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111.
Elsässer T Brons S Psonka K Scholz M Gudowska-Nowak E Taucher-Scholz G 《Radiation research》2008,169(6):649-659
The investigation of fragment length distributions of plasmid DNA gives insight into the influence of localized energy distribution on the induction of DNA damage, particularly the clustering of double-strand breaks. We present an approach that determines the fragment length distributions of plasmid DNA after heavy-ion irradiation by using the Local Effect Model. We find a good agreement of our simulations with experimental fragment distributions derived from atomic force microscopy (AFM) studies by including experimental constraints typical for AFM. Our calculations reveal that by comparing the fragmentation in terms of fluence, we can uniquely distinguish the effect of different radiation qualities. For very high-LET irradiation using nickel or uranium ions, no difference between their fragment distributions can be expected for the same dose level. However, for carbon ions with an intermediate LET, the fragmentation pattern differs from the distribution for very high-LET particles. The results of the model calculations can be used to determine the optimal experimental parameters for a demonstration of the influence of track structure on primary radiation damage. Additionally, we compare the results of our model for two different plasmid geometries. 相似文献
112.
113.
An arginine switch in the species B adenovirus knob determines high-affinity engagement of cellular receptor CD46 下载免费PDF全文
Persson BD Müller S Reiter DM Schmitt BB Marttila M Sumowski CV Schweizer S Scheu U Ochsenfeld C Arnberg N Stehle T 《Journal of virology》2009,83(2):673-686
Adenoviruses (Ads) are icosahedral, nonenveloped viruses with a double-stranded DNA genome. The 51 known Ad serotypes exhibit profound variations in cell tropism and disease types. The number of observed Ad infections is steadily increasing, sometimes leading to fatal outcomes even in healthy individuals. Species B Ads can cause kidney infections, hemorrhagic cystitis, and severe respiratory infections, and most of them use the membrane cofactor protein CD46 as a cellular receptor. The crystal structure of the human Ad type 11 (Ad11) knob complexed with CD46 is known; however, the determinants of CD46 binding in related species B Ads remain unclear. We report here a structural and functional analysis of the Ad11 knob, as well as the Ad7 and Ad14 knobs, which are closely related in sequence to the Ad11 knob but have altered CD46-binding properties. The comparison of the structures of the three knobs, which we determined at very high resolution, provides a platform for understanding these differences and allows us to propose a mechanism for productive high-affinity engagement of CD46. At the center of this mechanism is an Ad knob arginine that needs to switch its orientation in order to engage CD46 with high affinity. Quantum chemical calculations showed that the CD46-binding affinity of Ad11 is significantly higher than that of Ad7. Thus, while Ad7 and Ad14 also bind CD46, the affinity and kinetics of these interactions suggest that these Ads are unlikely to use CD46 productively. The proposed mechanism is likely to determine the receptor usage of all CD46-binding Ads. 相似文献
114.
Wang J Vollrath S Behrends T Bodelier PL Muyzer G Meima-Franke M Den Oudsten F Van Cappellen P Laanbroek HJ 《Applied and environmental microbiology》2011,77(7):2337-2344
Microbial iron oxidation is an integral part of the iron redox cycle in wetlands. Nonetheless, relatively little is known about the composition and ecology of iron-oxidizing communities in the soils and sediments of wetlands. In this study, sediment cores were collected across a freshwater tidal marsh in order to characterize the iron-oxidizing bacteria (FeOB) and to link their distributions to the geochemical properties of the sediments. We applied recently designed 16S rRNA primers targeting Gallionella-related FeOB by using a nested PCR-denaturing gradient gel electrophoresis (DGGE) approach combined with a novel quantitative PCR (qPCR) assay. Gallionella-related FeOB were detected in most of the samples. The diversity and abundance of the putative FeOB were generally higher in the upper 5 to 12 cm of sediment than in deeper sediment and higher in samples collected in April than in those collected in July and October. Oxygen supply by macrofauna appears to be a major force in controlling the spatial and temporal variations in FeOB communities. The higher abundance of Gallionella-related FeOB in April coincided with elevated concentrations of extractable Fe(III) in the sediments. Despite this coincidence, the distributions of FeOB did not exhibit a simple relationship to the redox zonation inferred from the geochemical depth profiles. 相似文献
115.
Sandoval R González A Caviedes A Pancetti F Smalla KH Kaehne T Michea L Gundelfinger ED Wyneken U 《Journal of neurochemistry》2011,118(5):760-772
Nitric oxide (NO) has been proposed to down-regulate NMDA receptors (NMDA-Rs) in a homeostatic manner. However, NMDA-R-dependent NO synthesis also can cause excitotoxic cell death. Using bicuculline-stimulated hippocampal and cortical cell cultures, we have addressed the role of the brain-derived neurotrophic factor-NO pathway in NMDA-R down-regulation. This pathway protected cortical cells from NMDA-induced death and led to NMDA-R inhibition. In contrast, no evidence was gained for the presence of this protective pathway in hippocampal neurons, in which NMDA-induced NO synthesis was confirmed to be toxic. Therefore, opposing effects of NO depended on the activation of different signalling pathways. The pathophysiological relevance of this observation was investigated in synaptosomes and post-synaptic densities isolated from rat hippocampi and cerebral cortices following kainic acid-induced status epilepticus. In cortical, but not in hippocampal synaptosomes, brain-derived neurotrophic factor induced NO synthesis and inhibited NMDA-R currents present in isolated post-synaptic densities. In conclusion, we identified a NO-dependent homeostatic response in the rat cerebral cortex induced by elevated activity. A low performance of this pathway in brain areas including the hippocampus may be related to their selective vulnerability in pathologies such as temporal lobe epilepsy. 相似文献
116.
117.
Micro-scale modeling of pesticide degradation coupled to carbon turnover in the detritusphere: model description and sensitivity analysis 总被引:1,自引:0,他引:1
Holger Pagel Joachim Ingwersen Christian Poll Ellen Kandeler Thilo Streck 《Biogeochemistry》2014,117(1):185-204
Microbiologically active biogeochemical interfaces are excellent systems to study soil functions such as pesticide degradation at the micro-scale. In particular, in the detritusphere pesticide degradation is accelerated by input of fresh organic carbon from litter into the adjacent soil. This observed priming effect suggests: (i) pesticide degradation is strongly coupled to carbon turnover, (ii) it is controlled by size and activity of the microbial community and (iii) sorption and transport of dissolved carbonaceous compounds and pesticides might regulate substrate availability and in turn decomposition processes. We present a new mechanistic 1D model (PEsticide degradation Coupled to CArbon turnover in the Detritusphere, PECCAD) which implements these hypotheses. The new model explicitly considers growth and activity of bacteria, fungi and specific pesticide degraders in response to substrate availability. Enhanced pesticide degradation due to availability of a second source of carbon (dissolved organic carbon) is implemented in the model structure via two mechanisms. First, additional substrate is utilized simultaneously with the pesticide by bacterial pesticide degraders resulting in an increase in their size and activity. Second, stimulation of fungal growth and activity by additional substrates leads directly to higher pesticide degradation via co-metabolism. Thus, PECCAD implicitly accounts for litter-stimulated production and activity of unspecific fungal enzymes responsible for co-metabolic pesticide degradation. With a global sensitivity analysis we identified high-leverage model parameters and input. In combination with appropriate experimental data, PECCAD can serve as a tool to elucidate regulation mechanisms of accelerated pesticide degradation in the detritusphere. 相似文献
118.
Molecular Analyses of Novel Methanotrophic Communities in Forest Soil That Oxidize Atmospheric Methane 总被引:12,自引:4,他引:8 下载免费PDF全文
Forest and other upland soils are important sinks for atmospheric CH4, consuming 20 to 60 Tg of CH4 per year. Consumption of atmospheric CH4 by soil is a microbiological process. However, little is known about the methanotrophic bacterial community in forest soils. We measured vertical profiles of atmospheric CH4 oxidation rates in a German forest soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting the pmoA gene, coding for the α subunit of the particulate methane monooxygenase, and the small-subunit rRNA gene (SSU rDNA) of all life. The forest soil was a sink for atmospheric CH4 in situ and in vitro at all times. In winter, atmospheric CH4 was oxidized in a well-defined subsurface soil layer (6 to 14 cm deep), whereas in summer, the complete soil core was active (0 cm to 26 cm deep). The content of total extractable DNA was about 10-fold higher in summer than in winter. It decreased with soil depth (0 to 28 cm deep) from about 40 to 1 μg DNA per g (dry weight) of soil. The PCR product concentration of SSU rDNA of all life was constant both in winter and in summer. However, the PCR product concentration of pmoA changed with depth and season. pmoA was detected only in soil layers with active CH4 oxidation, i.e., 6 to 16 cm deep in winter and throughout the soil core in summer. The same methanotrophic populations were present in winter and summer. Layers with high CH4 consumption rates also exhibited more bands of pmoA in DGGE, indicating that high CH4 oxidation activity was positively correlated with the number of methanotrophic populations present. The pmoA sequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH4 consumption. 相似文献
119.
We investigate the emergence of spatio-temporal patterns in ecological systems. In particular, we study a generalized predator-prey system on a spatial domain. On this domain diffusion is considered as the principal process of motion. We derive the conditions for Hopf and Turing instabilities without specifying the predator-prey functional responses and discuss their biological implications. Furthermore, we identify the codimension-2 Turing-Hopf bifurcation and the codimension-3 Turing-Takens-Bogdanov bifurcation. These bifurcations give rise to complex pattern formation processes in their neighborhood. Our theoretical findings are illustrated with a specific model. In simulations a large variety of different types of long-term behavior, including homogenous distributions, stationary spatial patterns and complex spatio-temporal patterns, are observed. 相似文献
120.
Diggle SP Stacey RE Dodd C Cámara M Williams P Winzer K 《Environmental microbiology》2006,8(6):1095-1104
LecA (PA-IL) is a cytotoxic lectin and adhesin produced by Pseudomonas aeruginosa which binds hydrophobic galactosides with high specificity and affinity. By using a lecA-egfp translation fusion and immunoblot analysis of the biofilm extracellular matrix, we show that lecA is expressed in biofilm-grown cells. In static biofilm assays on both polystyrene and stainless steel, biofilm depth and surface coverage was reduced by mutation of lecA and enhanced in the LecA-overproducing strain PAO-P47. Biofilm surface coverage by the parent strain, PAO-P47 but not the lecA mutant on steel coupons was also inhibited by growth in the presence of either isopropyl-beta-D-thiogalactoside (IPTG) or p-nitrophenyl-alpha-D-galactoside (NPG). Furthermore, mature wild-type biofilms formed in the absence of these hydrophobic galactosides could be dispersed by the addition of IPTG. In contrast, addition of p-nitrophenyl-alpha-L-fucose (NPF) which has a high affinity for the P. aeruginosa LecB (PA-IIL) lectin had no effect on biofilm formation or dispersal. Planktonic growth of P. aeruginosa PAO1 was unaffected by the presence of IPTG, NPG or NPF, nor was the strain able to utilize these sugars as carbon sources, suggesting that the observed effects on biofilm formation were due to the competitive inhibition of LecA-ligand binding. Similar results were also obtained for biofilms grown under dynamic flow conditions on steel coupons, suggesting that LecA contributes to P. aeruginosa biofilm architecture under different environmental conditions. 相似文献