs. For the sausage modes, while introducing the flow reduces P 1/2P 2 by typically case, it significantly increases the threshold aspect ratio only above which standing sausage modes can be supported, meaning that their detectability is restricted to even wider slabs. In the case of photospheric slabs, the flow effect is not as strong. However, standing modes are distinct from the coronal case in that standing kink modes show a P 1/2P 2 that deviates from unity even for a zero-width slab, while standing sausage modes no longer suffer from a threshold aspect ratio. We conclude that transverse structuring in plasma density and flow speed should be considered in seismological applications of multiple periodicities to solar atmospheric structures.

  20. Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function.

    Science.gov (United States)

    Mueller, Noel T; Shin, Hakdong; Pizoni, Aline; Werlang, Isabel C; Matte, Ursula; Goldani, Marcelo Z; Goldani, Helena A S; Dominguez-Bello, Maria G

    2017-12-04

    Cesarean (C-section) delivery, recently shown to cause excess weight gain in mice, perturbs human neonatal gut microbiota development due to the lack of natural mother-to-newborn transfer of microbes. Neonates excrete first the in-utero intestinal content (referred to as meconium) hours after birth, followed by intestinal contents reflective of extra-uterine exposure (referred to as transition stool) 2 to 3 days after birth. It is not clear when the effect of C-section on the neonatal gut microbiota emerges. We examined bacterial DNA in carefully-collected meconium, and the subsequent transitional stool, from 59 neonates [13 born by scheduled C-section and 46 born by vaginal delivery] in a private hospital in Brazil. Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq (San Diego, CA, USA) platform. We found evidence of bacterial DNA in the majority of meconium samples in our study. The bacterial DNA structure (i.e., beta diversity) of meconium differed significantly from that of the transitional stool microbiota. There was a significant reduction in bacterial alpha diversity (e.g., number of observed bacterial species) and change in bacterial composition (e.g., reduced Proteobacteria) in the transition from meconium to stool. However, changes in predicted microbiota metabolic function from meconium to transitional stool were only observed in vaginally-delivered neonates. Within sample comparisons showed that delivery mode was significantly associated with bacterial structure, composition and predicted microbiota metabolic function in transitional-stool samples, but not in meconium samples. Specifically, compared to vaginally delivered neonates, the transitional stool of C-section delivered neonates had lower proportions of the genera Bacteroides , Parabacteroides and Clostridium . These differences led to C-section neonates having lower predicted abundance of microbial genes related to metabolism of amino and

  1. Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function

    Directory of Open Access Journals (Sweden)

    Noel T. Mueller

    2017-12-01

    Full Text Available Cesarean (C-section delivery, recently shown to cause excess weight gain in mice, perturbs human neonatal gut microbiota development due to the lack of natural mother-to-newborn transfer of microbes. Neonates excrete first the in-utero intestinal content (referred to as meconium hours after birth, followed by intestinal contents reflective of extra-uterine exposure (referred to as transition stool 2 to 3 days after birth. It is not clear when the effect of C-section on the neonatal gut microbiota emerges. We examined bacterial DNA in carefully-collected meconium, and the subsequent transitional stool, from 59 neonates [13 born by scheduled C-section and 46 born by vaginal delivery] in a private hospital in Brazil. Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq (San Diego, CA, USA platform. We found evidence of bacterial DNA in the majority of meconium samples in our study. The bacterial DNA structure (i.e., beta diversity of meconium differed significantly from that of the transitional stool microbiota. There was a significant reduction in bacterial alpha diversity (e.g., number of observed bacterial species and change in bacterial composition (e.g., reduced Proteobacteria in the transition from meconium to stool. However, changes in predicted microbiota metabolic function from meconium to transitional stool were only observed in vaginally-delivered neonates. Within sample comparisons showed that delivery mode was significantly associated with bacterial structure, composition and predicted microbiota metabolic function in transitional-stool samples, but not in meconium samples. Specifically, compared to vaginally delivered neonates, the transitional stool of C-section delivered neonates had lower proportions of the genera Bacteroides, Parabacteroides and Clostridium. These differences led to C-section neonates having lower predicted abundance of microbial genes related to metabolism of

  2. Rice root-associated bacteria: insights into community structures across 10 cultivars

    NARCIS (Netherlands)

    Hardoim, P.R.; Andreote, F.D.; Reinhold-Hurek, B.; Sessitsch, A.; Overbeek, van L.S.; Elsas, van J.D.

    2011-01-01

    In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed

  3. Rice root-associated bacteria : insights into community structures across 10 cultivars

    NARCIS (Netherlands)

    Hardoim, P. R.; Andreote, F. D.; Reinhold-Hurek, B.; Sessitsch, A.; van Overbeek, L. S.; van Elsas, J. D.

    In this study, the effects of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Betaproteobacteria, Pseudomonas and Actinobacteria were studied using PCR, followed

  4. A model based on soil structural aspects describing the fate of genetically modified bacteria in soil

    NARCIS (Netherlands)

    Hoeven, van der N.; Elsas, van J.D.; Heijnen, C.E.

    1996-01-01

    A computer simulation model was developed which describes growth and competition of bacteria in the soil environment. In the model, soil was assumed to contain millions of pores of a few different size classes. An introduced bacterial strain, e.g. a genetically modified micro-organism (GEMMO), was

  5. Sulfate-reducing bacteria inhabiting natural corrosion depostis from marine steel structures

    NARCIS (Netherlands)

    Païssé, S.; Ghiglione, J.-F.; Marty, F.; Abbas, B.; Gueuné, H.; Sanchez Amaya, J.; Muyzer, G.; Quillet, L.

    2013-01-01

    In the present study, investigations were conducted on natural corrosion deposits to better understand the role of sulfate-reducing bacteria (SRB) in the accelerated corrosion process of carbon steel sheet piles in port environments. We describe the abundance and diversity of total and metabolically

  6. The structures of lipopolysaccharides from plant-associated gram-negative bacteria

    DEFF Research Database (Denmark)

    Molinaro, Antonio; Newman, Mari-Anne; Lanzetta, Rosa

    2009-01-01

    Gram-negative bacterial lipopolysaccharides (LPSs) have multiple roles in plant-microbe interactions. LPSs contribute to the low permeabilities of bacterial outer membranes, which act as barriers to protect bacteria from plant-derived antimicrobial substances. Conversely, perception of LPSs by pl...

  7. RF breakdown in "cold" slow wave structures operating at travelling wave mode of TM01

    Science.gov (United States)

    Yuan, Yuzhang; Zhang, Jun; Zhong, Huihuang; Zhang, Dian; Bai, Zhen; Zhu, Danni

    2018-01-01

    RF breakdown experiments and simulations in "cold" slow wave structures (SWSs) are executed. All the SWSs are designed as traveling wave structures, which operate at the π/2 mode of TM01 waves. The experimental results indicate that the input microwave energy is mainly absorbed, not reflected by the RF breakdown process in traveling wave SWSs. Both larger magnitude of Es-max and more numbers of periods of SWSs aggravate the microwave absorption in the breakdown process and bring about a shorter transmission pulse width. We think that the critical surface E-field of the multi-period SWSs is 1 MV/cm. However, little correlation between RF breakdown effects and Bext is observed in the experiments. The simulation conditions are coincident with the experimental setup. Explosive emissions of electrons in the rounded corner of SWSs together with the ionization of the gas layer close to it supply the breakdown plasma. The gas layer consists of water vapor and hydrogen gas and has a pressure of 1 Pa. Different kinds of circumstances of SWSs are simulated. We mainly concern about the characteristic of the plasma and its influence on microwave power. Comprehensive simulation results are obtained. The simulation results match the experimental results basically and are helpful in explaining the RF breakdown phenomenon physically.

  8. Imaging of lactic acid bacteria with AFM-elasticity and adhesion maps and their relationship to biological and structural data

    Energy Technology Data Exchange (ETDEWEB)

    Schaer-Zammaretti, Prisca; Ubbink, Job

    2003-10-15

    The adhesion of lactic acid bacteria to the intestinal epithelium is one of the most important factors determining probiotic ability of a bacterial strain. Studying bacterial adhesion requires knowledge of the structure and properties of the bacterial surface, which can be studied by atomic force microscopy under native conditions. The observation of the surface topography of bacteria from the species Lactobacillus crispatus, L. helveticus and L. johnsonii shows major differences between bacteria having a crystalline-like protein layer as part of the cell wall and those without such layers. Force volume images calculated into elasticity and adhesion force maps of different bacterial strains show that L. crispatus and L. helveticus have a surface with a homogeneous stiffness with no adhesion events. This is most likely caused by the S-layer, which completely covers the surface of the bacteria. We infer that the absence of adhesion peaks is caused by the semi-crystalline character of such protein layers, in agreement with the results obtained from electron microscopy. Analysis of a number of L. johnsonii strains shows that these bacteria have surface properties which strongly differ from the L. crispatus and L. helveticus strains. For L. johnsonii DMS20533 and L. johnsonii ATCC33200 high adhesion forces are observed, which can be related to a surface rich in polysaccharides. L. johnsonii ATCC332 has lower adhesion forces compared to the other two and, furthermore, the surface topography shows depressions. We suppose that this strain has a surface pattern consisting of crystalline-like proteins alternating with polysaccharide-rich domains. The wide variety in surface properties of lactobacilli could well have wide-ranging implications for food processing and for health benefits.

  9. Exploration of fluid dynamic indicators/causative factors in the formation of tower structures in staphylococci bacteria bio-films

    Science.gov (United States)

    Sherman, Erica; Derek, Moormeier; Bayles, Kenneth; Wei, Timothy

    2015-11-01

    Staphylococcus aureus bacteria form biofilms with distinct structures that facilitate their ability to tolerate treatment and to spread within the body. As such, staph infections represent one of the greatest threats to post-surgery patients. It has been found that flow conditions play a significant role in the developmental and dispersal activity of a biofilm. The coupling between the growing biofilm and surrounding flow, however, is not well understood. Indeed, little is know why bacteria form tower structures under certain conditions but not in a predictable way. μ-PTV measurements were made in a microchannel to try to identify fluid dynamic indicators for the formation of towers in biofilm growth. Preliminary experiments indicated changes in the near wall flow up to five hours before a tower formed. The reason for that is the target of this investigation. Staphylococcus aureus bacteria were cultured in the Bioflux Fluxion channel and subjected to a steady shear rate of 0.5 dynes. In addition to μ-PTV measurement, nuclease production and cell number density counts were observed prior to and during tower development. These were compared against measurements made under the same nominal flow conditions where a tower did not form.

  10. THE PERIOD RATIO FOR STANDING KINK AND SAUSAGE MODES IN SOLAR STRUCTURES WITH SIPHON FLOW. I. MAGNETIZED SLABS

    International Nuclear Information System (INIS)

    Li Bo; Habbal, Shadia Rifai; Chen Yanjun

    2013-01-01

    In the applications of solar magneto-seismology, the ratio of the period of the fundamental mode to twice the period of its first overtone, P 1 /2P 2 , plays an important role. We examine how field-aligned flows affect the dispersion properties, and hence the period ratios, of standing modes supported by magnetic slabs in the solar atmosphere. We numerically solve the dispersion relations and devise a graphic means to construct standing modes. For coronal slabs, we find that the flow effects are significant for the fast kink and sausage modes alike. For the kink ones, they may reduce P 1 /2P 2 by up to 23% compared with the static case, and the minimum allowed P 1 /2P 2 can fall below the lower limit analytically derived for static slabs. For the sausage modes, while introducing the flow reduces P 1 /2P 2 by typically ∼ 1 /2P 2 that deviates from unity even for a zero-width slab, while standing sausage modes no longer suffer from a threshold aspect ratio. We conclude that transverse structuring in plasma density and flow speed should be considered in seismological applications of multiple periodicities to solar atmospheric structures.

  11. Do freshwater macrophytes influence the community structure of ammonia-oxidizing and denitrifying bacteria in the rhizospere?

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2006-01-01

    DO FRESHWATER MACROPHYTES INFLUENCE THE COMMUNITY STRUCTURE OF AMMONIA-OXIDIZING AND DENITRIFYING BACTERIA IN THE RHIZOSPHERE? M. Herrmann, A. Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia...... to unvegetated sediment, especially with respect to the availability of oxygen, organic carbon, and inorganic nitrogen. We hypothesize that macrophyte species create specific niches for ammonia oxidizing and nitrate-reducing bacteria in their rhizosphere, leading to plant-dependant differences in abundance......-denitrification using the 15N isotope pairing technique. Ammonia-oxidizing and nitrate-reducing populations are analyzed based on the ammonia monooxygenase gene (amoA) and the nitrate reductase gene (narG) as functional markers. Preliminary data indicate that there in fact exist differences in the community composition...

  12. Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

    OpenAIRE

    Diallo, M. D.; Guisse, A.; Sall, S. N.; Dick, R. P.; Assigbetsé, Komi; Dieng, A. L.; Chotte, Jean-Luc

    2015-01-01

    Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB) community composition and nitrogen (N) availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C) and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. T...

  13. Matrix architecture dictates three-dimensional migration modes of human macrophages: differential involvement of proteases and podosome-like structures.

    Science.gov (United States)

    Van Goethem, Emeline; Poincloux, Renaud; Gauffre, Fabienne; Maridonneau-Parini, Isabelle; Le Cabec, Véronique

    2010-01-15

    Tissue infiltration of macrophages, although critical for innate immunity, is also involved in pathologies, such as chronic inflammation and cancer. In vivo, macrophages migrate mostly in a constrained three-dimensional (3D) environment. However, in vitro studies, mainly focused on two dimensions, do not provide meaningful clues about the mechanisms involved in 3D macrophage migration. In contrast, tumor cell 3D migration is well documented. It comprises a protease-independent and Rho kinase (ROCK)-dependent amoeboid migration mode and a protease-dependent and ROCK-independent mesenchymal migration mode. In this study, we examined the influence of extracellular matrix (composition, architecture, and stiffness) on 3D migration of human macrophages derived from blood monocytes (MDMs). We show that: 1) MDMs use either the amoeboid migration mode in fibrillar collagen I or the mesenchymal migration mode in Matrigel and gelled collagen I, whereas HT1080 tumor cells only perform mesenchymal migration; 2) when MDMs use the mesenchymal migratory mode, they form 3D collagenolytic structures at the tips of cell protrusions that share several markers with podosomes as described in two dimensions; 3) in contrast to tumor cells, matrix metalloproteinase inhibitors do not impair protease-dependent macrophage 3D migration, suggesting the involvement of other proteolytic systems; and 4) MDMs infiltrating matrices of similar composition but with variable stiffness adapt their migration mode primarily to the matrix architecture. In conclusion, although it is admitted that leukocytes 3D migration is restricted to the amoeboid mode, we show that human macrophages also perform the mesenchymal mode but in a distinct manner than tumor cells, and they naturally adapt their migration mode to the environmental constraints.

  14. Characterisation of community structure of bacteria in parallel mesophilic and thermophilic pilot scale anaerobe sludge digesters.

    Science.gov (United States)

    Tauber, T; Berta, Brigitta; Székely, Anna J; Gyarmati, I; Kékesi, Katalin; Márialigeti, K; Tóth, Erika M

    2007-03-01

    The aim of the present work was to compare the microbial communities of a mesophilic and a thermophilic pilot scale anaerobe sludge digester. For studying the communities cultivation independent chemotaxonomical methods (RQ and PLFA analyses) and T-RFLP were applied. Microbial communities of the mesophilic and thermophilic pilot digesters showed considerable differences, both concerning the species present, and their abundance. A Methanosarcina sp. dominated the thermophilic, while a Methanosaeta sp. the mesophilic digester among Archaea. Species diversity of Bacteria was reduced in the thermophilic digester. Based on the quinone patterns in both digesters the dominance of sulphate reducing respiratory bacteria could be detected. The PLFA profiles of the digester communities were similar though in minor components characteristic differences were shown. Level of branched chain fatty acids is slightly lower in the thermophilic digester that reports less Gram positive bacteria. The relative ratio of fatty acids characteristic to Enterobacteriaceae, Bacteroidetes and Clostridia shows differences between the two digesters: their importance generally decreased under thermophilic conditions. The sulphate reducer marker (15:1 and 17:1) fatty acids are present in low quantity in both digesters.

  15. Effect of the energy deposition modes on the structural stability of pure zirconia

    Energy Technology Data Exchange (ETDEWEB)

    Simeone, D. [Materiaux fonctionnels pour l' energie, CEA-CNRS-Ecole Centrale Paris, CEA/DEN/SRMA 91191 Gif-sur-Yvette and SPMS, 92295 Chatenay-Malabry (France)], E-mail: david.simeone@cea.fr; Baldinozzi, G.; Gosset, D. [Materiaux fonctionnels pour l' energie, CEA-CNRS-Ecole Centrale Paris, CEA/DEN/SRMA 91191 Gif-sur-Yvette and SPMS, 92295 Chatenay-Malabry (France); LeCaer, S. [DSM/DRECAM/SCM/URA 331 CNRS, CEA Saclay, 91191 Gif sur Yvette (France); Mazerolles, L. [CECM, UPR CNRS 2801, 94407 Vitry sur Seine (France); Monnet, I.; Bouffard, S. [CIRIL, CEA-CNRS-ENSICAEN, 14070 Caen Cedex 5 (France)

    2008-06-15

    One of the most important goals in materials science is to be able to design materials with specific properties. Irradiation seems to be a powerful tool for the design of advanced materials because of its ability to modify over different scales the microstructure of solids. Nowadays, it is clearly proved that irradiation induces order-disorder phase transitions in metallic alloys and in some ceramics. Recent investigations on pure monoclinic zirconia have clearly shown that a displacive phase transition can be induced by irradiation. In this work, the impact of the energy deposition modes on the structural stability of pure monoclinic ZrO{sub 2} is discussed in detail. Based on experimental evidences, a microscopic model is proposed to explain the displacive phase transition observed in this material after irradiation by low and high energy ions within the Landau theory framework. Even if defects generated by low and high energy ions are quite different, these defects are able to quench the same tetragonal phase in pure zirconia.

  16. Inferring long-distance dispersal modes in American amphitropically disjunct species through adaptive dispersal structures.

    Science.gov (United States)

    Schenk, John J; Saunders, Kelsey

    2017-11-22

    A repeated pattern of American amphitropical disjunct species or sister species distributed on either side of the equator has long-fascinated botanists, but the modes of these disjunctions remain untested. We evaluated diaspore morphology to generate hypotheses on probable dispersal mechanisms. The sizes and structures of diaspores, habit, habitat, distribution, and dispersal units were collected for 108 species from literature searches and herbarium specimens. Variation was evaluated with summary statistics, χ 2 tests with Monte Carlo simulations, ANOVAs, and the nonparametric Mann-Whitney test. Seeds were the dispersing diaspore in 38.0% of the species, 45.4 were dispersed as fruits, and the remaining were dispersed as infructescences or spores. Diaspores were epizoochorous (52.8%), anemochorous (20.4%), achorous (15.7%), endozoochorous (8.3%), and hydrochorous (2.8%). Epizoochory was significantly greater than expected. Zoochory occurred more frequently than expected when considering achorous diaspores as animal-dispersed. Most species were associated with wetland, woodland, and grassland habitats. An ANOVA revealed that diaspores associated with hydrochory were larger and anemochory was smaller; all other syndromes were not significantly different. Botanists have long-held the assumption that bird migrations are responsible for amphitropical disjunctions. Our results support this hypothesis, with the majority of these events occurring by external attachment of small fruits. However, our results also indicate that anemochory might play a greater role in producing amphitropical distributions than previously thought and at a greater rate than endozoochory or hydrochory. © 2017 Botanical Society of America.

  17. Alternating-Phase-Focused Linac with Interdigital H-Mode Structure for Medical Injectors

    CERN Document Server

    Iwata, Yoshiyuki; Fujimoto, Tetsuya; Fujisawa, Takashi; Furukawa, Takuji; Hojo, Satoru; Honma, T; Kanazawa, Mitsutaka; Kapin, Valery; Mitsumoto, Toshinori; Miyahara, Nobuyuki; Murakami, Takeshi; Muramatsu, Masayuki; Noda, Koji; Ogawa, Hirotsugu; Ogawa, Hiroyuki; Torikoshi, Masami; Tsutsui, Hiroshi; Yamada, Satoru; Yamamoto, Kazuo

    2005-01-01

    Tumor therapy using Heavy Ion Medical Accelerator in Chiba (HIMAC) has been performed at National Institute of Radiological Sciences (NIRS). With the successful clinical results over ten years, a project on developing compact accelerators has been started. To design these compact accelerators, a size of an injector as well as construction and operation costs plays an important role. To satisfy these requirements, we propose a compact injector consisting of a RFQ and Interdigital H-mode Drift-Tube-Linac (IH-DTL) having the resonant frequency of 200 MHz. The injector will accelerate carbon ion up to 4.0 AMeV. For the beam focusing of the IH-DTL, the method of Alternating-Phase-Focusing was employed. With the IH structure and rather high operating-frequency, the size of the cavities is compact; the radius is approximately 0.4 m, and the length of the RFQ and IH-DTL will be 2.5m and 3.5m respectively. The fabrication of the RFQ is in progress. For the IH-DTL, the full-scale model was fabricated. With the encourag...

  18. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xiaorui [Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030 (United States); Lu, Mingyang [Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030 (United States); Poon, Billy K. [Department of Bioengineering, Rice University, Houston, TX 77005 (United States); Wang, Qinghua [Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030 (United States); Ma, Jianpeng, E-mail: jpma@bcm.tmc.edu [Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030 (United States); Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, TX 77030 (United States); Department of Bioengineering, Rice University, Houston, TX 77005 (United States)

    2009-04-01

    The structural model of the unliganded and fully glycosylated simian immunodeficiency virus gp120 core determined to 4.0 Å resolution was substantially improved using a recently developed normal-mode-based anisotropic B-factor refinement method. The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 Å resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 Å resolution and of a membrane protein at 3.2 Å resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures.

  19. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

    International Nuclear Information System (INIS)

    Chen, Xiaorui; Lu, Mingyang; Poon, Billy K.; Wang, Qinghua; Ma, Jianpeng

    2009-01-01

    The structural model of the unliganded and fully glycosylated simian immunodeficiency virus gp120 core determined to 4.0 Å resolution was substantially improved using a recently developed normal-mode-based anisotropic B-factor refinement method. The envelope protein gp120/gp41 of simian and human immunodeficiency viruses plays a critical role in viral entry into host cells. However, the extraordinarily high structural flexibility and heavy glycosylation of the protein have presented enormous difficulties in the pursuit of high-resolution structural investigation of some of its conformational states. An unliganded and fully glycosylated gp120 core structure was recently determined to 4.0 Å resolution. The rather low data-to-parameter ratio limited refinement efforts in the original structure determination. In this work, refinement of this gp120 core structure was carried out using a normal-mode-based refinement method that has been shown in previous studies to be effective in improving models of a supramolecular complex at 3.42 Å resolution and of a membrane protein at 3.2 Å resolution. By using only the first four nonzero lowest-frequency normal modes to construct the anisotropic thermal parameters, combined with manual adjustments and standard positional refinement using REFMAC5, the structural model of the gp120 core was significantly improved in many aspects, including substantial decreases in R factors, better fitting of several flexible regions in electron-density maps, the addition of five new sugar rings at four glycan chains and an excellent correlation of the B-factor distribution with known structural flexibility. These results further underscore the effectiveness of this normal-mode-based method in improving models of protein and nonprotein components in low-resolution X-ray structures

  20. [Effects of methyl bromide fumigation on community structure of denitrifying bacteria with nitrousoxide reductase gene (nosZ) in soil].

    Science.gov (United States)

    Yan, Pingmei; Qiao, Hongping; Zhao, Wenjing; Chen, Yanfei; Shan, Shuhua; Cao, Aocheng

    2015-01-04

    We studied the effect of methyl bromide fumigation on soil edaphic denitrification. We adopted nosZ-PCR-RFLP (restriction fragment length polymorphism) method, nosZ-MPN-PCR (Most-Probable-Number- PCR) counting method and soil nitrate elimination rate method, to explore the effect of methyl bromide fumigation on community structure, quantity and activity of denitrifying bacteria in soil. After methyl bromide fumigating soil for 100 d, soil denitrification did not change obviously (P > 0. 05). Margalef index, Shannon-wiener index and Evenness index had no significant difference (P > 0.05) in nosZ denitrifying bacterial communities between fumigated soil and the control. There were Rhodopsendomonas, Pseudomonas fluorescens, Herbacspirillum, uncultured bacterium partial in both of them. However, Azospirillum, Rhizobium melibei, Nitrosospira multiformis were exclusively found in the control, and Uncultured Azospirillum sp, Mesorhizobium sp were in fumigated one. Moreover, the number of denitrifying bacteria in the control resolved by nosZ-MPN-PCR (Most-Probable-Number-PCR) was 1.4 times higher than that of the fumigated one. After 100 d fumigating soil, the composition of nosZ denitrifying microbial community and the population of denitrifying bacteria changed. Furthermore, there was no difference in denitrification between the fumigated soil and the control.

  1. Tamm-plasmon and surface-plasmon hybrid-mode based refractometry in photonic bandgap structures.

    Science.gov (United States)

    Das, Ritwick; Srivastava, Triranjita; Jha, Rajan

    2014-02-15

    The transverse magnetic (TM) polarized hybrid modes formed as a consequence of coupling between Tamm plasmon polariton (TM-TPP) mode and surface plasmon polariton (SPP) mode exhibit interesting dispersive features for realizing a highly sensitive and accurate surface plasmon resonance (SPR) sensor. We found that the TM-TPP modes, formed at the interface of distributed Bragg reflector and metal, are strongly dispersive as compared to SPP modes at optical frequencies. This causes an appreciably narrow interaction bandwidth between TM-TPP and SPP modes, which leads to highly accurate sensing. In addition, appropriate tailoring of dispersion characteristics of TM-TPP as well as SPP modes could ensure high sensitivity of a novel SPR platform. By suitably designing the Au/TiO₂/SiO₂-based geometry, we propose a TM-TPP/SPP hybrid-mode sensor and achieve a sensitivity ≥900  nm/RIU with high detection accuracy (≥30  μm⁻¹) for analyte refractive indices varying between 1.330 and 1.345 in 600-700 nm wavelength range. The possibility to achieve desired dispersive behavior in any spectral band makes the sensing configuration an extremely attractive candidate to design sensors depending on the availability of optical sources.

  2. Gain analysis of higher-order-mode amplification in a dielectric-implanted multi-beam traveling wave structure

    Energy Technology Data Exchange (ETDEWEB)

    Gee, Anthony; Shin, Young-Min

    2013-01-01

    A multi-beam traveling wave amplifier designed with an overmoded staggered double grating array was examined by small signal analysis combined with simulation. Eigenmode and S-parameter analyses show that the 2cm long slow wave structure (SWS) has 1-5dB insertion loss over the passband (TM31 mode) with ~28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM31-mode is amplified with 15–20 dB/beam at 64–84GHz with three elliptical beams of 10kV and 150mA/beam, which was compared with particle-in-cell (PIC) simulations. PIC analysis on the analysis of instability with zero-input driving excitations demonstrated that background noises and non-operating lower order modes are noticeably suppressed by implanting equidistant dielectric absorbers; the overmoded structure only allowed the desired 3rd order mode to propagate in the structure. The designed circuit structure can be widely applied to multi-beam devices for high power RF generation.

  3. Optimal design for crosstalk analysis in 12-core 5-LP mode homogeneous multicore fiber for different lattice structure

    Science.gov (United States)

    Kumar, Dablu; Ranjan, Rakesh

    2018-03-01

    12-Core 5-LP mode homogeneous multicore fibers have been proposed for analysis of inter-core crosstalk and dispersion, with four different lattice structures (circular, 2-ring, square lattice, and triangular lattice) having cladding diameter of 200 μm and a fixed cladding thickness of 35 μm. The core-to-core crosstalk impact has been studied numerically with respect to bending radius, core pitch, transmission distance, wavelength, and core diameter for all 5-LP modes. In anticipation of further reduction in crosstalk levels, the trench-assisted cores have been incorporated for all respective designs. Ultra-low crosstalk (-138 dB/100 km) has been achieved through the triangular lattice arrangement, with trench depth Δ2 = -1.40% for fundamental (LP01) mode. It has been noted that the impact of mode polarization on crosstalk behavior is minor, with difference in crosstalk levels between two polarized spatial modes as ≤0.2 dB. Moreover, the optimized cladding diameter has been obtained for all 5-LP modes for a target value of crosstalk of -50 dB/100 km, with all the core arrangements. The dispersion characteristic has also been analyzed with respect to wavelength, which is nearly 2.5 ps/nm km at operating wavelength 1550 nm. The relative core multiplicity factor (RCMF) for the proposed design is obtained as 64.

  4. Period ratios for standing kink and sausage modes in magnetized structures with siphon flow on the Sun

    Science.gov (United States)

    Yu, Hui; Chen, Shao-Xia; Li, Bo; Xia, Li-Dong

    2016-06-01

    Standing oscillations with multiple periods have been found in a number of atmospheric structures on the Sun. The ratio of the period of the fundamental to twice the one of its first overtone, P 1/2P 2, is important in applications of solar magneto-seismology. We examine how field-aligned flows impact P 1/2P 2 of standing modes in solar magnetic cylinders. For coronal loops, the flow effects are significant for both fast kink and sausage modes. For kink modes, they reduce P 1/2P 2 by up to 17% relative to the static case even when the density contrast between the loop and its surroundings approaches infinity. For sausage modes, the reduction in P 1/2P 2 due to flow is typically ≲ 5.5% compared with the static case. However, the threshold aspect ratio, only above which can trapped sausage modes be supported, may increase dramatically with the flow magnitude. For photospheric tubes, the flow effect on P 1/2P 2 is not as strong. However, when applied to sausage modes, introducing field-aligned flows offers more possibilities in interpreting the multiple periods that have recently been measured. We conclude that field-aligned flows should be taken into account to help better understand what causes the departure of P 1/2P 2 from unity.

  5. Structural changes in the cells of some bacteria during population growth: a Fourier transform infrared-attenuated total reflectance study.

    Science.gov (United States)

    Ede, Sarah M; Hafner, Louise M; Fredericks, Peter M

    2004-03-01

    Structural changes occurring in the cells of several bacteria during their growth curves have been investigated by Fourier transform infrared (FT-IR) spectroscopy using the sampling technique of attenuated total reflectance (ATR). Spectra reflect all of the components of the cells, including the cell walls, cell membranes, internal structures, and the cytoplasm. The bacteria studied were Bacillus stearothermophilus, Halobacterium salinarum, Halococcus morrhuae, and Acetobacter aceti. All species showed significant spectral changes during their growth curves, indicating structural changes in the cells during increases in cell numbers. The major change for B. stearothermophilus was in the lipid content, which was at a maximum during the exponential phase of the growth curve. For the halophiles H. salinarum and H. morrhuae, the major change was that the concentration of sulfate ion in the cells varied during the growth curve and was at a maximum during the mid-part of the exponential phase of the growth curve. A. aceti cells showed increasing polysaccharide content during the growth curve as well as maximum lipid content during the exponential phase of growth.

  6. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments

    DEFF Research Database (Denmark)

    Ravenschlag, K.; Sahm, K.; Knoblauch, C.

    2000-01-01

    The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburg-fjorden, Svalbard) a-as characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes......-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina...

  7. Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment: a multi-method approach

    DEFF Research Database (Denmark)

    Llobet-Brossa, Enrique; Rabus, Ralf; Böttcher, Michael E.

    2002-01-01

    The community structure of sulfate-reducing bacteria (SRB) in an intertidal mud flat of the German Wadden Sea (Site Dangast, Jade Bay) was studied and related to sedimentary biogeochemical gradients and processes. Below the penetration depths of oxygen (~3 mm) and nitrate (~4 mm), the presence...... and counting viable cells with the most probable number technique. Phylogenetic groups of SRB identified with these techniques were almost evenly distributed throughout the top 20 cm of the sediment. Application of fluorescence in situ hybridization, however, demonstrated a maximum of active members...

  8. Optical-cell model based on the lasing competition of mode structures with different Q-factors in high-power semiconductor lasers

    Energy Technology Data Exchange (ETDEWEB)

    Podoskin, A. A., E-mail: podoskin@mail.ioffe.ru; Shashkin, I. S.; Slipchenko, S. O.; Pikhtin, N. A.; Tarasov, I. S. [Russian Academy of Sciences, Ioffe Institute (Russian Federation)

    2015-08-15

    A model describing the operation of a completely optical cell, based on the competition of lasing of Fabry-Perot cavity modes and the high-Q closed mode in high-power semiconductor lasers is proposed. Based on rate equations, the conditions of lasing switching between Fabry-Perot modes for ground and excited lasing levels and the closed mode are considered in the case of increasing internal optical loss under conditions of high current pump levels. The optical-cell operation conditions in the mode of a high-power laser radiation switch (reversible mode-structure switching) and in the mode of a memory cell with bistable irreversible lasing switching between mode structures with various Q-factors are considered.

  9. The Nucleus 59Cu. Complex Structure, Shape Evolution, Exotic Decay Modes

    International Nuclear Information System (INIS)

    Andreoiu, Corina

    2002-08-01

    High-spin states in the mass A∼60 region were populated using the state-of-art γ-ray spectrometers Gammasphere, Euroball, and GASP in conjunction with dedicated ancillary detectors. In particular, the 59 Cu nucleus was studied in several experiments, and a very extensive level scheme was determined. It comprises more than 320 transitions connecting about 150 excited states. Relative to mass, it is the most extensive level scheme known to date. Next to the spherical states at low excitation energy eight regular sequences of high-energy γ-ray transitions have been observed. They form rotational bands with various degree of deformation, which are interpreted in the light of the shell model and the configuration-dependent Cranked Nilsson-Strutinsky approach. One of the experiments was dedicated to the study of prompt particle decays. It revealed five prompt proton decays connecting five deformed states in three of the rotational bands in 59 Cu with three spherical states in the daughter nucleus 58 Ni. It is the first observation of the fine structure of the newly discovered prompt proton decay mode. The proton decays compete with the γ decay-out from the second minimum of the nuclear potential into the low-spin spherical states in the first minimum of the potential. The discrete γ decay-out mechanism of the yrast superdeformed band is investigated in detail. The nucleus 59 Zn, the mirror partner of 59 Cu, was identified for the first time, and the mirror symmetry of the T=1/2 A=59 pair is discussed

  10. Edge transport and mode structure of a QCM-like fluctuation driven by the Shoelace antenna

    Science.gov (United States)

    Golfinopoulos, T.; LaBombard, B.; Brunner, D.; Terry, J. L.; Baek, S. G.; Ennever, P.; Edlund, E.; Han, W.; Burke, W. M.; Wolfe, S. M.; Irby, J. H.; Hughes, J. W.; Fitzgerald, E. W.; Granetz, R. S.; Greenwald, M. J.; Leccacorvi, R.; Marmar, E. S.; Pierson, S. Z.; Porkolab, M.; Vieira, R. F.; Wukitch, S. J.; The Alcator C-Mod Team

    2018-05-01

    The Shoelace antenna was built to drive edge fluctuations in the Alcator C-Mod tokamak, matching the wavenumber (k\\perp≈1.5 cm‑1) and frequency (30≲ f ≲ 200 kHz) of the quasi-coherent mode (QCM), which is responsible for regulating transport across the plasma boundary in the steady-state, ELM-free Enhanced D α (EDA) H-mode. Initial experiments in 2012 demonstrated that the antenna drove a resonant response in the edge plasma in steady-state EDA and transient, non-ELMy H-modes, but transport measurements were unavailable. In 2016, the Shoelace antenna was relocated to enable direct measurements of driven transport by a reciprocating Mirror Langmuir Probe, while also making available gas puff imaging and reflectometer data to provide additional radial localization of the driven fluctuation. This new data suggests a  ∼4 mm-wide mode layer centered on or just outside the separatrix. Fluctuations coherent with the antenna produced a radial electron flux with {Γ_e}/{n_e}∼4 m s‑1 in EDA H-mode, smaller than but comparable to the QCM level. But in transient ELM-free H-mode, {Γ_e}/{n_e} was an order of magnitude smaller, and driven fluctuations reduced by a factor of ≳ 3. The driven mode is quantitatively similar to the intrinsic QCM across measured spectral quantities, except that it is more coherent and weaker. This work informs the prospect of achieving control of edge transport by direct coupling to edge modes, as well as the use of such active coupling for diagnostic purposes.

  11. Seismic analysis of structures of nuclear power plants by Lanczos mode superposition method

    International Nuclear Information System (INIS)

    Coutinho, A.L.G.A.; Alves, J.L.D.; Landau, L.; Lima, E.C.P. de; Ebecken, N.F.F.

    1986-01-01

    The Lanczos Mode Superposition Method is applied in the seismic analysis of nuclear power plants. The coordinate transformation matrix is generated by the Lanczos algorithm. It is shown that, through a convenient choice of the starting vector of the algorithm, modes with participation factors are automatically selected. It is performed the Response Spectra analysis of a typical reactor building. The obtained results are compared with those determined by the classical aproach stressing the remarkable computer effectiveness of the proposed methodology. (Author) [pt

  12. Design and prototyping of self-centering optical single-mode fiber alignment structures

    International Nuclear Information System (INIS)

    Ebraert, Evert; Gao, Fei; Thienpont, Hugo; Van Erps, Jürgen; Beri, Stefano; Watté, Jan

    2016-01-01

    The European Commission’s goal of providing each European household with at least a 30 Mb s −1 Internet connection by 2020 would be facilitated by a widespread deployment of fibre-to-the-home, which would in turn be sped up by the development of connector essential components, such as high-precision alignment features. Currently, the performance of state-of-the-art physical contact optical fiber connectors is limited by the tolerance on the cladding of standard telecom-grade single-mode fiber (SMF), which is typically smaller than  ±1 μ m. We propose to overcome this limit by developing micro-spring-based self-centering alignment structures (SCAS) for SMF-connectors. We design these alignment structures with robustness and low-cost replication in mind, allowing for large-scale deployment. Both theoretical and finite element analysis (FEA) models are used to determine the optimal dimensions of the beams of which the micro-springs of the SCAS are comprised. Two topologies of the SCAS, consisting of three and four micro-springs respectively, are investigated for two materials: polysulfone (PSU) and polyetherimide (PEI). These materials hold great potential for high-performance fiber connectors while being compatible with low-cost production and with the harsh environmental operation conditions of those connectors. The theory and FEA agree well (<3% difference) for a simple micro-spring. When including a pedestal on the micro-spring (to bring it further away from the fiber) and for shorter spring lengths the agreement worsens. This is due to spring compression effects not being taken into account in our theoretical model. Prototypes are successfully fabricated using deep proton writing and subsequently characterized. The controlled insertion of an SMF in the SCAS is investigated and we determine that a force of 0.11 N is required. The fiber insertion also causes an out-of-plane deformation of the micro-springs in the SCAS of about 7 μ m, which is no

  13. Differences in the structure of the gut bacteria communities in development stages of the Chinese white pine beetle (Dendroctonus armandi).

    Science.gov (United States)

    Hu, Xia; Wang, Chunyan; Chen, Hui; Ma, Junning

    2013-10-18

    The Chinese white pine beetle Dendroctonus armandi Tsai and Li, is arguably the most destructive forest insect in the Qinling Mountains in Northern China. Little is known about the structure of the bacterial communities associated with D. armandi even though this wood-boring insect plays important roles in ecosystem and biological invasion processes that result in huge economic losses in pine forests. The aim of this study was to investigate the composition of the bacterial communities present in the guts of D. armandi at different developmental stages using a culture-independent method involving PCR-denaturing gradient gel electrophoresis (DGGE). Analysis of PCR-amplified 16S rRNA gene fragments of bacteria from the guts of larvae, pupae, and male and female adults revealed bacterial communities of low complexity that differed according to the developmental stage. Citrobacter spp. and Pantoea spp. predominated in larvae and adults, whereas Methylobacterium was the dominant genus at the pupal stage. The main difference between the guts of male and female adults was the greater dominance of Citrobacter in females. Previous studies suggest that the bacterial community associated with D. armandi guts may influence insect development. The data obtained in this study regarding the phylogenetic relationships and the community structure of intestinal bacteria at different developmental stages of the D. armandi life cycle contribute to our understanding of D. armandi and could aid the development of new pest control strategies.

  14. Differences in the Structure of the Gut Bacteria Communities in Development Stages of the Chinese White Pine Beetle (Dendroctonus armandi

    Directory of Open Access Journals (Sweden)

    Junning Ma

    2013-10-01

    Full Text Available The Chinese white pine beetle Dendroctonus armandi Tsai and Li, is arguably the most destructive forest insect in the Qinling Mountains in Northern China. Little is known about the structure of the bacterial communities associated with D. armandi even though this wood-boring insect plays important roles in ecosystem and biological invasion processes that result in huge economic losses in pine forests. The aim of this study was to investigate the composition of the bacterial communities present in the guts of D. armandi at different developmental stages using a culture-independent method involving PCR-denaturing gradient gel electrophoresis (DGGE. Analysis of PCR-amplified 16S rRNA gene fragments of bacteria from the guts of larvae, pupae, and male and female adults revealed bacterial communities of low complexity that differed according to the developmental stage. Citrobacter spp. and Pantoea spp. predominated in larvae and adults, whereas Methylobacterium was the dominant genus at the pupal stage. The main difference between the guts of male and female adults was the greater dominance of Citrobacter in females. Previous studies suggest that the bacterial community associated with D. armandi guts may influence insect development. The data obtained in this study regarding the phylogenetic relationships and the community structure of intestinal bacteria at different developmental stages of the D. armandi life cycle contribute to our understanding of D. armandi and could aid the development of new pest control strategies.

  15. Structure of picosecond pulses of a Q-switched and mode-locked diode-pumped Nd:YAG laser

    Science.gov (United States)

    Donin, V. I.; Yakovin, D. V.; Gribanov, A. V.

    2015-12-01

    The pulse duration of a diode-pumped Nd:YAG laser, in which Q-switching with mode-locking (QML regime) is achieved using a spherical mirror and a travelling-wave acousto-optic modulator, is directly measured with a streak camera. It is found that the picosecond pulses can have a non-single-pulse structure, which is explained by excitation of several competing transverse modes in the Q-switching regime with a pulse repetition rate of 1 kHz. In the case of cw mode-locking (without Q-switching), a new (auto-QML) regime is observed, in which the pulse train repetition rate is determined by the frequency of the relaxation oscillations of the laser field while the train contains single picosecond pulses.

  16. Structure of picosecond pulses of a Q-switched and mode-locked diode-pumped Nd:YAG laser

    Energy Technology Data Exchange (ETDEWEB)

    Donin, V I; Yakovin, D V; Gribanov, A V [Institute of Automation and Electrometry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk (Russian Federation)

    2015-12-31

    The pulse duration of a diode-pumped Nd:YAG laser, in which Q-switching with mode-locking (QML regime) is achieved using a spherical mirror and a travelling-wave acousto-optic modulator, is directly measured with a streak camera. It is found that the picosecond pulses can have a non-single-pulse structure, which is explained by excitation of several competing transverse modes in the Q-switching regime with a pulse repetition rate of 1 kHz. In the case of cw mode-locking (without Q-switching), a new (auto-QML) regime is observed, in which the pulse train repetition rate is determined by the frequency of the relaxation oscillations of the laser field while the train contains single picosecond pulses. (control of laser radiation parameters)

  17. Antibacterial prenylated isoflavonoids and stilbenoids : quantitative structure-activity relationships and mode of action

    NARCIS (Netherlands)

    Araya-Cloutier, Carla

    2017-01-01

    Prenylated phenolic compounds, i.e. those bearing a C5-isoprenoid  (prenyl) substituent, are abundant in plants from the Fabaceae (legume) family and are potential natural antibacterial agents against resistant pathogenic bacteria. To understand the antibacterial properties of these compounds,

  18. Influencing Mechanism of Potential Factors on Passengers’ Long-Distance Travel Mode Choices Based on Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Yun Wang

    2017-10-01

    Full Text Available Understanding the public transportation users’ preferences to long-distance travel modes would contribute to reasonable developing policies and resource allocation. This paper aims to explore the influencing mechanism of potential factors on the long-distance travel mode choice. A survey was conducted to collect the data. The analysis of variance (ANOVA approach was applied to analyze the correlation relationship between potential factors and travel mode choice behavior. The results showed that, except gender, service demand for safety and departure time, all of the other factors significantly influenced the travel mode choice behavior. Specifically, passengers with higher education level and income level were more likely to choose high-speed railway (HSR and plane; passengers caring about travel expense were more likely to choose ordinary train, whereas plane and HSR may be chosen more by passengers caring more about comfort, punctuality and efficiency; the more passengers were satisfied with travel modes’ service performance, the more they would be likely to choose them; the most competitive distance ranges for coach, ordinary train, HSR and plane were below 500 km, 500–1000 km, 500–1500 km and over 1500 km, respectively. Besides, the structural equation modeling (SEM technique was applied to investigate the influencing mechanism of factors on the long-distance travel mode choice. The results revealed that travel distance was the most significant variable directly influencing passengers’ mode choices, followed by the service demand, performance evaluation, and personal attributes. Furthermore, personal attributes were verified to have an indirect effect on travel mode choice behavior by significantly affecting the service demand and performance evaluation.

  19. Field profile and loading measurements on higher order modes in a two cell 500 MHz superconducting structure

    International Nuclear Information System (INIS)

    Barry, W.; Edighoffer, J.; Chattopadhyay, S.; Fornaco, S.

    1992-01-01

    The Infrared Free Electron Laser, being designed at LBL as part of the Chemical Dynamics Research Laboratory, is based on a 500 MHz superconducting linac driver that consists of five 4-cell structures of the CERN/DESY type. A 500 MHz, 2-cell version of this structure is being used in a joint Stanford/LBL/BNL program to study accelerator issues relevant to the FEL applications. As part of this study, field profile and loading measurements of higher order modes have been made on the prototype structure. (Author) 3 refs., 2 figs., tab

  20. Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

    KAUST Repository

    Pogoreutz, Claudia

    2018-01-25

    The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora-associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.

  1. Identifying the default mode network structure using dynamic causal modeling on resting-state functional magnetic resonance imaging.

    Science.gov (United States)

    Di, Xin; Biswal, Bharat B

    2014-02-01

    The default mode network is part of the brain structure that shows higher neural activity and energy consumption when one is at rest. The key regions in the default mode network are highly interconnected as conveyed by both the white matter fiber tracing and the synchrony of resting-state functional magnetic resonance imaging signals. However, the causal information flow within the default mode network is still poorly understood. The current study used the dynamic causal modeling on a resting-state fMRI data set to identify the network structure underlying the default mode network. The endogenous brain fluctuations were explicitly modeled by Fourier series at the low frequency band of 0.01-0.08Hz, and those Fourier series were set as driving inputs of the DCM models. Model comparison procedures favored a model wherein the MPFC sends information to the PCC and the bilateral inferior parietal lobule sends information to both the PCC and MPFC. Further analyses provide evidence that the endogenous connectivity might be higher in the right hemisphere than in the left hemisphere. These data provided insight into the functions of each node in the DMN, and also validate the usage of DCM on resting-state fMRI data. © 2013.

  2. Relationships between default-mode network connectivity, medial temporal lobe structure, and age-related memory deficits.

    Science.gov (United States)

    Ward, Andrew M; Mormino, Elizabeth C; Huijbers, Willem; Schultz, Aaron P; Hedden, Trey; Sperling, Reisa A

    2015-01-01

    Advanced aging negatively impacts memory performance. Brain aging has been associated with shrinkage in medial temporal lobe structures essential for memory--including hippocampus and entorhinal cortex--and with deficits in default-mode network connectivity. Yet, whether and how these imaging markers are relevant to age-related memory deficits remains a topic of debate. Using a sample of 182 older (age 74.6 ± 6.2 years) and 66 young (age 22.2 ± 3.6 years) participants, this study examined relationships among memory performance, hippocampus volume, entorhinal cortex thickness, and default-mode network connectivity across aging. All imaging markers and memory were significantly different between young and older groups. Each imaging marker significantly mediated the relationship between age and memory performance and collectively accounted for most of the variance in age-related memory performance. Within older participants, default-mode connectivity and hippocampus volume were independently associated with memory. Structural equation modeling of cross-sectional data within older participants suggest that entorhinal thinning may occur before reduced default-mode connectivity and hippocampal volume loss, which in turn lead to deficits in memory performance. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Vertical Mode Structure and Transport of Indonesian Throughflow in Makassar Strait

    Science.gov (United States)

    Susanto, R. D.

    2002-12-01

    As part of the Indonesian-US Arlindo program, velocity and temperature at various depths and travel time from pressure inverted echo sounders (PIES) were measured in the Makassar Strait from November 1996 to July 1998. Here, we improve our initial estimate of the throughflow in the 0-200m layer by incorporating the six-months of ADCP data, as well as scatterometer wind data; below 1500m PIES data are used to improve the estimate. Vertical mode decomposition of the improved velocity field indicates that mode-1 represents 81% of the total transport. Meanwhile mode-2, 3, 4 accounts for 10%, 4% and 3% of the total transport, respectively. Mode 1 reveals that most of the throughflow transport occurs in the thermocline (150-400m) with a maximum velocity of 40cm/s at the depth of 250m. All our previous results derived from the initial volume transport time series are observed in mode-1, such as: lower transport during El Nino as compared to La Nina, and semiannual Kelvin waves from the Indian Ocean reducing the volume transport in May/June and October/November 1997. We further refine our estimate of the transport weighted average temperature and it agrees with the previous Arlindo calculations, significantly cooler than values typically used by the community. This result is very important - not only for the observational point of view - but also for numerical models of the Indonesian throughflow transport and heat-flux in the Pacific and Indian Oceans.

  4. Distribution, organization and ecology of bacteria in chronic wounds

    DEFF Research Database (Denmark)

    Kirketerp-Møller, Klaus; Jensen, Peter Ø.; Fazli, Mustafa

    2008-01-01

    contained P. aeruginosa. Furthermore, PNA FISH revealed the structural organization of bacteria in the samples. It appeared that P. aeruginosa aggregated as microcolonies imbedded in the matrix component alginate, which is a characteristic hallmark of the biofilm mode of growth. The present investigation...

  5. Enhancement-Mode AlGaN/GaN High Electron Mobility Transistors Using a Nano-Channel Array Structure

    International Nuclear Information System (INIS)

    Liu Sheng-Hou; Cai Yong; Zeng Chun-Hong; Shi Wen-Hua; Zhang Bao-Shun; Gong Ru-Min; Wang Jin-Yan; Wen, Cheng P.; Feng Zhi-Hong; Wang Jing-Jing; Yin Jia-Yun; Qin Hua

    2011-01-01

    A nano-channel array (NCA) structure is applied to realize enhancement-mode (E-mode) AlGaN/GaN high-electron mobility transistors (HEMTs). The fabricated NCA-HEMT, consisting of 1000 channels connected in parallel with a channel width of 64 nm, shows a threshold voltage of 0.15 V and a subthreshold slope of 78 mV/dec, compared to −3.92 V and 99 mV/dec for a conventional HEMT (C-HEMT), respectively Both the NCA-HEMT and C-HEMT show similar gate leakage current, indicating no significant degradation in gate leakage characteristics for the NCA-HEMT. The surrounding-field effect and relieved polarization contribute to the very large positive threshold voltage shift, while the work function difference makes it positive. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  6. Abstract: Stoichiometry, Vibrational Modes and Structures of Molten Nb2O5-K2S2O7 Mixtures

    DEFF Research Database (Denmark)

    Boghosian, S.; Borup, F.; Berg, Rolf W.

    1998-01-01

    High temperature Raman spectroscopy is used tostudy the vibrational modes and structures of the Nb205-K2S207(0 < X(Nb2O5)<0.22) molten salt mixtures at 450-700 oC under static equilibria conditions. Band assignments and Raman band intensity correlations with complex stoichiometry are performed in...... in order to characterise the complex(es) formed. The determination of stoichiometry is done following a general procedure which is based on a simple formalism correlating measurements of relative Raman band intensities with the stoichiometry of solutes in molten salt solvents.......High temperature Raman spectroscopy is used tostudy the vibrational modes and structures of the Nb205-K2S207(0 X(Nb2O5)

  7. Production and structural characterization of exopolysaccharides from newly isolated probiotic lactic acid bacteria.

    Science.gov (United States)

    Abid, Yousra; Casillo, Angela; Gharsallah, Houda; Joulak, Ichrak; Lanzetta, Rosa; Corsaro, Maria Michela; Attia, Hamadi; Azabou, Samia

    2018-03-01

    In this work, four exopolysaccharide-producing lactic acid bacteria (LAB) strains, newly isolated from Tunisian spontaneously fermented foods and beverages, namely bovine and turkey meat sausages (BMS and TMS), date palm sap (DPS) and cow milk (CM), were identified as Leuconostoc citreum-BMS, Leuconostoc mesenteroides-TMS, Pediococcus pentosaceus-DPS and Leuconostoc pseudomesenteroides-CM, respectively. The isolated strains showed the ability to withstand simulated human gastrointestinal (GI) tract conditions (low pH, lysozyme, bile salts, pepsin and pancreatin) and showed high surface hydrophobicity (79-90%), besides their ability to act against Escherichia coli and Listeria monocytogenes and to produce exopolysaccharides (EPS). Therefore, these isolates can be served as potential probiotics. The produced EPS were growth-associated suggesting that they are primary metabolites. The molecular weights were higher than 10 6 Da using HPLC-SEC. 2D-NMR results indicated that all the samples were mixtures of dextran and levan, except for EPS-CM which was a levan-type EPS. Furthermore, the EPS samples showed an abitlity to inhibit and to disrupt pathogenic biofilms and showed high thermostability studied via differential scanning calorimetry (DSC) with melting points higher than 224°C making them promising to be used in thermal processed foods. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests.

    Science.gov (United States)

    Wang, Xiaoli; Wang, Xiaoling; Zhang, Weixin; Shao, Yuanhu; Zou, Xiaoming; Liu, Tao; Zhou, Lixia; Wan, Songze; Rao, Xingquan; Li, Zhian; Fu, Shenglei

    2016-01-12

    Soil bacteria may be influenced by vegetation and play important roles in global carbon efflux and nutrient cycling under global changes. Coniferous and broadleaved forests are two phyletically distinct vegetation types. Soil microbial communities in these forests have been extensively investigated but few studies have presented comparable data regarding the characteristics of bacterial communities in subtropical forests. We investigated soil bacterial biomass and community composition in three pairs of coniferous and broadleaved forests across a subtropical climatic gradient. We found that bacterial biomass differed between the coniferous and broadleaved forests across the subtropical climate gradient; however, this difference disappeared at some individual sites. In contrast, the same 90 bacterial genera were found in both forest types, and their relative abundances didn't differ between the forest types, with the exception of one genus that was more abundant in broadleaved forests. Soil nitrogen or moisture was associated with bacterial groups in the coniferous and broadleaved forests, respectively. Thus, we inferred that these forests can respond differently to future changes in nitrogen deposition or precipitation. This study highlights soil bacterial invariant community composition in contrasting subtropical forests and provides a new perspective on the potential response and feedback of forests to global changes.

  9. Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities

    Directory of Open Access Journals (Sweden)

    Josep M. Gasol

    2000-06-01

    Full Text Available Flow cytometry is rapidly becoming a routine methodology in aquatic microbial ecology. The combination of simple to use bench-top flow cytometers and highly fluorescent nucleic acid stains allows fast and easy determination of microbe abundance in the plankton of lakes and oceans. The different dyes and protocols used to stain and count planktonic bacteria as well as the equipment in use are reviewed, with special attention to some of the problems encountered in daily routine practice such as fixation, staining and absolute counting. One of the main advantages of flow cytometry over epifluorescence microscopy is the ability to obtain cell-specific measurements in large numbers of cells with limited effort. We discuss how this characteristic has been used for differentiating photosynthetic from non-photosynthetic prokaryotes, for measuring bacterial cell size and nucleic acid content, and for estimating the relative activity and physiological state of each cell. We also describe how some of the flow cytometrically obtained data can be used to characterize the role of microbes on carbon cycling in the aquatic environment and we prospect the likely avenues of progress in the study of planktonic prokaryotes through the use of flow cytometry.

  10. Phylogenetic diversity and community structure of sponge-associated bacteria from mangroves of the Caribbean Sea

    KAUST Repository

    Yang, Jiangke

    2011-02-08

    To gain insight into the species richness and phylogeny of the microbial communities associated with sponges in mangroves, we performed an extensive phylogenetic analysis, based on terminal restriction fragment length polymorphism profiling and 16S ribosomal RNA gene sequences, of the 4 sponge species Aplysina fulva, Haliclona hogarthi, Tedania ignis and Ircinia strobilina as well as of ambient seawater. The sponge-associated bacterial communities contained 13 phyla, including Poribacteria and an unclassified group not found in the ambient seawater community, 98% of which comprised Proteobacteria, Cyanobacteria and Bacteroidetes. Although the sponges themselves were phylogenetically distant and bacterial community variation within the host species was observed, microbial phyla such as Proteobacteria, Acidobacteria, Chloroflexi and the unclassified group were consistently observed as the dominant populations within the communities. The sponge-associated bacterial communities resident in the Caribbean Sea mangroves are phylogenetically similar but significantly distinct from communities found in other biogeographical sites such as the deep-water environments of the Caribbean Sea, the South China Sea and Australia. The interspecific variation within the host species and the distinct biogeographical characteristics that the sponge-associated bacteria exhibited indicate that the acquisition, establishment and formation of functional sponge-associated bacterial communities may initially be the product of both vertical and horizontal transmission, and is then shaped by the internal environment created by the sponge species and certain external environmental factors. © Inter-Research 2011.

  11. Efficacy of reactive mineral-based sorbents for phosphate, bacteria, nitrogen and TOC removal--column experiment in recirculation batch mode.

    Science.gov (United States)

    Nilsson, Charlotte; Lakshmanan, Ramnath; Renman, Gunno; Rajarao, Gunaratna Kuttuva

    2013-09-15

    Two mineral-based materials (Polonite and Sorbulite) intended for filter wells in on-site wastewater treatment were compared in terms of removal of phosphate (PO4-P), total inorganic nitrogen (TIN), total organic carbon (TOC) and faecal indicator bacteria (Escherichia coli and Enterococci). Using an innovative, recirculating system, septic tank effluent was pumped at a hydraulic loading rate of 3000 L m(2) d(-1) into triplicate bench-scale columns of each material over a 90-day period. The results showed that Polonite performed better with respect to removal of PO4-P, retaining on average 80% compared with 75% in Sorbulite. This difference was attributed to higher CaO content in Polonite and its faster dissolution. Polonite also performed better in terms of removal of bacteria because of its higher pH value. The total average reduction in E. coli was 60% in Polonite and 45% in Sorbulite, while for Enterococci the corresponding value was 56% in Polonite and 34% in Sorbulite. Sorbulite removed TIN more effectively, with a removal rate of 23%, while Polonite removed 11% of TIN, as well as TOC. Organic matter (measured as TOC) was accumulated in the filter materials but was also released periodically. The results showed that Sorbulite could meet the demand in removing phosphate and nitrogen with reduced microbial release from the wastewater treatment process. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Co-ordinated functions of Mms proteins define the surface structure of cubo-octahedral magnetite crystals in magnetotactic bacteria.

    Science.gov (United States)

    Arakaki, Atsushi; Yamagishi, Ayana; Fukuyo, Ayumi; Tanaka, Masayoshi; Matsunaga, Tadashi

    2014-08-01

    Magnetotactic bacteria synthesize magnetosomes comprised of membrane-enveloped single crystalline magnetite (Fe3 O4 ). The size and morphology of the nano-sized magnetite crystals (Mms (Mms5, Mms6, Mms7, and Mms13), was previously isolated from the surface of cubo-octahedral magnetite crystals in Magnetospirillum magneticum strain AMB-1. Analysis of an mms6 gene deletion mutant suggested that the Mms6 protein plays a major role in the regulation of magnetite crystal size and morphology. In this study, we constructed various mms gene deletion mutants and characterized the magnetite crystals formed by the mutant strains. Comparative analysis showed that all mms genes were involved in the promotion of crystal growth in different manners. The phenotypic characterization of magnetites also suggested that these proteins are involved in controlling the geometries of the crystal surface structures. Thus, the co-ordinated functions of Mms proteins regulate the morphology of the cubo-octahedral magnetite crystals in magnetotactic bacteria. © 2014 John Wiley & Sons Ltd.

  13. 6-Pyruvoyltetrahydropterin synthase orthologs of either a single or dual domain structure are responsible for tetrahydrobiopterin synthesis in bacteria.

    Science.gov (United States)

    Kong, Jin Sun; Kang, Ji-Youn; Kim, Hye Lim; Kwon, O-Seob; Lee, Kon Ho; Park, Young Shik

    2006-09-04

    6-Pyruvoyltetrahydropterin synthase (PTPS) catalyzes the second step of tetrahydrobiopterin (BH4) synthesis. We previously identified PTPS orthologs (bPTPS-Is) in bacteria which do not produce BH4. In this study we disrupted the gene encoding bPTPS-I in Synechococcus sp. PCC 7942, which produces BH4-glucoside. The mutant was normal in BH4-glucoside production, demonstrating that bPTPS-I does not participate in BH4 synthesis in vivo and bringing us a new PTPS ortholog (bPTPS-II) of a bimodular polypeptide. The recombinant Synechococcus bPTPS-II was assayed in vitro to show PTPS activity higher than human enzyme. Further computational analysis revealed the presence of mono and bimodular bPTPS-II orthologs mostly in green sulfur bacteria and cyanobacteria, respectively, which are well known for BH4-glycoside production. In summary we found new bacterial PTPS orthologs, having either a single or dual domain structure and being responsible for BH4 synthesis in vivo, thereby disclosing all the bacterial PTPS homologs.

  14. Slow light modes for optical delay lines: 2D photonic crystal-based design structures, performances and challenges

    International Nuclear Information System (INIS)

    Talneau, A

    2010-01-01

    This paper presents an overview of 2D photonic crystal-based structures designed to display low group velocity as well as reduced group velocity dispersions. Their main envisioned applications are optical delay lines for telecom transmissions at 1.55 µm. Optical mechanisms responsible for slowing down the optical modes and encountered in the slow light regime serve as a guideline for this paper. (review article)

  15. The effect of bacteria on diatom community structure - The 'antibiotics' approach

    Digital Repository Service at National Institute of Oceanography (India)

    DeCosta, P.M.; Anil, A.C.

    . The bacterial community preferred the ‘tolerance’ strategy over ‘resistance’ in response to treatment with penicillin; these changes in bacterial dynamics were probably linked to concurrent changes in diatom community structure. The observations with penicillin...

  16. Structural differences in gut bacteria communities in developmental stages of natural populations of Lutzomyia evansi from Colombia's Caribbean coast.

    Science.gov (United States)

    Vivero, Rafael José; Jaramillo, Natalia Gil; Cadavid-Restrepo, Gloria; Soto, Sandra I Uribe; Herrera, Claudia Ximena Moreno

    2016-09-13

    adult stages. Additionally, differences were found in bacterial community structure in fed females, unfed females, males and larvae. The intestinal bacteria detected by PCR-TTGE were Enterobacter cloacae and Bacillus thuringiensis, which were present in different life stages of Lu. evansi, and Burkholderia cenocepacia and Bacillus gibsonii, which were detected only in the larval stage. Wolbachia and Leishmania were not detected in gut samples of Lutzomyia evansi. The analyses conducted using microbiological and molecular approaches indicated significant variations in the bacterial communities associated with the gut of Lu. evansi, depending on the developmental stage and food source. We propose that these elements affect microbial diversity in L. evansi guts and may in turn influence pathogen transmission to humans bitten by this insect.

  17. Discriminating between the effects of founding events and reproductive mode on the genetic structure of Triops populations (Branchiopoda: Notostraca.

    Directory of Open Access Journals (Sweden)

    Rebekah L Horn

    Full Text Available Crustaceans that initially colonize a freshwater temporary pond can strongly bias the subsequent genetic composition of the population, causing nearby populations to be genetically distinct. In addition, these crustaceans have various reproductive modes that can influence genetic differentiation and diversity within and between populations. We report on two species of tadpole shrimp, Triops newberryi and Triops longicaudatus "short", with different reproductive modes. Reproduction in the tadpole shrimp can occur clonally (parthenogenesis, with self fertilization (hermaphroditism, or through outcrossing of hermaphrodites with males (androdioecy. For all these reproductive modes, population genetic theory predicts decreased genetic diversity and increased population differentiation. Here we use mitochondrial control region (mtCR sequences and nuclear microsatellite loci to determine if the difference in reproductive mode affects the high genetic structure typical of persistent founder effects. Previous authors indicated that T. newberryi is androdioecious because populations are composed of hermaphrodites and males, and T. longicaudatus "short" is hermaphroditic or parthenogenetic because males are absent. In our data, T. newberryi and T. longicaudatus "short" populations were highly structured genetically over short geographic distances for mtCR sequences and microsatellite loci (T. newberryi: ΦST = 0.644, FST = 0.252, respectively; T. l. "short": invariant mtCR sequences, FST = 0.600. Differences between the two Triops species in a number of diversity measures were generally consistent with expectations from population genetic theory regarding reproductive mode; however, three of four comparisons were not statistically significant. We conclude the high genetic differentiation between populations is likely due to founder effects and results suggest both species are composed of selfing hermaphrodites with some level of outcrossing

  18. An investigation into the functional and structural connectivity of the Default Mode Network

    NARCIS (Netherlands)

    van Oort, E.S.B.; van Cappellen van Walsum, Anne-Marie; Norris, David Gordon

    2014-01-01

    Connectivity analyses based on both resting-state (rs-)fMRI and diffusion weighted imaging studies suggest that the human brain contains regions that act as hubs for the entire brain, and that elements of the Default Mode Network (DMN) play a pivotal role in this network. In the present study, the

  19. Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

    DEFF Research Database (Denmark)

    Hansen, Benni Winding; Kesäniemi, Jenni E; Mustonen, Marina

    2014-01-01

    elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation...

  20. Linear-Space Data Structures for Range Mode Query in Arrays

    DEFF Research Database (Denmark)

    Chan, Timothy M.; Durocher, Stephane; Larsen, Kasper Green

    2012-01-01

    that supports range mode queries in O(sqrt(n / log n)) worst-case time. Furthermore, we present strong evidence that a query time significantly below sqrt(n) cannot be achieved by purely combinatorial techniques; we show that boolean matrix multiplication of two sqrt(n) by sqrt(n) matrices reduces to n range...

  1. Linear-Space Data Structures for Range Mode Query in Arrays

    DEFF Research Database (Denmark)

    Chan, Timothy M.; Durocher, Stephane; Larsen, Kasper Green

    2014-01-01

    that supports range mode queries in O(sqrt(n / log n)) worst-case time. Furthermore, we present strong evidence that a query time significantly below sqrt(n) cannot be achieved by purely combinatorial techniques; we show that boolean matrix multiplication of two sqrt(n) by sqrt(n) matrices reduces to n range...

  2. Effect of Thermal Fields on the Structure of Corrosion-Resistant Steels Under Different Modes of Laser Treatment

    Science.gov (United States)

    Tarasova, T. V.; Gusarov, A. V.; Protasov, K. E.; Filatova, A. A.

    2017-11-01

    The influence of temperature fields on the structure and properties of corrosion-resistant chromium steels under different modes of laser treatment is investigated. A model of heat transfer under laser impact on target is used to plot thermal fields and cycles and cooling rates. It is shown that the model used for computing thermal fields gives tentative geometric sizes of the fusion zones under laser treatment and selective laser fusion. The cooling rate is shown to have decisive influence on the structure of corrosion-resistant steels after laser treatment with surface fusion in devices for pulsed, continuous, and selective laser melting.

  3. Structural peculiarities of the O-specific polysaccharides of Azospirillum bacteria of serogroup III.

    Science.gov (United States)

    Fedonenko, Yu P; Boiko, A S; Zdorovenko, E L; Konnova, S A; Shashkov, A S; Ignatov, V V; Knirel, Yu A

    2011-07-01

    Lipopolysaccharides and O-specific polysaccharides were isolated from the outer membrane of bacterial cells of three strains belonging to two Azospirillum species, and their structures were established by monosaccharide analysis including determination of the absolute configurations, methylation analysis, and one- and two-dimensional NMR spectroscopy. It was shown that while having the identical composition, the O-polysaccharides have different branched tetrasaccharide repeating units. Two neutral polysaccharides were found in the lipopolysaccharide of A. brasilense 54, and the structure for the predominant O-polysaccharide was determined. The structural data, together with results of serological studies, enabled assignment of strains examined to a novel serogroup, III. The chemical basis for the serological relatedness among the azospirilla of this serogroup is presumably the presence of a common →3)-α-L-Rhap-(1→2)-α-L-Rhap-(1→3)-α-L-Rhap-(1→ oligosaccharide motif in their O-polysaccharides.

  4. Structural properties, crystal quality and growth modes of MOCVD-grown AlN with TMAl pretreatment of sapphire substrate

    KAUST Repository

    Sun, Haiding

    2017-08-08

    The growth of high quality AlN epitaxial films relies on precise control of the initial growth stages. In this work, we examined the influence of the trimethylaluminum (TMAl) pretreatment of sapphire substrates on the structural properties, crystal quality and growth modes of heteroepitaxial AlN films on (0001) sapphire substrates. Without the pretreatment, the AlN films nucleated on the smooth surface but exhibited mixed crystallographic Al- (N-) polarity, resulting in rough AlN film surfaces. With increasing the pretreatment time from 1 to 5 s, the N-polarity started to be impeded. However, small islands were formed on sapphire surface due to the decompostion of TMAl. As a result, small voids became noticeable at the nucleation layer (NL) because the growth started as quasi three-dimensional (3D) but transformed to 2D mode as the film grew thicker and got coalesced, leading to smoother and Al-polar films. On the other hand, longer pretreatment time of 40 s formed large 3D islands on sapphire, and thus initiated a 3D-growth mode of the AlN film, generating Al-polar AlN nanocolumns with different facets, which resulted into rougher film surfaces. The epitaxial growth modes and their correlation with the AlN film crystal quality under different TMAl pretreatments are also discussed.

  5. Emergence of time-horizon invariant correlation structure in financial returns by subtraction of the market mode

    Science.gov (United States)

    Borghesi, Christian; Marsili, Matteo; Miccichè, Salvatore

    2007-08-01

    We investigate the emergence of a structure in the correlation matrix of assets’ returns as the time horizon over which returns are computed increases from the minutes to the daily scale. We analyze data from different stock markets (New York, Paris, London, Milano) and with different methods. In addition to the usual correlations, we also analyze those obtained by subtracting the dynamics of the “center of mass” (i.e., the market mode). We find that when the center of mass is not removed the structure emerges, as the time horizon increases, from splitting a single large cluster into smaller ones. By contrast, when the market mode is removed the structure of correlations observed at the daily scale is already well defined at very high frequency ( 5min in the New York Stock Exchange). Moreover, this structure accounts for 80% of the classification of stocks in economic sectors. Similar results, though less sharp, are found for the other markets. We also find that the structure of correlations in the overnight returns is markedly different from that of intraday activity.

  6. Observation of beam-excited dipole modes in traveling wave accelerator structures

    International Nuclear Information System (INIS)

    Vetter, A.M.; Adamski, J.L.; Gallagher, W.J.

    1985-01-01

    Beamline tests on a series of waveguide models have recently been completed at the Boeing Radiation Effects Laboratory. The purpose of these tests has been to study beam excitation of the dipole modes which participate in regenerative and cumulative beam breakup processes in RF linac waveguides. Cell excitation patterns, dependence on transverse beam displacement from the axis, and comparative excitation levels in waveguides of different design were measured

  7. Relationship between the anterior forebrain mesocircuit and the default mode network in the structural bases of disorders of consciousness.

    Science.gov (United States)

    Lant, Nicholas D; Gonzalez-Lara, Laura E; Owen, Adrian M; Fernández-Espejo, Davinia

    2016-01-01

    The specific neural bases of disorders of consciousness (DOC) are still not well understood. Some studies have suggested that functional and structural impairments in the default mode network may play a role in explaining these disorders. In contrast, others have proposed that dysfunctions in the anterior forebrain mesocircuit involving striatum, globus pallidus, and thalamus may be the main underlying mechanism. Here, we provide the first report of structural integrity of fiber tracts connecting the nodes of the mesocircuit and the default mode network in 8 patients with DOC. We found evidence of significant damage to subcortico-cortical and cortico-cortical fibers, which were more severe in vegetative state patients and correlated with clinical severity as determined by Coma Recovery Scale-Revised (CRS-R) scores. In contrast, fiber tracts interconnecting subcortical nodes were not significantly impaired. Lastly, we found significant damage in all fiber tracts connecting the precuneus with cortical and subcortical areas. Our results suggest a strong relationship between the default mode network - and most importantly the precuneus - and the anterior forebrain mesocircuit in the neural basis of the DOC.

  8. Relationship between the anterior forebrain mesocircuit and the default mode network in the structural bases of disorders of consciousness

    Directory of Open Access Journals (Sweden)

    Nicholas D. Lant

    2016-01-01

    Full Text Available The specific neural bases of disorders of consciousness (DOC are still not well understood. Some studies have suggested that functional and structural impairments in the default mode network may play a role in explaining these disorders. In contrast, others have proposed that dysfunctions in the anterior forebrain mesocircuit involving striatum, globus pallidus, and thalamus may be the main underlying mechanism. Here, we provide the first report of structural integrity of fiber tracts connecting the nodes of the mesocircuit and the default mode network in 8 patients with DOC. We found evidence of significant damage to subcortico-cortical and cortico-cortical fibers, which were more severe in vegetative state patients and correlated with clinical severity as determined by Coma Recovery Scale—Revised (CRS-R scores. In contrast, fiber tracts interconnecting subcortical nodes were not significantly impaired. Lastly, we found significant damage in all fiber tracts connecting the precuneus with cortical and subcortical areas. Our results suggest a strong relationship between the default mode network – and most importantly the precuneus – and the anterior forebrain mesocircuit in the neural basis of the DOC.

  9. Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea.

    Science.gov (United States)

    Tomita, Takeo

    2017-11-01

    Amino acids are essential components in all organisms because they are building blocks of proteins. They are also produced industrially and used for various purposes. For example, L-glutamate is used as the component of "umami" taste and lysine has been used as livestock feed. Recently, many kinds of amino acids have attracted attention as biological regulators and are used for a healthy life. Thus, to clarify the mechanism of how amino acids are biosynthesized and how they work as biological regulators will lead to further effective utilization of them. Here, I review the leucine-induced-allosteric activation of glutamate dehydrogenase (GDH) from Thermus thermophilus and the relationship with the allosteric regulation of GDH from mammals. Next, I describe structural insights into the efficient production of L-glutamate by GDH from an excellent L-glutamate producer, Corynebacterium glutamicum. Finally, I review the structural biology of lysine biosynthesis of thermophilic bacterium and archaea.

  10. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Halavaty, Andrei S. [Center for Structural Genomics of Infectious Diseases, (United States); Northwestern University, Chicago, IL 60611 (United States); Kim, Youngchang [Center for Structural Genomics of Infectious Diseases, (United States); Argonne National Laboratory, Argonne, IL 60439 (United States); University of Chicago, Chicago, IL 60637 (United States); Minasov, George; Shuvalova, Ludmilla; Dubrovska, Ievgeniia; Winsor, James [Center for Structural Genomics of Infectious Diseases, (United States); Northwestern University, Chicago, IL 60611 (United States); Zhou, Min [Center for Structural Genomics of Infectious Diseases, (United States); Argonne National Laboratory, Argonne, IL 60439 (United States); University of Chicago, Chicago, IL 60637 (United States); Onopriyenko, Olena; Skarina, Tatiana [Center for Structural Genomics of Infectious Diseases, (United States); University of Toronto, Toronto, Ontario M5G 1L6 (Canada); Papazisi, Leka; Kwon, Keehwan; Peterson, Scott N. [Center for Structural Genomics of Infectious Diseases, (United States); J. Craig Venter Institute, Rockville, MD 20850 (United States); Joachimiak, Andrzej [Center for Structural Genomics of Infectious Diseases, (United States); Argonne National Laboratory, Argonne, IL 60439 (United States); University of Chicago, Chicago, IL 60637 (United States); Savchenko, Alexei [Center for Structural Genomics of Infectious Diseases, (United States); University of Toronto, Toronto, Ontario M5G 1L6 (Canada); Anderson, Wayne F., E-mail: wf-anderson@northwestern.edu [Center for Structural Genomics of Infectious Diseases, (United States); Northwestern University, Chicago, IL 60611 (United States)

    2012-10-01

    The structural characterization of acyl-carrier-protein synthase (AcpS) from three different pathogenic microorganisms is reported. One interesting finding of the present work is a crystal artifact related to the activity of the enzyme, which fortuitously represents an opportunity for a strategy to design a potential inhibitor of a pathogenic AcpS. Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS{sub SA}), Vibrio cholerae (AcpS{sub VC}) and Bacillus anthracis (AcpS{sub BA}) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS{sub BA} is emphasized because of the two 3′, 5′-adenosine diphosphate (3′, 5′-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3′, 5′-ADP is bound as the 3′, 5′-ADP part of CoA in the known structures of the CoA–AcpS and 3′, 5′-ADP–AcpS binary complexes. The position of the second 3′, 5′-ADP has never been described before. It is in close proximity to the first 3′, 5′-ADP and the ACP-binding site. The coordination of two ADPs in AcpS{sub BA} may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP.

  11. Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria

    International Nuclear Information System (INIS)

    Halavaty, Andrei S.; Kim, Youngchang; Minasov, George; Shuvalova, Ludmilla; Dubrovska, Ievgeniia; Winsor, James; Zhou, Min; Onopriyenko, Olena; Skarina, Tatiana; Papazisi, Leka; Kwon, Keehwan; Peterson, Scott N.; Joachimiak, Andrzej; Savchenko, Alexei; Anderson, Wayne F.

    2012-01-01

    The structural characterization of acyl-carrier-protein synthase (AcpS) from three different pathogenic microorganisms is reported. One interesting finding of the present work is a crystal artifact related to the activity of the enzyme, which fortuitously represents an opportunity for a strategy to design a potential inhibitor of a pathogenic AcpS. Some bacterial type II fatty-acid synthesis (FAS II) enzymes have been shown to be important candidates for drug discovery. The scientific and medical quest for new FAS II protein targets continues to stimulate research in this field. One of the possible additional candidates is the acyl-carrier-protein synthase (AcpS) enzyme. Its holo form post-translationally modifies the apo form of an acyl carrier protein (ACP), which assures the constant delivery of thioester intermediates to the discrete enzymes of FAS II. At the Center for Structural Genomics of Infectious Diseases (CSGID), AcpSs from Staphylococcus aureus (AcpS SA ), Vibrio cholerae (AcpS VC ) and Bacillus anthracis (AcpS BA ) have been structurally characterized in their apo, holo and product-bound forms, respectively. The structure of AcpS BA is emphasized because of the two 3′, 5′-adenosine diphosphate (3′, 5′-ADP) product molecules that are found in each of the three coenzyme A (CoA) binding sites of the trimeric protein. One 3′, 5′-ADP is bound as the 3′, 5′-ADP part of CoA in the known structures of the CoA–AcpS and 3′, 5′-ADP–AcpS binary complexes. The position of the second 3′, 5′-ADP has never been described before. It is in close proximity to the first 3′, 5′-ADP and the ACP-binding site. The coordination of two ADPs in AcpS BA may possibly be exploited for the design of AcpS inhibitors that can block binding of both CoA and ACP

  12. Can CFMIP2 models reproduce the leading modes of cloud vertical structure in the CALIPSO-GOCCP observations?

    Science.gov (United States)

    Wang, Fang; Yang, Song

    2018-02-01

    Using principal component (PC) analysis, three leading modes of cloud vertical structure (CVS) are revealed by the GCM-Oriented CALIPSO Cloud Product (GOCCP), i.e. tropical high, subtropical anticyclonic and extratropical cyclonic cloud modes (THCM, SACM and ECCM, respectively). THCM mainly reflect the contrast between tropical high clouds and clouds in middle/high latitudes. SACM is closely associated with middle-high clouds in tropical convective cores, few-cloud regimes in subtropical anticyclonic clouds and stratocumulus over subtropical eastern oceans. ECCM mainly corresponds to clouds along extratropical cyclonic regions. Models of phase 2 of Cloud Feedback Model Intercomparison Project (CFMIP2) well reproduce the THCM, but SACM and ECCM are generally poorly simulated compared to GOCCP. Standardized PCs corresponding to CVS modes are generally captured, whereas original PCs (OPCs) are consistently underestimated (overestimated) for THCM (SACM and ECCM) by CFMIP2 models. The effects of CVS modes on relative cloud radiative forcing (RSCRF/RLCRF) (RSCRF being calculated at the surface while RLCRF at the top of atmosphere) are studied in terms of principal component regression method. Results show that CFMIP2 models tend to overestimate (underestimated or simulate the opposite sign) RSCRF/RLCRF radiative effects (REs) of ECCM (THCM and SACM) in unit global mean OPC compared to observations. These RE biases may be attributed to two factors, one of which is underestimation (overestimation) of low/middle clouds (high clouds) (also known as stronger (weaker) REs in unit low/middle (high) clouds) in simulated global mean cloud profiles, the other is eigenvector biases in CVS modes (especially for SACM and ECCM). It is suggested that much more attention should be paid on improvement of CVS, especially cloud parameterization associated with particular physical processes (e.g. downwelling regimes with the Hadley circulation, extratropical storm tracks and others), which

  13. Crystal structure of the neutralizing Llama V(HH D7 and its mode of HIV-1 gp120 interaction.

    Directory of Open Access Journals (Sweden)

    Andreas Hinz

    2010-05-01

    Full Text Available HIV-1 entry into host cells is mediated by the sequential binding of the envelope glycoprotein gp120 to CD4 and a chemokine receptor. Antibodies binding to epitopes overlapping the CD4-binding site on gp120 are potent inhibitors of HIV entry, such as the llama heavy chain antibody fragment V(HH D7, which has cross-clade neutralizing properties and competes with CD4 and mAb b12 for high affinity binding to gp120. We report the crystal structure of the D7 V(HH at 1.5 A resolution, which reveals the molecular details of the complementarity determining regions (CDR and substantial flexibility of CDR3 that could facilitate an induced fit interaction with gp120. Structural comparison of CDRs from other CD4 binding site antibodies suggests diverse modes of interaction. Mutational analysis identified CDR3 as a key component of gp120 interaction as determined by surface plasmon resonance. A decrease in affinity is directly coupled to the neutralization efficiency since mutations that decrease gp120 interaction increase the IC50 required for HIV-1 IIIB neutralization. Thus the structural study identifies the long CDR3 of D7 as the key determinant of interaction and HIV-1 neutralization. Furthermore, our data confirm that the structural plasticity of gp120 can accommodate multiple modes of antibody binding within the CD4 binding site.

  14. A new surface fractal dimension for displacement mode shape-based damage identification of plate-type structures

    Science.gov (United States)

    Shi, Binkai; Qiao, Pizhong

    2018-03-01

    Vibration-based nondestructive testing is an area of growing interest and worthy of exploring new and innovative approaches. The displacement mode shape is often chosen to identify damage due to its local detailed characteristic and less sensitivity to surrounding noise. Requirement for baseline mode shape in most vibration-based damage identification limits application of such a strategy. In this study, a new surface fractal dimension called edge perimeter dimension (EPD) is formulated, from which an EPD-based window dimension locus (EPD-WDL) algorithm for irregularity or damage identification of plate-type structures is established. An analytical notch-type damage model of simply-supported plates is proposed to evaluate notch effect on plate vibration performance; while a sub-domain of notch cases with less effect is selected to investigate robustness of the proposed damage identification algorithm. Then, fundamental aspects of EPD-WDL algorithm in term of notch localization, notch quantification, and noise immunity are assessed. A mathematical solution called isomorphism is implemented to remove false peaks caused by inflexions of mode shapes when applying the EPD-WDL algorithm to higher mode shapes. The effectiveness and practicability of the EPD-WDL algorithm are demonstrated by an experimental procedure on damage identification of an artificially-induced notched aluminum cantilever plate using a measurement system of piezoelectric lead-zirconate (PZT) actuator and scanning laser Doppler vibrometer (SLDV). As demonstrated in both the analytical and experimental evaluations, the new surface fractal dimension technique developed is capable of effectively identifying damage in plate-type structures.

  15. Influence of modes of metal transfer on grain structure and direction of grain growth in low nickel austenitic stainless steel weld metals

    International Nuclear Information System (INIS)

    Mukherjee, Manidipto; Saha, Saptarshi; Pal, Tapan Kumar; Kanjilal, Prasanta

    2015-01-01

    The present study elaborately discussed the effect of different modes of metal transfer (i.e., short circuit mode, spray mode and pulse mode) on grain structure and direction of grain growth in low nickel austenitic stainless steel weld metals. Electron backscattered diffraction (EBSD) analysis was used to study the grain growth direction and grain structure in weld metals. The changes in grain structure and grain growth direction were found to be essentially varied with the weld pool shape and acting forces induced by modes of metal transfer at a constant welding speed. Short circuit mode of metal transfer owing to higher Marangoni force (M a ) and low electromagnetic force (R m ) promotes the lower weld pool volume (Γ) and higher weld pool maximum radius (r m ). Short circuit mode also shows curved and tapered columnar grain structures and the grain growth preferentially occurred in <001> direction. In contrast, spray mode of metal transfer increases the Γ and reduces the r m values due to very high R m and typically reveals straight and broad columnar grain structures with preferential growth direction in <111>. In the pulse mode of metal transfer relatively high M a and R m simultaneously increase the weld pool width and the primary penetration which might encourage relatively complex grain growth directions in the weld pool and cause a shift of major intensity from <001> to <111> direction. It can also be concluded that the fusion zone grain structure and direction of grain growth are solely dependent on modes of metal transfer and remain constant for a particular mode of metal transfer irrespective of filler wire used. - Highlights: • Welded joints of LNiASS were prepared by varying modes of metal transfer. • Weld pool shape, grain structure and grain growth direction were studied. • Short circuit mode shows curved and tapered grain growth in <001> direction. • Spray mode shows straight and broad columnar grain growth in <111> direction. • Pulse

  16. Are the soft, liquid-like structures detected around bacteria by ambient dynamic atomic force microscopy capsules?

    Science.gov (United States)

    Méndez-Vilas, A; Labajos-Broncano, L; Perera-Núñez, J; González-Martín, M L

    2011-05-01

    High-resolution imaging of bacterial capsules by microscopy is of paramount importance in microbiology due to their role in pathogenesis. This is, however, quite a challenging task due to their delicate nature. In this context, recent reports have claimed successful exploitation of the capacity of atomic force microscopy (AFM) for imaging of extremely deformable (even liquid) surfaces under ambient conditions to detect bacterial capsules in the form of tiny amounts of liquid-like substances around bacteria. In order to further explore this supposed capacity of AFM, in this work, three staphylococcal strains have been scrutinized for the presence of capsules using such an AFM-based approach with a phosphate buffer and water as the suspending liquids. Similar results were obtained with the three strains. AFM showed the presence of liquid-like substances identical to those attributed to bacterial capsules in the previous literature. Extensive imaging and chemical analysis point out the central role of the suspending liquid (buffer) in the formation of these substances. The phenomenon has been reproduced even by using nonliving particles, a finding that refutes the biological origin of the liquid-like substances visualized around the cells. Deliquescence of major components of biological buffers, such as K(2)HPO(4), CaCl(2), or HEPES, is proposed as the fundamental mechanism of the formation of these ultrasmall liquid-like structures. Such an origin could explain the high similarity of our results obtained with three very different strains and also the high similarity of these results to others reported in the literature based on other bacteria and suspending liquids. Finally, possible biological/biomedical implications of the presence of these ultrasmall amounts of liquids wrapping microorganisms are discussed.

  17. High Power Test of X-band Single Cell HOM-free Choke-mode Damped Accelerating Structure made by Tsinghua University

    OpenAIRE

    Wu, Xiaowei; Abe, Tetsuo; Chen, Huaibi; Higo, Toshiyasu; Shi, Jiaru; Wuensch, Walter; Zha, Hao

    2016-01-01

    As an alternative design for CLIC main accelerating structures, X-band choke-mode damped structures had been studied for several years. However, the performance of choke-mode cavity under high power is still in lack of research. Two standing wave single cell choke-mode damped accelerating structures with different choke dimensions which are working at 11.424 GHz were designed, manufactured and bench tested by accelerator group in Tsinghua University. High power test was carried out on it to s...

  18. Structural and electron paramagnetic resonance (EPR) studies of mononuclear molybdenum enzymes from sulfate-reducing bacteria.

    Science.gov (United States)

    Brondino, Carlos D; Rivas, María G; Romão, Maria J; Moura, José J G; Moura, Isabel

    2006-10-01

    Molybdenum and tungsten are found in biological systems in a mononuclear form in the active site of a diverse group of enzymes that generally catalyze oxygen-atom-transfer reactions. The metal atom (Mo or W) is coordinated to one or two pyranopterin molecules and to a variable number of ligands such as oxygen (oxo, hydroxo, water, serine, aspartic acid), sulfur (cysteines), and selenium (selenocysteines) atoms. In addition, these proteins contain redox cofactors such as iron-sulfur clusters and heme groups. All of these metal cofactors are along an electron-transfer pathway that mediates the electron exchange between substrate and an external electron acceptor (for oxidative reactions) or donor (for reductive reactions). We describe in this Account a combination of structural and electronic paramagnetic resonance studies that were used to reveal distinct aspects of these enzymes.

  19. Potential seismic structural failure modes associated with the Zion Nuclear Plant. Seismic safety margins research program (Phase I). Project VI. Fragilities

    International Nuclear Information System (INIS)

    1979-10-01

    The Zion 1 and 2 Nuclear Power Plant consists of a number of structures. The most important of these from the viewpoint of safety are the containment buildings, the auxiliary building, the turbine building, and the crib house (or intake structure). The evaluation of the potential seismic failure modes and determination of the ultimate seismic capacity of the structures is a complex undertaking which will require a large number of detailed calculations. As the first step in this evaluation, a number of potential modes of structural failure have been determined and are discussed. The report is principally directed towards seismically induced failure of structures. To some extent, modes involving soil foundation failures are discussed in so far as they affect the buildings. However, failure modes involving soil liquefaction, surface faulting, tsunamis, etc., are considered outside the scope of this evaluation

  20. Structural Basis for Recognizing Phosphoarginine and Evolving Residue-Specific Protein Phosphatases in Gram-Positive Bacteria

    Directory of Open Access Journals (Sweden)

    Jakob Fuhrmann

    2013-06-01

    Full Text Available Many cellular pathways are regulated by the competing activity of protein kinases and phosphatases. The recent identification of arginine phosphorylation as a protein modification in bacteria prompted us to analyze the molecular basis of targeting phospho-arginine. In this work, we characterize an annotated tyrosine phosphatase, YwlE, that counteracts the protein arginine kinase McsB. Strikingly, structural studies of YwlE reaction intermediates provide a direct view on a captured arginine residue. Together with biochemical data, the crystal structures depict the evolution of a highly specific phospho-arginine phosphatase, with the use of a size-and-polarity filter for distinguishing phosphorylated arginine from other phosphorylated side chains. To confirm the proposed mechanism, we performed bioinformatic searches for phosphatases, employing a similar selectivity filter, and identified a protein in Drosophila melanogaster exhibiting robust arginine phosphatase activity. In sum, our findings uncover the molecular framework for specific targeting of phospho-arginine and suggest that protein arginine (dephosphorylation may be relevant in eukaryotes.

  1. Effect of repeat unit structure and molecular mass of lactic acid bacteria hetero-exopolysaccharides on binding to milk proteins.

    Science.gov (United States)

    Birch, Johnny; Harðarson, Hörður Kári; Khan, Sanaullah; Van Calsteren, Marie-Rose; Ipsen, Richard; Garrigues, Christel; Almdal, Kristoffer; Hachem, Maher Abou; Svensson, Birte

    2017-12-01

    Interactions of exopolysaccharides and proteins are of great importance in food science, but complicated to analyze and quantify at the molecular level. A surface plasmon resonance procedure was established to characterize binding of seven structure-determined, branched hetero-exopolysaccharides (HePSs) of 0.14-4.9MDa from lactic acid bacteria to different milk proteins (β-casein, κ-casein, native and heat-treated β-lactoglobulin) at pH 4.0-5.0. Maximum binding capacity (RU max ) and apparent affinity (K A,app ) were HePS- and protein-dependent and varied for example 10- and 600-fold, respectively, in the complexation with native β-lactoglobulin at pH 4.0. Highest RU max and K A,app were obtained with heat-treated β-lactoglobulin and β-casein, respectively. Overall, RU max and K A,app decreased 6- and 20-fold, respectively, with increasing pH from 4.0 to 5.0. K A,app was influenced by ionic strength and temperature, indicating that polar interactions stabilize HePS-protein complexes. HePS size as well as oligosaccharide repeat structure, conferring chain flexibility and hydrogen bonding potential, influence the K A,app . Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

    Directory of Open Access Journals (Sweden)

    Mariusz Cycoń

    2015-01-01

    Full Text Available The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB in soil using the denaturing gradient gel electrophoresis (DGGE approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S and the Shannon-Wiener index (H values for soil treated with the field rate (FR dosage of imidacloprid (1 mg/kg soil showed no changes in measured indices for the AOA and AOB community members. In turn, the 10*FR dosage of insecticide (10 mg/kg soil negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4+, known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

  3. Prediction of pressure induced structural phase transitions and internal mode frequency changes in solid N/sub 2/+

    Energy Technology Data Exchange (ETDEWEB)

    Etters, R.D.; Kobashi, K.; Chandrasekharan, V.

    1983-01-01

    A rhombohedral distortion of the Pm3n structure is introduced which shows that a low temperature phase transition occurs from P4/sup 2//mnm into the R3c calcite structure at P approx. = 19.2 kbar with a volume change of 0.125 cm/sup 3//mole. This transition agrees with recent Raman scattering measurements. Another transition from R3c into R3m is predicted at P approx. = 67.5 kbar, with a volume change of 0.1 cm/sup 3//mole. The pressure dependence of the intramolecular mode frequencies for the R3c structure is in reasonably good agreement with the two main branches observed experimentally.

  4. Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites and in Relation to Mode of Delivery

    Science.gov (United States)

    Chu, Derrick M.; Ma, Jun; Prince, Amanda L.; Antony, Kathleen M.; Seferovic, Maxim D.; Aagaard, Kjersti M.

    2017-01-01

    Human microbial communities are characterized by their taxonomic, metagenomic, and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to assess the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites, and assess the impact of mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early 3rd trimester (n=81) were prospectively enrolled for longitudinal sampling through 6 weeks post-delivery, and a second matched cross-sectional cohort (n=81) was additionally recruited for sampling once at delivery. Samples were collected for each maternal-infant dyad across multiple body sites, including stool, oral gingiva, nares, skin and vagina. 16S rRNA gene sequencing analysis and whole genome shotgun sequencing was performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogenous across all body sites at delivery, with the notable exception of neonatal meconium. However, by 6 weeks, the infant microbiota structure and function had significantly expanded and diversified, with body site serving as the primary determinant of the bacterial community composition and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with Cesarean delivery in some body sites (oral, nares, and skin; R2 = 0.038), this was not true in neonatal stool (meconium, Mann-Whitney p>0.05) and there was no observable difference in community function regardless of delivery mode. By 6 weeks of age, the infant microbiota structure and function had expanded and diversified with

  5. Effects of Different Working Modes of Ultrasound on Structural Characteristics of Zein and ACE Inhibitory Activity of Hydrolysates

    Directory of Open Access Journals (Sweden)

    Xiaofeng Ren

    2017-01-01

    Full Text Available Ultrasound was used as a new technology to pretreat protein prior to proteolysis to improve enzymolysis efficiency. The effects of different working modes of ultrasound on the angiotensin I-converting enzyme (ACE inhibitory activity of zein hydrolysates and the structural characteristics of zein were investigated. The solubility, surface hydrophobicity (H0, ultraviolet-visible (UV-Vis spectra, intrinsic fluorescence spectra, and circular dichroism (CD spectra of zein pretreated with ultrasound were determined. All ultrasound pretreatments significantly improved the ACE inhibitory activity of zein hydrolysates (p<0.05. The highest ACE inhibitory activity, representing an increase of 99.21% over the control, was obtained with dual sweeping frequency ultrasound of 33±2 and 68±2 kHz. The effects of single sweeping frequency and dual fixed frequency ultrasound were stronger than those of single fixed frequency ultrasound for improving the ACE inhibitory activity of zein. Structural changes in zein were induced by ultrasound, as confirmed by changes in the solubility, H0, UV-Vis spectra, intrinsic fluorescence spectra, and CD spectra of zein, and these were consistent with the corresponding ACE inhibitory activities of zein hydrolysates. Thus, ultrasound working mode and frequency have significant effects on the structure of zein and the ACE inhibitory activity of zein hydrolysates.

  6. [A study of phonon vibration like modes for aggregation structure in silicate melts by high temperature Raman spectrum].

    Science.gov (United States)

    Xu, Pei-Cang; Li, Ru-Bi; Shang, Tong-Ming; Zhou, Jian; Sun, Jian-Hua; You, Jing-Lin

    2010-05-01

    Silicate melts are special fractal dimension system that is metastable state of near-way order and far-way disorder. In this paper, the size of nanometer aggregation structure and the frequences of phonon vibration like mode in the low dimension silicate series (CaO-Al2O3-SiO2 and Na2-Al2O3-SiO2 series) synthesized via high temperature melting and sol gel methods were measured by means of small-angle X-ray scattering (SAXS), low wavenumber Raman spectrum (LWRS) and high temperature Raman spectrum (HTRS in situ measuring). The nanometer self-similarity aggregation structure(it's size is about a few nm to a few tens nm) and phonic phonon vibration like modes of low temperature silicate gel, high temperature silicate melts and it's quenching glasses phases were obtained. So a quantitative method by HTRS for measuring the aggregation size in the high temperature melts was established. The results showed that the aggregation size of the silicate melts is smaller at high temperature than at room temperature and the number of bridge oxygen in one Si-O tetrahedron in network structure units is decreasing at high temperature. This study work provides important theory and information for deliberating geochemistry characteristic, crystallization & evolution of natural magma and enhancing performance of low dimension silicate matelials.

  7. The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding

    Czech Academy of Sciences Publication Activity Database

    Tarbouriech, N.; Ducournau, C.; Hutin, S.; Mas, P.J.; Man, Petr; Forest, E.; Hart, D.J.; Peyrefitte, Ch.N.; Burmeister, W.P.; Iseni, F.

    2017-01-01

    Roč. 8, NOV 13 (2017), s. 1-12, č. článku 1455. ISSN 2041-1723 R&D Projects: GA MŠk(CZ) LQ1604 Institutional support: RVO:61388971 Keywords : PROTEIN SECONDARY STRUCTURE * CRYSTAL- STRUCTURE * GENETIC-CHARACTERIZATION Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 12.124, year: 2016

  8. Mode of production of monomolecular structuring water in liquid crystalline form

    International Nuclear Information System (INIS)

    Hasanov, A.M.

    2011-01-01

    Full text : Mode to protect living organisms from the biological effects of electromagnetic radiation of mobile phones and personal computers, including the determination of the energy absorbed by the body over time, depending on the biological factors of the body, characterized in that a biological factor using the total amount of water contained in the body, with time corresponding to the absorbed energy is equated to the maximum allowable rate, determined by the formula dt=dEBBNH/EodEeksp. Here K is the coefficient of the percentage of water in biological tissues, dEeksp. - Experimentally established energy flux density of the mobile phone or personal computer, dEBBNH ∼10mkVt/si 2 - maximum permissible rate of absorbed energy.

  9. Finite element modeling of temperature load effects on the vibration of local modes in multi-cable structures

    Science.gov (United States)

    Treyssède, Fabien

    2018-01-01

    Understanding thermal effects on the vibration of local (cable-dominant) modes in multi-cable structures is a complicated task. The main difficulty lies in the modification by temperature change of cable tensions, which are then undetermined. This paper applies a finite element procedure to investigate the effects of thermal loads on the linear dynamics of prestressed self-weighted multi-cable structures. Provided that boundary conditions are carefully handled, the discretization of cables with nonlinear curved beam elements can properly represent the thermoelastic behavior of cables as well as their linearized dynamics. A three-step procedure that aims to replace applied pretension forces with displacement continuity conditions is used. Despite an increase in the computational cost related to beam rotational degrees of freedom, such an approach has several advantages. Nonlinear beam finite elements are usually available in commercial codes. The overall method follows a thermoelastic geometrically non-linear analysis and hereby includes the main sources of non-linearities in multi-cable structures. The effects of cable bending stiffness, which can be significant, are also naturally accounted for. The accuracy of the numerical approach is assessed thanks to an analytical model for the vibration of a single inclined cable under temperature change. Then, the effects of thermal loads are investigated for two cable bridges, highlighting how natural frequencies can be affected by temperature. Although counterintuitive, a reverse relative change of natural frequency may occur for certain local modes. This phenomenon can be explained by two distinct mechanisms, one related to the physics intrinsic to cables and the other related to the thermal deflection of the superstructure. Numerical results show that cables cannot be isolated from the rest of the structure and the importance of modeling the whole structure for a quantitative analysis of temperature effects on the

  10. Crystal structure mediates mode of cell death in TiO{sub 2} nanotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Braydich-Stolle, Laura K.; Schaeublin, Nicole M.; Murdock, Richard C. [Wright-Patterson AFB, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force Research Laboratory (United States); Jiang, Jingkun; Biswas, Pratim [Washington University in St. Louis, Department of Energy, Environmental, and Chemical Engineering (United States); Schlager, John J.; Hussain, Saber M., E-mail: Saber.Hussain@wpafb.af.mi [Wright-Patterson AFB, Applied Biotechnology Branch, Human Effectiveness Directorate, Air Force Research Laboratory (United States)

    2009-08-15

    Certain properties that nanoparticles possess differentiate them from their bulk counterparts, and these characteristics must be evaluated prior to nanoparticle studies and include: size, shape, dispersion, physical and chemical properties, surface area, and surface chemistry. Early nanotoxicity studies evaluating TiO{sub 2} have yielded conflicting data which identify either size or crystal structure as the mediating property for nano-TiO{sub 2} toxicity. However, it is important to note that none of these studies examined size with the crystal structure composition controlled for or examined crystal structure while controlling the nanoparticle size. The goal of this study was to evaluate the role of size and crystal structure in TiO{sub 2} nanotoxicity while controlling for as many other nanoproperties as possible using the HEL-30 mouse keratinocyte cell line as a model for dermal exposure. In the size-dependent studies, all the nanoparticles are 100% anatase, and aggregate sizes were determined in order to take into account the effect of agglomeration on size-dependent toxicity. In addition, varying crystal structures were assessed while the size of the nanoparticles was controlled. We were able to identify that both size and crystal structure contribute to cytotoxicity and that the mechanism of cell death varies based on crystal structure. The 100% anatase TiO{sub 2} nanoparticles, regardless of size, induced cell necrosis, while the rutile TiO{sub 2} nanoparticles initiated apoptosis through formation of reactive oxygen species (ROS).

  11. Crystal structure mediates mode of cell death in TiO2 nanotoxicity

    International Nuclear Information System (INIS)

    Braydich-Stolle, Laura K.; Schaeublin, Nicole M.; Murdock, Richard C.; Jiang, Jingkun; Biswas, Pratim; Schlager, John J.; Hussain, Saber M.

    2009-01-01

    Certain properties that nanoparticles possess differentiate them from their bulk counterparts, and these characteristics must be evaluated prior to nanoparticle studies and include: size, shape, dispersion, physical and chemical properties, surface area, and surface chemistry. Early nanotoxicity studies evaluating TiO 2 have yielded conflicting data which identify either size or crystal structure as the mediating property for nano-TiO 2 toxicity. However, it is important to note that none of these studies examined size with the crystal structure composition controlled for or examined crystal structure while controlling the nanoparticle size. The goal of this study was to evaluate the role of size and crystal structure in TiO 2 nanotoxicity while controlling for as many other nanoproperties as possible using the HEL-30 mouse keratinocyte cell line as a model for dermal exposure. In the size-dependent studies, all the nanoparticles are 100% anatase, and aggregate sizes were determined in order to take into account the effect of agglomeration on size-dependent toxicity. In addition, varying crystal structures were assessed while the size of the nanoparticles was controlled. We were able to identify that both size and crystal structure contribute to cytotoxicity and that the mechanism of cell death varies based on crystal structure. The 100% anatase TiO 2 nanoparticles, regardless of size, induced cell necrosis, while the rutile TiO 2 nanoparticles initiated apoptosis through formation of reactive oxygen species (ROS).

  12. A Sliding-Mode Triboelectric Nanogenerator with Chemical Group Grated Structure by Shadow Mask Reactive Ion Etching.

    Science.gov (United States)

    Shang, Wanyu; Gu, Guang Qin; Yang, Feng; Zhao, Lei; Cheng, Gang; Du, Zu-Liang; Wang, Zhong Lin

    2017-09-26

    The sliding-mode triboelectric nanogenerator (S-TENG) with grated structure has important applications in energy harvest and active sensors; however its concavo-convex structure leads to large frictional resistance and abrasion. Here, we developed a S-TENG with a chemical group grated structure (S-TENG-CGG), in which the triboelectric layer's triboelectric potential has a positive-negative alternating charged structure. The triboelectric layer of the S-TENG-CGG was fabricated through a reactive ion etching process with a metal shadow mask with grated structure. In the etched region, the nylon film, originally positively charged as in friction with stainless steel, gained opposite triboelectric potential and became negatively charged because of the change of surface functional groups. The output signals of the S-TENG-CGG are alternating and the frequency is determined by both the segment numbers and the moving speed. The applications of the S-TENG-CGG in the charging capacitor and driving calculator are demonstrated. In the S-TENG-CGG, since there is no concavo-convex structure, the frictional resistance and abrasion are largely reduced, which enhances its performances in better stability and longer working time.

  13. Mechanical low-frequency filter via modes separation in 3D periodic structures

    Science.gov (United States)

    D'Alessandro, L.; Belloni, E.; Ardito, R.; Braghin, F.; Corigliano, A.

    2017-12-01

    This work presents a strategy to design three-dimensional elastic periodic structures endowed with complete bandgaps, the first of which is ultra-wide, where the top limits of the first two bandgaps are overstepped in terms of wave transmission in the finite structure. Thus, subsequent bandgaps are merged, approaching the behaviour of a three-dimensional low-pass mechanical filter. This result relies on a proper organization of the modal characteristics, and it is validated by performing numerical and analytical calculations over the unit cell. A prototype of the analysed layout, made of Nylon by means of additive manufacturing, is experimentally tested to assess the transmission spectrum of the finite structure, obtaining good agreement with numerical predictions. The presented strategy paves the way for the development of a class of periodic structures to be used in robust and reliable wave attenuation over a wide frequency band.

  14. Coupling Neumann development and component mode synthesis methods for stochastic analysis of random structures

    Directory of Open Access Journals (Sweden)

    Driss Sarsri

    2014-05-01

    Full Text Available In this paper, we propose a method to calculate the first two moments (mean and variance of the structural dynamics response of a structure with uncertain variables and subjected to random excitation. For this, Newmark method is used to transform the equation of motion of the structure into a quasistatic equilibrium equation in the time domain. The Neumann development method was coupled with Monte Carlo simulations to calculate the statistical values of the random response. The use of modal synthesis methods can reduce the dimensions of the model before integration of the equation of motion. Numerical applications have been developed to highlight effectiveness of the method developed to analyze the stochastic response of large structures.

  15. Structural and magnetic studies on heavy-metal-adsorbing iron sulphide nanoparticles produced by sulphate-reducing bacteria

    International Nuclear Information System (INIS)

    Watson, J.H.P; Cressey, B.A.; Roberts, A.P.; Ellwood, D.C.; Charnock, J.M.; Soper, A.K.

    2000-01-01

    In previous and in work to be published, it has been shown that iron sulphide material, produced by sulphate-reducing bacteria (SRB), is an excellent adsorbent for a wide range of heavy metals. The material adsorbs between 100 and 400 mg g -1 and residual levels in solutions can be of the order of pg per litre. Further, strongly magnetic forms of this material can now be produced which can be effectively and cheaply removed from suspension together with the adsorbate by magnetic separation. This paper examines the structure of weakly magnetic and strongly magnetic iron sulphide material produced by SRB with a view to increasing the understanding of its adsorbent and the magnetic properties. The structural properties have been examined using high-resolution imaging and electron diffraction in a transmission electron microscope (TEM), the measurements of magnetisation versus field and temperature, extended X-ray absorption fine-structure (EXAFS) spectroscopy, X-ray absorption near-edge structure (XANES) spectroscopy and neutron diffraction. Before drying the surface area of both the weakly magnetic and the strongly magnetic iron sulphide is of the order of 400-500 m 2 g -1 as revealed by the magnetic properties, neutron scattering and the adsorption of a number of heavy metals. After freeze-drying the surface area falls to between 18 and 19 m 2 g -1 . The initial inocula came from a semi-saline source and when fed with nutrient containing Fe 2+ and Fe 3+ produced a weakly magnetic iron sulphide (Watson et al., Minerals Eng. 8 (1995) 1097) and a few % of a more strongly magnetic material. Further work using a novel method (Keller-Besrest, Collin, J. Solid State Chem. 84 (1990) 211) produced a strongly magnetic iron sulphide material. EXAFS and XANES spectroscopy revealed (Keller-Besrest and Collin, 1990) that the weakly magnetic iron sulphide material had the Ni-As structure in which the Fe is tetrahedrally coordinated with the composition Fe 1-x S. The strongly

  16. Nonlinear Development of Unstable Modes and Formation of Coherent Vortex Structures in Weakly Supercritical Zonal Shear Flows

    Science.gov (United States)

    Shagalov, S. V.; Rybushkina, G. V.

    This study explores the nonlinear development of the barotropic instability in weakly supercritical horizontally sheared zonal currents in the presence of vertical stratification. The energy exchange between unstable normal modes and the flow is shown to be confined to the common critical layer-region where the modal wave speed matches the flow velocity. A closed system of equations governing the evolution of instability wave amplitudes and critical layer vorticity distributions is derivedwith the aid of an asymptotic procedure. The dependence of the evolutionary scenarios of the flow on the values of the supercriticality and dissipation parameters is examined within the framework of qualitative and numerical analysis of the obtained equations. Nonlinear growth and saturation of the unstable barotropic and baroclinic modes lead to development of periodic coherent structures in the vorticity distribution inside the common modal critical layer. These structures take on the appearance of two-dimensional vortex chain or three-dimensional baroclinic vortex pattern depending on the flow regime at the stage of the instability equilibration.

  17. An integrated approach to the probabilistic assessments of aircraft strikes and structural mode of damages to nuclear power plants

    International Nuclear Information System (INIS)

    Godbout, P.; Brais, A.

    1975-01-01

    The possibilities of an aircraft striking a Canadian nuclear power plant in the vicinity of an airport and of inducing structural failure modes have been evaluated. This evaluation, together with other studies, may enhance decisions in the development of general criteria for the siting of reactors near airports. The study made use, for assessment, of the probabilistic approach and made judicious applications of the finite Canadian, French, German, American and English resources that were available. The tools, techniques and methods used for achieving the above, form what may be called an integrated approach. This method of approach requires that the study be made in six consecutive steps as follows: the qualitative evaluation of having an aircraft strike on a site situated near an airport with the use of the logic model technique; the statistical data gathering on aircraft movements and accidents; evaluating the probability distribution and calculating the basic event probabilities; evaluating the probability of an aircraft strike and the application of the sensitivity approach; generating the probability density distribution versus strike impact energy, that is, the evaluation of the energy envelope; and the probabilistic evaluation of structural failure mode inducements

  18. Crystal structure of TAZ-TEAD complex reveals a distinct interaction mode from that of YAP-TEAD complex.

    Science.gov (United States)

    Kaan, Hung Yi Kristal; Chan, Siew Wee; Tan, Siew Kim Joyce; Guo, Fusheng; Lim, Chun Jye; Hong, Wanjin; Song, Haiwei

    2017-05-17

    The Hippo pathway is a tumor suppressor pathway that is implicated in the regulation of organ size. The pathway has three components: the upstream regulatory factors, the kinase core, and the downstream transcriptional machinery, which consists of YAP, TAZ (transcription co-activators) and TEAD (transcription factor). Formation of YAP/TAZ-TEAD complexes leads to the transcription of growth-promoting genes. Herein, we report the crystal structure of TAZ-TEAD4 complex, which reveals two binding modes. The first is similar to the published YAP-TEAD structure. The second is a unique binding mode, whereby two molecules of TAZ bind to and bridge two molecules of TEAD4. We validated the latter using cross-linking and multi-angle light scattering. Using siRNA, we showed that TAZ knockdown leads to a decrease in TEAD4 dimerization. Lastly, results from luciferase assays, using YAP/TAZ transfected or knockdown cells, give support to the non-redundancy of YAP/TAZ co-activators in regulating gene expression in the Hippo pathway.

  19. Weighted spiking neural P systems with structural plasticity working in sequential mode based on maximum spike number

    Science.gov (United States)

    Sun, Mingming; Qu, Jianhua

    2017-10-01

    Spiking neural P systems (SNP systems, in short) are a group of parallel and distributed computing devices inspired by the function and structure of spiking neurons. Recently, a new variant of SNP systems, called SNP systems with structural plasticity (SNPSP systems, in short) was proposed. In SNPSP systems, neuron can use plasticity ru les to create and delete synapses. In this work, we consider many restrictions sequentiality on SNPSP systems: (1) neuron with the maximum number of spikes is chosen to fire; (2) we use the weighted synapses. Specifically, we investigate the computational power of weighted SNPSP systems working in the sequential mode based on maximum spike number (WSNPSPM systems, in short) and we proved that SNPSP systems with these new restrictions are universal as generating devices.

  20. Nonlinear Spring Finite Elements for Predicting Mode I-Dominated Delamination Growth in Laminated Structure with Through-Thickness reinforcement

    Science.gov (United States)

    Ratcliffe, James G.; Krueger, Ronald

    2006-01-01

    adopted by Cartie and Partridge was used to represent z-pin failure under mode I loading conditions. In the current work spring elements available in most commercial finite element codes were used to model z-pins. The traction law used in previous analyses [4-6] was employed to represent z-pin damage. This method is intended for and is limited to simulating z-pins in composite laminate structure containing mode I-dominated delamination cracking. The current technique differs from previous analyses in that spring finite elements (available in commercial codes) are employed for simulating zpins, reducing the complexity of the analysis construction process. Furthermore, the analysis method can be applied to general structure that experiences mode I-dominated delamination cracking, in contrast to existing analytical solutions that are only applicable to coupon DCB specimens.

  1. Xylo- and arabinoxylooligosaccharides from wheat bran by endoxylanases, utilisation by probiotic bacteria, and structural studies of the enzymes.

    Science.gov (United States)

    Mathew, Sindhu; Aronsson, Anna; Karlsson, Eva Nordberg; Adlercreutz, Patrick

    2018-04-01

    Xylooligosaccharides (XOS) and arabinoxylooligosaccharides (AXOS) were produced from the insoluble arabinoxylan fraction of pretreated wheat bran by endoxylanases. The glycoside hydrolase (GH) family 10 xylanases GsXyn10A from Geobacillus stearothermophilus and RmXyn10A-CM from Rhodothermus marinus produced the AXOS A 3 X, A 2 XX and A 2 + 3 XX in addition to XOS. RmXyn10A-CM also produced XA 2 + 3 XX due to its non-conserved aglycone region accommodating additional arabinose substitutions in subsite +2. The GH11 enzymes, Pentopan from Thermomyces lanuginosus and NpXyn11A from Neocallimastix patriciarum had minor structural differences affecting hydrogen bonds in subsites -3 and +3, with similar hydrolysis profiles producing XA 3 XX as major AXOS and minor amounts of XA 2 XX but different ratios of X 3 /X 2 . In vitro analysis of the prebiotic properties of (A)XOS produced by Pentopan revealed nearly complete uptake of X 2 and X 3 by the probiotic bacteria Lactobacillus brevis and Bifidobacterium adolescentis. In contrast to previous reports, the GH43 arabinofuranosidase BaAXHd-3 from B. adolescentis cleaved α-1,3-linked arabinose on some single substituted AXOS.

  2. A novel set of symmetric methylene blue derivatives exhibits effective bacteria photokilling - a structure-response study.

    Science.gov (United States)

    Gollmer, Anita; Felgenträger, Ariane; Bäumler, Wolfgang; Maisch, Tim; Späth, Andreas

    2015-02-01

    This study focuses on the structure-response relationship of symmetrically substituted phenothiazinium dyes. Four hydrophilic derivatives with the ability of additional hydrogen bonding (, ) or additional electrostatic interaction (, ) were synthesized, photophysically characterized and compared to the parent compound methylene blue (MB, ) and a lipophilic derivative () without additional coordination sites. Derivative was most effective against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli reaching a maximum photodynamic efficacy of >5log10 steps (≥99.999%) of bacteria killing in 10 minutes (5 μM, 30 J cm(-2)) without inherent dark toxicity after one single treatment with the incoherent light source PDT1200 (λmax = 660 nm, 50 mW cm(-2)). Interestingly, one derivative with two additional primary positive charges () showed selective killing of Escherichia coli (5 μM, 30 J cm(-2), 4log10 steps inactivation (≥99.99%)) and no antimicrobial effect on Staphylococcus aureus. This might allow the development of a new generation of photosensitizers with higher antimicrobial efficacy and selectivity for future applications.

  3. Separate structure of two branches of sheared slab ηi mode and effects of plasma rotation shear in weak magnetic shear region

    International Nuclear Information System (INIS)

    Jiquan Li; Kishimoto, Y.; Tuda, T.

    2000-01-01

    The separate structure of two branches of the sheared slab η i mode near the minimum-q magnetic surface is analysed and the effects of plasma rotation shears are considered in the weak magnetic shear region. Results show that the separation condition depends on the non-monotonous q profile and the deviation of rational surface from the minimum-q surface. Furthermore, it is found that the diamagnetic rotation shear may suppress the perturbation of the sheared slab η i mode at one side of the minimum-q surface, the poloidal rotation shear from the sheared E-vector x B-vector flow has a similar role to the slab mode structure when it possesses a direction same as the diamagnetic shear. A plausible interrelation between the separate structures of the two branches of the sheared slab mode and the discontinuity or gap of the radially global structure of the drift wave near the minimum-q surface observed in the toroidal particle simulation (Kishimoto Y et al 1998 Plasma Phys. Control. Fusion 40 A663) is discussed. It seems to support such a viewpoint: the double or/and global branches of the sheared slab η i mode near the minimum-q surface may become a bridge to connect the radially global structures of the drift wave at two sides of the minimum-q surface and the discontinuity may originate from the separate structures of these slab modes for a flatter q profile. (author)

  4. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

    Science.gov (United States)

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

  5. Analog circuit design structured mixed-mode design, multi-bit sigma-delta converters, short range RF circuits

    CERN Document Server

    van Roermund, Arthur

    2007-01-01

    Preface. Part I: Structured Mixed-Mode Design. Introduction. Structured Oscillator Design; C. Verhoeven, A. van Staveren. Systematic Design of High-frequency gm-C Filters; E. Lauwers, G. Gielen. Structured LNA Design; E.H. Nordholt. High-Level Simulation and Modeling Tools for Mixed-Signal Front-ends of Wireless Systems; P. Wambacq, et al. Structured Simulation-Based Analog Design Synthesis; R.A. Rutenbar. Structured Analog layout Design; K. Lampaert. Part II: Multi-Bit Sigma Delta Converters. Introduction. Architecture Considerations for Multi-Bit SigmaDelta ADCs; T. Brooks. Multirate Sigma-Delta Modulators, an Alternative to Multibit; F. Colodro, A. Torralba. Circuit Design Aspects of Multi-Bit Delta-Sigma Converters; Y. Geerts, et al. High-speed Digital to Analog Converter Issues with Applications to Sigma Delta Modulators; K. Doris, et al. Correction-Free Multi-Bit Sigma-Delta Modulators for ADSL; R. del Rio, et al. Sigma Delta Converters in Wireline Communications; A. Wiesbauer, et al. Part III: Short Ra...

  6. Structural insights into the binding mode and conformational changes of BSA induced by bixin and crocin.

    Science.gov (United States)

    Mohan, Sankari; Hemachandran, Hridya; Sneha, P; George Priya Doss, C; Godwin Christopher, J; Jayaraman, Gurunathan; Ramamoorthy, Siva

    2017-06-30

    Bixin and crocin are natural apocarotenoids utilized as food colorants and additives in food industries worldwide. For safety assessment, it is necessary to understand the biological interaction of food colorants. In our present study, we report the interaction of two apocarotenoids with bovine serum albumin (BSA) at physiological pH using spectroscopic techniques and in silico tools. The binding constant and the mode of binding sites have been studied. The enthalpic and entropic contribution to the intermolecular binding event was analyzed and it was found that the contribution of hydrogen bonding and hydrophobic interactions was dominant. The adverse temperature dependence in the unusual static quenching is found to be a reasonable consequence of the large activation energy requirement in the binding process, which is required to overcome the fundamental block and is a direct result of the unique microstructure of the binding sites. To confirm the experimental analysis, we investigated the binding patterns using different in silico tools. A combination of molecular docking, molecular dynamics, and toxicity analysis was performed, and the obtained results revealed that both the apocarotenoids had high binding affinity with a binding energy of -5.44 and -5.93 kcal/mol for bixin and crocin, respectively, with no toxic effects and are in accordance with our experimental analysis. The results directly revealed the flexibility of the protein toward bixin and crocin which has a great impact on the interaction. Thus bixin and crocin can guardedly be used as food colorants in food industries.

  7. Failure mode prediction for composite structural insulated panels with MgO board facings

    Science.gov (United States)

    Smakosz, Łukasz; Kreja, Ireneusz

    2018-01-01

    Sandwich panels are readily used in civil engineering due to their high strength to weight ratio and the ease and speed of assembly. The idea of a sandwich section is to combine thin and durable facings with a light-weight core and the choice of materials used allows obtaining the desired behaviour. Panels in consideration consist of MgO (magnesium oxide) board facings and expanded polystyrene core and are characterized by immunity to biological corrosion, a high thermal insulation and a relatively low impact on environment. Customizing the range of panels to meet market needs requires frequent size changes, leading to different failure modes, which are identified in a series of costly full-scale laboratory tests. A nonlinear numerical model was created with a use of a commercial ABAQUS code and a user-defined procedure, which is able to reproduce observed failure mechanisms; its parameters were established on the basis of small-scale tests and numerical experiments. The model was validated by a comparison with the results of the full-scale bending and compression tests. The results obtained were in satisfactory agreement with the test data.

  8. Superparamagnetic plasmonic nanohybrids: shape-controlled synthesis, TEM-induced structure evolution, and efficient sunlight-driven inactivation of bacteria.

    Science.gov (United States)

    Zhai, Yueming; Han, Lei; Wang, Ping; Li, Gaiping; Ren, Wen; Liu, Ling; Wang, Erkang; Dong, Shaojun

    2011-11-22

    Magnetic materials and noble metal-based multifunctional hybrids have attracted much attention recently due to their unique properties and potential applications in a variety of fields. However, substantial challenges remain to directly obtain water-soluble hybrids with well-defined structures and to directly combine magnetic nanoparticles with nonspherical noble metals. We describe here for the first time a simple solvothermal method to synthesize a series of novel water-soluble nanohybrids composed of shape-tuned Ag cores and a Fe(3)O(4) shell. We found that small Fe(3)O(4) grains can be well-distributed directly on the surface on the Ag seeds. Such hybrids have both plasmonic and significant superparamagnetic properties, enabling magnetic separation. The plasmon resonance frequency of Ag nanostructures can be fine-tuned through the interactions between the two components. In addition, the decorated Fe(3)O(4) nanoparticles stabilized the Ag nanostructures when exposed to air and natural light for a long time. Furthermore, an interesting structural transformation is observed in the one-dimensional Ag-Fe(3)O(4) nanowires under high-energy electron beam. The Ag core can diffuse through the porous iron oxide shell, break away, and result in the formation of Ag nanocluster-decorated iron oxide tubes. Finally, the hybrids acted as a chemical template for the synthesis of Fe(3)O(4)/Au-AgCl double-layer nanotubes that display obvious near-infrared absorption. Importantly, the double-layer nanotubes exhibited enhanced photocatalytic inactivation of bacteria at very low concentrations under natural sunlight. © 2011 American Chemical Society

  9. The Importance of the Default Mode Network in Creativity--A Structural MRI Study

    Science.gov (United States)

    Kühn, Simone; Ritter, Simone M.; Müller, Barbara C. N.; van Baaren, Rick B.; Brass, Marcel; Dijksterhuis, Ap

    2014-01-01

    Anecdotal reports as well as behavioral studies have suggested that creative performance benefits from unconscious processes. So far, however, little is known about how creative ideas arise from the brain. In the current study, we aimed to investigate the neural correlates of creativity by means of structural MRI research. Given that unconscious…

  10. Sperm competition and reproductive mode influence sperm dimensions and structure among snakes.

    Science.gov (United States)

    Tourmente, Maximiliano; Gomendio, Montserrat; Roldan, Eduardo R S; Giojalas, Laura C; Chiaraviglio, Margarita

    2009-10-01

    The role of sperm competition in increasing sperm length is a controversial issue, because findings from different taxa seem contradictory. We present a comparative study of 25 species of snakes with different levels of sperm competition to test whether it influences the size and structure of different sperm components. We show that, as levels of sperm competition increase, so does sperm length, and that this elongation is largely explained by increases in midpiece length. In snakes, the midpiece is comparatively large and it contains structures, which in other taxa are present in the rest of the flagellum, suggesting that it may integrate some of its functions. Thus, increases in sperm midpiece size would result in more energy as well as greater propulsion force. Sperm competition also increases the area occupied by the fibrous sheath and outer dense fibers within the sperm midpiece, revealing for the first time an effect upon structural elements within the sperm. Finally, differences in male-male encounter rates between oviparous and viviparous species seem to lead to differences in levels of sperm competition. We conclude that the influence of sperm competition upon different sperm components varies between taxa, because their structure and function is different.

  11. Towards consistent modes of e-health implementation : structurational analysis of a telecare programmes limited success

    NARCIS (Netherlands)

    Boonstra, A.; van Offenbeek, M.A.G.

    2010-01-01

    Telecare is the use of information and communication systems to facilitate care delivery to individuals in their homes. Although the expectations of telecare are high, its implementation has proved complex. This case study demonstrates this complexity through a structurational analysis of a telecare

  12. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    Directory of Open Access Journals (Sweden)

    Tsunetomo Yamada

    2016-07-01

    Full Text Available The detailed atomic structure of the binary icosahedral (i ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP, both resulting from a close-packing of a large (Sc and a small (Zn atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K2/K1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason Debye–Waller factor, which explains the vanishing of `high-Qperp' reflections.

  13. Atomic structure and phason modes of the Sc–Zn icosahedral quasicrystal

    Science.gov (United States)

    Yamada, Tsunetomo; Takakura, Hiroyuki; Euchner, Holger; Pay Gómez, Cesar; Bosak, Alexei; Fertey, Pierre; de Boissieu, Marc

    2016-01-01

    The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom. The difference in chemical composition between i-ScZn7.33 and i-YbCd5.7 was found to lie in the icosahedron shell and the DFP where in i-ScZn7.33 chemical disorder occurs on the large atom sites, which induces a significant distortion to the structure units. The intensity in reciprocal space displays a substantial amount of diffuse scattering with anisotropic distribution, located around the strong Bragg peaks, that can be fully interpreted as resulting from phason fluctuations, with a ratio of the phason elastic constants K 2/K 1 = −0.53, i.e. close to a threefold instability limit. This induces a relatively large perpendicular (or phason) Debye–Waller factor, which explains the vanishing of ‘high-Q perp’ reflections. PMID:27437112

  14. Wannier–Stark electro-optical effect, quasi-guided and photonic modes in 2D macroporous silicon structures with SiO{sub 2} coatings

    Energy Technology Data Exchange (ETDEWEB)

    Karachevtseva, L., E-mail: lakar@isp.kiev.ua [Ningbo University of Technology, No. 55-155 Cui Bai Road, Ningbo 315016 (China); V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, 41 Nauky Pr., 03028 Kyiv (Ukraine); Goltviansky, Yu., E-mail: ecoflam@voliacable.com [V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, 41 Nauky Pr., 03028 Kyiv (Ukraine); Sapelnikova, O., E-mail: e_kolesnik84@mail.ru [V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, 41 Nauky Pr., 03028 Kyiv (Ukraine); Lytvynenko, O., E-mail: lytvole@gmail.com [V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, 41 Nauky Pr., 03028 Kyiv (Ukraine); Stronska, O., E-mail: yaschichek@ukr.net [V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, 41 Nauky Pr., 03028 Kyiv (Ukraine); Bo, Wang, E-mail: bo305@hotmail.com [Ningbo University of Technology, No. 55-155 Cui Bai Road, Ningbo 315016 (China); Kartel, M., E-mail: nikar@kartel.kiev.ua [Ningbo University of Technology, No. 55-155 Cui Bai Road, Ningbo 315016 (China)

    2016-12-01

    Highlights: • The IR absorption spectra of oxidized macroporous silicon were studied. • The Wannier–Stark electro-optical effect on Si-SiO{sub 2} boundary was confirmed. • An additional electric field of quasi-guided optical modes was evaluated. • The photonic modes and band gaps were measured as peculiarities in absorption spectra. - Abstract: Opportunities to enhance the properties of structured surfaces were demonstrated on 2D macroporous silicon structures with SiO{sub 2} coatings. We investigated the IR light absorption oscillations in macroporous silicon structures with SiO2 coatings 0–800 nm thick. The Wannier–Stark electro-optical effect due to strong electric field on Si-SiO{sub 2}boundary and an additional electric field of quasi-guided optical modes were taken into account. The photonic modes and band gaps were also considered as peculiarities in absorbance spectra of macroporous silicon structures with a thick SiO{sub 2} coating. The photonic modes do not coincide with the quasi-guided modes in the silicon matrix and do not appear in absorption spectra of 2D macroporous silicon structures with surface nanocrystals.

  15. Structural basis for PPAR partial or full activation revealed by a novel ligand binding mode

    Science.gov (United States)

    Capelli, Davide; Cerchia, Carmen; Montanari, Roberta; Loiodice, Fulvio; Tortorella, Paolo; Laghezza, Antonio; Cervoni, Laura; Pochetti, Giorgio; Lavecchia, Antonio

    2016-10-01

    The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors involved in the regulation of the metabolic homeostasis and therefore represent valuable therapeutic targets for the treatment of metabolic diseases. The development of more balanced drugs interacting with PPARs, devoid of the side-effects showed by the currently marketed PPARγ full agonists, is considered the major challenge for the pharmaceutical companies. Here we present a structure-based virtual screening approach that let us identify a novel PPAR pan-agonist with a very attractive activity profile and its crystal structure in the complex with PPARα and PPARγ, respectively. In PPARα this ligand occupies a new pocket whose filling is allowed by the ligand-induced switching of the F273 side chain from a closed to an open conformation. The comparison between this pocket and the corresponding cavity in PPARγ provides a rationale for the different activation of the ligand towards PPARα and PPARγ, suggesting a novel basis for ligand design.

  16. Structural combination of established 5-HT(2A) receptor ligands: new aspects of the binding mode

    DEFF Research Database (Denmark)

    Kramer, Vasko; Herth, Matthias M; Santini, Martin A

    2010-01-01

    MH.MZ, MDL 100907, and altanserin are structurally similar 4-benzoyl-piperidine derivatives and are well accommodated to receptor interaction models. We combined structural elements of different high-affinity and selective 5-HT(2A) antagonists, as MH.MZ, altanserin, and SR 46349B, to improve......) with a moderate affinity toward the 5-HT(2A) receptor (K(i) = 57 nm). The remarkably reduced affinity of other compounds (4a), (4b), and (4c) (K(i) = 411, 360 and 356 nm respectively) indicates that MH.MZ can only bind to the 5-HT(2A) receptor with the p-fluorophenylethyl residue in a sterically restricted...

  17. The effect of the solidification mode on eutectic structure in Fe-C-V alloys

    International Nuclear Information System (INIS)

    Fras, E.; Guzik, E.

    1980-01-01

    The aim of the study was to determine such a chemical composition of Fe-C-V alloys which would ensure the formation of perfectly eutectic structures as well as to investigate the eutectic morphology of these alloys when undergoing bulk and directional solidification. Attempts have been done to get in situ composites from Fe-C-V alloys. The adopted testing methods as well as obtained results are described in detail. (H.M.)

  18. Comparing Two Modes of Instruction in English Passive Structures (Processing and Meaning-Based Output Instruction

    Directory of Open Access Journals (Sweden)

    Asma Dabiri

    2018-04-01

    Full Text Available This research compared the effects of two types of instruction: Processing Instruction (PI and Meaning-based Output Instruction (MOI on the interpretation and production of English passive structures.  Ninety EFL intermediate tertiary level female students (PI group= 30, MOI group= 30 and control group = 30 participated in this study. The instruments were a proficiency test, a test to assess English passive structures and two instructional materials (PI and MOI. The data were analyzed by running one-way analysis of variance (ANOVA and mixed between-within ANOVA. The study indicated the effectiveness of PI and MOI on English passive structures. PI had considerable enhancement on interpretation tasks all the time. It supported the use of PI rather than the use of traditional instructions in which mechanical components were emphasized. Also, the PI and MOI had long term effects on the interpretation and production of English passive sentences.  This study supported the use of PI and MOI rather than the use of traditional instruction (TI in EFL settings. The implication for particularly classroom teaching is that successful grammar instruction has to related to ultimate learning outcomes. Also, creating communicative tasks to offer opportunities for teaching grammar can lead to long-lasting learning effects.

  19. Order or chaos? Origin and mode of emplacement of breccias in floors of large impact structures

    Science.gov (United States)

    Dressler, B. O.; Reimold, W. U.

    2004-09-01

    Breccias in the crater floor of large impact structures are pseudotachylites (sensu largo), authigenic monomict and polymict clastic-matrix breccias, so-called footwall breccias, and impact melt breccias. Pseudotachylite bodies in the center of large impact structures (e.g., Vredefort Dome, South Africa) appear to have a random distribution and orientation, but most dip steeply or vertically. Large bodies of pseudotachylite in the more distal sectors of the >200-km-diameter Sudbury Structure have been interpreted as ring and terrace collapse features. In the Vredefort Dome, networks of randomly distributed pseudotachylite veins accompany large ("mother lode") pseudotachylite dikes. In general, pseudotachylites in the floors of central parts of impact craters may form through explosive transfer of thermal shock energy, in a process that could be termed "flash replacement melting", whereas pseudotachylites at large distances from the centers of large impact structure are believed to have formed through friction leading to partial or complete melting, similar to the formation of tectonic pseudotachylites. In smaller structures (e.g., Ries and Slate Islands), clastic-matrix breccias instead of pseudotachylites occur as the most common breccias in the crater floors. They have a chaotic distribution pattern. Their dips are commonly also steep to vertical. Melt breccia dikes in the target rocks of the crater floor are associated with melt sheets that fill the lower part of the excavation cavity. At Vredefort, erosion has removed the coherent melt sheet, but melt breccia dikes (Vredefort Granophyre) in the crater floor are preserved. They are characterized by a remarkably homogeneous chemical composition and are believed to represent the initial, undifferentiated impact melt. Near the Vredefort collar, the Granophyre forms more or less concentric dikes. In the more central parts of the Dome, their orientation is more random, but, in places, may be controlled by the Archean

  20. Bacteria at glacier surfaces: microbial community structures in debris covered glaciers and cryoconites in the Italian Alps

    Science.gov (United States)

    Azzoni, Roberto; Franzetti, Andrea; Ambrosini, Roberto; D'Agata, Carlo; Senese, Antonella; Minora, Umberto; Tagliaferri, Ilario; Diolaiuti, Guglielmina

    2014-05-01

    bacteria and the copy of Rubisco genes found on cryoconite holes collected on a wide Italian DFG (Forni Glacier - Central Alps). The structure of the microbial communities in cryoconite holes seem to be determined mainly by a turnover process. This work was carried out under the umbrella of the SHARE Stelvio Project which has been funded by the Lombardy Region government and managed by FLA (Lombardy Foundation for the Enviroment) and EvK2-CNR Committee.

  1. FEA modeling of CMUT with membrane stand-off structures to enable selectable frequency-mode operation.

    Science.gov (United States)

    Eames, Matthew D C; Reck, Theodore J; Kilroy, Joseph P; Hossack, John A

    2011-12-01

    A selectable, dual-frequency, capacitive micro- machined ultrasonic transducer (CMUT) designed for both high-frequency imaging and low-frequency therapeutic effect is presented. A validated finite element analysis (FEA) CMUT model was used to examine the performance of the proposed dual-frequency transducer. CMUT device simulations were used to design a hybrid device incorporating stand-off structures that divide a large, low-frequency membrane into smaller, high-frequency sub-membranes when the membrane is partially collapsed so that the stand-offs contact the substrate. In low-frequency operation, simulations indicated that the peak negative pressure achieved by the hybrid device, when biased by 30.0 VDC and excited by a 2-MHz signal with 30.0 V amplitude, exceeded 190 kPa, which is sufficient for microbubble rupture. Low-frequency mode bandwidth was 93% at a center frequency of 2.1 MHz. In the high-frequency mode of operation, the device was excited by 175 Vdc and 87.5 Vac, which generated a peak negative pressure of 247 kPa. Device center frequency was 44.1 MHz with a - 6-dB fractional bandwidth of 42%.

  2. Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: Insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family

    Energy Technology Data Exchange (ETDEWEB)

    Nath, Seema; Banerjee, Ramanuj; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in

    2014-07-18

    Highlights: • VcLMWPTP-1 forms dimer in solution. • The dimer is catalytically active unlike other reported dimeric LMWPTPs. • The formation of extended dimeric surface excludes the active site pocket. • The surface bears closer resemblance to eukaryotic LMWPTPs. - Abstract: Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45 Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.

  3. Substrate structure dependence of the growth modes of p-quaterphenyl thin films on gold

    International Nuclear Information System (INIS)

    Muellegger, S.; Mitsche, S.; Poelt, P.; Haenel, K.; Birkner, A.; Woell, C.; Winkler, A.

    2005-01-01

    The variably oriented crystallite surfaces of a recrystallized polycrystalline gold sample served as substrates for the investigation of the structure dependence of p-quaterphenyl (4P) thin film growth. The films were prepared in ultrahigh vacuum by organic molecular beam evaporation. Optical microscopy, scanning electron microscopy, combined with laterally resolved electron backscatter diffraction and scanning tunnelling microscopy have been applied to determine the correlation between the substrate surface structure and 4P film morphology. Crystallite surfaces consisting of (110) terraces favour highly anisotropic needle-like 4P growth with the needle orientation normal to the Au directions. Atomic steps on vicinal planes with narrow terraces (< 2 nm) can also induce anisotropy in the 4P thin film growth, in particular elongated 4P islands normal to the step direction. In contrast to that, a nearly isotropic distribution of the needle orientations is observed on Au grains terminated by highly symmetric (111) or (100) crystal planes. Additionally, patches of continuous 4P layers can be found on these surfaces. There is strong evidence that the 4P molecules within the needle-like crystallites are oriented parallel to the Au surface, whereas for the continuous layers the 4P molecules are oriented nearly upright on the surface

  4. Lack of Population Structure and Mixed Reproduction Modes in Exserohilum turcicum from South Africa.

    Science.gov (United States)

    Human, Maria Petronella; Barnes, Irene; Craven, Maryke; Crampton, Bridget Genevieve

    2016-11-01

    Exserohilum turcicum is the causal agent of northern corn leaf blight, a destructive foliar disease of maize that results in yield losses worldwide. In South Africa, typical yield losses range from 15 to 30%. Previous studies found high haplotypic diversity with evidence for sexual recombination in E. turcicum populations from tropical climates such as Kenya. However, the population genetic structure and method of reproduction of E. turcicum in South Africa is unknown and, therefore, was investigated. Twelve polymorphic microsatellite markers were screened on 258 E. turcicum isolates from maize collected during 2012 and 2013 from three maize fields in South Africa. A multiplex polymerase chain reaction assay amplifying both mating type idiomorphs was applied to investigate the distribution of mating types. No distinct genetic clusters were observed. Shared haplotypes were identified between isolates separated by distances of up to 762 km, which provided evidence of migration. High haplotypic diversity indicated that sexual reproduction is occurring among E. turcicum isolates, although mating type ratios and linkage disequilibrium analyses did not support the hypothesis of random mating. The population genetic structure of E. turcicum in South Africa is likely due to the direct movement and spread of isolates undergoing a mixed reproductive lifecycle.

  5. HIGHER MODE FREQUENCY EFFECTS ON RESONANCE IN MACHINERY, STRUCTURES, AND PIPE SYSTEMS

    Energy Technology Data Exchange (ETDEWEB)

    Leishear, R.

    2010-05-02

    The complexities of resonance in multi-degree of freedom systems (multi-DOF) may be clarified using graphic presentations. Multi-DOF systems represent actual systems, such as beams or springs, where multiple, higher order, natural frequencies occur. Resonance occurs when a cyclic load is applied to a structure, and the frequency of the applied load equals one of the natural frequencies. Both equations and graphic presentations are available in the literature for single degree of freedom (SDOF) systems, which describe the response of spring-mass-damper systems to harmonically applied, or cyclic, loads. Loads may be forces, moments, or forced displacements applied to one end of a structure. Multi-DOF systems are typically described only by equations in the literature, and while equations certainly permit a case by case analysis for specific conditions, graphs provide an overall comprehension not gleaned from single equations. In fact, this collection of graphed equations provides novel results, which describe the interactions between multiple natural frequencies, as well as a comprehensive description of increased vibrations near resonance.

  6. Toroidally Resolved Structure of Divertor Heat Flux in RMP H-mode Discharges on DIII-D

    International Nuclear Information System (INIS)

    Jakubowski, M.W.; Evans, T.E.; Fenstermacher, M.E.; Lasnier, C.J.; Wolf, R.C.; Baylor, Larry R.; Boedo, J.A.; Burrell, K.H.; DeGrassie, J.S.; Gohil, P.; Mordijck, S.; Laengner, R.; Leonard, A.W.; Moyer, R.A.; Petrie, T.W.; Petty, C.C.; Pinsker, R.I.; Rhodes, T.L.; Schaffer, M.J.; Schmitz, O.; Snyder, P.B.; Stoschus, H.; Osborne, T.H.; Orlov, D.M.; Unterberg, Ezekial A.; Watkins, J.G.

    2011-01-01

    As shown on DIII-D edge localized modes (ELMs) can be either completely eliminated or mitigated with resonant magnetic perturbation (RMP) fields. Two infrared cameras, separated 105 degrees toroidally, were used to make simultaneous measurements of ELM heat loads with high frame rates. Without the RMP fields ELMs display a variety of different heat load dynamics and a range of toroidal variability that is characteristic of their 3D structure. Comparing radial averages there is no asymmetry between two toroidal locations. With RMP-mitigated ELMs, the variability in the radially averaged power loads is significantly reduced and toroidal asymmetries in power loads are introduced. In addition to RMP ELM suppression scenarios an RMP scenario with only very small ELMs and very good confinement has been achieved.

  7. Synthesis, Structure, and Rigid Unit Mode-like Anisotropic Thermal Expansion of BaIr2In9.

    Science.gov (United States)

    Calta, Nicholas P; Han, Fei; Kanatzidis, Mercouri G

    2015-09-08

    This Article reports the synthesis of large single crystals of BaIr2In9 using In flux and their characterization by variable-temperature single-crystal and synchrotron powder X-ray diffraction, resistivity, and magnetization measurements. The title compound adopts the BaFe2Al9-type structure in the space group P6/mmm with room temperature unit cell parameters a = 8.8548(6) Å and c = 4.2696(4) Å. BaIr2In9 exhibits anisotropic thermal expansion behavior with linear expansion along the c axis more than 3 times larger than expansion in the ab plane between 90 and 400 K. This anisotropic expansion originates from a rigid unit mode-like mechanism similar to the mechanism of zero and negative thermal expansion observed in many anomalous thermal expansion materials such as ZrW2O8 and ScF3.

  8. Body-insensitive Multi-Mode MIMO Terminal Antenna of Double-Ring Structure

    DEFF Research Database (Denmark)

    Zhao, Kun; Zhang, Shuai; Ishimiya, Katsunori

    2015-01-01

    In this paper, we propose a novel multimode multi-input multi-output (MIMO) antenna system composed of a dual-element MIMO cellular antenna and dual-element MIMO Wi-Fi antenna for mobile terminal applications. The antenna system has a double-ring structure and can be integrated with the metal frame...... of mobile terminals. With the multimode excitation, the MIMO cellular antenna can operate at 830-900 MHz, 1700-2200 MHz, and 2400-2700 MHz, for 2G, 3G, and LTE bands, respectively. The MIMO Wi-Fi antenna can cover two Wi-Fi bands from 2.4 to 2.5 GHz and from 5.2 to 5.8 GHz. The effect of a user's body...

  9. Diverse modes of binding in structures of Leishmania majorN-myristoyltransferase with selective inhibitors

    Directory of Open Access Journals (Sweden)

    James A. Brannigan

    2014-07-01

    Full Text Available The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed.

  10. A review of output-only structural mode identification literature employing blind source separation methods

    Science.gov (United States)

    Sadhu, A.; Narasimhan, S.; Antoni, J.

    2017-09-01

    Output-only modal identification has seen significant activity in recent years, especially in large-scale structures where controlled input force generation is often difficult to achieve. This has led to the development of new system identification methods which do not require controlled input. They often work satisfactorily if they satisfy some general assumptions - not overly restrictive - regarding the stochasticity of the input. Hundreds of papers covering a wide range of applications appear every year related to the extraction of modal properties from output measurement data in more than two dozen mechanical, aerospace and civil engineering journals. In little more than a decade, concepts of blind source separation (BSS) from the field of acoustic signal processing have been adopted by several researchers and shown that they can be attractive tools to undertake output-only modal identification. Originally intended to separate distinct audio sources from a mixture of recordings, mathematical equivalence to problems in linear structural dynamics have since been firmly established. This has enabled many of the developments in the field of BSS to be modified and applied to output-only modal identification problems. This paper reviews over hundred articles related to the application of BSS and their variants to output-only modal identification. The main contribution of the paper is to present a literature review of the papers which have appeared on the subject. While a brief treatment of the basic ideas are presented where relevant, a comprehensive and critical explanation of their contents is not attempted. Specific issues related to output-only modal identification and the relative advantages and limitations of BSS methods both from theoretical and application standpoints are discussed. Gap areas requiring additional work are also summarized and the paper concludes with possible future trends in this area.

  11. Structural and functional abnormalities of default mode network in minimal hepatic encephalopathy: a study combining DTI and fMRI.

    Directory of Open Access Journals (Sweden)

    Rongfeng Qi

    Full Text Available BACKGROUND AND PURPOSE: Live failure can cause brain edema and aberrant brain function in cirrhotic patients. In particular, decreased functional connectivity within the brain default-mode network (DMN has been recently reported in overt hepatic encephalopathy (HE patients. However, so far, little is known about the connectivity among the DMN in the minimal HE (MHE, the mildest form of HE. Here, we combined diffusion tensor imaging (DTI and resting-state functional MRI (rs-fMRI to test our hypothesis that both structural and functional connectivity within the DMN were disturbed in MHE. MATERIALS AND METHODS: Twenty MHE patients and 20 healthy controls participated in the study. We explored the changes of structural (path length, tracts count, fractional anisotropy [FA] and mean diffusivity [MD] derived from DTI tractography and functional (temporal correlation coefficient derived from rs-fMRI connectivity of the DMN in MHE patients. Pearson correlation analysis was performed between the structural/functional indices and venous blood ammonia levels/neuropsychological tests scores of patients. All thresholds were set at P<0.05, Bonferroni corrected. RESULTS: Compared to the healthy controls, MHE patients showed both decreased FA and increased MD in the tract connecting the posterior cingulate cortex/precuneus (PCC/PCUN to left parahippocampal gyrus (PHG, and decreased functional connectivity between the PCC/PCUN and left PHG, and medial prefrontal cortex (MPFC. MD values of the tract connecting PCC/PCUN to the left PHG positively correlated to the ammonia levels, the temporal correlation coefficients between the PCC/PCUN and the MPFC showed positive correlation to the digital symbol tests scores of patients. CONCLUSION: MHE patients have both disturbed structural and functional connectivity within the DMN. The decreased functional connectivity was also detected between some regions without abnormal structural connectivity, suggesting that the

  12. Crustal structure and inferred extension mode in the northern margin of the South China Sea

    Science.gov (United States)

    Gao, J.; Wu, S.; McIntosh, K. D.; Mi, L.; Spence, G.

    2016-12-01

    Combining multi-channel seismic reflection and satellite gravity data, this study has investigated the crustal structure and magmatic activities of the northern South China Sea (SCS) margin. Results show that a broad continent-ocean transition zone (COT) with more than 140 km wide is characterized by extensive igneous intrusion/extrusion and hyper-extended continental crust in the northeastern SCS margin, a broader COT with 220-265 km wide is characterized by crustal thinning, rift depression, structural highs with igneous rock and perhaps a volcanic zone or a zone of tilted fault blocks at the distal edge in the mid-northern SCS margin, and a narrow COT with 65 km wide bounded seawards by a volcanic buried seamount is characterized by extremely hyper-extended continental crust in the northwestern SCS margin, where the remnant crust with less than 3 km thick is bounded by basin-bounding faults corresponding to an aborted rift below the Xisha Trough with a sub-parallel fossil ridge in the adjacent Northwest Sub-basin. Results from gravity modeling and seismic refraction data show that a high velocity layer (HVL) is present in the outer shelf and slope below extended continental crust in the eastern portion of the northern SCS margin and is thickest (up to 10 km) in the Dongsha Uplift where the HVL gradually thins to east and west below the lower slope and finally terminates at the Manila Trench and Baiyun sag of the Pearl River Mouth Basin. The magmatic intrusions/extrusions and HVL may be related to partial melting caused by decompression of passive, upwelling asthenosphere which resulted primarily in post-rifting underplating and magmatic emplacement or modification of the crust. The northern SCS margin is closer to those of the magma-poor margins than those of volcanic margins, but the aborted rift near the northwestern continental margin shows that there may be no obvious detachment fault like that in the Iberia-Newfoundland type margin. The symmetric aborted

  13. Design of the Pi-Mode Structure (PIMS) for Linac4

    CERN Document Server

    Gerigk, F

    2010-01-01

    The PIMS will accelerate an H| − | beam from 100 MeV to 160 MeV, the output energy of Linac4. The cell length is constant within each of the 12 seven-cell cavities, but increases from cavity to cavity according to the increasing beam velocity. Its mechanical design is derived from the five-cell normal conducting LEP cavities, which were in operation at CERN for approximately 15 years. Even though the shunt impedance is around 10% lower than for a Side-Coupled Linac (SCL) operating at 704 MHz, the PIMS has the advantage of using the same RF frequency (352 MHz) as all the other accelerating structures in Linac4, thus simplifying and standardising the linac RF system. Furthermore, the simplified mechanical construction of the PIMS, which uses only 84 cells instead of over 400 for the SCL, also reduces construction costs and tuning effort. In this paper we present the electromagnetic design of the PIMS, including the arguments for the choice of a 5% cell-to-cell coupling factor, the shape of the coupling cells,...

  14. Population structure of manganese-oxidizing bacteria in stratified soils and properties of manganese oxide aggregates under manganese-complex medium enrichment.

    Directory of Open Access Journals (Sweden)

    Weihong Yang

    Full Text Available Manganese-oxidizing bacteria in the aquatic environment have been comprehensively investigated. However, little information is available about the distribution and biogeochemical significance of these bacteria in terrestrial soil environments. In this study, stratified soils were initially examined to investigate the community structure and diversity of manganese-oxidizing bacteria. Total 344 culturable bacterial isolates from all substrata exhibited Mn(II-oxidizing activities at the range of 1 µM to 240 µM of the equivalent MnO2. The high Mn(II-oxidizing isolates (>50 mM MnO2 were identified as the species of phyla Actinobacteria, Firmicutes and Proteobacteria. Seven novel Mn(II-oxidizing bacterial genera (species, namely, Escherichia, Agromyces, Cellulomonas, Cupriavidus, Microbacterium, Ralstonia, and Variovorax, were revealed via comparative phylogenetic analysis. Moreover, an increase in the diversity of soil bacterial community was observed after the combined enrichment of Mn(II and carbon-rich complex. The phylogenetic classification of the enriched bacteria represented by predominant denaturing gradient gel electrophoresis bands, was apparently similar to culturable Mn(II-oxidizing bacteria. The experiments were further undertaken to investigate the properties of the Mn oxide aggregates formed by the bacterial isolates with high Mn(II-oxidizing activity. Results showed that these bacteria were closely encrusted with their Mn oxides and formed regular microspherical aggregates under prolonged Mn(II and carbon-rich medium enrichment for three weeks. The biotic oxidation of Mn(II to Mn(III/IV by these isolates was confirmed by kinetic examinations. X-ray diffraction assays showed the characteristic peaks of several Mn oxides and rhodochrosite from these aggregates. Leucoberbelin blue tests also verified the Mn(II-oxidizing activity of these aggregates. These results demonstrated that Mn oxides were formed at certain amounts under the

  15. Reduced-order computational model in nonlinear structural dynamics for structures having numerous local elastic modes in the low-frequency range. Application to fuel assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Batou, A., E-mail: anas.batou@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France); Soize, C., E-mail: christian.soize@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallee (France); Brie, N., E-mail: nicolas.brie@edf.fr [EDF R and D, Département AMA, 1 avenue du général De Gaulle, 92140 Clamart (France)

    2013-09-15

    Highlights: • A ROM of a nonlinear dynamical structure is built with a global displacements basis. • The reduced order model of fuel assemblies is accurate and of very small size. • The shocks between grids of a row of seven fuel assemblies are computed. -- Abstract: We are interested in the construction of a reduced-order computational model for nonlinear complex dynamical structures which are characterized by the presence of numerous local elastic modes in the low-frequency band. This high modal density makes the use of the classical modal analysis method not suitable. Therefore the reduced-order computational model is constructed using a basis of a space of global displacements, which is constructed a priori and which allows the nonlinear dynamical response of the structure observed on the stiff part to be predicted with a good accuracy. The methodology is applied to a complex industrial structure which is made up of a row of seven fuel assemblies with possibility of collisions between grids and which is submitted to a seismic loading.

  16. Polymorphic transformation of helical flagella of bacteria

    Science.gov (United States)

    Lim, Sookkyung; Howard Berg Collaboration; William Ko Collaboration; Yongsam Kim Collaboration; Wanho Lee Collaboration; Charles Peskin Collaboration

    2016-11-01

    Bacteria such as E. coli swim in an aqueous environment by utilizing the rotation of flagellar motors and alternate two modes of motility, runs and tumbles. Runs are steady forward swimming driven by bundles of flagellar filaments whose motors are turning CCW; tumbles involve a reorientation of the direction of swimming triggered by motor reversals. During tumbling, the helical flagellum undergoes polymorphic transformations, which is a local change in helical pitch, helical radius, and handedness. In this work, we investigate the underlying mechanism of structural conformation and how this polymorphic transition plays a role in bacterial swimming. National Science Foundation.

  17. Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea.

    Science.gov (United States)

    Zhang, Yu; Wang, Xungong; Zhen, Yu; Mi, Tiezhu; He, Hui; Yu, Zhigang

    2017-01-01

    Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB , and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

  18. Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2017-11-01

    Full Text Available Sulfate-reducing bacteria (SRB and sulfur-oxidizing bacteria (SOB have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99% and revealed the high diversity, richness, and operational taxonomic unit (OTU numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

  19. Differences in fungal and bacterial physiology alter soil carbon and nitrogen cycling: synthesizing effects of microbial community structure using the Fungi and Bacteria (FAB) model. (Invited)

    Science.gov (United States)

    Averill, C.; Hawkes, C. V.; Waring, B. G.

    2013-12-01

    Most biogeochemical models of soil carbon and nitrogen cycling include a simplified representation of the soil microbial community as a single pool, despite good evidence that shifts in the composition or relative abundance of microbial taxa can affect process rates. Incorporating a more realistic depiction of the microbial community in these models may increase their predictive accuracy, but this must be balanced against the feasibility of modeling the enormous diversity present in soil. We propose that explicitly including two major microbial functional groups with distinct physiologies, fungi and bacteria, will improve model predictions. To this end, we created the fungi and bacteria (FAB) model, building off previous enzyme-driven biogeochemical models that explicitly represent microbial physiology. We compared this model to a complementary biogeochemical model that does not include microbial community structure (';single-pool'). We also performed a cross-ecosystem meta-analysis of fungi-to-bacteria ratios to determine if model predictions of community structure matched empirical data. There were large differences in process rates and pool sizes between the single-pool and FAB models. In the FAB model, inorganic N pools were reduced by 5-95% depending on the soil C:N ratio due to bacterial immobilization of fungal mineralization products. This nitrogen subsidy also increased microbial biomass at some C:N ratios. Although there were changes in some components of respiration, particularly overflow respiration, there was no net effect of community structure on total respiration fluxes. The FAB model predicted a breakpoint in the relationship between the ratio of fungi to bacteria and soil C:N, after which the fungi-to-bacteria ratio should begin to increase. Break-point analysis of the meta-analysis data set revealed a consistent pattern and matched the slope of the change in F:B with soil C:N, but not the precise breakpoint. We argue that including microbial

  20. The impact of a freshwater fish farm on the community of tetracycline-resistant bacteria and the structure of tetracycline resistance genes in river water.

    Science.gov (United States)

    Harnisz, Monika; Korzeniewska, Ewa; Gołaś, Iwona

    2015-06-01

    The aim of this study was to assess the impact of a fish farm on the structure of antibiotic resistant bacteria and antibiotic resistance genes in water of Drwęca River. Samples of upstream river waters; post-production waters and treated post-production waters from fish farm; as well as downstream river waters were monitored for tetracycline resistant bacteria, tetracycline resistant genes, basic physico-chemical parameters and tetracyclines concentration. The river waters was characterized by low levels of pollution, which was determined based on water temperature, pH and concentrations of dissolved oxygen and tetracycline antibiotics. Culture-dependent (heterotrophic plate counts, counts of bacteria resistant to oxytetracycline (OTC(R)) and doxycycline (DOX(R)), minimum inhibitory concentrations for oxytetracycline and doxycycline, multidrug resistance of OTC(R) and DOX(R), qualitative composition of OTC(R) and DOX(R), prevalence of tet genes in resistant isolates) and culture-independent surveys (quantity of tet gene copies) revealed no significant differences in the abundance of antibiotic-resistant bacteria and antibiotic resistance genes between the studied samples. The only way in which the fish farm influenced water quality in the Drwęca River was by increasing the diversity of tetracycline-resistance genes. However, it should also be noted that the bacteria of the genera Aeromonas sp. and Acinetobacter sp. were able to transfer 6 out of 13 tested tet genes into Escherichiacoli, which can promote the spread of antibiotic resistance in the environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Elucidation of the mode of interaction of thermolysin with a proteinaceous metalloproteinase inhibitor, SMPI, based on a model complex structure and a structural dynamics analysis.

    Science.gov (United States)

    Tate, S; Ohno, A; Seeram, S S; Hiraga, K; Oda, K; Kainosho, M

    1998-09-18

    SMPI is a proteinaceous microbial metalloproteinase inhibitor that was isolated from Streptomyces nigrescens TK-23 in 1979. SMPI is known to selectively inhibit the metalloproteinases in the gluzincin family, according to the Rawling and Barrett classification. There has been no report on the interaction of a metalloproteinase in the family of gluzincins with its specific proteinaceous inhibitor. We have solved the solution structure of SMPI by NMR. Here, we report the binding mode of SMPI to thermolysin, based on the model complex structure generated using our high-resolution NMR structure of SMPI and the crystal structure of thermolysin. The obtained complex model shows that the extruded loop of SMPI, with the scissile bond Cys64-Val65, is complementary in shape to the active cleft of thermolysin. In the complex, the Cys64 (P1) carbonyl oxygen atom can form a tetrahedral coordination to the active zinc in thermolysin, and simultaneously, the methyl groups of Val65 (P1') are closely located in the hydrophobic S1' pocket in thermolysin. From the electrostatic potential surface calculation, the active loop of SMPI and the active cleft in thermolysin have been shown to be complementary in the surface charge distribution, resulting in the stabilization of the complex. The apparently large active loop is less flexible, but maintains a conformation in the nano- to picosecond time-scale, as elucidated from the 15N spin relaxation analysis. This is a quite different structural feature of SMPI from the flexible binding loop generally found in the serine proteinase inhibitors, such as SSI and eglin c, and can be related to the narrow specificity of SMPI. The present study provides the first insight into the interaction between a proteinaceous inhibitor and a gluzincin metalloproteinase. Copyright 1998 Academic Press.

  2. Distribution, Organization, and Ecology of Bacteria in Chronic Wounds▿

    Science.gov (United States)

    Kirketerp-Møller, Klaus; Jensen, Peter Ø.; Fazli, Mustafa; Madsen, Kit G.; Pedersen, Jette; Moser, Claus; Tolker-Nielsen, Tim; Høiby, Niels; Givskov, Michael; Bjarnsholt, Thomas

    2008-01-01

    Between 1 and 2% of the population in the developed world experiences a nonhealing or chronic wound characterized by an apparent arrest in a stage dominated by inflammatory processes. Lately, research groups have proposed that bacteria might be involved in and contribute to the lack of healing of these wounds. To investigate this, we collected and examined samples from chronic wounds obtained from 22 different patients, all selected because of suspicion of Pseudomonas aeruginosa colonization. These wound samples were investigated by standard culturing methods and peptide nucleic acid-based fluorescence in situ hybridization (PNA FISH) for direct identification of bacteria. By means of the culturing methods, Staphylococcus aureus was detected in the majority of the wounds, whereas P. aeruginosa was observed less frequently. In contrast, using PNA FISH, we found that a large fraction of the wounds contained P. aeruginosa. Furthermore, PNA FISH revealed the structural organization of bacteria in the samples. It appeared that P. aeruginosa aggregated as microcolonies imbedded in the matrix component alginate, which is a characteristic hallmark of the biofilm mode of growth. The present investigation suggests that bacteria present within these wounds tend to be aggregated in microcolonies imbedded in a self-produced matrix, characteristic of the biofilm mode of growth. Additionally, we must conclude that there exists no good correlation between bacteria detected by standard culturing methods and those detected by direct detection methods such as PNA FISH. This strongly supports the development of new diagnostic and treatment strategies for chronic wounds. PMID:18508940

  3. The structural basis for the exo-mode of action in GH74 oligoxyloglucan reducing end-specific cellobiohydrolase.

    Science.gov (United States)

    Yaoi, Katsuro; Kondo, Hidemasa; Hiyoshi, Ayako; Noro, Natsuko; Sugimoto, Hiroshi; Tsuda, Sakae; Mitsuishi, Yasushi; Miyazaki, Kentaro

    2007-06-29

    Oligoxyloglucan reducing end-specific cellobiohydrolase (OXG-RCBH) is a unique exo-beta-1,4-glucanase that belongs to glycoside hydrolase family 74. The enzyme recognizes the reducing end of xyloglucan oligosaccharides and releases two glucosyl residue segments from the reducing end of the main chain. Previously, we reported that OXG-RCBH consists of two seven-bladed beta-propeller domains. There is a large cleft between the two domains, and a unique loop encloses one side of the active site cleft. Here, we report the X-ray crystal structure of the OXG-RCBH-substrate complex determined to a resolution of 2.4 A. The substrate bound to the cleft, and its reducing end was arranged near the loop region that is believed to impart OXG-RCBH with its activity. We constructed a deletion mutant of the loop region and conducted a detailed analysis. A deletion mutant of the loop region showed endo-activity with altered substrate recognition. More specifically, cleavage occurred randomly instead of at specific sites, most likely due to the misalignment of the substrate within the subsite. We believe that the loop imparts unique substrate specificity with exo-mode hydrolysis in OXG-RCBH.

  4. Integrated Flight/Structural Mode Control for Very Flexible Aircraft Using L1 Adaptive Output Feedback Controller

    Science.gov (United States)

    Che, Jiaxing; Cao, Chengyu; Gregory, Irene M.

    2012-01-01

    This paper explores application of adaptive control architecture to a light, high-aspect ratio, flexible aircraft configuration that exhibits strong rigid body/flexible mode coupling. Specifically, an L(sub 1) adaptive output feedback controller is developed for a semi-span wind tunnel model capable of motion. The wind tunnel mount allows the semi-span model to translate vertically and pitch at the wing root, resulting in better simulation of an aircraft s rigid body motion. The control objective is to design a pitch control with altitude hold while suppressing body freedom flutter. The controller is an output feedback nominal controller (LQG) augmented by an L(sub 1) adaptive loop. A modification to the L(sub 1) output feedback is proposed to make it more suitable for flexible structures. The new control law relaxes the required bounds on the unmatched uncertainty and allows dependence on the state as well as time, i.e. a more general unmatched nonlinearity. The paper presents controller development and simulated performance responses. Simulation is conducted by using full state flexible wing models derived from test data at 10 different dynamic pressure conditions. An L(sub 1) adaptive output feedback controller is designed for a single test point and is then applied to all the test cases. The simulation results show that the L(sub 1) augmented controller can stabilize and meet the performance requirements for all 10 test conditions ranging from 30 psf to 130 psf dynamic pressure.

  5. Recent Results from Analysis of Flow Structures and Energy Modes Induced by Viscous Wave around a Surface-Piercing Cylinder

    Directory of Open Access Journals (Sweden)

    Giancarlo Alfonsi

    2017-01-01

    Full Text Available Due to its relevance in ocean engineering, the subject of the flow field generated by water waves around a vertical circular cylinder piercing the free surface has recently started to be considered by several research groups. In particular, we studied this problem starting from the velocity-potential framework, then the implementation of the numerical solution of the Euler equations in their velocity-pressure formulation, and finally the performance of the integration of the Navier-Stokes equations in primitive variables. We also developed and applied methods of extraction of the flow coherent structures and most energetic modes. In this work, we present some new results of our research directed, in particular, toward the clarification of the main nonintuitive character of the phenomenon of interaction between a wave and a surface-piercing cylinder, namely, the fact that the wave exerts its maximum force and exhibits its maximum run-up on the cylindrical obstacle at different instants. The understanding of this phenomenon becomes of crucial importance in the perspective of governing the entity of the wave run-up on the obstacle by means of wave-flow-control techniques.

  6. Population structure of the ash dieback pathogen, Hymenoscyphus fraxineus, in relation to its mode of arrival in the UK.

    Science.gov (United States)

    Orton, E S; Brasier, C M; Bilham, L J; Bansal, A; Webber, J F; Brown, J K M

    2018-02-01

    The ash dieback fungus, Hymenoscyphus fraxineus , a destructive, alien pathogen of common ash ( Fraxinus excelsior ), has spread across Europe over the past 25 years and was first observed in the UK in 2012. To investigate the relationship of the pathogen's population structure to its mode of arrival, isolates were obtained from locations in England and Wales, either where established natural populations of ash had been infected by wind-dispersed ascospores or where the fungus had been introduced on imported planting stock. Population structure was determined by tests for vegetative compatibility (VC), mating type and single-nucleotide polymorphisms (SNPs). VC heterogeneity was high at all locations, with 96% of isolate pairings being incompatible. Frequencies of the MAT1-1-1 and MAT1-2-1 idiomorphs were approximately equal, consistent with H. fraxineus being an obligate outbreeder. Most SNP variation occurred within study location and there was little genetic differentiation between the two types of location in the UK, or between pathogen populations in the UK and continental Europe. There was modest differentiation between UK subpopulations, consistent with genetic variation between source populations in continental Europe. However, there was no evidence of strong founder effects, indicating that numerous individuals of H. fraxineus initiated infection at each location, regardless of the route of pathogen transmission. The ssRNA virus HfMV1 was present at moderate to high frequencies in all UK subpopulations. The results imply that management of an introduced plant pathogen requires action against its spread at the continental level involving coordinated efforts by European countries.

  7. A scorpion venom neurotoxin paralytic to insects that affects sodium current inactivation: Purification, primary structure, and mode of action

    Energy Technology Data Exchange (ETDEWEB)

    Eitan, M.; Fowler, E.; Herrmann, R.; Duval, A.; Pelhate, M.; Zlotkin, E. (Hebrew Univ., Jerusalem (Israel))

    1990-06-26

    A new toxin, Lqh alpha IT, which caused a unique mode of paralysis of blowfly larvae, was purified from the venom of the scorpion Leiurus quinquestriatus hebraeus, and its structural and pharmacological properties were compared to those of three other groups of neurotoxins found in Buthinae scorpion venoms. Like the excitatory and depressant insect-selective neurotoxins, Lqh alpha IT was highly toxic to insects, but it differed from these toxins in two important characteristics: (a) Lqh alpha IT lacked strict selectivity for insects; it was highly toxic to crustaceans and had a measurable but low toxicity to mice. (b) It did not displace an excitatory insect toxin, 125I-AaIT, from its binding sites in the insect neuronal membrane; this indicates that the binding sites for Lqh alpha IT are different from those shared by the excitatory and depressant toxins. However, in its primary structure and its effect on excitable tissues, Lqh alpha IT strongly resembled the well-characterized alpha scorpion toxins, which affect mammals. The amino acid sequence was identical with alpha toxin sequences in 55%-75% of positions. This degree of similarity is comparable to that seen among the alpha toxins themselves. Voltage- and current-clamp studies showed that Lqh alpha IT caused an extreme prolongation of the action potential in both cockroach giant axon and rat skeletal muscle preparations as a result of the slowing and incomplete inactivation of the sodium currents. These observations indicate that Lqh alpha IT is an alpha toxin which acts on insect sodium channels.

  8. A scorpion venom neurotoxin paralytic to insects that affects sodium current inactivation: Purification, primary structure, and mode of action

    International Nuclear Information System (INIS)

    Eitan, M.; Fowler, E.; Herrmann, R.; Duval, A.; Pelhate, M.; Zlotkin, E.

    1990-01-01

    A new toxin, Lqh alpha IT, which caused a unique mode of paralysis of blowfly larvae, was purified from the venom of the scorpion Leiurus quinquestriatus hebraeus, and its structural and pharmacological properties were compared to those of three other groups of neurotoxins found in Buthinae scorpion venoms. Like the excitatory and depressant insect-selective neurotoxins, Lqh alpha IT was highly toxic to insects, but it differed from these toxins in two important characteristics: (a) Lqh alpha IT lacked strict selectivity for insects; it was highly toxic to crustaceans and had a measurable but low toxicity to mice. (b) It did not displace an excitatory insect toxin, 125I-AaIT, from its binding sites in the insect neuronal membrane; this indicates that the binding sites for Lqh alpha IT are different from those shared by the excitatory and depressant toxins. However, in its primary structure and its effect on excitable tissues, Lqh alpha IT strongly resembled the well-characterized alpha scorpion toxins, which affect mammals. The amino acid sequence was identical with alpha toxin sequences in 55%-75% of positions. This degree of similarity is comparable to that seen among the alpha toxins themselves. Voltage- and current-clamp studies showed that Lqh alpha IT caused an extreme prolongation of the action potential in both cockroach giant axon and rat skeletal muscle preparations as a result of the slowing and incomplete inactivation of the sodium currents. These observations indicate that Lqh alpha IT is an alpha toxin which acts on insect sodium channels

  9. Magnetic Bacteria.

    Science.gov (United States)

    Nelson, Jane Bray; Nelson, Jim

    1992-01-01

    Describes the history of Richard Blakemore's discovery of magnetotaxic organisms. Discusses possible reasons why the magnetic response in bacteria developed. Proposes research experiments integrating biology and physics in which students investigate problems using cultures of magnetotaxic organisms. (MDH)

  10. Big bacteria

    DEFF Research Database (Denmark)

    Schulz, HN; Jørgensen, BB

    2001-01-01

    A small number of prokaryotic species have a unique physiology or ecology related to their development of unusually large size. The biomass of bacteria varies over more than 10 orders of magnitude, from the 0.2 mum wide nanobacteria to the largest cells of the colorless sulfur bacteria......, Thiomargarita namibiensis, with a diameter of 750 mum. All bacteria, including those that swim around in the environment, obtain their food molecules by molecular diffusion. Only the fastest and largest swimmers known, Thiovulum majus, are able to significantly increase their food supply by motility...... and by actively creating an advective flow through the entire population. Diffusion limitation generally restricts the maximal size of prokaryotic cells and provides a selective advantage for mum-sized cells at the normally low substrate concentrations in the environment. The largest heterotrophic bacteria...

  11. Big bacteria

    DEFF Research Database (Denmark)

    Schulz, HN; Jørgensen, BB

    2001-01-01

    A small number of prokaryotic species have a unique physiology or ecology related to their development of unusually large size. The biomass of bacteria varies over more than 10 orders of magnitude, from the 0.2 mum wide nanobacteria to the largest cells of the colorless sulfur bacteria...... and by actively creating an advective flow through the entire population. Diffusion limitation generally restricts the maximal size of prokaryotic cells and provides a selective advantage for mum-sized cells at the normally low substrate concentrations in the environment. The largest heterotrophic bacteria......, the 80 x 600 mum large Epulopiscium sp. from the gut of tropical fish, are presumably living in a very nutrient-rich medium. Many large bacteria contain numerous inclusions in the cells that reduce the volume of active cytoplasm. The most striking examples of competitive advantage from large cell size...

  12. Planck intermediate results XXXVIII. E- and B-modes of dust polarization from the magnetized filamentary structure of the interstellar medium

    DEFF Research Database (Denmark)

    Ade, P. A. R.; Aghanim, N.; Arnaud, M.

    2016-01-01

    The quest for a B-mode imprint from primordial gravity waves on the polarization of the cosmic microwave background (CMB) requires the characterization of foreground polarization from Galactic dust. We present a statistical study of the filamentary structure of the 353 GHz Planck Stokes maps at h...

  13. Density perturbation mode structure of high frequency compressional and global Alfvén eigenmodes in the National Spherical Torus Experiment using a novel reflectometer analysis technique

    Science.gov (United States)

    Crocker, N. A.; Kubota, S.; Peebles, W. A.; Rhodes, T. L.; Fredrickson, E. D.; Belova, E.; Diallo, A.; LeBlanc, B. P.; Sabbagh, S. A.

    2018-01-01

    Reflectometry measurements of compressional (CAE) and global (GAE) Alfvén eigenmodes are analyzed to obtain the amplitude and spatial structure of the density perturbations associated with the modes. A novel analysis technique developed for this purpose is presented. The analysis also naturally yields the amplitude and spatial structure of the density contour radial displacement, which is found to be 2–4 times larger than the value estimated directly from the reflectometer measurements using the much simpler ‘mirror approximation’. The modes were driven by beam ions in a high power (6 MW) neutral beam heated H-mode discharge (#141398) in the National Spherical Torus Experiment. The results of the analysis are used to assess the contribution of the modes to core energy transport and ion heating. The total displacement amplitude of the modes, which is shown to be larger than previously estimated (Crocker et al 2013 Nucl. Fusion 53 43017), is compared to the predicted threshold (Gorelenkov et al 2010 Nucl. Fusion 50 84012) for the anomalously high heat diffusion inferred from transport modeling in similar NSTX discharges. The results of the analysis also have strong implications for the energy transport via coupling of CAEs to kinetic Alfvén waves seen in simulations with the Hybrid MHD code (Belova et al 2015 Phys. Rev. Lett. 115 15001). Finally, the amplitudes of the observed CAEs fall well below the threshold for causing significant ion heating by stochastic velocity space diffusion (Gates et al 2001 Phys. Rev. Lett. 87 205003).

  14. Analytical expression of giant Goos-Hänchen shift in terms of proper and improper modes in waveguide structures with arbitrary refractive index profile.

    Science.gov (United States)

    Alishahi, Fatemeh; Mehrany, Khashayar

    2010-06-01

    We analytically relate the giant Goos-Hänchen shift, observed at the interface of a high refractive index prism and a waveguide structure with an arbitrary refractive index profile, to the spatial resonance phenomenon. The proximity effect of the high refractive index prism on modal properties of the waveguide is discussed, and the observed shift is expressed in terms of proper and improper electromagnetic modes supported by the waveguide with no prism. The transversely increasing improper modes are shown playing an increasingly important role as the high refractive index prism comes closer to the waveguide.

  15. Intima-media thickness evaluation by B-mode ultrasound: Correlation with blood pressure levels and cardiac structures

    Directory of Open Access Journals (Sweden)

    F.L. Plavnik

    2000-01-01

    Full Text Available The aim of this study was to analyze the thickness of the intima-media complex (IMC using a noninvasive method. The carotid and femoral common arteries were evaluated by noninvasive B-mode ultrasound in 63 normotensive and in 52 hypertensive subjects and the thickness of the IMC was tested for correlation with blood pressure, cardiac structures and several clinical and biological parameters. The IMC was thicker in hypertensive than in normotensive subjects (0.67 ± 0.13 and 0.62 ± 0.16 vs 0.54 ± 0.09 and 0.52 ± 0.11 mm, respectively, P<0.0001. In normotensive patients, the simple linear regression showed significant correlations between IMC and age, body mass index and 24-h systolic blood pressure for both the carotid and femoral arteries. In hypertensives the carotid IMC was correlated with age and 24-h systolic blood pressure while femoral IMC was correlated only with 24-h diastolic blood pressure. Forward stepwise regression showed that age, body mass index and 24-h systolic blood pressure influenced the carotid IMC relationship (r2 = 0.39 in normotensives. On the other hand, the femoral IMC relationship was influenced by 24-h systolic blood pressure and age (r2 = 0.40. In hypertensives, age and 24-h systolic blood pressure were the most important determinants of carotid IMC (r2 = 0.37, while femoral IMC was influenced only by 24-h diastolic blood pressure (r2 = 0.10. There was an association between carotid IMC and echocardiographic findings in normotensives, while in hypertensives only the left posterior wall and interventricular septum were associated with femoral IMC. We conclude that age and blood pressure influence the intima-media thickness, while echocardiographic changes are associated with the IMC.

  16. Full-scale photobioreactor for biotreatment of olive washing water: Structure and diversity of the microalgae-bacteria consortium.

    Science.gov (United States)

    Maza-Márquez, P; González-Martínez, A; Rodelas, B; González-López, J

    2017-08-01

    The performance of a full-scale photobioreactor (PBR) for the treatment of olive washing water (OWW) was evaluated under different HRTs (5-2days). The system was able to treat up to 3926L OWWday -1 , and consisted of an activated-carbon pretreatment column and a tubular PBR unit (80 tubes, 98.17L volume, 2-m height, 0.25m diameter). PBR was an effective and environmentally friendly method for the removal of phenols, COD, BOD 5 , turbidity and color from OWW (average efficiencies 94.84±0.55%, 85.86±1.24%, 99.12±0.17%, 95.86±0.98% and 87.24±0.91%, respectively). The diversity of total bacteria and microalgae in the PBR was analyzed using Illumina-sequencing, evaluating the efficiency of two DNA extraction methods. A stable microalgae-bacteria consortium was developed throughout the whole experimentation period, regardless of changes in HRT, temperature or solar radiation. MDS analyses revealed that the interplay between green algae (Sphaeropleales), cyanobacteria (Hapalosiphon) and Proteobacteria (Rhodopseudomonas, Azotobacter) played important roles in OWW bioremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. The mode of emplacement of Neogene flood basalts in eastern Iceland: Facies architecture and structure of simple aphyric basalt groups

    Science.gov (United States)

    Óskarsson, Birgir V.; Riishuus, Morten S.

    2014-12-01

    Simple flows (tabular) in the Neogene flood basalt sections of Iceland are described and their mode of emplacement assessed. The flows belong to three aphyric basalt groups: the Kumlafell group, the Hólmatindur group and the Hjálmadalur group. The groups can be traced over 50 km and originate in the Breiðdalur-Thingmuli volcanic zone. The groups have flow fields that display mixed volcanic facies architecture and can be classified after dominating type morphology. The Kumlafell and the Hólmatindur groups have predominantly simple flows of pāhoehoe and rubbly pāhoehoe morphologies with minor compound or lobate pāhoehoe flows. The Hjálmadalur group has simple flows of rubbly pāhoehoe, but also includes minor compound or lobate flows of rubble and 'a'ā. Simple flows are most common in the distal and medial areas from the vents, while more lobate flows in proximal areas. The simple flows are formed by extensive sheet lobes that are several kilometers long with plane-parallel contacts, some reaching thicknesses of ~ 40 m (aspect ratios structures. Their internal structure consists generally of a simple upper vesicular crust, a dense core and a thin basal vesicular zone. The brecciated flow-top is formed by clinker and crustal rubble, the clinker often welded or agglutinated. The simple flows erupted from seemingly short-lived fissures and have the characteristics of cooling-limited flows. We estimate the effusion rates to be ~ 105 m3/s for the simple flows of the Kumlafell and Hólmatindur groups and ~ 104 m3/s for the Hjálmadalur group. The longest flows advanced 15-20 km from the fissures, with lava streams of fast propagating flows inducing tearing and brecciation of the chilled crust. Compound or lobate areas appear to reflect areas of low effusion rates or the interaction of the lava with topographic barriers or wetlands, resulting in chaotic flowage. Slowing lobes with brecciated flow-tops developed into 'a'ā flows. The groups interdigitated with lava

  18. Study of complex modes

    International Nuclear Information System (INIS)

    Pastrnak, J.W.

    1986-01-01

    This eighteen-month study has been successful in providing the designer and analyst with qualitative guidelines on the occurrence of complex modes in the dynamics of linear structures, and also in developing computer codes for determining quantitatively which vibration modes are complex and to what degree. The presence of complex modes in a test structure has been verified. Finite element analysis of a structure with non-proportional dumping has been performed. A partial differential equation has been formed to eliminate possible modeling errors

  19. Effect of repeat unit structure and molecular mass of lactic acid bacteria hetero-exopolysaccharides on binding to milk proteins

    DEFF Research Database (Denmark)

    Birch, Johnny; HarÐarson, HörÐur Kári; Khan, Sanaullah

    2017-01-01

    -exopolysaccharides (HePSs) of 0.14–4.9 MDa from lactic acid bacteria to different milk proteins (β-casein, κ-casein, native and heat-treated β-lactoglobulin) at pH 4.0–5.0. Maximum binding capacity (RUmax) and apparent affinity (KA,app) were HePS- and protein-dependent and varied for example 10- and 600-fold......, respectively, in the complexation with native β-lactoglobulin at pH 4.0. Highest RUmax and KA,app were obtained with heat-treated β-lactoglobulin and β-casein, respectively. Overall, RUmax and KA,app decreased 6- and 20-fold, respectively, with increasing pH from 4.0 to 5.0. KA,app was influenced by ionic...

  20. STUDY ON THE STRUCTURAL BASIS OF PERIPHERAL LIGHT HARVESTING COMPLEXES (LH2 IN PURPLE NON-SULPHUR PHOTOSYNTHETIC BACTERIA

    Directory of Open Access Journals (Sweden)

    Tatas H.P. Brotosudarmo

    2010-12-01

    Full Text Available Photosynthesis provides an example of a natural process that has been optimized during evolution to harness solar energy efficiently and safely, and finally to use it to produce a carbon-based fuel. Initially, solar energy is captured by the light harvesting pigment-protein complexes. In purple bacteria these antenna complexes are constructed on a rather simple modular basis. Light absorbed by these antenna complexes is funnelled downhill to reaction centres, where light drives a trans-membrane redox reaction. The light harvesting proteins not only provide the scaffolding that correctly positions the bacteriochlorophyll a and carotenoid pigments for optimal energy transfer but also creates an environment that can modulate the wavelength at which different bacteriochlorophyll molecules absorb light thereby creating the energy funnel. How these proteins can modulate the absorption spectra of the bacteriochlorophylls will be discussed in this review.

  1. Using New Mode Choice Model Nesting Structures to Address Emerging Policy Questions: A Case Study of the Pittsburgh Central Business District

    Directory of Open Access Journals (Sweden)

    Zulqarnain H. Khattak

    2017-11-01

    Full Text Available As transportation activities affect a region’s environmental quality, knowing why individuals prefer certain modes can help a region make judicious transportation investments. Using a nested logit model, this paper studies the behavior of commuters to downtown Pittsburgh who use auto, bus, light rail, walking, and biking. Although statistical measures influence the selection of a nesting structure, another criterion for model selection is the policy questions such models inform. Hence this paper demonstrates how an alternative model structure allows planners to consider new policy questions. For example, how might a change in parking fee affect greenhouse gas emission (GHGs? The proposed model showed that a 5%, 10% and 15% increase in parking cost reduces GHGs by 7.3%, 9% and 13.2%, respectively, through increasing carpoolers’ mode share. Because the proposed model forecasts mode choices of certain groups of travelers with higher accuracy (compared to an older model that did not consider the model selection criteria presented here, the proposed model strengthens policymakers’ ability to consider environmental impacts of interest to the region (in this case, GHGs. The paper does not suggest that one nesting structure is always preferable; rather the nesting structure must be chosen with the policy considerations in mind.

  2. Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

    Energy Technology Data Exchange (ETDEWEB)

    Ławniczak, Ł., E-mail: lukasz.k.lawniczak@wp.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Syguda, A., E-mail: Anna.Syguda@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Borkowski, A., E-mail: a.borkowski@uw.edu.pl [Faculty of Geology, University of Warsaw, 02-089 Warsaw (Poland); Cyplik, P., E-mail: pcyplik@wp.pl [Department of Biotechnology and Food Microbiology, University of Life Sciences in Poznan, 60-627 Poznan (Poland); Marcinkowska, K., E-mail: k.marcinkowska@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Wolko, Ł., E-mail: wolko@o2.pl [Department of Biochemistry and Biotechnology, Poznań University of Life Sciences in Poznan, 60-632 Poznan (Poland); Praczyk, T., E-mail: t.praczyk@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Chrzanowski, Ł., E-mail: Lukasz.Chrzanowski@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Pernak, J., E-mail: Juliusz.Pernak@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland)

    2016-09-01

    The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing {sup 1}H and {sup 13}C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. - Highlights: • Impact of herbicidal ionic liquids on bacterial community structure was studied. • Oligomeric herbicidal ionic liquids were effective but not readily biodegradable. • Next generation sequencing was used to evaluate shifts in bacterial abundance. • Treatment during field trials resulted in changes at class and species level. • Use of herbicidal ionic liquids affects the structure of autochthonic soil bacteria.

  3. Structural modification of resveratrol leads to increased anti-tumor activity, but causes profound changes in the mode of action

    Energy Technology Data Exchange (ETDEWEB)

    Scherzberg, Maria-Christina; Kiehl, Andreas; Zivkovic, Aleksandra; Stark, Holger [Institute of Pharmaceutical Chemistry, Biozentrum, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main (Germany); Stein, Jürgen [Institute of Pharmaceutical Chemistry, Biozentrum, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main (Germany); Department of Internal Medicine, Sachsenhausen Hospital, Frankfurt am Main (Germany); Fürst, Robert [Institute of Pharmaceutical Biology, Biozentrum, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main (Germany); Steinhilber, Dieter [Institute of Pharmaceutical Chemistry, Biozentrum, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main (Germany); Ulrich-Rückert, Sandra, E-mail: sandra.ulrich@em.uni-frankfurt.de [Institute of Pharmaceutical Chemistry, Biozentrum, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main (Germany)

    2015-08-15

    (Z)-3,5,4′-Trimethoxystilbene (Z-TMS) is a resveratrol analog with increased antiproliferative activity towards a number of cancer cell lines compared to resveratrol, which has been shown to inhibit tubulin polymerization in vitro. The purpose of this study was to investigate if Z-TMS still shows potential for the prevention of metabolic diseases as known for resveratrol. Cell growth inhibition was determined with IC{sub 50} values for Z-TMS between 0.115 μM and 0.473 μM (resveratrol: 110.7 μM to 190.2 μM). Flow cytometric analysis revealed a G{sub 2}/M arrest after Z-TMS treatment, whereas resveratrol caused S phase arrest. Furthermore, Z-TMS was shown to impair microtubule polymerization. Beneficial effects on lipid accumulation were observed for resveratrol, but not for Z-TMS in an in vitro steatosis model. (E)-Resveratrol was confirmed to elevate cAMP levels, and knockdown of AMPK attenuated the antiproliferative activity, while Z-TMS did not show significant effects in these experiments. SIRT1 and AMPK activities were further measured indirectly via induction of the target gene small heterodimer partner (SHP). Thereby, (E)-resveratrol, but not Z-TMS, showed potent induction of SHP mRNA levels in an AMPK- and SIRT1-dependent manner, as confirmed by knockdown experiments. We provide evidence that Z-TMS does not show beneficial metabolic effects, probably due to loss of activity towards resveratrol target genes. Moreover, our data support previous findings that Z-TMS acts as an inhibitor of tubulin polymerization. These findings confirm that the methylation of resveratrol leads to profound changes in the mode of action, which should be taken into consideration when conducting lead structure optimization approaches. - Highlights: • Methylation of resveratrol leads to profound changes in biologic activity. • Z-TMS does not prevent hepatic steatosis, but inhibits tubulin polymerization. • Resveratrol analog Z-TMS does not influence known targets like

  4. An Insight into the Interaction Mode Between CheB and Chemoreceptor from Two Crystal Structures of CheB Methylesterase Catalytic Domain

    Energy Technology Data Exchange (ETDEWEB)

    K Cho; B Crane; S Park

    2011-12-31

    We have determined 2.2 {angstrom} resolution crystal structure of Thermotoga maritima CheB methylesterase domain to provide insight into the interaction mode between CheB and chemoreceptors. T. maritima CheB methylesterase domain has identical topology of a modified doubly-wound {alpha}/{beta} fold that was observed from the previously reported Salmonella typhimurium counterpart, but the analysis of the electrostatic potential surface near the catalytic triad indicated considerable charge distribution difference. As the CheB demethylation consensus sites of the chemoreceptors, the CheB substrate, are not uniquely conserved between T. maritima and S. typhimurium, such surfaces with differing electrostatic properties may reflect CheB regions that mediate protein-protein interaction. Via the computational docking of the two T. maritima and S. typhimurium CheB structures to the respective T. maritima and Escherichia coli chemoreceptors, we propose a CheB:chemoreceptor interaction mode.

  5. Bacterial structure of aerobic granules is determined by aeration mode and nitrogen load in the reactor cycle.

    Science.gov (United States)

    Cydzik-Kwiatkowska, Agnieszka

    2015-04-01

    This study investigated how the microbial composition of biomass and kinetics of nitrogen conversions in aerobic granular reactors treating high-ammonium supernatant depended on nitrogen load and the number of anoxic phases in the cycle. Excellent ammonium removal and predomination of full nitrification was observed in the reactors operated at 1.1 kg TKN m(-3) d(-1) and with anoxic phases in the cycle. In all reactors, Proteobacteria and Actinobacteria predominated, comprising between 90.14% and 98.59% of OTUs. Extracellular polymeric substances-producing bacteria, such as Rhodocyclales, Xanthomonadaceae, Sphingomonadales and Rhizobiales, were identified in biomass from all reactors, though in different proportions. Under constant aeration, bacteria capable of autotrophic nitrification were found in granules, whereas under variable aeration heterotrophic nitrifiers such as Pseudomonas sp. and Paracoccus sp. were identified. Constant aeration promoted more even bacteria distribution among taxa; with 1 anoxic phase, Paracoccus aminophilus predominated (62.73% of OTUs); with 2 phases, Corynebacterium sp. predominated (65.10% of OTUs). Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Local structural properties and attribute characteristisc in 2-mode networks: p* models to map choices of theater events

    NARCIS (Netherlands)

    Agneessens, F.; Roose, H.

    2008-01-01

    Choices of plays made by theatergoers can be considered as a 2-mode or affiliation network. In this article we illustrate how p* models (an exponential family of distributions for random graphs) can be used to uncover patterns of choices. Based on audience research in three theater institutions in

  7. The fecal bacteria

    Science.gov (United States)

    Sadowsky, Michael J.; Whitman, Richard L.

    2011-01-01

    The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

  8. Production of structured lipids by acidolysis of an EPA-enriched fish oil and caprylic acid in a packed bed reactor: analysis of three different operation modes.

    Science.gov (United States)

    González Moreno, P A; Robles Medina, A; Camacho Rubio, F; Camacho Páez, B; Molina Grima, E

    2004-01-01

    Structured triacylglycerols (ST) enriched in eicosapentaenoic acid (EPA) in position 2 of the triacylglycerol (TAG) backbone were synthesized by acidolysis of a commercially available EPA-rich oil (EPAX4510, 40% EPA) and caprylic acid (CA), catalyzed by the 1,3-specific immobilized lipase Lipozyme IM. The reaction was carried out in a packed bed reactor (PBR) operating in two ways: (1) by recirculating the reaction mixture from the exit of the bed to the substrate reservoir (discontinuous mode) and (2) in continuous mode, directing the product mixture leaving the PBR to a product reservoir. By operating in these two ways and using a simple kinetic model, representative values for the apparent kinetic constants (kX) for each fatty acid (native, Li or odd, M) were obtained. The kinetic model assumes that the rate of incorporation of a fatty acid into TAG per amount of enzyme, rX (mole/(h g lipase)) is proportional to the extent of the deviation from the equilibrium for each fatty acid (i.e., the difference of concentration between the fatty acid in the triacylglycerol and the concentration of the same fatty acid in the triacylglycerol once the equilibrium of the acidolysis reaction is reached). The model allows comparing the two operating modes through the processing intensity, defined as mLt/(V[TG]0) and mL/(q[TG]0), for the discontinuous and continuous operation modes, respectively. In discontinuous mode, ST with 59.5% CA and 9.6% EPA were obtained. In contrast, a ST with 51% CA and 19.6% EPA were obtained when using the continuous operation mode. To enhance the CA incorporation when operating in continuous mode, a two-step acidolysis reaction was performed (third operation mode). This continuous two-step process yields a ST with a 64% CA and a 15% EPA. Finally, after purifying the above ST in a preparative silica gel column, impregnated with boric acid, a ST with 66.9% CA and 19.6% EPA was obtained. The analysis by reverse phase and Ag+ liquid chromatography of

  9. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    Science.gov (United States)

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  10. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

    Science.gov (United States)

    Piatkowski, Pawel; Kasprzak, Joanna M; Kumar, Deepak; Magnus, Marcin; Chojnowski, Grzegorz; Bujnicki, Janusz M

    2016-01-01

    RNA encompasses an essential part of all known forms of life. The functions of many RNA molecules are dependent on their ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that either utilize information derived from known structures of other RNA molecules (by way of template-based modeling) or attempt to simulate the physical process of RNA structure formation (by way of template-free modeling). All computational methods suffer from various limitations that make theoretical models less reliable than high-resolution experimentally determined structures. This chapter provides a protocol for computational modeling of RNA 3D structure that overcomes major limitations by combining two complementary approaches: template-based modeling that is capable of predicting global architectures based on similarity to other molecules but often fails to predict local unique features, and template-free modeling that can predict the local folding, but is limited to modeling the structure of relatively small molecules. Here, we combine the use of a template-based method ModeRNA with a template-free method SimRNA. ModeRNA requires a sequence alignment of the target RNA sequence to be modeled with a template of the known structure; it generates a model that predicts the structure of a conserved core and provides a starting point for modeling of variable regions. SimRNA can be used to fold small RNAs (models for larger RNAs that have a correctly modeled core. ModeRNA can be either downloaded, compiled and run locally or run through a web interface at http://genesilico.pl/modernaserver/ . SimRNA is currently available to download for local use as a precompiled software package at http://genesilico.pl/software/stand-alone/simrna and as a

  11. In vitro activity of tedizolid against gram-positive bacteria in patients with skin and skin structure infections and hospital-acquired pneumonia: a Korean multicenter study.

    Science.gov (United States)

    Lee, Yangsoon; Hong, Sung Kuk; Choi, Sunghak; Im, Weonbin; Yong, Dongeun; Lee, Kyungwon

    2015-09-01

    We compared the activities of tedizolid to those of linezolid and other commonly used antimicrobial agents against gram-positive cocci recovered from patients with skin and skin structure infections (SSSIs) and hospital-acquired pneumonia (HAP) in Korean hospitals. Gram-positive isolates were collected from 356 patients with SSSIs and 144 patients with HAP at eight hospitals in Korea from 2011 to 2014. SSSIs included impetigo, cellulitis, erysipelas, furuncles, abscesses, and infected burns. Antimicrobial susceptibility was tested by using the CLSI agar dilution method. All of the gram-positive isolates were inhibited by ≤1 μg/mL tedizolid. The minimum inhibitory concentration [MIC]₉₀ of tedizolid was 0.5 μg/mL for methicillin-resistant Staphylococcus aureus, which was 4-fold lower than that of linezolid. Tedizolid may become a useful option for the treatment of SSSIs and HAP caused by gram-positive bacteria.

  12. Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4

    Directory of Open Access Journals (Sweden)

    Elena N. Sigida

    2016-04-01

    Full Text Available An O-specific polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide isolated by the phenol–water extraction from the halotolerant soil bacteria Azospirillum halopraeferens type strain Au4. The polysaccharide was studied by sugar and methylation analyses, selective cleavages by Smith degradation and solvolysis with trifluoroacetic acid, one- and two-dimensional 1H and 13C NMR spectroscopy. The following masked repeating structure of the O-specific polysaccharide was established: →3-α-L-Rhap2Me-(1→3-[β-D-Glcp-(1→4]-α-D-Fucp-(1→2-β-D-Xylp-(1→, where non-stoichiometric substituents, an O-methyl group (~45% and a side-chain glucose residue (~65%, are shown in italics.

  13. Modeling the Joint Choice Decisions on Urban Shopping Destination and Travel-to-Shop Mode: A Comparative Study of Different Structures

    Directory of Open Access Journals (Sweden)

    Chuan Ding

    2014-01-01

    Full Text Available The joint choice of shopping destination and travel-to-shop mode in downtown area is described by making use of the cross-nested logit (CNL model structure that allows for potential interalternative correlation along the both choice dimensions. Meanwhile, the traditional multinomial logit (MNL model and nested logit (NL model are also formulated, respectively. This study uses the data collected in the downtown areas of Maryland-Washington, D.C. region, for shopping trips, considering household, individual, land use, and travel related characteristics. The results of the model reveal the significant influencing factors on joint choice travel behavior between shopping destination and travel mode. A comparison of the different models shows that the proposed CNL model structure offers significant improvements in capturing unobserved correlations between alternatives over MNL model and NL model. Moreover, a Monte Carlo simulation for a group of scenarios assuming that there is an increase in parking fees in downtown area is undertaken to examine the impact of a change in car travel cost on the joint choice of shopping destination and travel mode switching. The results are expected to give a better understanding on the shopping travel behavior.

  14. TDP-43 inclusion bodies formed in bacteria are structurally amorphous, non-amyloid and inherently toxic to neuroblastoma cells.

    Directory of Open Access Journals (Sweden)

    Claudia Capitini

    Full Text Available Accumulation of ubiquitin-positive, tau- and α-synuclein-negative intracellular inclusions of TDP-43 in the central nervous system represents the major hallmark correlated to amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin-positive inclusions. Such inclusions have variably been described as amorphous aggregates or more structured deposits having an amyloid structure. Following the observations that bacterial inclusion bodies generally consist of amyloid aggregates, we have overexpressed full-length TDP-43 and C-terminal TDP-43 in E. coli, purified the resulting full-length and C-terminal TDP-43 containing inclusion bodies (FL and Ct TDP-43 IBs and subjected them to biophysical analyses to assess their structure/morphology. We show that both FL and Ct TDP-43 aggregates contained in the bacterial IBs do not bind amyloid dyes such as thioflavin T and Congo red, possess a disordered secondary structure, as inferred using circular dichroism and infrared spectroscopies, and are susceptible to proteinase K digestion, thus possessing none of the hallmarks for amyloid. Moreover, atomic force microscopy revealed an irregular structure for both types of TDP-43 IBs and confirmed the absence of amyloid-like species after proteinase K treatment. Cell biology experiments showed that FL TDP-43 IBs were able to impair the viability of cultured neuroblastoma cells when added to their extracellular medium and, more markedly, when transfected into their cytosol, where they are at least in part ubiquitinated and phosphorylated. These data reveal an inherently high propensity of TDP-43 to form amorphous aggregates, which possess, however, an inherently high ability to cause cell dysfunction. This indicates that a gain of toxic function caused by TDP-43 deposits is effective in TDP-43 pathologies, in addition to possible loss of function mechanisms originating from the cellular mistrafficking of the protein.

  15. Potential role of bacteria packaging by protozoa in the persistence and transmission of pathogenic bacteria

    OpenAIRE

    Denoncourt, Alix M.; Paquet, Valérie E.; Charette, Steve J.

    2014-01-01

    Many pathogenic bacteria live in close association with protozoa. These unicellular eukaryotic microorganisms are ubiquitous in various environments. A number of protozoa such as amoebae and ciliates ingest pathogenic bacteria, package them usually in membrane structures, and then release them into the environment. Packaged bacteria are more resistant to various stresses and are more apt to survive than free bacteria. New evidence indicates that protozoa and not bacteria control the packaging...

  16. Monolithic integration of enhancement-mode vertical driving transistorson a standard InGaN/GaN light emitting diode structure

    Science.gov (United States)

    Lu, Xing; Liu, Chao; Jiang, Huaxing; Zou, Xinbo; Zhang, Anping; Lau, Kei May

    2016-08-01

    In this letter, monolithic integration of InGaN/GaN light emitting diodes (LEDs) with vertical metal-oxide-semiconductor field effect transistor (VMOSFET) drivers have been proposed and demonstrated. The VMOSFET was achieved by simply regrowing a p- and n-GaN bilayer on top of a standard LED structure. After fabrication, the VMOSFET is connected with the LED through the conductive n-GaN layer, with no need of extra metal interconnections. The junction-based VMOSFET is inherently an enhancement-mode (E-mode) device with a threshold voltage of 1.6 V. By controlling the gate bias of the VMOSFET, the light intensity emitted from the integrated VMOSFET-LED device could be well modulated, which shows great potential for various applications, including solid-state lighting, micro-displays, and visible light communications.

  17. Stable and High OSNR Compound Linear-Cavity Single-Longitudinal-Mode Erbium-Doped Silica Fiber Laser Based on an Asymmetric Four-Cavity Structure

    International Nuclear Information System (INIS)

    Feng Ting; Yan Feng-Ping; Li Qi; Peng Wan-Jing; Feng Su-Chun; Wen Xiao-Dong; Tan Si-Yu; Liu Peng

    2012-01-01

    We propose a stable and high optical signal-to-noise ratio (OSNR) compound linear-cavity single-longitudinal-mode (SLM) erbium-doped silica fiber laser. It consists of three uniform fiber Bragg gratings (FBGs) and two fiber couplers to form a simple asymmetric four-cavity structure to select the longitudinal mode. The stable SLM operation at the wavelength of 1544.053 nm with a 3 dB bandwidth of 0.014 nm and an OSNR of ∼60 dB was verified experimentally. Under laboratory conditions, a power fluctuation performance of less than 0.05 dB for 5 h and wavelength variation of less than 0.01 nm for about 150 min is demonstrated. Finally, the characteristic of laser output power as a function of pump power is investigated. The proposed system provides a simple and cost-effective approach to realize a stable SLM fiber laser

  18. Antiresonance and decoupling in electronic transport through parallel-coupled quantum-dot structures with laterally-coupled Majorana zero modes

    Science.gov (United States)

    Zhang, Ya-Jing; Zhang, Lian-Lian; Jiang, Cui; Gong, Wei-Jiang

    2018-02-01

    We theoretically investigate the electronic transport through a parallel-coupled multi-quantum-dot system, in which the terminal dots of a one-dimensional quantum-dot chain are embodied in the two arms of an Aharonov-Bohm interferometer. It is found that in the structures of odd(even) dots, all their even(odd) molecular states have opportunities to decouple from the leads, and in this process antiresonance occurs which are accordant with the odd(even)-numbered eigenenergies of the sub-molecule without terminal dots. Next when Majorana zero modes are introduced to couple laterally to the terminal dots, the antiresonance and decoupling phenomena still co-exist in the quantum transport process. Such a result can be helpful in understanding the special influence of Majorana zero mode on the electronic transport through quantum-dot systems.

  19. Detection of Ammonia-Oxidizing Bacteria (AOB) Using a Porous Silicon Optical Biosensor Based on a Multilayered Double Bragg Mirror Structure.

    Science.gov (United States)

    Zhang, Hongyan; Lv, Jie; Jia, Zhenhong

    2018-01-01

    We successfully demonstrate a porous silicon (PS) double Bragg mirror by electrochemical etching at room temperature as a deoxyribonucleic acid (DNA) label-free biosensor for detecting ammonia-oxidizing bacteria (AOB). Compared to various other one-dimension photonic crystal configurations of PS, the double Bragg mirror structure is quite easy to prepare and exhibits interesting optical properties. The width of high reflectivity stop band of the PS double Bragg mirror is about 761 nm with a sharp and deep resonance peak at 1328 nm in the reflectance spectrum, which gives a high sensitivity and distinguishability for sensing performance. The detection sensitivity of such a double Bragg mirror structure is illustrated through the investigation of AOB DNA hybridization in the PS pores. The redshifts of the reflectance spectra show a good linear relationship with both complete complementary and partial complementary DNA. The lowest detection limit for complete complementary DNA is 27.1 nM and the detection limit of the biosensor for partial complementary DNA is 35.0 nM, which provides the feasibility and effectiveness for the detection of AOB in a real environment. The PS double Bragg mirror structure is attractive for widespread biosensing applications and provides great potential for the development of optical applications.

  20. Intrinsic localized modes and nonlinear impurity modes in curved ...

    Indian Academy of Sciences (India)

    structure of the localized modes induced by an isotopic light-mass impurity in this chain. We further demonstrate that a ... direct physical meaning and can describe polymers and biomolecular systems. The motion of the chain is confined to .... mode center (n = 0) the local mode must obey the expression (10). Equation (8).

  1. Study of the influence of semiconductor material parameters on acoustic wave propagation modes in GaSb/AlSb bi-layered structures by Legendre polynomial method

    Science.gov (United States)

    Othmani, Cherif; Takali, Farid; Njeh, Anouar; Ben Ghozlen, Mohamed Hédi

    2016-09-01

    The propagation of Rayleigh-Lamb waves in bi-layered structures is studied. For this purpose, an extension of the Legendre polynomial (LP) method is proposed to formulate the acoustic wave equation in the bi-layered structures induced by thin film Gallium Antimonide (GaSb) and with Aluminum Antimonide (AlSb) substrate in moderate thickness. Acoustic modes propagating along a bi-layer plate are shown to be quite different than classical Lamb modes, contrary to most of the multilayered structures. The validation of the LP method is illustrated by a comparison between the associated numerical results and those obtained using the ordinary differential equation (ODE) method. The convergency of the LP method is discussed through a numerical example. Moreover, the influences of thin film GaSb parameters on the characteristics Rayleigh-Lamb waves propagation has been studied in detail. Finally, the advantages of the Legendre polynomial (LP) method to analyze the multilayered structures are described. All the developments performed in this work were implemented in Matlab software.

  2. Study of the influence of semiconductor material parameters on acoustic wave propagation modes in GaSb/AlSb bi-layered structures by Legendre polynomial method

    Energy Technology Data Exchange (ETDEWEB)

    Othmani, Cherif, E-mail: othmanicheriffss@gmail.com; Takali, Farid; Njeh, Anouar; Ben Ghozlen, Mohamed Hédi

    2016-09-01

    The propagation of Rayleigh–Lamb waves in bi-layered structures is studied. For this purpose, an extension of the Legendre polynomial (LP) method is proposed to formulate the acoustic wave equation in the bi-layered structures induced by thin film Gallium Antimonide (GaSb) and with Aluminum Antimonide (AlSb) substrate in moderate thickness. Acoustic modes propagating along a bi-layer plate are shown to be quite different than classical Lamb modes, contrary to most of the multilayered structures. The validation of the LP method is illustrated by a comparison between the associated numerical results and those obtained using the ordinary differential equation (ODE) method. The convergency of the LP method is discussed through a numerical example. Moreover, the influences of thin film GaSb parameters on the characteristics Rayleigh–Lamb waves propagation has been studied in detail. Finally, the advantages of the Legendre polynomial (LP) method to analyze the multilayered structures are described. All the developments performed in this work were implemented in Matlab software.

  3. Differences in the Structure of the Gut Bacteria Communities in Development Stages of the Chinese White Pine Beetle (Dendroctonus armandi)

    OpenAIRE

    Hu, Xia; Wang, Chunyan; Chen, Hui; Ma, Junning

    2013-01-01

    The Chinese white pine beetle Dendroctonus armandi Tsai and Li, is arguably the most destructive forest insect in the Qinling Mountains in Northern China. Little is known about the structure of the bacterial communities associated with D. armandi even though this wood-boring insect plays important roles in ecosystem and biological invasion processes that result in huge economic losses in pine forests. The aim of this study was to investigate the composition of the bacterial communities presen...

  4. Nitrification activity and community structure of nitrite-oxidizing bacteria in the bioreactors operated with addition of pharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Kraigher, Barbara, E-mail: barbara.kraigher@bf.uni-lj.si [University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Microbiology, Vecna pot 111, 1000 Ljubljana (Slovenia); Mandic-Mulec, Ines [University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Chair of Microbiology, Vecna pot 111, 1000 Ljubljana (Slovenia)

    2011-04-15

    Pharmaceuticals represent a group of the new emerging contaminants, which might influence microbial communities in the activated sludge. Nitrification activity and Nitrospira community structure in the small-scale reactors supplied with different concentrations (0, 50, 200, 500 {mu}g L{sup -1}) of the selected pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid) were evaluated. Ammonia removal was not influenced by selected pharmaceuticals. However, in the two reactors operated with 50 {mu}g L{sup -1} of pharmaceuticals (R50 and R50P), the effluent concentration of N-(NO{sub 2}{sup -} + NO{sub 3}{sup -}) was significantly higher than in the other reactors. Nitrospira community structure was assessed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequencing of the partial genes for 16S rRNA. Nitrospira spp. were detected in all reactors. The two dominant T-RFs represented the sublineages I and II of the genus Nitrospira. Main shifts were observed in the reactors R50 and R50P, where the T-RF representing sublineage II was much higher as compared to the other reactors. Consistent with this, the Nitrospira sublineage II was detected only in the clone libraries from the reactors R50 and R50P. Our results suggest that the relative abundance of Nitrospira sublineage II could be related to the effluent N-(NO{sub 2}{sup -} + NO{sub 3}{sup -}) concentration.

  5. Nitrification activity and community structure of nitrite-oxidizing bacteria in the bioreactors operated with addition of pharmaceuticals

    International Nuclear Information System (INIS)

    Kraigher, Barbara; Mandic-Mulec, Ines

    2011-01-01

    Pharmaceuticals represent a group of the new emerging contaminants, which might influence microbial communities in the activated sludge. Nitrification activity and Nitrospira community structure in the small-scale reactors supplied with different concentrations (0, 50, 200, 500 μg L -1 ) of the selected pharmaceuticals (ibuprofen, naproxen, ketoprofen, diclofenac and clofibric acid) were evaluated. Ammonia removal was not influenced by selected pharmaceuticals. However, in the two reactors operated with 50 μg L -1 of pharmaceuticals (R50 and R50P), the effluent concentration of N-(NO 2 - + NO 3 - ) was significantly higher than in the other reactors. Nitrospira community structure was assessed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequencing of the partial genes for 16S rRNA. Nitrospira spp. were detected in all reactors. The two dominant T-RFs represented the sublineages I and II of the genus Nitrospira. Main shifts were observed in the reactors R50 and R50P, where the T-RF representing sublineage II was much higher as compared to the other reactors. Consistent with this, the Nitrospira sublineage II was detected only in the clone libraries from the reactors R50 and R50P. Our results suggest that the relative abundance of Nitrospira sublineage II could be related to the effluent N-(NO 2 - + NO 3 - ) concentration.

  6. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors

    Science.gov (United States)

    Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

    2018-02-01

    Optimization of fragment size d-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

  7. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

    Science.gov (United States)

    Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

    2015-01-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

  8. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

    Directory of Open Access Journals (Sweden)

    Wakene C Negassa

    Full Text Available Physical protection of soil carbon (C is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i decomposition of added plant residue, (ii CO2 emission from soil, and (iii structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of

  9. Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

    Science.gov (United States)

    Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

    2015-01-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

  10. Structure-activity relationships of the antimicrobial peptide arasin 1 - and mode of action studies of the N-terminal, proline-rich region.

    Directory of Open Access Journals (Sweden)

    Victoria S Paulsen

    Full Text Available Arasin 1 is a 37 amino acid long proline-rich antimicrobial peptide isolated from the spider crab, Hyas araneus. In this work the active region of arasin 1 was identified through structure-activity studies using different peptide fragments derived from the arasin 1 sequence. The pharmacophore was found to be located in the proline/arginine-rich NH(2 terminus of the peptide and the fragment arasin 1(1-23 was almost equally active to the full length peptide. Arasin 1 and its active fragment arasin 1(1-23 were shown to be non-toxic to human red blood cells and arasin 1(1-23 was able to bind chitin, a component of fungal cell walls and the crustacean shell. The mode of action of the fully active N-terminal arasin 1(1-23 was explored through killing kinetic and membrane permeabilization studies. At the minimal inhibitory concentration (MIC, arasin 1(1-23 was not bactericidal and had no membrane disruptive effect. In contrast, at concentrations of 5×MIC and above it was bactericidal and interfered with membrane integrity. We conclude that arasin 1(1-23 has a different mode of action than lytic peptides, like cecropin P1. Thus, we suggest a dual mode of action for arasin 1(1-23 involving membrane disruption at peptide concentrations above MIC, and an alternative mechanism of action, possibly involving intracellular targets, at MIC.

  11. Semi-analytical quasi-normal mode theory for the local density of states in coupled photonic crystal cavity-waveguide structures

    DEFF Research Database (Denmark)

    de Lasson, Jakob Rosenkrantz; Kristensen, Philip Trøst; Mørk, Jesper

    2015-01-01

    We present and validate a semi-analytical quasi-normal mode (QNM) theory for the local density of states (LDOS) in coupled photonic crystal (PhC) cavity-waveguide structures. By means of an expansion of the Green's function on one or a few QNMs, a closed-form expression for the LDOS is obtained......-trivial spectrum with a peak and a dip is found, which is reproduced only when including both the two relevant QNMs in the theory. In both cases, we find relative errors below 1% in the bandwidth of interest....

  12. Full Article: Stoichiometry, Vibrational Modes and Structure of Molten Nb2O5-K2S2O7 Mixtures

    DEFF Research Database (Denmark)

    Boghosian, S.; Borup, F.; Berg, Rolf W.

    1998-01-01

    The dissolution reaction of Nb205 in pure molten K2S207 has been studied and high temperature Raman spectroscopy has been used for determining the vibrational and structural properties of the Nb(V) complex(es) formed according to the reaction Nb205 + n S207(2-) -> complex. By means of a recently...... of a possible structural model....

  13. Molecular Structures, Vibrational Spectroscopy, and Normal-Mode Analysis of M(2)(C&tbd1;CR)(4)(PMe(3))(4) Dimetallatetraynes. Observation of Strongly Mixed Metal-Metal and Metal-Ligand Vibrational Modes.

    Science.gov (United States)

    John, Kevin D.; Miskowski, Vincent M.; Vance, Michael A.; Dallinger, Richard F.; Wang, Louis C.; Geib, Steven J.; Hopkins, Michael D.

    1998-12-28

    The nature of the skeletal vibrational modes of complexes of the type M(2)(C&tbd1;CR)(4)(PMe(3))(4) (M = Mo, W; R = H, Me, Bu(t)(), SiMe(3)) has been deduced. Metrical data from X-ray crystallographic studies of Mo(2)(C&tbd1;CR)(4)(PMe(3))(4) (R = Me, Bu(t)(), SiMe(3)) and W(2)(C&tbd1;CMe)(4)(PMe(3))(4) reveal that the core bond distances and angles are within normal ranges and do not differ in a statistically significant way as a function of the alkynyl substituent, indicating that their associated force constants should be similarly invariant among these compounds. The crystal structures of Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) and Mo(2)(C&tbd1;CBu(t)())(4)(PMe(3))(4) are complicated by 3-fold disorder of the Mo(2) unit within apparently ordered ligand arrays. Resonance-Raman spectra ((1)(delta-->delta) excitation, THF solution) of Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) and its isotopomers (PMe(3)-d(9), C&tbd1;CSiMe(3)-d(9), (13)C&tbd1;(13)CSiMe(3)) exhibit resonance-enhanced bands due to a(1)-symmetry fundamentals (nu(a) = 362, nu(b) = 397, nu(c) = 254 cm(-)(1) for the natural-abundance complex) and their overtones and combinations. The frequencies and relative intensities of the fundamentals are highly sensitive to isotopic substitution of the C&tbd1;CSiMe(3) ligands, but are insensitive to deuteration of the PMe(3) ligands. Nonresonance-Raman spectra (FT-Raman, 1064 nm excitation, crystalline samples) for the Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) compounds and for Mo(2)(C&tbd1;CR)(4)(PMe(3))(4) (R = H, D, Me, Bu(t)(), SiMe(3)) and W(2)(C&tbd1;CMe)(4)(PMe(3))(4) exhibit nu(a), nu(b), and nu(c) and numerous bands due to alkynyl- and phosphine-localized modes, the latter of which are assigned by comparisons to FT-Raman spectra of Mo(2)X(4)L(4) (X = Cl, Br, I; L = PMe(3), PMe(3)-d(9))(4) and Mo(2)Cl(4)(AsMe(3))(4). Valence force-field normal-coordinate calculations on the model compound Mo(2)(C&tbd1;CH)(4)P(4), using core force constants transferred from a calculation

  14. Microbial community structure and biodegradation activity of particle-associated bacteria in a coal tar contaminated creek

    Energy Technology Data Exchange (ETDEWEB)

    Jennifer M. DeBruyn; Gary S. Sayler [University of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology and Department of Microbiology

    2009-05-01

    The Chattanooga Creek Superfund site (Chattanooga, TN) is one of the most polluted waterways in the southeastern U.S. with high polycyclic aromatic hydrocarbon (PAH) concentrations in the sediments. PAHs associate with suspended solids in the water column, and may be redeposited onto the floodplain. These suspended particles represent an interesting but understudied environment for PAH-degrading microbial communities. This study tested the hypotheses that particle-associated bacterial (PAB) communities have genotypic potential (PAH-dioxygenase genes) and activity (naphthalene and pyrene mineralization), and can contribute to natural attenuation of PAHs in Chattanooga Creek. Upstream of the Superfund site, mineralization ranged from 0.2 to 2.0% of added {sup 14}C-naphthalene and 0 to 0.1% {sup 14}C-pyrene (after 40 h), with first order biodegradation rate constants (k{sub 1}) ranging from 1.09 to 9.18 x 10{sup -5} h{sup -1} and 0 to 1.13 x 10{sup -6} h{sup -1}, respectively. Mineralization was significantly greater in PAB communities within the contaminated zone, with 11.8 to 31.2% {sup 14}C-naphthalene (k{sup 1} 5.34 to 14.2 x 10-4 h{sup -1}) and 1.3 to 6.6% {sup 14}C-pyrene mineralized (k{sub 1} 2.89 to 15.0 x 10{sup -5} h{sup -1}). Abundances of nagAc (naphthalene dioxygenase) and nidA (pyrene dioxygenase) genes indicated that PAB communities harbored populations with genetic potential for both low- and high-molecular weight PAH degradation, and quantification of Mycobacterium 16S rDNA genes indicated that PAH-degrading mycobacteria are also prevalent in this environment. Phylogenetic comparisons (T-RFLPs) between PAB and sediments indicated these microbial communities were taxonomically distinct, but shared some functional similarities, namely PAH catabolic genotypes, mineralization capabilities, and community structuring along a contamination gradient. 38 refs., 4 figs., 2 tabs.

  15. The Atomic Structure of Ti2C and Ti3C2 MXenes is Responsible for Their Antibacterial Activity Toward E. coli Bacteria

    Science.gov (United States)

    Jastrzębska, Agnieszka Maria; Karwowska, Ewa; Wojciechowski, Tomasz; Ziemkowska, Wanda; Rozmysłowska, Anita; Chlubny, Leszek; Olszyna, Andrzej

    2018-02-01

    The expanded Ti2C and Ti3C2 MXene phases were synthesized from their parent Ti2AlC and Ti3AlC2 MAX phases using the same conditions of the classical acidic aluminum extraction method. The assumption for the study was that the expanded Ti2C and Ti3C2 MXenes are composed of the same atoms and if are synthesized from MAX phases using the same conditions of the classical acidic aluminum extraction method, the observed bio-effects can be related only to the changes in their structures. The scanning electron microscope investigations indicated that the expanded Ti2C and Ti3C2 sheets formed the specific network of slit-shaped nano-pores. The x-ray photoelectron spectroscopy for chemical analysis (ESCA-XPS) showed almost no difference in surface chemistry of Ti2C and Ti3C2 MXenes. The high-resolution transmission electron microscope investigations revealed, however, differences in atomic structure of the individual Ti2C and Ti3C2 sheets. Measured distance between Ti-C atomic layers in Ti2C was 9.76 Å and was larger by 0.53 Å in comparison with Ti3C2 (9.23 Å). Our investigations of bioactive properties toward model gram-negative Escherichia coli bacterial strain showed that the Ti2C MXene did not influence the viability of bacteria. Contrarily, the Ti3C2 MXene showed antibacterial properties. The results of the study indicate that the structure at the atomic scale may play a key role in the bioactivity of MXenes of the same chemical composition, but different stoichiometry, just like in case of Ti2C and Ti3C2.

  16. "Supramolecular" assembly of gold nanorods end-terminated with polymer "pom-poms": effect of pom-pom structure on the association modes.

    Science.gov (United States)

    Nie, Zhihong; Fava, Daniele; Rubinstein, Michael; Kumacheva, Eugenia

    2008-03-19

    We report a predefined self-organization of gold nanorods (NRs) end-terminated with multiple polymer arms ("pom-poms") in higher-order structures. The assembly of polymer-tethered NRs was controlled by changing the structure of the polymer pom-poms. We show that the variation in the molecular weight of the polymer molecules and their relative location with respect to the long side of the NRs resulted in two competing association modes of the nanorods, that is, their side-by-side and end-to-end assembly, and produced bundles, chains, rings, and bundled chains of the NRs. The superposition of the two variables controlling the organization of NRs allowed us to create a map showing the variation in the longitudinal plasmonic bands of the NRs achieved by their self-assembly.

  17. Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lenong; Chang, Zhenzhan; Pan, Zhiqiang; Fu, Zheng-Qing; Wang, Xiaoqiang (US-Agriculture); (SRNF); (Georgia)

    2009-01-12

    Cytochrome P450s exist ubiquitously in all organisms and are involved in many biological processes. Allene oxide synthase (AOS) is a P450 enzyme that plays a key role in the biosynthesis of oxylipin jasmonates, which are involved in signal and defense reactions in higher plants. The crystal structures of guayule (Parthenium argentatum) AOS (CYP74A2) and its complex with the substrate analog 13(S)-hydroxyoctadeca-9Z,11E-dienoic acid have been determined. The structures exhibit a classic P450 fold but possess a heme-binding mode with an unusually long heme binding loop and a unique I-helix. The structures also reveal two channels through which substrate and product may access and leave the active site. The entrances are defined by a loop between {beta}3-2 and {beta}3-3. Asn-276 in the substrate binding site may interact with the substrate's hydroperoxy group and play an important role in catalysis, and Lys-282 at the entrance may control substrate access and binding. These studies provide both structural insights into AOS and related P450s and a structural basis to understand the distinct reaction mechanism.

  18. The Use of Contact Mode Atomic Force Microscopy in Aqueous Medium for Structural Analysis of Spinach Photosynthetic Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Phuthong, Witchukorn; Huang, Zubin; Wittkopp, Tyler M.; Sznee, Kinga; Heinnickel, Mark L.; Dekker, Jan P.; Frese, Raoul N.; Prinz, Fritz B.; Grossman, Arthur R.

    2015-07-28

    To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach (Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsic domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.

  19. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

    Science.gov (United States)

    Nandy, Suman Kumar; Seal, Alpana

    2016-01-01

    Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

  20. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

    Directory of Open Access Journals (Sweden)

    Suman Kumar Nandy

    Full Text Available Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

  1. ``GodMode is his video game name'': situating learning and identity in structures of social practice

    Science.gov (United States)

    Bricker, Leah A.; Bell, Philip

    2012-12-01

    In this paper, we report on the structural nexus of one youth's gaming practices across contexts and over time. We utilize data from an ethnography of youth science and technology learning, as well as expertise development, across settings and developmental time. We use Ole Dreier's theory of persons to understand how this youth is able to develop considerable gaming expertise. Additionally, we explicate the learning practices embedded in the structural nexus of this youth's gaming and we examine associated issues of learning and identity. We problematize the lack of continuity between his formal schooling experiences and the structural nexus of his gaming practices as situated in a variety of other contexts and we reflect on the implications for the design of STEM gaming experiences in formal school environments.

  2. Bathymetric highs in the mid-slope region of the western continental margin of India - Structure and mode of origin

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, D.G.; Paropkari, A.L.; Krishna, K.S.; Chaubey, A.K.; Ajay, K.K.; Kodagali, V.N.

    -filled depression of ~0.2 km wide. Over all the seafloor relief’s shows a broad anticline with gentle and evenly deepening flanks on either side overlain by ~2 s (TWT) thick sediments. The seismic reflectors of relatively wide structure E (Fig. 7) show a series... 'horst' structure that is bounded on both sides by steep faults. Sediments thickness patterns and faulted basement are confirmed from the fault-bounded trough, named the 'Kori-Comorin Depression' (Biswas, 1989) or "eastern part of shelf margin basin...

  3. Study of the modes of adsorption and electronic structure of hydrogen peroxide and ethanol over TiO2 rutile (110) surface within the context of water splitting

    Science.gov (United States)

    Alghamdi, H.; Idriss, H.

    2018-03-01

    While photocatalytic water splitting over many materials is favourable thermodynamically the kinetic of the reaction is very slow. One of the proposed reasons linked to the slow oxidation reaction rate is H2O2 formation as a reaction intermediate. Using Density Functional Theory (DFT) H2O2 is investigated on TiO2 rutile (110) surface to determine its most stable adsorption modes: molecular, (H)O(H)O - (a), partially dissociated, (H)OO - (a), and fully dissociated (a) - OO - (a). We then compare H2O2 interaction to that of a fast hole scavenger molecule, ethanol. Geometry, electronic structure, charge density difference and work function determination of both adsorbates are presented and compared using DFT with different functionals (PBE, PBE-D, PBE-U, and HSE + D). H2O2 is found to be strongly adsorbed on TiO2 rutile (110) surface with adsorption energies reaching 0.95 eV, comparable to that of ethanol (0.89 eV); using GGA PBE. The negative changes in the work function upon adsorption were found to be highest for molecular adsorption ( - 1.23 eV) and lowest for the fully dissociated mode ( - 0.54 eV) of H2O2. This may indicate that electrons flow from the surface to the adsorbate in order to make O(s)-H partially offset the overall magnitude of the oxygen lone pair interaction (of H2O2) with Ti4+ cations. Examination of the electronic structure through density of states (DOS) at the PBE level of computation, indicates that the H2O2 highest occupied molecular orbital (HOMO) level is not overlapping with oxygen atoms of TiO2 surface at any of its adsorption modes and at any of the computation methods. Some overlap is seen using the HSE + D computational method. On the other hand the dissociated mode of ethanol (ethoxides) does overlap with all computational methods used. The high adsorption energy and the absence of overlapping of the HOMO level of H2O2 with TiO2 rutile (110) surface may explain why water splitting is slow.

  4. Polymorphism in Developmental Mode and Its Effect on Population Genetic Structure of a Spionid Polychaete, Pygospio elegans

    NARCIS (Netherlands)

    Kesaniemi, Jenni E.; Geuverink, Elzemiek; Knott, K. Emily

    Population genetic structure of sedentary marine species is expected to be shaped mainly by the dispersal ability of their larvae. Long-lived planktonic larvae can connect populations through migration and gene flow, whereas species with nondispersive benthic or direct-developing larvae are expected

  5. "GodMode Is His Video Game Name": Situating Learning and Identity in Structures of Social Practice

    Science.gov (United States)

    Bricker, Leah A.; Bell, Philip

    2012-01-01

    In this paper, we report on the structural nexus of one youth's gaming practices across contexts and over time. We utilize data from an ethnography of youth science and technology learning, as well as expertise development, across settings and developmental time. We use Ole Dreier's theory of persons to understand how this youth is able to develop…

  6. Three-way SIMPLIMAX for oblique rotation of the three-mode factor analysis core to simple structure

    NARCIS (Netherlands)

    Kiers, Henk A.L.

    1998-01-01

    SIMPLIMAX is proposed as a procedure for oblique rotation of a factor loadings matrix to simple structure. The distinguishing feature of this method is that it rotates the loading matrix so that after rotation the m smallest elements have a minimal sum of squares (where m is specified in advance).

  7. High-gradient low-β accelerating structure using the first negative spatial harmonic of the fundamental mode

    Science.gov (United States)

    Kutsaev, Sergey V.; Agustsson, Ronald; Boucher, Salime; Fischer, Richard; Murokh, Alex; Mustapha, Brahim; Nassiri, Alireza; Ostroumov, Peter N.; Plastun, Alexander; Savin, Evgeny; Smirnov, Alexander Yu.

    2017-12-01

    The development of high-gradient accelerating structures for low-β particles is the key for compact hadron linear accelerators. A particular example of such a machine is a hadron therapy linac, which is a promising alternative to cyclic machines, traditionally used for cancer treatment. Currently, the practical utilization of linear accelerators in radiation therapy is limited by the requirement to be under 50 m in length. A usable device for cancer therapy should produce 200-250 MeV protons and/or 400 - 450 MeV /u carbon ions, which sets the requirement of having 35 MV /m average "real-estate gradient" or gradient per unit of actual accelerator length, including different accelerating sections, focusing elements and beam transport lines, and at least 50 MV /m accelerating gradients in the high-energy section of the linac. Such high accelerating gradients for ion linacs have recently become feasible for operations at S-band frequencies. However, the reasonable application of traditional S-band structures is practically limited to β =v /c >0.4 . However, the simulations show that for lower phase velocities, these structures have either high surface fields (>200 MV /m ) or low shunt impedances (issue, we have designed a novel radio frequency structure where the beam is synchronous with the higher spatial harmonic of the electromagnetic field. In this paper, we discuss the principles of this approach, the related beam dynamics and especially the electromagnetic and thermomechanical designs of this novel structure. Besides the application to ion therapy, the technology described in this paper can be applied to future high gradient normal conducting ion linacs and high energy physics machines, such as a compact hadron collider. This approach preserves linac compactness in settings with limited space availability.

  8. Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States.

    Science.gov (United States)

    Taniguchi, Takeshi; Imada, Shogo; Acharya, Kumud; Iwanaga, Fumiko; Yamanaka, Norikazu

    2015-01-01

    Tamarix ramosissima is a tree species that is highly resistant to salt and drought. The Tamarix species survives in a broad range of environmental salt levels, and invades major river systems in southwestern United States. It may affect root-associated bacteria (RB) by increasing soil salts and nutrients. The effects of RB on host plants may vary even under saline conditions, and the relationship may be important for T. ramosissima. However, to the best of our knowledge, there have been no reports relating to T. ramosissima RB and its association with salinity and nutrient levels. In this study, we have examined this association and the effect of arbuscular mycorrhizal colonization of T. ramosissima on RB because a previous study has reported that colonization of arbuscular mycorrhizal fungi affected the rhizobacterial community (Marschner et al., 2001). T. ramosissima roots were collected from five locations with varying soil salinity and nutrient levels. RB community structures were examined by terminal restriction fragment (T-RF) length polymorphism, cloning, and sequencing analyses. The results suggest that RB richness, or the diversity of T. ramosissima, have significant negative relationships with electrical conductivity (EC), sodium concentration (Na), and the colonization of arbuscular mycorrhizal fungi, but have a significant positive relationship with phosphorus in the soil. However, at each T-RF level, positive correlations between the emergence of some T-RFs and EC or Na were observed. These results indicate that high salinity decreased the total number of RB species, but some saline-tolerant RB species multiplied with increasing salinity levels. The ordination scores of nonmetric multidimensional scale analysis of RB community composition show significant relationships with water content, calcium concentration, available phosphorus, and total nitrogen. These results indicate that the RB diversity and community composition of T. ramosissima are affected

  9. Conjugation in Gram-Positive Bacteria.

    Science.gov (United States)

    Goessweiner-Mohr, Nikolaus; Arends, Karsten; Keller, Walter; Grohmann, Elisabeth

    2014-08-01

    Conjugative transfer is the most important means of spreading antibiotic resistance and virulence factors among bacteria. The key vehicles of this horizontal gene transfer are a group of mobile genetic elements, termed conjugative plasmids. Conjugative plasmids contain as minimum instrumentation an origin of transfer (oriT), DNA-processing factors (a relaxase and accessory proteins), as well as proteins that constitute the trans-envelope transport channel, the so-called mating pair formation (Mpf) proteins. All these protein factors are encoded by one or more transfer (tra) operons that together form the DNA transport machinery, the Gram-positive type IV secretion system. However, multicellular Gram-positive bacteria belonging to the streptomycetes appear to have evolved another mechanism for conjugative plasmid spread reminiscent of the machinery involved in bacterial cell division and sporulation, which transports double-stranded DNA from donor to recipient cells. Here, we focus on the protein key players involved in the plasmid spread through the two different modes and present a new secondary structure homology-based classification system for type IV secretion protein families. Moreover, we discuss the relevance of conjugative plasmid transfer in the environment and summarize novel techniques to visualize and quantify conjugative transfer in situ.

  10. Pepsin homologues in bacteria

    Directory of Open Access Journals (Sweden)

    Bateman Alex

    2009-09-01

    Full Text Available Abstract Background Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been suggested that the gene has arisen from an ancient duplication and fusion event. The only sequence similarity between the lobes is restricted to the motif around the active site aspartate and a hydrophobic-hydrophobic-Gly motif. Together, these contribute to an essential structural feature known as a psi-loop. There is one such psi-loop in each lobe, and so each lobe presents an active Asp. The human immunodeficiency virus peptidase, retropepsin, from peptidase family A2 also has a similar fold but consists of one lobe only and has to dimerize to be active. All known members of family A1 show the bilobed structure, but it is unclear if the ancestor of family A1 was similar to an A2 peptidase, or if the ancestral retropepsin was derived from a half-pepsin gene. The presence of a pepsin homologue in a prokaryote might give insights into the evolution of the pepsin family. Results Homologues of the aspartic peptidase pepsin have been found in the completed genomic sequences from seven species of bacteria. The bacterial homologues, unlike those from eukaryotes, do not possess signal peptides, and would therefore be intracellular acting at neutral pH. The bacterial homologues have Thr218 replaced by Asp, a change which in renin has been shown to confer activity at neutral pH. No pepsin homologues could be detected in any archaean genome. Conclusion The peptidase family A1 is found in some species of bacteria as well as eukaryotes. The bacterial homologues fall into two groups, one from oceanic bacteria and one from plant symbionts. The bacterial homologues are all predicted to be intracellular proteins, unlike the eukaryotic enzymes. The bacterial homologues are bilobed like pepsin, implying that if no horizontal gene transfer has occurred the duplication

  11. Synthesis and characterization of p-xylylenediaminium bis(nitrate). Effects of the coordination modes of nitrate groups on their structural and vibrational properties

    Science.gov (United States)

    Gatfaoui, S.; Issaoui, N.; Brandán, Silvia Antonia; Roisnel, T.; Marouani, H.

    2018-01-01

    The p-xylylenediaminium bis(nitrate) compound have been synthesized and then, it was characterized by using Fourier Transform infrared (FT-IR) in the solid phase and, by using the Ultraviolet-Visible (UV-Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance (1H- and 13C-NMR) spectra in aqueous solution and in dimethylsulfoxide solvent. In this work, two monodentate and bidentate coordination modes were considered for the nitrate ligands in both media in order to study the structural and vibrational properties of that salt. Hence, the natural bond orbital (NBO), atoms in molecules (AIM), Merz-Kollman (MK) charges, molecular electrostatic potentials (MEP) and frontier orbitals studies were performed for p-xylylenediaminium bis(nitrate) and their cation and anion species taking into account for the salt those two coordination modes for the nitrate ligands. The intermolecular interactions of this salt were also evaluated by Hirshfeld surface analysis. The B3LYP calculations performed by using the hybrid method and the 6-311G* and 6-311++G** basis sets generate monodentate and bidentate structures with Ci and C2 symmetries, respectively. The force fields and the force constants values for these two structures were also computed and their complete vibrational assignments were performed by using those both levels of theory. The strong band at 1536 cm-1, the bands between 2754 and 2547 cm-1 and the bands between 1779 and 1704 cm-1 support clearly the presence of the dimeric species while the IR bands at 1986/1856 cm-1 could justify the presence of the bidentate species in the solid phase.

  12. Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation.

    Science.gov (United States)

    Nagata, Ryuhei; Fujihashi, Masahiro; Sato, Takaaki; Atomi, Haruyuki; Miki, Kunio

    2015-06-09

    The TK2285 protein from Thermococcus kodakarensis was recently characterized as an enzyme catalyzing the phosphorylation of myo-inositol. Only two myo-inositol kinases have been identified so far, the TK2285 protein and Lpa3 from Zea mays, both of which belong to the ribokinase family. In either case, which of the six hydroxyl groups of myo-inositol is phosphorylated is still unknown. In addition, little is known about the myo-inositol binding mechanism of these enzymes. In this work, we determined two crystal structures: those of the TK2285 protein complexed with the substrates (ATP analogue and myo-inositol) or the reaction products formed by the enzyme. Analysis of the ternary substrates-complex structure and site-directed mutagenesis showed that five residues were involved in the interaction with myo-inositol. Structural comparison with other ribokinase family enzymes indicated that two of the five residues, Q136 and R140, are characteristic of myo-inositol kinase. The crystal structure of the ternary products-complex, which was prepared by incubating the TK2285 protein with myo-inositol and ATP, holds 1d-myo-inositol 3-phosphate (Ins(3)P) in the active site. NMR and HPLC analyses with a chiral column also indicated that the TK2285 reaction product was Ins(3)P. The results obtained here showed that the TK2285 protein specifically catalyzes the phosphorylation of the 3-OH of myo-inositol. We thus designated TK2285 as myo-inositol 3-kinase (MI3K). The precise identification of the reaction product should provide a sound basis to further explore inositol metabolism in Archaea.

  13. FR-type radio sources in COSMOS: relation of radio structure to size, accretion modes and large-scale environment

    Science.gov (United States)

    Vardoulaki, Eleni; Faustino Jimenez Andrade, Eric; Delvecchio, Ivan; Karim, Alexander; Smolčić, Vernesa; Magnelli, Benjamin; Bertoldi, Frank; Schinnener, Eva; Sargent, Mark; Finoguenov, Alexis; VLA COSMOS Team

    2018-01-01

    The radio sources associated with active galactic nuclei (AGN) can exhibit a variety of radio structures, from simple to more complex, giving rise to a variety of classification schemes. The question which still remains open, given deeper surveys revealing new populations of radio sources, is whether this plethora of radio structures can be attributed to the physical properties of the host or to the environment. Here we present an analysis on the radio structure of radio-selected AGN from the VLA-COSMOS Large Project at 3 GHz (JVLA-COSMOS; Smolčić et al.) in relation to: 1) their linear projected size, 2) the Eddington ratio, and 3) the environment their hosts lie within. We classify these as FRI (jet-like) and FRII (lobe-like) based on the FR-type classification scheme, and compare them to a sample of jet-less radio AGN in JVLA-COSMOS. We measure their linear projected sizes using a semi-automatic machine learning technique. Their Eddington ratios are calculated from X-ray data available for COSMOS. As environmental probes we take the X-ray groups (hundreds kpc) and the density fields (~Mpc-scale) in COSMOS. We find that FRII radio sources are on average larger than FRIs, which agrees with literature. But contrary to past studies, we find no dichotomy in FR objects in JVLA-COSMOS given their Eddington ratios, as on average they exhibit similar values. Furthermore our results show that the large-scale environment does not explain the observed dichotomy in lobe- and jet-like FR-type objects as both types are found on similar environments, but it does affect the shape of the radio structure introducing bents for objects closer to the centre of an X-ray group.

  14. Structural, mutational and biophysical studies reveal a canonical mode of molecular recognition between immune receptor TIGIT and nectin-2

    Energy Technology Data Exchange (ETDEWEB)

    Samanta, Dibyendu; Guo, Haisu; Rubinstein, Rotem; Ramagopal, Udupi A.; Almo, Steven C.

    2017-01-01

    In addition to antigen-specific stimulation of T cell receptor (TCR) by a peptide-MHC complex, the functional outcome of TCR engagement is regulated by antigen-independent costimulatory signals. Costimulatory signals are provided by an array of interactions involving activating and inhibitory receptors expressed on T cells and their cognate ligands on antigen presenting cells. T cell immunoglobulin and ITIM domain (TIGIT), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or poliovirus receptor (PVR), inhibits activation of T and NK cells. Here we report the crystal structure of the human TIGIT ectodomain, which exhibits the classic two-layer β-sandwich topology observed in other immunoglobulin super family (IgSF) members. Biophysical studies indicate that TIGIT is monomeric in solution but can form a dimer at high concentrations, consistent with the observation of a canonical immunoglobulin-like dimer interface in the crystalline state. Based on existing structural data, we present a model of the TIGIT:nectin-2 complex and utilized complementary biochemical studies to map the nectin-binding interface on TIGIT. Our data provide important structural and biochemical determinants responsible for the recognition of nectin-2 by TIGIT. Defining the TIGIT:nectin-2 binding interface provides the basis for rational manipulation of this molecular interaction for the development of immunotherapeutic reagents in autoimmunity and cancer.

  15. Self-centering fiber alignment structures for high-precision field installable single-mode fiber connectors

    Science.gov (United States)

    Van Erps, Jürgen; Ebraert, Evert; Gao, Fei; Vervaeke, Michael; Berghmans, Francis; Beri, Stefano; Watté, Jan; Thienpont, Hugo

    2014-05-01

    There is a steady increase in the demand for internet bandwidth, primarily driven by cloud services and high-definition video streaming. Europe's Digital Agenda states the ambitious objective that by 2020 all Europeans should have access to internet at speeds of 30Mb/s or above, with 50% or more of households subscribing to connections of 100Mb/s. Today however, internet access in Europe is mainly based on the first generation of broadband, meaning internet accessed over legacy telephone copper and TV cable networks. In recent years, Fiber-To-The-Home (FTTH) networks have been adopted as a replacement of traditional electrical connections for the `last mile' transmission of information at bandwidths over 1Gb/s. However, FTTH penetration is still very low (FTTH networks. Indeed, the success and adoption of optical access networks critically depend on the quality and reliability of connections between optical fibers. In particular a further reduction of insertion loss of field- installable connectors must be achieved without a significant increase in component cost. This requires precise alignment of fibers that can differ in terms of ellipticity, eccentricity or diameter and seems hardly achievable using today's widespread ferrule-based alignment systems. In this paper, we present a field-installable connector based on deflectable/compressible spring structures, providing a self-centering functionality for the fiber. This way, it can accommodate for possible fiber cladding diameter variations (the tolerance on the cladding diameter of G.652 fiber is typically +/-0.7μm). The mechanical properties of the cantilever are derived through an analytical approximation and a mathematical model of the spring constant, and finite element-based simulations are carried out to find the maximum first principal stress as well as the stress distribution distribution in the fiber alignment structure. Elastic constants of the order of 104N=m are found to be compatible with a proof

  16. Failure Modes

    DEFF Research Database (Denmark)

    Jakobsen, K. P.; Burcharth, H. F.; Ibsen, Lars Bo

    1999-01-01

    The present appendix contains the derivation of ten different limit state equations divided on three different failure modes. Five of the limit state equations can be used independently of the characteristics of the subsoil, whereas the remaining five can be used for either drained or undrained...

  17. Interpretation of Mutation Induction by Accelerated Very Heavy Ions in Bacteria

    International Nuclear Information System (INIS)

    Kozubek, S.; Ryznar, L.; Krasavin, E.A.

    1994-01-01

    We propose a simple approach for the calculation of the frequency of mutation induction in bacteria. The approach is based on the calculation of the fraction of energy deposited by accelerated particles in indirect hits, e.i. events in which the particle does not pass through the cell, however, the cell is hit by δ-electrons. This descriptor of the radiation field has been evaluated for different values of the particle energy and different radii of sensitive structure. Four models of the track structure have been used for calculations. The results have been compared with experimental data on mutation induction in bacteria. Two different modes of particle mutagenic action can be distinguished. Available experimental data agree reasonably well with the results of the presented theory if appropriate track structure is taken. Very good results have been obtained with the track structure models of Kudryashov, 1973 and Chatterjee and Magee, 1973. 23 refs., 6 figs., 1 tab

  18. Structure of Bacillus subtilis γ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

    Energy Technology Data Exchange (ETDEWEB)

    Ida, Tomoyo [Osaka University, Toyonaka, Osaka 560-0043 (Japan); Suzuki, Hideyuki [Kyoto Institute of Technology, Goshokaido-cho, Matsugasaki, Sakyo-ku, Kyoto 606-8585 (Japan); Fukuyama, Keiichi [Osaka University, Toyonaka, Osaka 560-0043 (Japan); Hiratake, Jun [Kyoto University, Uji, Kyoto 611-0011 (Japan); Wada, Kei, E-mail: keiwada@med.miyazaki-u.ac.jp [University of Miyazaki, Miyazaki 889-1692 (Japan); Osaka University, Toyonaka, Osaka 560-0043 (Japan)

    2014-02-01

    The binding modes of acivicin, a classical and an electrophilic active-site-directed glutamate analogue, to bacterial γ-glutamyltranspeptidases were found to be diverse. γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp{sup 2} hybridization to Thr403 O{sup γ}, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.

  19. Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.

    Science.gov (United States)

    Gristick, Harry B; von Boehmer, Lotta; West, Anthony P; Schamber, Michael; Gazumyan, Anna; Golijanin, Jovana; Seaman, Michael S; Fätkenheuer, Gerd; Klein, Florian; Nussenzweig, Michel C; Bjorkman, Pamela J

    2016-10-01

    HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-Å- and 3.9-Å-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46-derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs.

  20. Structure of Calmodulin Bound to a Calcineurin Peptide: A New Way of Making an Old Binding Mode

    International Nuclear Information System (INIS)

    Ye, Q.; Li, X.; Wong, A.; Wei, Q.; Jia, Z.

    2006-01-01

    Calcineurin is a calmodulin-binding protein in brain and the only serine/threonine protein phosphatase under the control of Ca 2+ /calmodulin (CaM), which plays a critical role in coupling Ca 2+ signals to cellular responses. CaM up-regulates the phosphatase activity of calcineurin by binding to the CaM-binding domain (CBD) of calcineurin subunit A. Here, we report crystal structural studies of CaM bound to a CBD peptide. The chimeric protein containing CaM and the CBD peptide forms an intimate homodimer, in which CaM displays a native-like extended conformation and the CBD peptide shows -helical structure. Unexpectedly, the N-terminal lobe from one CaM and the C-terminal lobe from the second molecule form a combined binding site to trap the peptide. Thus, the dimer provides two binding sites, each of which is reminiscent of the fully collapsed conformation of CaM commonly observed in complex with, for example, the myosin light chain kinase (MLCK) peptide. The interaction between the peptide and CaM is highly specific and similar to MLCK

  1. Effect of Different Connection Modes on Bolt Structural Properties of TC4 Alloy in Selective Laser Melting

    Science.gov (United States)

    Li, Xiaodan; Huang, Shuangjun; Xu, Liang; Hui, Li; Zhou, Song

    2017-12-01

    The bolt structural properties of selective laser melted (SLM) samples produced from TC4 powder metal has been investigated. Two different connection molds relative to single lap joint and bilateral lap joint as well as two different state of surface quality were considered. Samples and test procedures were designed in accordance with HB 5143 and HB 5287 standard. The results show that there is a strong influence of connection molds on the dynamic behavior of SLM produced TC4. The mechanical properties of bilateral lap joint are better than those of the single lap joint. Meanwhile the fatigue performance of the bilateral lap joint is much stronger than that of the single lap joint which it is a symmetrical structure of the two-shear test on both sides of the force evenly, while the single lap joint is a single shear sample of the uneven force. There are two kinds of fracture form most of which are broken in the first row of screw and a small part in the middle of the connecting plate.

  2. Purification Techniques of Bacteriocins from Lactic Acid Bacteria and Other Gram-Positive Bacteria

    Science.gov (United States)

    Saavedra, Lucila; Sesma, Fernando

    The search for new antimicrobial peptides produced by lactic acid ­bacteria and other Gram-positive microorganisms has become an interesting field of research in the past decades. The fact that bacteriocins are active against numerous foodborne and human pathogens, are produced by generally regarded as safe (GRAS) microorganisms, and are readily degraded by proteolytic host systems makes them attractive candidates for biotechnological applications. However, before suggesting or choosing a new bacteriocin for future technology developments, it is necessary to elucidate its biochemical structure and its mode of action, which may be carried out once the bacteriocin is purified to homogeneity. This chapter focuses on describing the main strategies used for the purification of numerous bacteriocins.

  3. Molecular dynamics simulation and x-ray structural studies of mode-coupling in monoclinic K2ZnBr4

    International Nuclear Information System (INIS)

    Machida, Mitsuo; Itoh, Hideaki; Koyano, Nobumitsu

    2003-01-01

    The mode-coupling between the rotational and translational motions in the monoclinic K 2 ZnBr 4 was studied by the molecular dynamics simulation and X-ray structure analysis. In the structure analysis, the Fourier analysis indicates that, in the paraelectric phase, electron densities of the bromines Br1 and Br2 on the mirror plane are fairly elongated in the b direction, while the density of the bromine Br3 at the general position spreads more or less in the a direction. In the ferroelectric phase, the elongation is suppressed in particular for Br1 and Br2, and the densities of Br3 and Br4, which are equivalent each other in the paraelectric phase, are nearly isotropic. In addition, Br1 and Br2 displace in the b direction through the rotation of the ZnBr 4 2- ion about the a axis. In the simulation, the ZnBr 4 2- ions are treated as rigid-bodies. The trajectories of the bromines reproduce satisfactorily the characteristic feature of the Fourier maps. This means that the ZnBr 4 2- ions are approximately regarded as rigid-bodies even in the real K 2 ZnBr 4 . The mode-coupling analysis shows that, in the ZnBr 4 2- rigid-bodies, the rotational motion about the a axis and the translational motion in the b direction couple strongly. Moreover, the displacements of rotational and translational motions in the b direction are almost synchronous for Br1 and Br2, and almost asynchronous for Br3 and Br4. (author)

  4. Synthesis, structural, magnetic and phase-transition studies of the ferromagnetic La2CoMnO6 double perovskite by symmetry-adapted modes.

    Science.gov (United States)

    Orayech, B; Urcelay-Olabarria, I; López, G A; Fabelo, O; Faik, A; Igartua, J M

    2015-08-21

    A powdered La2CoMnO6 double perovskite was synthesized by the solid-state reaction method, and its crystal structure was investigated by (mode-crystallography) Rietveld analysis using X-ray and neutron powder diffraction data. La2CoMnO6 material is a monoclinic perovskite at room temperature, adopting the space group P21/n (a(-)a(-)b(+)), , c ≈ 2ap and Z = 2. The P21/n phase can be described effectively by three distortion modes (GM4(+), X3(+), X5(+)) of the Fm3[combining macron]m (a(0)a(0)a(0)) parent phase. The comparative study of the material and those in the Ln2CoMnO6 and Ln2NiMnO6 families has shown a general trend in nearly all the materials, has served to select a common direction in the sub-space spanned by X5(+), tri-linearly coupled to the order parameters of the cubic to monoclinic first order phase transition. This direction has been used to parametrize the refinements and to perform reliable refinements in the high-temperature intermediate distorted trigonal phase, R3[combining macron] (a(-)a(-)a(-)), for which only one effectively acting irrep has been deduced: GM5(+), physically a tilt of the oxygen sharing octahedra of Co and Mn. Its temperature evolution up to the prototype cubic phase has been fitted in the framework of the Landau Theory of Phase Transitions, showing a behavior typical of a tricritical point. The low-temperature neutron powder diffraction data have served to solve the magnetic structure: three indistinguishable ferromagnetic models with the space groups P21/n and P2/n' are proposed.

  5. The effect of cobalt substitution in crystal structure and vibrational modes of CuFe{sub 2}O{sub 4} powders obtained by polymeric precursor method

    Energy Technology Data Exchange (ETDEWEB)

    Silva, M.D.P.; Silva, F.C. [Departamento de Química, CCET, Universidade Federal do Maranhão, 65085-580 São Luís, MA (Brazil); Sinfrônio, F.S.M. [Departamento de Engenharia Elétrica, CCET, Universidade Federal do Maranhão, 65085-580 São Luís, MA (Brazil); Paschoal, A.R. [Departamento de Física, Universidade Federal do Ceará, Campus do Pici, 60455-760 Fortaleza, CE (Brazil); Silva, E.N. [Departamento de Física, CCET, Universidade Federal do Maranhão, 65085-580 São Luís, MA (Brazil); Paschoal, C.W.A., E-mail: paschoal@ufma.br [Departamento de Física, CCET, Universidade Federal do Maranhão, 65085-580 São Luís, MA (Brazil); Department of Materials Science and Engineering, University of California Berkeley, 94720-1760 Berkeley, CA (United States); Department of Physics, University of California Berkeley, 94720-7300 Berkeley, CA (United States)

    2014-01-25

    Highlights: • We synthesized mixed spinels by polymeric precursor method. • We investigated the structural and vibrational properties of the mixed. • We investigated the synthesis condition effects in these properties. • We proposed a complete phonon description for CuFe{sub 2}O{sub 4} and CoFe{sub 2}O{sub 4} spinels. -- Abstract: In this work Co–Cu mixed spinel Co{sub 1−x}Cu{sub x}Fe{sub 2}O{sub 4} powders were obtained by polymeric precursors method at several annealing temperatures between 700 and 1200 °C. The samples were characterized by means of X-ray powder diffraction, confirming the ideal inverse spinel structure for CoFe{sub 2}O{sub 4} sample and the tetragonal distorted inverse spinel structure for CuFe{sub 2}O{sub 4} sample. Based on FWHM evaluation, we estimated that crystallite sizes varies between 27 and 37 nm for the non-substituted samples. The optical-active modes were determined by infrared and Raman spectroscopies. The phonon spectra showed a local tetragonal distortion for mixed samples.

  6. Differences in individual empowerment outcomes of socially disadvantaged women: effects of mode of participation and structural changes in a physical activity promotion program.

    Science.gov (United States)

    Röger, Ulrike; Rütten, Alfred; Frahsa, Annika; Abu-Omar, Karim; Morgan, Antony

    2011-10-01

    This study explored the differences in individual empowerment outcomes of a group of socially disadvantaged women participating in physical activity promotion. The outcomes observed were assessed in the context of the women's mode of participation and the structural organizational and community level changes, which took place during the implementation of the program. Fifteen semi-structured qualitative interviews were conducted and analyzed using qualitative content analysis. Two groups of women participated in the interviews--those involved in the whole process of planning, implementation and evaluation of the program and those who took part in the program activities. Individual empowerment outcomes were achieved for all those interviewed, although those participating in the planning, implementation and evaluation of the program achieved the greatest. A number of organizational and community level processes were also identified that supported the individual empowerment of those taking part. This study supports the use of multilevel empowerment approaches to health as they help to identify the ideal characteristics that organizations and communities should possess and the potential structural changes required to support individual empowerment.

  7. The Default Mode Network is functionally and structurally disrupted in amnestic mild cognitive impairment — A bimodal MEG–DTI study

    Directory of Open Access Journals (Sweden)

    Pilar Garcés

    2014-01-01

    Full Text Available Over the past years, several studies on Mild Cognitive Impairment (MCI and Alzheimer's disease (AD have reported Default Mode Network (DMN deficits. This network is attracting increasing interest in the AD community, as it seems to play an important role in cognitive functioning and in beta amyloid deposition. Attention has been particularly drawn to how different DMN regions are connected using functional or structural connectivity. To this end, most studies have used functional Magnetic Resonance Imaging (fMRI, Positron Emission Tomography (PET or Diffusion Tensor Imaging (DTI. In this study we evaluated (1 functional connectivity from resting state magnetoencephalography (MEG and (2 structural connectivity from DTI in 26 MCI patients and 31 age-matched controls. Compared to controls, the DMN in the MCI group was functionally disrupted in the alpha band, while no differences were found for delta, theta, beta and gamma frequency bands. In addition, structural disconnection could be assessed through a decreased fractional anisotropy along tracts connecting different DMN regions. This suggests that the DMN functional and anatomical disconnection could represent a core feature of MCI.

  8. The influence of physical and technological magnetron sputtering modes on the structure and optical properties of CdS and CdTe films

    Directory of Open Access Journals (Sweden)

    G.S. Khrypunov

    2017-07-01

    Full Text Available To create technology for preparation of CdS and CdTe thin films by direct current magnetron sputtering, the influence of physical and technological condensation modes on the crystal structure and optical properties of these films were investigated. The laboratory method of DC magnetron sputtering with preheating of the target for the mentioned films on glass substrates was developed. We obtained the CdS layers with hexagonal structure 150…200 nm thick under conditions when the plasma discharge current density was 1.1 mA/cm2 and the deposition rate – 30…40 nm/min. The bandgap in the obtained CdS films is Eg = 2.38…2.41 eV. After annealing in vacuum, the optical transparence of CdS films reaches 80…90%, which allows to use these films as a transparent window layer in solar cells based on heterojunctions of CdS/CdTe. When the plasma discharge current density is 2.2…5.4 mA/cm2 and the deposition rate is 200 nm/min, we obtained CdTe layers with hexagonal structure up to 5 µm thick. The transmittance of CdTe films with hexagonal structure in the wavelength range of the visible spectrum is up to 5%, and in the infrared spectral range is about 60%. The bandgap in the obtained CdTe layers of different thickness is 1.52…1.54 eV. After chloride treatment as a result of the phase transition wurtzite–sphalerite, the investigated CdTe films contain only the stable cubic structure and can be used as a base layer of solar cells.

  9. Q-mode curve resolution of UV-vis spectra for structural transformation studies of anthocyanins in acidic solutions

    Energy Technology Data Exchange (ETDEWEB)

    Marco, Paulo Henrique [Laboratorio de Quimiometria em Ciencias Naturais, Departamento de Quimica, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-970 Londrina, Parana (Brazil); Scarminio, Ieda Spacino [Laboratorio de Quimiometria em Ciencias Naturais, Departamento de Quimica, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-970 Londrina, Parana (Brazil)]. E-mail: ieda@qui.uel.br

    2007-01-30

    Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH{sup +}), the pseudobase or carbinol pseudobase (B), cis-chalcone (C{sub C}), trans-chalcone (C{sub t}), and ionized cis-chalcone (C{sub C}{sup -}). Four equilibrium constant values were calculated using relative concentrations, hydration, pK{sub h}=2.60+/-0.01, tautomeric, K{sub T}=0.14+/-0.01, acid-base, pK{sub a}=4.24+/-0.04, and ionization of the cis-chalcone, pK{sub C{sub C}}=8.74+/-1.5x10{sup -2}. The calculated protonation rate of the tautomers is K{sub H{sup +}}=0.08+/-7.6x10{sup -3}. These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature.

  10. Q-mode curve resolution of UV-vis spectra for structural transformation studies of anthocyanins in acidic solutions

    International Nuclear Information System (INIS)

    Marco, Paulo Henrique; Scarminio, Ieda Spacino

    2007-01-01

    Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH + ), the pseudobase or carbinol pseudobase (B), cis-chalcone (C C ), trans-chalcone (C t ), and ionized cis-chalcone (C C - ). Four equilibrium constant values were calculated using relative concentrations, hydration, pK h =2.60+/-0.01, tautomeric, K T =0.14+/-0.01, acid-base, pK a =4.24+/-0.04, and ionization of the cis-chalcone, pK C C =8.74+/-1.5x10 -2 . The calculated protonation rate of the tautomers is K H + =0.08+/-7.6x10 -3 . These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature

  11. The evolution of angiosperm lianescence without vessels--climbing mode and wood structure-function in Tasmannia cordata (Winteraceae).

    Science.gov (United States)

    Feild, Taylor S; Chatelet, David S; Balun, Lawong; Schilling, Edward E; Evans, Robert

    2012-01-01

    • The lack of extant lianescent vessel-less seed plants supports a hypothesis that liana evolution requires large-diameter xylem conduits. Here, we demonstrate an unusual example of a lianoid vessel-less angiosperm, Tasmannia cordata (Winteraceae), from New Guinea. • Wood mechanical, hydraulic and structural measurements were used to determine how T. cordata climbs and to test for ecophysiological shifts related to liana evolution vs 13 free-standing congeners. • The tracheid-based wood of T. cordata furnished low hydraulic capacity compared with that of vessel-bearing lianas. In comparison with most nonclimbing relatives, T. cordata possessed lower photosynthetic rates and leaf and stem hydraulic capacities. However, T. cordata exhibited a two- to five-fold greater wood elastic modulus than its relatives. • Tasmannia cordata provides an unusual example of angiosperm liana evolution uncoupled from xylem conduit gigantism, as well as high plasticity and cell type diversity in vascular development. Because T. cordata lacks vessels, our results suggest that a key limitation for a vessel-less liana is that strong and low hydraulically conductive wood is required to meet the mechanical demands of lianescence. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

  12. The mode of inhibitor binding to peptidyl-tRNA hydrolase: binding studies and structure determination of unbound and bound peptidyl-tRNA hydrolase from Acinetobacter baumannii.

    Science.gov (United States)

    Kaushik, Sanket; Singh, Nagendra; Yamini, Shavait; Singh, Avinash; Sinha, Mau; Arora, Ashish; Kaur, Punit; Sharma, Sujata; Singh, Tej P

    2013-01-01

    The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design.

  13. The mode of inhibitor binding to peptidyl-tRNA hydrolase: binding studies and structure determination of unbound and bound peptidyl-tRNA hydrolase from Acinetobacter baumannii.

    Directory of Open Access Journals (Sweden)

    Sanket Kaushik

    Full Text Available The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design.

  14. Hierarchical super-structure identified by polarized light microscopy, electron microscopy and nanoindentation: Implications for the limits of biological control over the growth mode of abalone sea shells

    Directory of Open Access Journals (Sweden)

    Schneider Andreas S

    2012-09-01

    American Chemical Society 2008, 130:17519–17527]. Polarized optical microscopy revealed unprecedented super-structures in the calcitic shell part. This bears, in principle, the potential for in vivo studies, which might be useful for investigating the growth modes of nacre and other shell types.

  15. Accurate mode characterization of two-mode optical fibers by in-fiber acousto-optics.

    Science.gov (United States)

    Alcusa-Sáez, E; Díez, A; Andrés, M V

    2016-03-07

    Acousto-optic interaction in optical fibers is exploited for the accurate and broadband characterization of two-mode optical fibers. Coupling between LP 01 and LP 1m modes is produced in a broadband wavelength range. Difference in effective indices, group indices, and chromatic dispersions between the guided modes, are obtained from experimental measurements. Additionally, we show that the technique is suitable to investigate the fine modes structure of LP modes, and some other intriguing features related with modes' cut-off.

  16. The proteolytic systems of lactic acid bacteria

    NARCIS (Netherlands)

    Kunji, Edmund R.S.; Mierau, Igor; Hagting, Anja; Poolman, Bert; Konings, Wil N.

    1996-01-01

    Proteolysis in dairy lactic acid bacteria has been studied in great detail by genetic, biochemical and ultrastructural methods. From these studies the picture emerges that the proteolytic systems of lactococci and lactobacilli are remarkably similar in their components and mode of action. The

  17. Structure, antimicrobial activities and mode of interaction with membranes of novel [corrected] phylloseptins from the painted-belly leaf frog, Phyllomedusa sauvagii.

    Directory of Open Access Journals (Sweden)

    Zahid Raja

    Full Text Available Transcriptomic and peptidomic analysis of skin secretions from the Painted-belly leaf frog Phyllomedusa sauvagii led to the identification of 5 novel phylloseptins (PLS-S2 to -S6 and also of phylloseptin-1 (PSN-1, here renamed PLS-S1, the only member of this family previously isolated in this frog. Synthesis and characterization of these phylloseptins revealed differences in their antimicrobial activities. PLS-S1, -S2, and -S4 (79-95% amino acid sequence identity; net charge  = +2 were highly potent and cidal against Gram-positive bacteria, including multidrug resistant S. aureus strains, and killed the promastigote stage of Leishmania infantum, L. braziliensis and L. major. By contrast, PLS-S3 (95% amino acid identity with PLS-S2; net charge  = +1 and -S5 (net charge  = +2 were found to be almost inactive against bacteria and protozoa. PLS-S6 was not studied as this peptide was closely related to PLS-S1. Differential scanning calorimetry on anionic and zwitterionic multilamellar vesicles combined with circular dichroism spectroscopy and membrane permeabilization assays on bacterial cells indicated that PLS-S1, -S2, and -S4 are structured in an amphipathic α-helix that disrupts the acyl chain packing of anionic lipid bilayers. As a result, regions of two coexisting phases could be formed, one phase rich in peptide and the other lipid-rich. After reaching a threshold peptide concentration, the disruption of lipid packing within the bilayer may lead to local cracks and disintegration of the microbial membrane. Differences in the net charge, α-helical folding propensity, and/or degree of amphipathicity between PLS-S1, -S2 and -S4, and between PLS-S3 and -S5 appear to be responsible for their marked differences in their antimicrobial activities. In addition to the detailed characterization of novel phylloseptins from P. sauvagii, our study provides additional data on the previously isolated PLS-S1 and on the mechanism of action of

  18. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

    Energy Technology Data Exchange (ETDEWEB)

    Stanek, Kimberly A.; Patterson-West, Jennifer; Randolph, Peter S.; Mura, Cameron

    2017-03-31

    The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophileAquifex aeolicus(Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore,AaeHfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6RNA reveals that the outer rim of theAaeHfq hexamer features a well defined binding pocket that is selective for uracil. ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

  19. Bleach vs. Bacteria

    Science.gov (United States)

    ... Articles | Inside Life Science Home Page Bleach vs. Bacteria By Sharon Reynolds Posted April 2, 2014 Your ... hypochlorous acid to help kill invading microbes, including bacteria. Researchers funded by the National Institutes of Health ...

  20. Effect of Cr-N codoping on structural phase transition, Raman modes, and optical properties of TiO2 nanoparticles

    Science.gov (United States)

    Hassnain Jaffari, G.; Tahir, Adnan; Ali, Naveed Zafar; Ali, Awais; Qurashi, Umar S.

    2018-04-01

    Noncompensated cation-anion codoping in TiO2 nanoparticles has been achieved by a chemical synthesis route. Significant reduction in the optical bandgap and enhancement in the absorption of visible light have been observed. Structural phase transformation has been tracked in detail as a function of doping and heat treatment temperature. Anatase to rutile phase transition temperature for doped samples was higher in comparison to the pure TiO2 nanoparticles. Nitrogen and chromium addition increases the phase transformation barrier, where the effect of the former dopant is of more significance. The Raman results showed an increase in the oxygen content with higher post annealing temperatures. With Cr incorporation, the peak associated with the Eg mode has been found to shift towards a higher wave number, while with nitrogen incorporation, the shift was towards a lower wave number. A decrease in reflectance with N co-doping for all samples, irrespective of phase and annealing temperatures, has been observed. In compositions with nitrogen of the same content, bandgap reduction was higher in the rutile phase in comparison to the anatase phase. In general, overall results revealed that with a higher loading fraction of ammonia, the N content increases, while Cr addition prevents nitrogen loss even up to high post annealing temperatures, i.e., 850 °C.

  1. New insights into the structure and mode of action of Mo-CBP3, an antifungal chitin-binding protein of Moringa oleifera seeds.

    Directory of Open Access Journals (Sweden)

    Adelina B Batista

    Full Text Available Mo-CBP3 is a chitin-binding protein purified from Moringa oleifera Lam. seeds that displays inhibitory activity against phytopathogenic fungi. This study investigated the structural properties and the antifungal mode of action of this protein. To this end, circular dichroism spectroscopy, antifungal assays, measurements of the production of reactive oxygen species and microscopic analyses were utilized. Mo-CBP3 is composed of 30.3% α-helices, 16.3% β-sheets, 22.3% turns and 30.4% unordered forms. The Mo-CBP3 structure is highly stable and retains its antifungal activity regardless of temperature and pH. Fusarium solani was used as a model organism for studying the mechanisms by which this protein acts as an antifungal agent. Mo-CBP3 significantly inhibited spore germination and mycelial growth at 0.05 mg.mL-1. Mo-CBP3 has both fungistatic and fungicidal effects, depending on the concentration used. Binding of Mo-CBP3 to the fungal cell surface is achieved, at least in part, via electrostatic interactions, as salt was able to reduce its inhibitory effect. Mo-CBP3 induced the production of ROS and caused disorganization of both the cytoplasm and the plasma membrane in F. solani cells. Based on its high stability and specific toxicity, with broad-spectrum efficacy against important phytopathogenic fungi at low inhibitory concentrations but not to human cells, Mo-CBP3 has great potential for the development of new antifungal drugs or transgenic crops with enhanced resistance to phytopathogens.

  2. Crystal structures and high-temperature phase-transitions in SrNdMRuO{sub 6} (M=Zn,Co,Mg,Ni) new double perovskites studied by symmetry-mode analysis

    Energy Technology Data Exchange (ETDEWEB)

    Iturbe-Zabalo, E., E-mail: iturbe@ill.fr [Institut Laue-Langevin (ILL), 6 rue Jules Horowitz, BP156, 38042 Grenoble Cedex 9 (France); Fisika Aplikatua II Saila, Zientzia eta Teknologia Fakultatea, UPV/EHU, P.O. Box 644, 48080 Bilbao (Spain); Igartua, J.M. [Fisika Aplikatua II Saila, Zientzia eta Teknologia Fakultatea, UPV/EHU, P.O. Box 644, 48080 Bilbao (Spain); Faik, A. [CICEnergigune, Parque Tecnologico, Albert Einstein 48, 01510 Minano, Alava (Spain); Larranaga, A. [X-Izpien Zerbitzu Orokorra, SGIKer, UPV/EHU, P.O. Box 644, 48080 Bilbao (Spain); Hoelzel, M. [Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM II), TUM, 85747 Garching (Germany); Cuello, G.J. [Institut Laue-Langevin (ILL), 6 rue Jules Horowitz, BP156, 38042 Grenoble Cedex 9 (France)

    2013-02-15

    Crystal structures of SrNdZnRuO{sub 6}, SrNdCoRuO{sub 6}, SrNdMgRuO{sub 6} and SrNdNiRuO{sub 6} double perovskites have been studied by X-ray, synchrotron radiation and neutron powder diffraction method, at different temperatures, and using the symmetry-mode analysis. All compounds adopt the monoclinic space group P2{sub 1}/n at room-temperature, and contain a completely ordered array of the tilted MO{sub 6} and RuO{sub 6} octahedra, whereas Sr/Nd cations are completely disordered. The analysis of the structures in terms of symmetry-adapted modes of the parent phase allows the identification of the modes responsible for the phase-transition. The high-temperature study (300-1250 K) has shown that the compounds present a temperature induced structural phase-transition: P2{sub 1}/n{yields}P4{sub 2}/n{yields}Fm3{sup Macron }m. - Graphical abstract: Representation of the dominant distortion modes of the symmetry mode decomposition of the room-temperature (P2{sub 1}/n), intermediate (P4{sub 2}/n) and cubic (Fm-3m) phase SrNdMRuO{sub 6} (M=Zn,Co,Mg,Ni), with respect to the parent phase Fm-3m. The dominant distortion modes are: in the monoclinic phase-GM{sub 4}{sup +} (blue arrow), X{sub 3}{sup +} (green arrow) and X{sub 5}{sup +} acting on A-site cations (red arrow); in the tetragonal phase-GM{sub 4}{sup +} (pink arrow), X{sub 3}{sup +} (light blue arrow) and X{sub 5}{sup +} acting on A-site cations (brown arrow). Highlights: Black-Right-Pointing-Pointer Structural study of four ruthenate double perovskites. Black-Right-Pointing-Pointer Room-temperature structural determination using symmetry-mode procedure. Black-Right-Pointing-Pointer Determination of temperature induced structural phase-transitions. Black-Right-Pointing-Pointer Symmetry adapted-mode analysis.

  3. Ballooning modes or Fourier modes in a toroidal plasma?

    International Nuclear Information System (INIS)

    Connor, J.W.; Taylor, J.B.

    1987-01-01

    The relationship between two different descriptions of eigenmodes in a torus is investigated. In one the eigenmodes are similar to Fourier modes in a cylinder and are highly localized near a particular rational surface. In the other they are the so-called ballooning modes that extend over many rational surfaces. Using a model that represents both drift waves and resistive interchanges the transition from one of these structures to the other is investigated. In this simplified model the transition depends on a single parameter which embodies the competition between toroidal coupling of Fourier modes (which enhances ballooning) and variation in frequency of Fourier modes from one rational surface to another (which diminishes ballooning). As the coupling is increased each Fourier mode acquires a sideband on an adjacent rational surface and these sidebands then expand across the radius to form the extended mode described by the conventional ballooning mode approximation. This analysis shows that the ballooning approximation is appropriate for drift waves in a tokamak but not for resistive interchanges in a pinch. In the latter the conventional ballooning effect is negligible but they may nevertheless show a ballooning feature. This is localized near the same rational surface as the primary Fourier mode and so does not lead to a radially extended structure

  4. [Chitinolytic activity of bacteria].

    Science.gov (United States)

    Saks, Elzbieta; Jankiewicz, Urszula

    2010-01-01

    Chitinolytic bacteria play an important role in degradation of chitin, one of the most abundant biopolymers in nature. These microorganisms synthesize specific enzymes, that catalyze hydrolysis of beta-1,4-glycosidic bonds in low-digestible chitin polymers, turning it into low-molecular, easy to digest compounds. During last decades many bacterial chitinolytic enzymes have been studied and characterized, mainly for their potential applications in agriculture, industry and medicine. Several chitinase classifications have been proposed, either on the base of substrate specificity or amino acid sequence similarities. X-ray crystallography and NMR spectroscopy techniques enabled the determination of three dimensional structure of some chitinases, what was helpful in explaining their catalytic mechanism. Development of biotechnology and molecular biology enables a deep research in regulation and cloning of bacterial chitinase genes.

  5. Potential role of bacteria packaging by protozoa in the persistence and transmission of pathogenic bacteria

    Directory of Open Access Journals (Sweden)

    Alix M Denoncourt

    2014-05-01

    Full Text Available Many pathogenic bacteria live in close association with protozoa. These unicellular eukaryotic microorganisms are ubiquitous in various environments. A number of protozoa such as amoebae and ciliates ingest pathogenic bacteria, package them usually in membrane structures, and then release them into the environment. Packaged bacteria are more resistant to various stresses and are more apt to survive than free bacteria. New evidence indicates that protozoa and not bacteria control the packaging process. It is possible that packaging is more common than suspected and may play a major role in the persistence and transmission of pathogenic bacteria. To confirm the role of packaging in the propagation of infections, it is vital that the molecular mechanisms governing the packaging of bacteria by protozoa be identified as well as elements related to the ecology of this process in order to determine whether packaging acts as a Trojan Horse.

  6. Plant n-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan

    Science.gov (United States)

    Huang, Tung-Yi; Hsu, Bing-Mu; Chao, Wei-Chun; Fan, Cheng-Wei

    2018-03-01

    n-Alkane and alkane-degrading bacteria have long been used as crucial biological indicators of paleoecology, petroleum pollution, and oil and gas prospecting. However, the relationship between n-alkane and alkane-degrading bacteria in natural forests is still poorly understood. In this study, long-chain n-alkane (C14-C35) concentrations in litterfall, litter layer, and topsoil as well as the diversity and abundance of n-alkane-degrading bacterial communities in litter layers were investigated in three habitats across a lowland subtropical rainforest in southern Taiwan: ravine, windward, and leeward habitats in Nanjenshan. Our results demonstrate that the litterfall yield and productivity of long-chain n-alkane were highest in the ravine habitats. However, long-chain n-alkane concentrations in all habitats were decreased drastically to a similar low level from the litterfall to the bulk soil, suggesting a higher rate of long-chain n-alkane degradation in the ravine habitat. Operational taxonomic unit (OTU) analysis using next-generation sequencing data revealed that the relative abundances of microbial communities in the windward and leeward habitats were similar and different from that in the ravine habitat. Data mining of community amplicon sequencing using the NCBI database revealed that alkB-gene-associated bacteria (95 % DNA sequence similarity to alkB-containing bacteria) were most abundant in the ravine habitat. Empirical testing of litter layer samples using semi-quantitative polymerase chain reaction for determining alkB gene levels confirmed that the ravine habitat had higher alkB gene levels than the windward and leeward habitats. Heat map analysis revealed parallels in pattern color between the plant and microbial species compositions of the habitats, suggesting a causal relationship between the plant n-alkane production and microbial community diversity. This finding indicates that the diversity and relative abundance of microbial communities in the

  7. Antibacterial and Antioxidant Activity of Essential Oil Terpenes against Pathogenic and Spoilage-Forming Bacteria and Cell Structure-Activity Relationships Evaluated by SEM Microscopy

    Directory of Open Access Journals (Sweden)

    Hatice Zengin

    2014-11-01

    Full Text Available The antibacterial activity and antioxidant effect of the compounds α-terpineol, linalool, eucalyptol and α-pinene obtained from essential oils (EOs, against pathogenic and spoilage forming bacteria were determined. The antibacterial activities of these compounds were observed in vitro on four Gram-negative and three Gram-positive strains. S. putrefaciens was the most resistant bacteria to all tested components, with MIC values of 2% or higher, whereas E. coli O157:H7 was the most sensitive strain among the tested bacteria. Eucalyptol extended the lag phase of S. Typhimurium, E. coli O157:H7 and S. aureus at the concentrations of 0.7%, 0.6% and 1%, respectively. In vitro cell growth experiments showed the tested compounds had toxic effects on all bacterial species with different level of potency. Synergistic and additive effects were observed at least one dose pair of combination against S. Typhimurium, E. coli O157:H7 and S. aureus, however antagonistic effects were not found in these combinations. The results of this first study are encouraging for further investigations on mechanisms of antimicrobial activity of these EO components.

  8. [Teichoic acids from lactic acid bacteria].

    Science.gov (United States)

    Livins'ka, O P; Harmasheva, I L; Kovalenko, N K

    2012-01-01

    The current view of the structural diversity of teichoic acids and their involvement in the biological activity of lactobacilli has been reviewed. The mechanisms of effects of probiotic lactic acid bacteria, in particular adhesive and immunostimulating functions have been described. The prospects of the use of structure data of teichoic acid in the assessment of intraspecific diversity of lactic acid bacteria have been also reflected.

  9. Measurement of magnetic turbulence structure and nonlinear mode coupling of tearing fluctuations in the Madison Symmetric Torus reversed field pinch edge

    International Nuclear Information System (INIS)

    Assadi, S.

    1994-01-01

    Linear and nonlinear magnetohydrodynamic (MHD) stability of current-driven modes are studied in the MST reversed field pinch. Measured low frequency (f < 35 kHz) magnetic fluctuations are consistent with the global resistive tearing instabilities predicted by 3-D MHD simulations. At frequencies above 35 kHz, the magnetic fluctuations were detected to be localized and externally resonant. Discrete dynamo events, ''sawtooth oscillations,'' have been observed in the experimental RFP plasmas. This phenomenon causes the plasma to become unstable to m = 1 tearing modes. The modes that may be important in different phases of these oscillations are identified. These results then assist in nonlinear studies and also help to interpret the spectral broadening of the measured data during a discrete dynamo event. Three-wave nonlinear coupling of spectral Fourier modes is measured in the MST by applying bispectral analysis to magnetic fluctuations measured at the plasma edge at 64 toroidal locations and 16 poloidal locations, permitting observation of coupling over 8 poloidal and 32 toroidal modes. Comparison to bispectra predicted by resistive MHD computation indicates reasonably good agreement. However, during the crash phase of the sawtooth oscillation the nonlinear coupling is strongly enhanced, concomitant with a broadened k-spectrum. During the sawtooth formation the plasma is undergoing a pure diffusive process. The dynamo only occurs during the sawtooth crash. High frequency activity prior to a sawtooth crash is caused by nonlinear frequency (small-scale) mode coupling. Growth rate and coupling coefficients of toroidal mode spectra are calculated by statistical modeling. Temporal evolution of edge toroidal mode spectra has been predicted by transfer function analysis. The driving sources of electrostatic fields are different than for the magnetic fields. The characteristics of tearing modes can be altered by external field errors and addition of impurities to the plasma

  10. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

    DEFF Research Database (Denmark)

    Priemé, Anders; Wolsing, Martin

    2004-01-01

    Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...

  11. ef1097 and ypkK encode enterococcin V583 and corynicin JK, members of a new family of antimicrobial proteins (bacteriocins) with modular structure from Gram-positive bacteria.

    Science.gov (United States)

    Swe, Pearl M; Heng, Nicholas C K; Ting, Yi-Tian; Baird, Hayley J; Carne, Alan; Tauch, Andreas; Tagg, John R; Jack, Ralph W

    2007-10-01

    Unlike the colicins, microcins and related peptide antibiotics, little is known about antibiotic proteins (M(r)>10,000) from Gram-positive bacteria, since only few examples have been described to date. In this study we used heterologous expression of recombinant proteins to access the 17 kDa antibiotic protein SA-M57 from Streptococcus pyogenes, along with two proteins of unknown function identified in publicly available databases: EF1097 from Enterococcus faecalis and YpkK from Corynebacterium jeikeium. Here we show that all three are antibiotic proteins with different spectra of antimicrobial activity that kill sensitive bacteria at nanomolar concentrations. In silico structure predictions indicate that although the three proteins share little sequence similarity, they may be composed of conserved secondary structural elements: a relatively unstructured, acidic N-terminal portion and a basic C-terminal portion characterized by two helical elements separated by a loop structure and stabilized by an essential disulphide. Expression of individual segments as well as protein chimaeras revealed that, at least in the case of YpkK, the C-terminal portion is responsible for the killing action of the protein, whereas the role of the N-terminal portion remains unclear. Both scnM57 and ef1097 appear to be widely distributed in Strep. pyogenes and Ent. faecalis (respectively), whereas ypkK is found only rarely amongst clinical isolates of C. jeikeium. Finally, we determined that the proteins kill sensitive bacteria without lysis, a feature that distinguishes them from known murolytic proteins.

  12. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Corona, Angela; Steinmann, Casper

    2018-01-01

    with innovative mechanisms. The HIV-1 reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only viral encoded enzyme that still lacks an efficient inhibitor despite the fact that it is a well-validated target whose functional abrogation compromises viral infectivity. Identification of new drugs...... inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly...

  13. Genomics of Probiotic Bacteria

    Science.gov (United States)

    O'Flaherty, Sarah; Goh, Yong Jun; Klaenhammer, Todd R.

    Probiotic bacteria from the Lactobacillus and Bifidobacterium species belong to the Firmicutes and the Actinobacteria phylum, respectively. Lactobacilli are members of the lactic acid bacteria (LAB) group, a broadly defined family of microorganisms that ferment various hexoses into primarily lactic acid. Lactobacilli are typically low G + C gram-positive species which are phylogenetically diverse, with over 100 species documented to date. Bifidobacteria are heterofermentative, high G + C content bacteria with about 30 species of bifidobacteria described to date.

  14. Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies.

    Science.gov (United States)

    Istyastono, Enade P; Nijmeijer, Saskia; Lim, Herman D; van de Stolpe, Andrea; Roumen, Luc; Kooistra, Albert J; Vischer, Henry F; de Esch, Iwan J P; Leurs, Rob; de Graaf, Chris

    2011-12-08

    The histamine H(4) receptor (H(4)R) is a G protein-coupled receptor (GPCR) that plays an important role in inflammation. Similar to the homologous histamine H(3) receptor (H(3)R), two acidic residues in the H(4)R binding pocket, D(3.32) and E(5.46), act as essential hydrogen bond acceptors of positively ionizable hydrogen bond donors in H(4)R ligands. Given the symmetric distribution of these complementary pharmacophore features in H(4)R and its ligands, different alternative ligand binding mode hypotheses have been proposed. The current study focuses on the elucidation of the molecular determinants of H(4)R-ligand binding modes by combining (3D) quantitative structure-activity relationship (QSAR), protein homology modeling, molecular dynamics simulations, and site-directed mutagenesis studies. We have designed and synthesized a series of clobenpropit (N-(4-chlorobenzyl)-S-[3-(4(5)-imidazolyl)propyl]isothiourea) derivatives to investigate H(4)R-ligand interactions and ligand binding orientations. Interestingly, our studies indicate that clobenpropit (2) itself can bind to H(4)R in two distinct binding modes, while the addition of a cyclohexyl group to the clobenpropit isothiourea moiety allows VUF5228 (5) to adopt only one specific binding mode in the H(4)R binding pocket. Our ligand-steered, experimentally supported protein modeling method gives new insights into ligand recognition by H(4)R and can be used as a general approach to elucidate the structure of protein-ligand complexes.

  15. Self-assembly of metal-organic coordination polymers constructed from a bent dicarboxylate ligand: diversity of coordination modes, structures, and gas adsorption.

    Science.gov (United States)

    Yang, Wenbin; Lin, Xiang; Blake, Alexander J; Wilson, Claire; Hubberstey, Peter; Champness, Neil R; Schröder, Martin

    2009-12-07

    We have synthesized five new metal-organic coordination polymers incorporating the bent ligand H(2)hfipbb [4,4'-(hexafluoroisopropylidene)bis(benzoic acid)] with different transition metal ions and co-ligands via solvothermal reactions to give [Zn(2)(hfipbb)(2)(py)(2)] x DMF (1), [Zn(2)(hfipbb)(2)(4,4'-bipy)(H(2)O)] (2), [Zn(2)(hfipbb)(2)(bpdab)].2DMF (3), [Cd(2)(hfipbb)(2)(DMF)(2)] x 2 DMF (4), and [Co(hfipbb)(dpp)] x MeOH (5) (py = pyridine, 4,4'-bipy = 4,4'-bipyridine, bpdab = 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene, dpp = 1,3-di(4-pyridyl)propane). Compound 1 displays a 2-fold 2D-->2D parallel interpenetrated layer network with one-dimensional (1D) helical channels, while 3 exhibits a three-dimensional pillared helical-layer open framework of alpha-Po topology based upon binuclear paddlewheel units. In compounds 2 and 5, binuclear motifs with double carboxylate bridges are linked by hfipbb(2-) ligands into a 1D ribbon, which are further assembled into two-dimensional non-interpenetrated (4,4) layers via bipyridyl co-ligands. However, the different bridging modes of hfipbb(2-) ligands and the different disposition of the coordinated co-ligands around metal ions result in subtle differences in the final architecture. Thus, 2 is based on a binuclear cluster node, double-stranded hfipbb(2-) linkers, and single-stranded 4,4'-bipy linkers, while 5 is based on a binuclear cluster node and hfipbb(2-) and dpp linkers which are both double-stranded. Among these compounds, the Cd(II) complex 4 is possibly the most interesting because it represents a rare example in which metal centers are linked by carboxylate groups into infinite chains further joined together by hfipbb(2-) spacers to form a 2D network with tubular helical channels. All these coordination polymers exhibit low solvent-accessible volumes. Both 3 and 4 retain structural integrity and permanent microporosity upon evacuation of guest molecules, with hydrogen uptakes of 0.57 and 0.78 wt %, respectively, at

  16. Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

    Science.gov (United States)

    Sauer-Heilborn, Annette; Welte, Tobias; Guzman, Carlos A.; Abraham, Wolf-Rainer; Höfle, Manfred G.

    2015-01-01

    The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF. PMID:26135861

  17. How honey kills bacteria

    NARCIS (Netherlands)

    Kwakman, Paulus H. S.; te Velde, Anje A.; de Boer, Leonie; Speijer, Dave; Vandenbroucke-Grauls, Christina M. J. E.; Zaat, Sebastian A. J.

    2010-01-01

    With the rise in prevalence of antibiotic-resistant bacteria, honey is increasingly valued for its antibacterial activity. To characterize all bactericidal factors in a medical-grade honey, we used a novel approach of successive neutralization of individual honey bactericidal factors. All bacteria

  18. Antioxidant Properties of Probiotic Bacteria.

    Science.gov (United States)

    Wang, Yang; Wu, Yanping; Wang, Yuanyuan; Xu, Han; Mei, Xiaoqiang; Yu, Dongyou; Wang, Yibing; Li, Weifen

    2017-05-19

    Oxidative stress defines a condition in which the prooxidant-antioxidant balance in the cell is disturbed, resulting in DNA hydroxylation, protein denaturation, lipid peroxidation, and apoptosis, ultimately compromising cells' viability. Probiotics have been known for many beneficial health effects, and the consumption of probiotics alone or in food shows that strain-specific probiotics can present antioxidant activity and reduce damages caused by oxidation. However, the oxidation-resistant ability of probiotics, especially the underling mechanisms, is not properly understood. In this view, there is interest to figure out the antioxidant property of probiotics and summarize the mode of action of probiotic bacteria in antioxidation. Therefore, in the present paper, the antioxidant mechanisms of probiotics have been reviewed in terms of their ability to improve the antioxidant system and their ability to decrease radical generation. Since in recent years, oxidative stress has been associated with an altered gut microbiota, the effects of probiotics on intestinal flora composition are also elaborated.

  19. A structured analysis of in vitro failure loads and failure modes of fiber, metal, and ceramic post-and-core systems.

    NARCIS (Netherlands)

    Fokkinga, W.A.; Kreulen, C.M.; Vallittu, P.K.; Creugers, N.H.J.

    2004-01-01

    PURPOSE: This study sought to aggregate literature data on in vitro failure loads and failure modes of prefabricated fiber-reinforced composite (FRC) post systems and to compare them to those of prefabricated metal, custom-cast, and ceramic post systems. MATERIALS AND METHODS: The literature was

  20. Modes of fossil preservation

    Science.gov (United States)

    Schopf, J.M.

    1975-01-01

    The processes of geologic preservation are important for understanding the organisms represented by fossils. Some fossil differences are due to basic differences in organization of animals and plants, but the interpretation of fossils has also tended to be influenced by modes of preservation. Four modes of preservation generally can be distinguished: (1) Cellular permineralization ("petrifaction") preserves anatomical detail, and, occasionally, even cytologic structures. (2) Coalified compression, best illustrated by structures from coal but characteristic of many plant fossils in shale, preserves anatomical details in distorted form and produces surface replicas (impressions) on enclosing matrix. (3) Authigenic preservation replicates surface form or outline (molds and casts) prior to distortion by compression and, depending on cementation and timing, may intergrade with fossils that have been subject to compression. (4) Duripartic (hard part) preservation is characteristic of fossil skeletal remains, predominantly animal. Molds, pseudomorphs, or casts may form as bulk replacements following dissolution of the original fossil material, usually by leaching. Classification of the kinds of preservation in fossils will aid in identifying the processes responsible for modifying the fossil remains of both animals and plants. ?? 1975.

  1. Principal Metabolic Flux Mode Analysis.

    Science.gov (United States)

    Bhadra, Sahely; Blomberg, Peter; Castillo, Sandra; Rousu, Juho; Wren, Jonathan

    2018-02-06

    In the analysis of metabolism, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, are able to capture the metabolic flux modes, however, they are primarily designed for the analysis of single samples at a time, and not best suited for exploratory analysis on a large sets of samples. We propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology. The proposed method can be applied to genome-scale metabolic network in efficient way as PMFA does not enumerate elementary modes. In addition, the method is more robust on out-of-steady steady-state experimental data than competing flux mode analysis approaches. Matlab software for PMFA and SPMFA and data set used for experiments are available in https://github.com/aalto-ics-kepaco/PMFA. sahely@iitpkd.ac.in, juho.rousu@aalto.fi, Peter.Blomberg@vtt.fi, Sandra.Castillo@vtt.fi. Detailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

  2. Antibiotics from predatory bacteria

    Directory of Open Access Journals (Sweden)

    Juliane Korp

    2016-03-01

    Full Text Available Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism.

  3. Hydrogen production by nonphotosynthetic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Huang, S.D.; Secor, C.K.; Zweig, R.M.; Ascione, R.

    1984-01-01

    H-producing nonphotosynthetic bacteria are identified and H from sewage treatment plants, H from rumen bacteria, and large-scale production of H through the genetic manipulation of H-producing nonphotosynthetic bacteria are discussed. (Refs. 36).

  4. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    Science.gov (United States)

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

  5. Single-mode ytterbium-doped large-mode-area photonic bandgap rod fiber amplifier

    DEFF Research Database (Denmark)

    Alkeskjold, Thomas Tanggaard; Scolari, Lara; Broeng, Jes

    2011-01-01

    Enabling Single-Mode (SM) operation in Large-Mode-Area (LMA) fiber amplifiers and lasers is critical, since a SM output ensures high beam quality and excellent pointing stability. In this paper, we demonstrate and test a new design approach for achieving SM LMA rod fibers by using a photonic...... bandgap structure. The structure allows resonant coupling of higher-order modes from the core and acts as a spatially Distributed Mode Filter (DMF). With this approach, we demonstrate passive SM performance in an only ~50cm long and straight ytterbium-doped rod fiber. The amplifier has a mode field...

  6. H-mode physics

    International Nuclear Information System (INIS)

    Itoh, Sanae.

    1991-06-01

    After the discovery of the H-mode in ASDEX ( a tokamak in Germany ) the transition between the L-mode ( Low confinement mode ) and H-mode ( High confinement mode ) has been observed in many tokamaks in the world. The H-mode has made a breakthrough in improving the plasma parameters and has been recognized to be a universal phenomena. Since its discovery, the extensive studies both in experiments and in theory have been made. The research on H-mode has been casting new problems of an anomalous transport across the magnetic surface. This series of lectures will provide a brief review of experiments for explaining H-mode and a model theory of H-mode transition based on the electric field bifurcation. If the time is available, a new theoretical model of the temporal evolution of the H-mode will be given. (author)

  7. [Darwin and bacteria].

    Science.gov (United States)

    Ledermann D, Walter

    2009-02-01

    As in 2009 the scientific world celebrates two hundreds years from the birthday of Charles Darwin and one hundred and fifty from the publication of The Origin of Species, an analysis of his complete work is performed, looking for any mention of bacteria. But it seems that the great naturahst never took knowledge about its existence, something rather improbable in a time when the discovery of bacteria shook the medical world, or he deliberately ignored them, not finding a place for such microscopic beings into his theory of evolution. But the bacteria badly affected his familiar life, killing scarlet fever one of his children and worsening to death the evolution of tuberculosis of his favourite Annie. Darwin himself could suffer the sickness of Chagas, whose etiological agent has a similar level to bacteria in the scale of evolution.

  8. Extracellular communication in bacteria

    DEFF Research Database (Denmark)

    Chhabra, S.R.; Philipp, B.; Eberl, L.

    2005-01-01

    molecules, in different Gram-positive and Gram-negative bacteria they control pathogenicity, secondary metabolite production, biofilm differentiation, DNA transfer and bioluminescence. The development of biosensors for the detection of these signal molecules has greatly facilitated their subsequent chemical...

  9. From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8

    Science.gov (United States)

    Verchot, Louis V.; Ward, Naomi L.; Belnap, Jayne; Bossio, Deborah; Coughenour, Michael; Gibson, John; Hanotte, Olivier; Muchiru, Andrew N.; Phillips, Susan L.; Steven, Blaire; Wall, Diana H.; Reid, Robin S.

    2015-01-01

    Generally, ecological research has considered the aboveground and belowground components of ecosystems separately. Consequently, frameworks for integrating the two components are not well developed. Integrating the microbial components into ecosystem ecology requires different approaches from those offered by plant ecology, partly because of the scales at which microbial processes operate and partly because of measurement constraints. Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways.

  10. Investigation of cavity mode and excitonic transition in an InGaAs/GaAs/AlGaAs vertical-cavity surface emitting laser structure by variable-temperature micro-photoluminescence, reflectance and photomodulated reflectance

    International Nuclear Information System (INIS)

    Yu, J L; Chen, Y H; Jiang, C Y; Zhang, H Y

    2012-01-01

    Variable-temperature micro-photoluminescence (μ-PL), reflectance (R) and photomodulated reflectance (PR) have been used to study an InGaAs/GaAs/AlGaAs vertical-cavity surface emitting laser (VCSEL) structure. μ-PL and R spectra have been recorded at different temperatures between 80 K and 300 K By comparing μ-PL with R spectra, both the excitonic transition and cavity mode are clearly identified. The Variable-temperature μ-PL and PR results of the etched sample with the top distributed Bragg reflectors (DBR) being removed further confirmed our identification. Our results demonstrate that variable-temperature μ-PL is a powerful noninvasive tool to measure accurate the quantum well transition and the cavity mode alignment.

  11. First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough.

    Science.gov (United States)

    Sun, Qing-Lei; Zeng, Zhi-Gang; Chen, Shuai; Sun, Li

    2016-01-01

    Alvinocaris longirostris is a species of shrimp existing in the hydrothermal fields of Okinawa Trough. To date the structure and function of the microbial community associated with A. longirostris are essentially unknown. In this study, by employment of the techniques of high through-put sequencing and clone library construction and analysis, we compared for the first time the community structures and metabolic profiles of microbes associated with the gill and gut of A. longirostris in a hydrothermal field of Okinawa Trough. Fourteen phyla were detected in the gill and gut communities, of which 11 phyla were shared by both tissues. Proteobacteria made up a substantial proportion in both tissues, while Firmicutes was abundant only in gut. Although gill and gut communities were similar in bacterial diversities, the bacterial community structures in these two tissues were significantly different. Further, we discovered for the first time the existence in the gill and gut communities of A. longirostris the genes (cbbM and aclB) encoding the key enzymes of Calvin-Benson-Bassham (CBB) cycle and the reductive tricarboxylic acid (rTCA) cycle, and that both cbbM and aclB were significantly more abundant in gill than in gut. Taken together, these results provide the first evidence that at least two carbon fixation pathways are present in both the gill and the gut communities of A. longirostris, and that the communities in different tissues likely differ in autotrophic productivity.

  12. Transient analysis mode participation for modal survey target mode selection using MSC/NASTRAN DMAP

    Science.gov (United States)

    Barnett, Alan R.; Ibrahim, Omar M.; Sullivan, Timothy L.; Goodnight, Thomas W.

    1994-01-01

    Many methods have been developed to aid analysts in identifying component modes which contribute significantly to component responses. These modes, typically targeted for dynamic model correlation via a modal survey, are known as target modes. Most methods used to identify target modes are based on component global dynamic behavior. It is sometimes unclear if these methods identify all modes contributing to responses important to the analyst. These responses are usually those in areas of hardware design concerns. One method used to check the completeness of target mode sets and identify modes contributing significantly to important component responses is mode participation. With this method, the participation of component modes in dynamic responses is quantified. Those modes which have high participation are likely modal survey target modes. Mode participation is most beneficial when it is used with responses from analyses simulating actual flight events. For spacecraft, these responses are generated via a structural dynamic coupled loads analysis. Using MSC/NASTRAN DMAP, a method has been developed for calculating mode participation based on transient coupled loads analysis results. The algorithm has been implemented to be compatible with an existing coupled loads methodology and has been used successfully to develop a set of modal survey target modes.

  13. Transient analysis mode participation for modal survey target mode selection using MSC/NASTRAN DMAP

    Science.gov (United States)

    Barnett, Alan R.; Ibrahim, Omar M.; Sullivan, Timothy L.; Goodnight, Thomas W.

    1994-03-01

    Many methods have been developed to aid analysts in identifying component modes which contribute significantly to component responses. These modes, typically targeted for dynamic model correlation via a modal survey, are known as target modes. Most methods used to identify target modes are based on component global dynamic behavior. It is sometimes unclear if these methods identify all modes contributing to responses important to the analyst. These responses are usually those in areas of hardware design concerns. One method used to check the completeness of target mode sets and identify modes contributing significantly to important component responses is mode participation. With this method, the participation of component modes in dynamic responses is quantified. Those modes which have high participation are likely modal survey target modes. Mode participation is most beneficial when it is used with responses from analyses simulating actual flight events. For spacecraft, these responses are generated via a structural dynamic coupled loads analysis. Using MSC/NASTRAN DMAP, a method has been developed for calculating mode participation based on transient coupled loads analysis results. The algorithm has been implemented to be compatible with an existing coupled loads methodology and has been used successfully to develop a set of modal survey target modes.

  14. Viscous, Resistive Magnetorotational Modes

    DEFF Research Database (Denmark)

    Pessah, Martin Elias; Chan, Chi-kwan

    2008-01-01

    We carry out a comprehensive analysis of the behavior of the magnetorotational instability (MRI) in viscous, resistive plasmas. We find exact, non-linear solutions of the non-ideal magnetohydrodynamic (MHD) equations describing the local dynamics of an incompressible, differentially rotating...... background threaded by a vertical magnetic field when disturbances with wavenumbers perpendicular to the shear are considered. We provide a geometrical description of these viscous, resistive MRI modes and show how their physical structure is modified as a function of the Reynolds and magnetic Reynolds...... momentum transport is always directed outwards. We also find that, for any combination of the Reynolds and magnetic Reynolds numbers, magnetic disturbances dominate both the energetics and the transport of angular momentum and that the total mean energy density is an upper bound for the total mean stress...

  15. The conjugation protein TcpC from Clostridium perfringens is structurally related to the type IV secretion system protein VirB8 from Gram-negative bacteria.

    Science.gov (United States)

    Porter, Corrine J; Bantwal, Radhika; Bannam, Trudi L; Rosado, Carlos J; Pearce, Mary C; Adams, Vicki; Lyras, Dena; Whisstock, James C; Rood, Julian I

    2012-01-01

    Bacterial conjugation is important for the acquisition of virulence and antibiotic resistance genes. We investigated the mechanism of conjugation in Gram-positive pathogens using a model plasmid pCW3 from Clostridium perfringens. pCW3 encodes tetracycline resistance and contains the tcp locus, which is essential for conjugation. We showed that the unique TcpC protein (359 amino acids, 41 kDa) was required for efficient conjugative transfer, localized to the cell membrane independently of other conjugation proteins, and that membrane localization was important for its function, oligomerization and interaction with the conjugation proteins TcpA, TcpH and TcpG. The crystal structure of the C-terminal component of TcpC (TcpC(99-359)) was determined to 1.8-Å resolution. TcpC(99-359) contained two NTF2-like domains separated by a short linker. Unexpectedly, comparative structural analysis showed that each of these domains was structurally homologous to the periplasmic region of VirB8, a component of the type IV secretion system from Agrobacterium tumefaciens. Bacterial two-hybrid studies revealed that the C-terminal domain was critical for interactions with other conjugation proteins. The N-terminal region of TcpC was required for efficient conjugation, oligomerization and protein-protein interactions. We conclude that by forming oligomeric complexes, TcpC contributes to the stability and integrity of the conjugation apparatus, facilitating efficient pCW3 transfer. © 2011 Blackwell Publishing Ltd.

  16. Studies on the structure and function of intestinal microbes of surgeonfishes in the central Red Sea with a focus on the giant bacteria Epulopiscium spp.

    KAUST Repository

    Miyake, Sou

    2015-05-01

    The intestinal tract microbiota – microbial community of the gut – is an important field in microbiology not only because of its critical role in the host development, but also increasingly large number of diseases are associated with certain state of the gut microbiota. The community structure and function of the gut microbiota is relatively well studied in humans and related higher vertebrates, but is severely understudied in fish. This is especially true for the coral reef fishes, who constitute the most diverse assemblage of vertebrates spread over a very local scale, and are essential for the resilience of the reefs. In order to bridge this gap in knowledge, this dissertation studied the community structure, interactions and functions of the gut microbial community from the surgeonfishes in the Red Sea – with special focus on the surgeonfish enteric symbiont Epulopiscium spp. Initially, I studied the composition of the gut microbiota of nine surgeonfish and three nonsurgeonfish species from the Red Sea using 454 pyrosequencing. Upon discovering the high abundance of Epulopiscium spp. in herbivorous surgeonfishes, I then proceeded to identify their phylogenetic diversity, distribution, as well as deducing their coevolutionary relationship with the host. Because Epulopiscium spp. undergo substantial changes in the cell size (grow up to ~600μm) and the DNA concentration (from 85 to over 250pg per cell) throughout their diel lifecycle, I also studied the temporal changes in their expression pattern using RNA-seq. Overall, this dissertation shed light on the complex structure, interaction and function of an important family of coral reef fish from the Red Sea through range of molecular techniques.

  17. Experimental investigation on multidisciplinary geophysical characterization of deep underground structure using multi-scale, multi-mode seismic profiling for the evaluation of ground motion and seismic model building

    International Nuclear Information System (INIS)

    Abe, Susumu

    2014-01-01

    Recent advancements in data acquisition and velocity estimation for multi-mode, multiscale seismic exploration were explained along with the basic concept of strategic geophysical surveys for NPP siting assessment. Then, as a case study using this concept, multidisciplinary geophysical characterization results pertaining to the deep underground structure beneath the JNES Kashiwazaki Center were explained in detail. At the site, reflection/refraction surveys and magnetotelluric/gravity surveys were also conducted. It was shown that these surveys can be used complementary because at the upsurge part, where clear images cannot be obtained by reflection/refraction surveys, magnetotelluric /gravity surveys can be used to obtain clear images. (author)

  18. Seeing green bacteria in a new light: genomics-enabled studies of the photosynthetic apparatus in green sulfur bacteria and filamentous anoxygenic phototrophic bacteria

    DEFF Research Database (Denmark)

    Frigaard, Niels-Ulrik; Bryant, Donald A

    2004-01-01

    Based upon their photosynthetic nature and the presence of a unique light-harvesting antenna structure, the chlorosome, the photosynthetic green bacteria are defined as a distinctive group in the Bacteria. However, members of the two taxa that comprise this group, the green sulfur bacteria...... (Chlorobi) and the filamentous anoxygenic phototrophic bacteria ("Chloroflexales"), are otherwise quite different, both physiologically and phylogenetically. This review summarizes how genome sequence information facilitated studies of the biosynthesis and function of the photosynthetic apparatus...... and carotenoid species also allow the functions of these pigments to be studied in vivo....

  19. SNV's modes of ordering

    NARCIS (Netherlands)

    Hummel, John; Duim, van der Rene

    2016-01-01

    This article adopts an aidnographic approach to examine how internal organizational modes of ordering have influenced tourism development practices of SNV Netherlands Development Organisation (SNV). Our research revealed six modes of ordering: administration, project management, enterprising,

  20. High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl-CoA ligand

    DEFF Research Database (Denmark)

    Taskinen, Jukka P; van Aalten, Daan M; Knudsen, Jens

    2007-01-01

    The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described. The...