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  • 1
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    Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-01
    Description: The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1–119) and a C-terminal DNA-binding domain (DBD, residues 130–236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein–DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Fungal Planet description sheets: 785– 867 (2018)
    Naturalis Biodiversity Center
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 41, pp. 238-417
    Details
    Publication Date: 2024-04-02
    Description: Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora corymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia corymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniella eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis. Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, Inocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia × europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.
    Keywords: Ecology ; Evolution ; Behavior and Systematics ; ITS nrDNA barcodes ; LSU ; new taxa ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 3
    Electronic Resource
    Electronic Resource
    A high precision ultrasonic system for vibration measurements (1992)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 63 (1992), S. 5435-5441 
    Details
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: A microcomputer-aided ultrasonic system that can be used to measure the vibratory displacements of an object is presented. A pair of low cost 40-kHz ultrasonic transducers is used to transmit ultrasound toward an object and receive the ultrasound reflected from the object. The relative motion of the object modulates the phase angle difference between the transmitted and received ultrasound signals. A single-chip microcomputer-based phase detector was designed to record and analyze the phase shift information which is then sent to a PC-AT microcomputer for processing. We have developed an ingenious method to reconstruct the relative motion of an object from the acquired data of the phase difference changes. A digital plotter based experiment was also designed for testing the performance of the whole system. The measured accuracy of the system in the reported experiments is within ±0.4 mm and the theoretical maximal measurable speed of the object is 89.6 cm/s. The main advantages of this ultrasonic vibration measurement system are high resolution, low cost, noncontact measurement and it is easily installed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1143415
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  • 4
    Electronic Resource
    Electronic Resource
    Electron inelastic interactions with overlayer systems (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 85 (1999), S. 8247-8254 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: An overlayer system composed of a thin film on the top of a semi-infinite substrate was studied in this work for electron inelastic interactions. Analytical expressions for the depth-dependent inelastic differential and integral inverse mean free paths were derived for both incident and escaping electrons. The interface (film-substrate) effect and the surface (vacuum-film) effect were analyzed by comparing the results of an overlayer system and a semi-infinite system. It was found that the interface effect extended to several angstroms on both sides of the interface for a 500 eV electron incident into or escaping from the vacuum–SiO2–Si and the vacuum–Au–Ni systems. An application of the spatial-varying inelastic differential inverse mean free paths was made by Monte Carlo simulations of the electron elastic backscattering from an overlayer system. Good agreement was found between results calculated presently and data measured experimentally on the elastic reflection coefficient. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.370666
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  • 5
    Electronic Resource
    Electronic Resource
    Improved methods for working with fish chromosomes with a review of metaphase chromosome banding (1990)
    Oxford, UK : Blackwell Publishing Ltd
    Journal of fish biology 37 (1990), S. 0 
    Details
    ISSN: 1095-8649
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Improved methods for obtaining, preparing, and staining fish chromosomes are described. Included are procedures for resolving serial or G-type bands. A brief review of various metaphase banding procedures and their use in fishes is also presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1095-8649.1990.tb05889.x
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  • 6
    Electronic Resource
    Electronic Resource
    Improved Gravimetric Terrain Corrections (1994)
    Oxford, UK : Blackwell Publishing Ltd
    Geophysical journal international 119 (1994), S. 0 
    Details
    ISSN: 1365-246X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences
    Notes: The objective of this paper is to improve gravimetric terrain corrections by: (1) investigating the effect of different topographic representations that are suitable for efficient processing of high volumes of data (e.g. the mass prism and the mass line models) on terrain corrections and on geiod computations; (2) accelerating the convergence of fast Fourier transform (FFT)-based terrain-correction formulae; and (3) developing a set of new formulae corresponding to the mass prism topographic model, which can be evaluated efficiently with the 2-D FFT.Terrain corrections were computed on a grid of 600 by 600 points with spacing 30″ by 60″ in the Rocky Mountains of British Columbia, Canada. the effect of using the mass line model instead of the mass prism model is 7.4 mGal (maximum) and 0.7mGal (rms) on the terrain corrections, and 24cm (maximum) and 16cm (rms) on the geoid undulations. the optimizations made on the FFT-based terrain-correction formulae effectively speed up the convergence. the newly developed mass prism terrain-correction formula significantly reduced the required computer time and provided identical results with those from the rigorous numerical integration. On an IBM/RISC machine running AIX, the computation of the 15 convolutions (the matrix size was expanded to 1200 by 1200 after 100 per cent zero-padding) via the new formulae only took 15 min (user time), while the numerical summation method required 83.5 days.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-246X.1994.tb04013.x
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  • 7
    Electronic Resource
    Electronic Resource
    Transactivation of the 'promoterless' luciferase-encoding vectors pXP1 and pXP2 by C/EBPα
    Amsterdam : Elsevier
    Gene 138 (1994), S. 257-258 
    Details
    ISSN: 0378-1119
    Keywords: Recombinant DNA ; cryptic promoters ; electroporation ; reporter gene ; transient gene expression
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0378-1119(94)90819-2
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  • 8
    Electronic Resource
    Electronic Resource
    Early neutron stars and quark matter
    Amsterdam : Elsevier
    Chinese Astronomy and Astrophysics 12 (1988), S. 1-6 
    Details
    ISSN: 0275-1062
    Keywords: Stars: neutron star - quark matter
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0275-1062(88)90016-1
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  • 9
    Electronic Resource
    Electronic Resource
    Deflagration to detonation transition fueled by dust layers (1995)
    Springer
    Shock waves 5 (1995), S. 249-258 
    Details
    ISSN: 1432-2153
    Keywords: Detonation ; Shock wave ; Heterogeneous combustion ; Dust explosion ; Supersonic combustion ; Unsteady flame
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics , Technology
    Notes: Abstract The roles which dust layers play in severe dust explosions were investigated in a 70 m long and 30 cm inside diameter horizontal Flame Acceleration Tube (FAT) with one end closed and the other end open to the atmosphere. A variety of dusts such as corn dust, cornstarch, Mira Gel starch, wheat dust, and wood flour were layered on the bottom half of the FAT. To initiate the combustion process, a detonation tube filled with a stoichiometric H2/O2 mixture at room temperature and 1 atm pressure was used to ignite a short presuspended dust cloud with a dust concentration of 500–600 g/m3. Combustion waves generated by this dust cloud travel toward the open end of the FAT and are continuously fueled by the dust/air mixtures. Flame propagation processes in the FAT were closely monitored by a variety of measuring instruments at different locations. The study demonstrates that stable quasi-detonation were reached in some runs, but self-sustained Chapman-Jouguet detonations were not observed possibly due to the limitation of the tube length. Attempts were made to determine the structure of dust detonations fueled by a dust layer. Preliminary evidence indicates that for Mira Gel starch the leading shock is essentially a triple shock configuration which involves a Mach stem and for wheat and wood dusts there possibly exists a multi-headed spin structure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01419006
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  • 10
    Electronic Resource
    Electronic Resource
    Natural selection causing microsatellite divergence in wild emmer wheat at the ecologically variable microsite at Ammiad, Israel (2000)
    Springer
    Theoretical and applied genetics 100 (2000), S. 985-999 
    Details
    ISSN: 1432-2242
    Keywords: Key words Natural selection ; Microecological diversity ; Microsatellites ; Adaptation ; T. dicoccoides ; Wild emmer wheat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Genetic diversity at 28 microsatellite loci was studied in a natural population of Triticum dicoccoides at the Ammiad microsite, north of the Sea of Galilee, Israel. This microsite was subdivided into four major habitats, North, Valley, Ridge and Karst, and further subdivided into nine subhabitats. The units thus defined showed strong and highly significant differentiation in ecological factors; in particular with respect to cover, proximity and height of rocks, and surface soil moisture after early rains. The results showed that allele distributions at microsatellite loci were nonrandom and associated with habitats. Significant genetic differentiation and variation in repeat number were found among subpopulations in the four major habitats and nine subhabitats. Habitat-specific and -unique alleles and linkage disequilibria were observed in the Karst subpopulation. The subpopulations dwelling in drier habitats and subhabitats showed higher genetic diversities at microsatellite loci. These results suggest that natural selection, presumably through aridity stress, acts upon microsatellite divergence predominantly on noncoding sequences, thereby contributing to differences in fitness.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001220051380
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